Running as unit: rb-build-arm64_12-92900.service ==================================================================================== Sun Apr 27 19:26:05 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_12) on jenkins, called using "codethink04-arm64 codethink03-arm64" as arguments. Sun Apr 27 19:26:05 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-16b1VTol" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sun Apr 27 19:26:05 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Sun Apr 27 19:26:05 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-p0EsbF' Sun Apr 27 19:26:06 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Sun Apr 27 19:26:06 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-82F7jL' ok, let's check if hisat2 is building anywhere yet… ok, hisat2 is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of hisat2 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. ============================================================================= Sun Apr 27 19:26:21 UTC 2025 I: starting to build hisat2/unstable/arm64 on jenkins on '2025-04-27 19:26' Sun Apr 27 19:26:21 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_12/92900/console.log 1745781981 arm64 unstable hisat2 Sun Apr 27 19:26:21 UTC 2025 I: Downloading source for unstable/hisat2=2.2.1-5 --2025-04-27 19:26:21-- http://deb.debian.org/debian/pool/main/h/hisat2/hisat2_2.2.1-5.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2104 (2.1K) [text/prs.lines.tag] Saving to: ‘hisat2_2.2.1-5.dsc’ 0K .. 100% 318M=0s 2025-04-27 19:26:21 (318 MB/s) - ‘hisat2_2.2.1-5.dsc’ saved [2104/2104] --2025-04-27 19:26:21-- http://deb.debian.org/debian/pool/main/h/hisat2/hisat2_2.2.1-5.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2104 (2.1K) [text/prs.lines.tag] Saving to: ‘hisat2_2.2.1-5.dsc’ 0K .. 100% 318M=0s 2025-04-27 19:26:21 (318 MB/s) - ‘hisat2_2.2.1-5.dsc’ saved [2104/2104] Sun Apr 27 19:26:21 UTC 2025 I: hisat2_2.2.1-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: hisat2 Binary: hisat2, python3-hisat2 Architecture: any all Version: 2.2.1-5 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe Homepage: https://daehwankimlab.github.io/hisat2/ Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/hisat2 Vcs-Git: https://salsa.debian.org/med-team/hisat2.git Testsuite: autopkgtest Testsuite-Triggers: bcftools, samtools Build-Depends: debhelper-compat (= 13), libsimde-dev, help2man , pandoc , python3:any Package-List: hisat2 deb science optional arch=any python3-hisat2 deb python optional arch=all Checksums-Sha1: e09c36d93952eff1ebfd19545c38e173636bf662 6761242 hisat2_2.2.1.orig.tar.gz 96871cfbd92f3e6d11393aba14344550f57ff8d2 29576 hisat2_2.2.1-5.debian.tar.xz Checksums-Sha256: f3f4f867d0a6b1f880d64efc19deaa5788c62050e0a4d614ce98b3492f702599 6761242 hisat2_2.2.1.orig.tar.gz 70d19cce728774d945e65a341721be568980cbd42c4449e8cb4677850c62607d 29576 hisat2_2.2.1-5.debian.tar.xz Files: 0d1fcfcaf7ba1e64eb68006bba5a3855 6761242 hisat2_2.2.1.orig.tar.gz 0168dcca6cecdd97887bb4330c189aaa 29576 hisat2_2.2.1-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmaNEIYACgkQPCZ2P2xn 5uKpuw/9HA+ly3oYGrYHwPjr4hsKtUAqP6YK1GgbrVylLefTL1kjIwr7m6hNGCzu 99X3wix8CRksJoEqqxw3TyVlMx9f4NQ247lKsJrejwGBK7S+GB5h2SgnKIYqUkKM Wgl/BkMQWgAYR1zHJ/nx+DD/gjx3ZqlG9JHzaECFTrIMdhHprWnOX5wGLZhaRpZA uKBFQqvYUVOIc5gyBZqP+tynQAqPk9cQ4YfcAU037Ew7ANtyxq+8DeXfgpn/t7lA /uba4uCfs7rxm4PmH/rroSrrny7nkF5YZiWd0wMIHkiWvty0fdgVJ1Y3rg/IgAgi 2fLJSRT7jVx2V8LfOcolXOMIC6pCsltpKG8WY42lZTB1nIUpR46i0OG+fVUAhd5N 4FsmK3YnBUBfY6Nx/CWq6SL1MzxdKoDxC88i4P8Ie6tZZxTJi5G0o8WCX/UgB4uS llD1hPGJVGszV4eTQyjNBk798Ac0+x2joThxuiwHedyG/41AyYXAUGJ7XJnITqPm GNeBvCZAJxtDyz9bmAPEAIteP9FczwWZHEB16IYB8pG+pwfRd7Dp/BFYQWwyVaD2 m6FEF/spuP9m5IdbwHbx2uEKxWGtm/bYBqSKdIGoyPFMMRu9aAlG70iaWKC2n+QL Aqq/FvUD9DBcfDfU5IqL07a2QYgECbcgR0gANrC9Yamz4Jzu7rc= =vP68 -----END PGP SIGNATURE----- Sun Apr 27 19:26:21 UTC 2025 I: Checking whether the package is not for us Sun Apr 27 19:26:21 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Sun Apr 27 19:26:21 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Sun Apr 27 19:26:21 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Sun Apr 27 19:26:21 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-guhWKH' ==================================================================================== Sun Apr 27 19:26:23 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "1 hisat2 unstable /srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL 2.2.1-5" as arguments. Sun Apr 27 19:26:23 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-0nYkl0yb" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sun Apr 27 19:26:23 UTC 2025 I: Downloading source for unstable/hisat2=2.2.1-5 Reading package lists... NOTICE: 'hisat2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/hisat2.git Please use: git clone https://salsa.debian.org/med-team/hisat2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 6793 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main hisat2 2.2.1-5 (dsc) [2104 B] Get:2 http://deb.debian.org/debian unstable/main hisat2 2.2.1-5 (tar) [6761 kB] Get:3 http://deb.debian.org/debian unstable/main hisat2 2.2.1-5 (diff) [29.6 kB] Fetched 6793 kB in 9s (797 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'hisat2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/hisat2.git Please use: git clone https://salsa.debian.org/med-team/hisat2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 6793 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main hisat2 2.2.1-5 (dsc) [2104 B] Get:2 http://deb.debian.org/debian unstable/main hisat2 2.2.1-5 (tar) [6761 kB] Get:3 http://deb.debian.org/debian unstable/main hisat2 2.2.1-5 (diff) [29.6 kB] Fetched 6793 kB in 9s (797 kB/s) Download complete and in download only mode ============================================================================= Building hisat2 in unstable on arm64 on codethink04-arm64 now. Date: Sun Apr 27 20:26:32 BST 2025 Date UTC: Sun Apr 27 19:26:32 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: Sun Apr 27 07:26:32 -12 2025 I: pbuilder-time-stamp: 1745781992 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 [hisat2_2.2.1-5.dsc] I: copying [./hisat2_2.2.1.orig.tar.gz] I: copying [./hisat2_2.2.1-5.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./hisat2_2.2.1-5.dsc: unsupported subcommand dpkg-source: info: extracting hisat2 in hisat2-2.2.1 dpkg-source: info: unpacking hisat2_2.2.1.orig.tar.gz dpkg-source: info: unpacking hisat2_2.2.1-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_imp dpkg-source: info: applying hardening dpkg-source: info: applying reproducibile dpkg-source: info: applying fix-freebsd dpkg-source: info: applying compilerflags dpkg-source: info: applying simde dpkg-source: info: applying python3 dpkg-source: info: applying fix-manual dpkg-source: info: applying riscv5 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/966878/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='a8df00f6df85426e9e404fa7e51a5354' 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='966878' 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.8bp91aLL/pbuilderrc_PHmI --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.8bp91aLL/b1 --logfile b1/build.log hisat2_2.2.1-5.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 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/966878/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), libsimde-dev, help2man, pandoc, python3:any dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19953 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 libsimde-dev; however: Package libsimde-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on pandoc; however: Package pandoc is not installed. pbuilder-satisfydepends-dummy depends on python3:any. 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} 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} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} liblocale-gettext-perl{a} liblua5.4-0{a} libmagic-mgc{a} libmagic1t64{a} libnuma1{a} libpipeline1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libsimde-dev{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} netbase{a} pandoc{a} pandoc-data{a} po-debconf{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 51 newly installed, 0 to remove and 0 not upgraded. Need to get 44.7 MB of archives. After unpacking 296 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 3.13.3-2 [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 3.13.3-2 [1998 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.3-1 [27.2 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-2 [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 3.13.3-2 [1890 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.3-2 [751 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.3-1 [10.2 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.3-1 [28.2 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2 [241 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41-4 [93.9 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-4 [862 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 37 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.4 [629 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2 [1611 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.2 [919 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 liblua5.4-0 arm64 5.4.7-1+b2 [134 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libnuma1 arm64 2.0.19-1 [21.6 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libsimde-dev all 0.8.2-3 [467 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-2 [49.2 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 pandoc-data all 3.1.11.1-3 [459 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 pandoc arm64 3.1.11.1+ds-2 [26.2 MB] Fetched 44.7 MB in 0s (125 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 ... 19953 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_3.13.3-2_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.3-2) ... 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_3.13.3-2_arm64.deb ... Unpacking python3.13-minimal (3.13.3-2) ... Setting up libpython3.13-minimal:arm64 (3.13.3-2) ... Setting up libexpat1:arm64 (2.7.1-1) ... Setting up python3.13-minimal (3.13.3-2) ... Selecting previously unselected package python3-minimal. (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 ... 20302 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.3-1_arm64.deb ... Unpacking python3-minimal (3.13.3-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... 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Setting up libdebhelper-perl (13.24.2) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up tzdata (2025b-2) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Apr 27 19:26:59 UTC 2025. Universal Time is now: Sun Apr 27 19:26:59 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up libffi8:arm64 (3.4.8-2) ... Setting up libnuma1:arm64 (2.0.19-1) ... 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 liblua5.4-0:arm64 (5.4.7-1+b2) ... Setting up netbase (6.5) ... Setting up pandoc-data (3.1.11.1-3) ... Setting up readline-common (8.2-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2) ... Setting up libtool (2.5.4-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3+b1) ... Setting up dh-autoreconf (20) ... Setting up pandoc (3.1.11.1+ds-2) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up libpython3.13-stdlib:arm64 (3.13.3-2) ... Setting up libpython3-stdlib:arm64 (3.13.3-1) ... Setting up python3.13 (3.13.3-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.3-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.2) ... Processing triggers for libc-bin (2.41-7) ... Reading package lists... Building dependency tree... Reading state information... 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/hisat2-2.2.1/ && 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 > ../hisat2_2.2.1-5_source.changes dpkg-buildpackage: info: source package hisat2 dpkg-buildpackage: info: source version 2.2.1-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/hisat2-2.2.1' rm -f hisat2-build-s hisat2-build-l hisat2-align-s hisat2-align-l hisat2-inspect-s hisat2-inspect-l hisat2-repeat hisat2-build-s-debug hisat2-build-l-debug hisat2-align-s-debug hisat2-align-l-debug hisat2-inspect-s-debug hisat2-inspect-l-debug hisat2-repeat-debug \ hisat2-build-s.exe hisat2-build-l.exe hisat2-align-s.exe hisat2-align-l.exe hisat2-inspect-s.exe hisat2-inspect-l.exe hisat2-repeat.exe hisat2-build-s-debug.exe hisat2-build-l-debug.exe hisat2-align-s-debug.exe hisat2-align-l-debug.exe hisat2-inspect-s-debug.exe hisat2-inspect-l-debug.exe hisat2-repeat-debug.exe \ hisat2-src.zip hisat2-bin.zip rm -f core.* .tmp.head rm -rf *.dSYM rm -rf .ht2lib-obj* rm -f libhisat2lib*.a libhisat2lib*.so make[1]: Leaving directory '/build/reproducible-path/hisat2-2.2.1' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/hisat2-2.2.1' dh_auto_build -- BUILD_HOST='Debian' BUILD_TIME="09 July 2024" all doc make -j12 "INSTALL=install --strip-program=true" BUILD_HOST=Debian "BUILD_TIME=09 July 2024" all doc make[2]: Entering directory '/build/reproducible-path/hisat2-2.2.1' /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/reproducible-path/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \ -I. -I third_party \ -o hisat2-build-s hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/reproducible-path/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-build-l hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/reproducible-path/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-align-s hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/reproducible-path/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-align-l hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \ -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/reproducible-path/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DHISAT2_INSPECT_MAIN -Wall \ -I. -I third_party -I . \ -o hisat2-inspect-s hisat2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \ -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/reproducible-path/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN -Wall \ -I. -I third_party -I . \ -o hisat2-inspect-l hisat2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/reproducible-path/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-repeat hisat2_repeat.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp mask.cpp qual.cpp aligner_bt.cpp scoring.cpp simple_func.cpp dp_framer.cpp aligner_result.cpp aligner_sw_driver.cpp aligner_sw.cpp aligner_swsse_ee_i16.cpp aligner_swsse_ee_u8.cpp aligner_swsse_loc_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse.cpp bit_packed_array.cpp repeat_builder.cpp diff_sample.cpp hisat2_repeat_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now make[2]: Nothing to be done for 'doc'. In file included from hisat2_build.cpp:35: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h: In instantiation of ‘void GFM::initFromVector(TStr&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::string&, bool, index_t, index_t, index_t, int, EList*, EList >*, uint32_t, bool) [with TStr = SString; index_t = long unsigned int; std::string = std::__cxx11::basic_string; std::ofstream = std::basic_ofstream; uint32_t = unsigned int]’: gfm.h:1039:23: required from ‘GFM::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, index_t, index_t, index_t, int, EList&, EList&, index_t, const RefReadInParams&, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ 1039 | initFromVector( | ~~~~~~~~~~~~~~~~~~~~^ 1040 | s, | ~~ 1041 | snpfile, | ~~~~~~~~ 1042 | htfile, | ~~~~~~~ 1043 | ssfile, | ~~~~~~~ 1044 | exonfile, | ~~~~~~~~~ 1045 | svfile, | ~~~~~~~ 1046 | repeatfile, | ~~~~~~~~~~~ 1047 | is, | ~~~ 1048 | szs, | ~~~~ 1049 | sztot, | ~~~~~~ 1050 | refparams, | ~~~~~~~~~~ 1051 | fout1, | ~~~~~~ 1052 | fout2, | ~~~~~~ 1053 | outfile, | ~~~~~~~~ 1054 | useBlockwise, | ~~~~~~~~~~~~~ 1055 | bmax, | ~~~~~ 1056 | bmaxSqrtMult, | ~~~~~~~~~~~~~ 1057 | bmaxDivN, | ~~~~~~~~~ 1058 | dcv, | ~~~~ 1059 | parent_szs, | ~~~~~~~~~~~ 1060 | parent_refnames, | ~~~~~~~~~~~~~~~~ 1061 | seed, | ~~~~~ 1062 | verbose); | ~~~~~~~~ hgfm.h:1989:14: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long unsigned int; uint32_t = unsigned int]’ 1989 | _in6(NULL) | ^ hisat2_build.cpp:535:15: required from ‘void driver(const std::string&, EList >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::string = std::__cxx11::basic_string]’ 535 | gfm = new HGFM( | ^~~~~~~~~~~~~~~~~~~~~ 536 | s, | ~~ 537 | packed, | ~~~~~~~ 538 | 1, // TODO: maybe not? | ~~~~~~~~~~~~~~~~~~~~~~~ 539 | lineRate, | ~~~~~~~~~ 540 | offRate, // suffix-array sampling rate | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 541 | ftabChars, // number of chars in initial arrow-pair calc | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 542 | localOffRate, | ~~~~~~~~~~~~~ 543 | localFtabChars, | ~~~~~~~~~~~~~~~ 544 | nthreads, | ~~~~~~~~~ 545 | snpfile, | ~~~~~~~~ 546 | htfile, | ~~~~~~~ 547 | ssfile, | ~~~~~~~ 548 | exonfile, | ~~~~~~~~~ 549 | svfile, | ~~~~~~~ 550 | repeatfile, | ~~~~~~~~~~~ 551 | outfile, // basename for .?.ht2 files | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 552 | reverse == 0, // fw | ~~~~~~~~~~~~~~~~~~~ 553 | !entireSA, // useBlockwise | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 554 | bmax, // block size for blockwise SA builder | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 555 | bmaxMultSqrt, // block size as multiplier of sqrt(len) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 556 | bmaxDivN, // block size as divisor of len | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 557 | noDc? 0 : dcv,// difference-cover period | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 558 | is, // list of input streams | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 559 | szs, // list of reference sizes | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 560 | (TIndexOffU)sztot.first, // total size of all unambiguous ref chars | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 561 | refparams, // reference read-in parameters | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 562 | localindex, // create local indexes? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 563 | parent_szs, // parent szs | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 564 | parent_refnames, // parent refence names | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 565 | seed, // pseudo-random number generator seed | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 566 | -1, // override offRate | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 567 | verbose, // be talkative | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 568 | autoMem, // pass exceptions up to the toplevel so that we can adjust memory settings automatically | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 569 | sanityCheck); // verify results and internal consistency | ~~~~~~~~~~~~ hisat2_build.cpp:786:39: required from here 786 | driver >(infile, | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ 787 | infiles, | ~~~~~~~~ 788 | snp_fname, | ~~~~~~~~~~ 789 | ht_fname, | ~~~~~~~~~ 790 | ss_fname, | ~~~~~~~~~ 791 | exon_fname, | ~~~~~~~~~~~ 792 | sv_fname, | ~~~~~~~~~ 793 | dummy_fname, | ~~~~~~~~~~~~ 794 | outfile, | ~~~~~~~~ 795 | false, | ~~~~~~ 796 | REF_READ_FORWARD, | ~~~~~~~~~~~~~~~~~ 797 | true, // create local indexes | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 798 | NULL, // no parent szs | ~~~~~~~~~~~~~~~~~~~~~~ 799 | NULL, // no parent refnames | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 800 | &parent_szs, // get parent szs | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 801 | &parent_refnames); // get parent refnames | ~~~~~~~~~~~~~~~~~ gfm.h:2167:33: warning: variable ‘template_len’ set but not used [-Wunused-but-set-variable] 2167 | index_t template_len = 0; | ^~~~~~~~~~~~ In file included from hisat2_build.cpp:35: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76, from aligner_sw_driver.h:86, from hi_aligner.h:42, from spliced_aligner.h:23, from hisat2.cpp:46: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void parseOptions(int, const char**)’: hisat2.cpp:1823:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1823 | auto_ptr presets(new PresetsV0()); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h: In instantiation of ‘void GFM::initFromVector(TStr&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::string&, bool, index_t, index_t, index_t, int, EList*, EList >*, uint32_t, bool) [with TStr = SString; index_t = unsigned int; std::string = std::__cxx11::basic_string; std::ofstream = std::basic_ofstream; uint32_t = unsigned int]’: gfm.h:1039:23: required from ‘GFM::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, index_t, index_t, index_t, int, EList&, EList&, index_t, const RefReadInParams&, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ 1039 | initFromVector( | ~~~~~~~~~~~~~~~~~~~~^ 1040 | s, | ~~ 1041 | snpfile, | ~~~~~~~~ 1042 | htfile, | ~~~~~~~ 1043 | ssfile, | ~~~~~~~ 1044 | exonfile, | ~~~~~~~~~ 1045 | svfile, | ~~~~~~~ 1046 | repeatfile, | ~~~~~~~~~~~ 1047 | is, | ~~~ 1048 | szs, | ~~~~ 1049 | sztot, | ~~~~~~ 1050 | refparams, | ~~~~~~~~~~ 1051 | fout1, | ~~~~~~ 1052 | fout2, | ~~~~~~ 1053 | outfile, | ~~~~~~~~ 1054 | useBlockwise, | ~~~~~~~~~~~~~ 1055 | bmax, | ~~~~~ 1056 | bmaxSqrtMult, | ~~~~~~~~~~~~~ 1057 | bmaxDivN, | ~~~~~~~~~ 1058 | dcv, | ~~~~ 1059 | parent_szs, | ~~~~~~~~~~~ 1060 | parent_refnames, | ~~~~~~~~~~~~~~~~ 1061 | seed, | ~~~~~ 1062 | verbose); | ~~~~~~~~ hgfm.h:1989:14: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = unsigned int; uint32_t = unsigned int]’ 1989 | _in6(NULL) | ^ hisat2_build.cpp:535:15: required from ‘void driver(const std::string&, EList >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::string = std::__cxx11::basic_string]’ 535 | gfm = new HGFM( | ^~~~~~~~~~~~~~~~~~~~~ 536 | s, | ~~ 537 | packed, | ~~~~~~~ 538 | 1, // TODO: maybe not? | ~~~~~~~~~~~~~~~~~~~~~~~ 539 | lineRate, | ~~~~~~~~~ 540 | offRate, // suffix-array sampling rate | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 541 | ftabChars, // number of chars in initial arrow-pair calc | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 542 | localOffRate, | ~~~~~~~~~~~~~ 543 | localFtabChars, | ~~~~~~~~~~~~~~~ 544 | nthreads, | ~~~~~~~~~ 545 | snpfile, | ~~~~~~~~ 546 | htfile, | ~~~~~~~ 547 | ssfile, | ~~~~~~~ 548 | exonfile, | ~~~~~~~~~ 549 | svfile, | ~~~~~~~ 550 | repeatfile, | ~~~~~~~~~~~ 551 | outfile, // basename for .?.ht2 files | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 552 | reverse == 0, // fw | ~~~~~~~~~~~~~~~~~~~ 553 | !entireSA, // useBlockwise | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 554 | bmax, // block size for blockwise SA builder | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 555 | bmaxMultSqrt, // block size as multiplier of sqrt(len) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 556 | bmaxDivN, // block size as divisor of len | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 557 | noDc? 0 : dcv,// difference-cover period | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 558 | is, // list of input streams | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 559 | szs, // list of reference sizes | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 560 | (TIndexOffU)sztot.first, // total size of all unambiguous ref chars | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 561 | refparams, // reference read-in parameters | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 562 | localindex, // create local indexes? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 563 | parent_szs, // parent szs | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 564 | parent_refnames, // parent refence names | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 565 | seed, // pseudo-random number generator seed | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 566 | -1, // override offRate | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 567 | verbose, // be talkative | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 568 | autoMem, // pass exceptions up to the toplevel so that we can adjust memory settings automatically | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 569 | sanityCheck); // verify results and internal consistency | ~~~~~~~~~~~~ hisat2_build.cpp:786:39: required from here 786 | driver >(infile, | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ 787 | infiles, | ~~~~~~~~ 788 | snp_fname, | ~~~~~~~~~~ 789 | ht_fname, | ~~~~~~~~~ 790 | ss_fname, | ~~~~~~~~~ 791 | exon_fname, | ~~~~~~~~~~~ 792 | sv_fname, | ~~~~~~~~~ 793 | dummy_fname, | ~~~~~~~~~~~~ 794 | outfile, | ~~~~~~~~ 795 | false, | ~~~~~~ 796 | REF_READ_FORWARD, | ~~~~~~~~~~~~~~~~~ 797 | true, // create local indexes | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 798 | NULL, // no parent szs | ~~~~~~~~~~~~~~~~~~~~~~ 799 | NULL, // no parent refnames | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 800 | &parent_szs, // get parent szs | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 801 | &parent_refnames); // get parent refnames | ~~~~~~~~~~~~~~~~~ gfm.h:2167:33: warning: variable ‘template_len’ set but not used [-Wunused-but-set-variable] 2167 | index_t template_len = 0; | ^~~~~~~~~~~~ In file included from hisat2_inspect.cpp:25: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from hisat2_repeat.cpp:36: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’: hisat2.cpp:3167:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3167 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3168:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3168 | auto_ptr ps(patsrcFact->create()); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3189:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3189 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void driver(const char*, const std::string&, const std::string&)’: hisat2.cpp:4035:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 4035 | auto_ptr refs( | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hi_aligner.h: In instantiation of ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’: hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:5688:105: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] 5688 | if(coord.off() + pepol.maxFragLen() * 2 < toff || toff + pepol.maxFragLen() * 2 < coord.off()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gfm.h: In instantiation of ‘void GFM::checkOrigs(const EList >&, bool) const [with index_t = unsigned int]’: hisat2.cpp:3815:17: required from ‘void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’ 3815 | gfm.checkOrigs(os, false); | ~~~~~~~~~~~~~~^~~~~~~~~~~ hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ gfm.h:6935:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^~~~~~~~ In file included from hisat2_inspect.cpp:25: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41: group_walk.h: In instantiation of ‘std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:1517:14: required from ‘bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ 1517 | st.advance( | ~~~~~~~~~~^ 1518 | gfmFw, | ~~~~~~ 1519 | ref, | ~~~~ 1520 | sa, | ~~~ 1521 | hit_, | ~~~~~ 1522 | (index_t)range, | ~~~~~~~~~~~~~~~ 1523 | false, | ~~~~~~ 1524 | NULL, | ~~~~~ 1525 | st_, | ~~~~ 1526 | gws, | ~~~~ 1527 | met, | ~~~~ 1528 | prm); | ~~~~ hi_aligner.h:5901:34: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’ 5901 | _gws_local.advanceElement( | ~~~~~~~~~~~~~~~~~~~~~~~~~^ 5902 | off, | ~~~~ 5903 | gfm, // forward Bowtie index for walking left | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5904 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5905 | _sas_local, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5906 | _gwstate_local, // GroupWalk state; scratch space | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5907 | wr, // put the result here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5908 | met, // metrics | ~~~~~~~~~~~~~~~~~~~~~~~~ 5909 | prm); // per-read metrics | ~~~~ hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ 5664 | getGenomeCoords_local( | ^~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ group_walk.h:1147:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1147 | if(new_node_bot - new_node_top < gws.map.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ group_walk.h:1158:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1158 | for(index_t j = 0; j + 1 < gws.map.size(); j++) { | ~~~~~~^~~~~~~~~~~~~~~~ group_walk.h:1213:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1213 | if(node_range.second - node_range.first < st.back().map_.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1224:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1224 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’: hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ 718 | alts, | ~~~~~ 719 | haplotypes, | ~~~~~~~~~~~ 720 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 721 | joinedOff, | ~~~~~~~~~~ 722 | rdseq, | ~~~~~~ 723 | rdoff - base_rdoff, | ~~~~~~~~~~~~~~~~~~~ 724 | rdoff, | ~~~~~~ 725 | rdlen, | ~~~~~~ 726 | ref, | ~~~~ 727 | sharedVar.raw_refbufs, | ~~~~~~~~~~~~~~~~~~~~~~ 728 | ASSERT_ONLY(sharedVar.destU32,) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 729 | alt_edits, | ~~~~~~~~~~ 730 | best_rdoff, | ~~~~~~~~~~~ 731 | NULL, /* rfseq */ | ~~~~~~~~~~~~~~~~~ 732 | tidx, | ~~~~~ 733 | rfoff, | ~~~~~~ 734 | rflen, | ~~~~~~ 735 | left, | ~~~~~ 736 | edits, | ~~~~~~ 737 | mm, | ~~~ 738 | ht_llist, | ~~~~~~~~~ 739 | cmp_ht, | ~~~~~~~ 740 | candidate_edits, | ~~~~~~~~~~~~~~~~ 741 | 0, /* tmp_numNs */ | ~~~~~~~~~~~~~~~~~~ 742 | numNs, | ~~~~~~ 743 | 0, /* dep */ | ~~~~~~~~~~~~~~~ 744 | gpol, | ~~~~~ 745 | numALTsTried); | ~~~~~~~~~~~~~ hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’ 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, | ~~~~~ 2339 | altdb.haplotypes(), | ~~~~~~~~~~~~~~~~~~~ 2340 | altdb.haplotype_maxrights(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2341 | genomeHit._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~ 2342 | seq, | ~~~~ 2343 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2344 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2345 | genomeHit._len, | ~~~~~~~~~~~~~~~ 2346 | ref, | ~~~~ 2347 | sharedVars, | ~~~~~~~~~~~ 2348 | genomeHit._tidx, | ~~~~~~~~~~~~~~~~ 2349 | (int)genomeHit._toff, | ~~~~~~~~~~~~~~~~~~~~~ 2350 | reflen, | ~~~~~~~ 2351 | false, /* left? */ | ~~~~~~~~~~~~~~~~~~ 2352 | gpol, | ~~~~~ 2353 | *genomeHit._edits, | ~~~~~~~~~~~~~~~~~~ 2354 | sharedVars.ht_llist, | ~~~~~~~~~~~~~~~~~~~~ 2355 | *genomeHit._ht_list, | ~~~~~~~~~~~~~~~~~~~~ 2356 | sharedVars.cmp_ht, | ~~~~~~~~~~~~~~~~~~ 2357 | &candidate_edits); | ~~~~~~~~~~~~~~~~~ hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:2801:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2801 | if(rfoff >= contig_len) return 0; | ~~~~~~^~~~~~~~~~~~~ hi_aligner.h:2879:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2879 | if(alt_range.first >= alts.size()) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:3044:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 3044 | for(int i = 0; i < alt.len; i++) { | ~~^~~~~~~~~ hi_aligner.h:3085:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 3085 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { | ~~~~~^~~~~~~~ hi_aligner.h:3161:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 3161 | if(alignedLen == next_rdlen) return rdlen; | ~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3197:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 3197 | if(mm_max_rd_i + rdoff > best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:3202:39: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 3202 | } else if(mm_max_rd_i + rdoff == best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3454:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 3454 | if(best_rdoff < rdoff + rd_i) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ group_walk.h: In instantiation of ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:494:14: required from ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’ 494 | return init(gfm, ref, sa, sts, hit, range, reportList, res, met); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1453:18: required from ‘void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ 1453 | st_.back().init( | ~~~~~~~~~~~~~~~^ 1454 | gfmFw, // Bowtie index | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1455 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1456 | sa, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1457 | st_, // EList | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1458 | hit_, // GWHit | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1459 | 0, // range 0 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1460 | false, // put resolved elements into res_? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1461 | NULL, // put resolved elements here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1462 | top, // GBW row at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1463 | bot, // GBW row at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1464 | node_top, // node at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1465 | node_bot, // node at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1466 | sa.node_iedge_count, | ~~~~~~~~~~~~~~~~~~~~ 1467 | 0, // # steps taken | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1468 | met); // update metrics here | ~~~~ hi_aligner.h:5896:20: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’ 5896 | _gws_local.init(gfm, ref, _sas_local, rnd, met); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ 5664 | getGenomeCoords_local( | ^~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ group_walk.h:785:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 785 | if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) { | ~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ group_walk.h:789:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 789 | if(new_top - top == tmp_gbwt_to_node.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:795:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 795 | if(i + 1 < tmp_zOffs.size()) { | ~~~~~~^~~~~~~~~~~~~~~~~~ group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 801 | if(new_bot - top < tmp_gbwt_to_node.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = unsigned int]’: hi_aligner.h:2915:39: required from ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ 2915 | add_haplotypes(alts, | ~~~~~~~~~~~~~~^~~~~~ 2916 | haplotypes, | ~~~~~~~~~~~ 2917 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 2918 | cmp_ht, | ~~~~~~~ 2919 | ht_list, | ~~~~~~~~ 2920 | rdlen); | ~~~~~~ hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ 718 | alts, | ~~~~~ 719 | haplotypes, | ~~~~~~~~~~~ 720 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 721 | joinedOff, | ~~~~~~~~~~ 722 | rdseq, | ~~~~~~ 723 | rdoff - base_rdoff, | ~~~~~~~~~~~~~~~~~~~ 724 | rdoff, | ~~~~~~ 725 | rdlen, | ~~~~~~ 726 | ref, | ~~~~ 727 | sharedVar.raw_refbufs, | ~~~~~~~~~~~~~~~~~~~~~~ 728 | ASSERT_ONLY(sharedVar.destU32,) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 729 | alt_edits, | ~~~~~~~~~~ 730 | best_rdoff, | ~~~~~~~~~~~ 731 | NULL, /* rfseq */ | ~~~~~~~~~~~~~~~~~ 732 | tidx, | ~~~~~ 733 | rfoff, | ~~~~~~ 734 | rflen, | ~~~~~~ 735 | left, | ~~~~~ 736 | edits, | ~~~~~~ 737 | mm, | ~~~ 738 | ht_llist, | ~~~~~~~~~ 739 | cmp_ht, | ~~~~~~~ 740 | candidate_edits, | ~~~~~~~~~~~~~~~~ 741 | 0, /* tmp_numNs */ | ~~~~~~~~~~~~~~~~~~ 742 | numNs, | ~~~~~~ 743 | 0, /* dep */ | ~~~~~~~~~~~~~~~ 744 | gpol, | ~~~~~ 745 | numALTsTried); | ~~~~~~~~~~~~~ hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’ 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, | ~~~~~ 2339 | altdb.haplotypes(), | ~~~~~~~~~~~~~~~~~~~ 2340 | altdb.haplotype_maxrights(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2341 | genomeHit._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~ 2342 | seq, | ~~~~ 2343 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2344 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2345 | genomeHit._len, | ~~~~~~~~~~~~~~~ 2346 | ref, | ~~~~ 2347 | sharedVars, | ~~~~~~~~~~~ 2348 | genomeHit._tidx, | ~~~~~~~~~~~~~~~~ 2349 | (int)genomeHit._toff, | ~~~~~~~~~~~~~~~~~~~~~ 2350 | reflen, | ~~~~~~~ 2351 | false, /* left? */ | ~~~~~~~~~~~~~~~~~~ 2352 | gpol, | ~~~~~ 2353 | *genomeHit._edits, | ~~~~~~~~~~~~~~~~~~ 2354 | sharedVars.ht_llist, | ~~~~~~~~~~~~~~~~~~~~ 2355 | *genomeHit._ht_list, | ~~~~~~~~~~~~~~~~~~~~ 2356 | sharedVars.cmp_ht, | ~~~~~~~~~~~~~~~~~~ 2357 | &candidate_edits); | ~~~~~~~~~~~~~~~~~ hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:2660:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2660 | if(ht_range.first >= haplotypes.size()) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ hi_aligner.h:2675:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2675 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2713:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2713 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2737:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2737 | for(; ht_range.second < haplotypes.size(); ht_range.second++) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ hi_aligner.h:2744:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2744 | if(ht_list[h].first == ht_range.second) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long int]’: spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:408:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] 408 | bool another_spliced = false; | ^~~~~~~~~~~~~~~ In file included from aligner_sw.h:76, from aligner_sw_driver.h:86, from hi_aligner.h:42, from spliced_aligner.h:23, from hisat2.cpp:46: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void parseOptions(int, const char**)’: hisat2.cpp:1823:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1823 | auto_ptr presets(new PresetsV0()); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’: hisat2.cpp:3167:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3167 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3168:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3168 | auto_ptr ps(patsrcFact->create()); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3189:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3189 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void driver(const char*, const std::string&, const std::string&)’: hisat2.cpp:4035:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 4035 | auto_ptr refs( | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76, from hisat2_repeat.cpp:37: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ hi_aligner.h: In instantiation of ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’: hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:4385:84: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4385 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:4404:55: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefId’ {aka ‘long int’} [-Wsign-compare] 4404 | if(positions[p].first.tid != res.refid()) continue; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:4405:63: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] 4405 | if(positions[p].first.toff + 1000 < res.refoff() || | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:4406:52: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] 4406 | res.refoff() + 1000 < positions[p].first.toff) continue; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:4407:88: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4407 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:4489:92: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4489 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:4578:69: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4578 | align2repeat = (numBestPair == 0 || numBestPair > rp.khits); | ~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:4584:83: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4584 | align2repeat = (rs->size() == 0 || sink.numBestUnp(rdi).first > rp.khits); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:4614:55: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4614 | if(sink.numBestUnp(rdi).first > rp.khits) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h: In instantiation of ‘bool HI_Aligner::pairReads(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, WalkMetrics&, PerReadMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’: hi_aligner.h:4088:17: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 4088 | pairReads(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, wlm, prm, him, rnd, sink); | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:5990:51: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] 5990 | if(_repeatConcordant[r].first == left.off() && | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:5991:52: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] 5991 | _repeatConcordant[r].second == left2.off()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h: In instantiation of ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’: hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:5661:33: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 5661 | if(nelt > 0 && nelt <= rp.kseeds && hitlen > max_hitlen) { | ~~~~~^~~~~~~~~~~~ hi_aligner.h:5688:105: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] 5688 | if(coord.off() + pepol.maxFragLen() * 2 < toff || toff + pepol.maxFragLen() * 2 < coord.off()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gfm.h: In instantiation of ‘void GFM::checkOrigs(const EList >&, bool) const [with index_t = long unsigned int]’: hisat2.cpp:3815:17: required from ‘void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’ 3815 | gfm.checkOrigs(os, false); | ~~~~~~~~~~~~~~^~~~~~~~~~~ hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ gfm.h:6935:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^~~~~~~~ hi_aligner.h: In instantiation of ‘index_t HI_Aligner::getAnchorHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const BitPairReference&, RandomSource&, index_t, bool, EList >&, index_t, SharedTempVars&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool) [with index_t = long unsigned int; local_index_t = short unsigned int]’: hi_aligner.h:5525:23: required from ‘bool HI_Aligner::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 5525 | index_t numHits = getAnchorHits(gfm, | ^~~~~~~~~~~~~ hi_aligner.h:4080:31: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 4080 | found[rdi][fwi] = align(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, swa, ssdb, rdi, fw, wlm, prm, swm, him, rnd, sink); | ^~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:5150:32: warning: comparison of integer expressions of different signedness: ‘TRefId’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] 5150 | if(coord.ref() == numeric_limits::max()) | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long unsigned int]’: hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:2267:47: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] 2267 | findSSOffs(gfm, altdb, (coord.joinedOff() >= width ? (index_t)(coord.joinedOff() - width) : 0), (index_t)(coord.joinedOff() + width), ssOffs); | ~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41: group_walk.h: In instantiation of ‘std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:1517:14: required from ‘bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ 1517 | st.advance( | ~~~~~~~~~~^ 1518 | gfmFw, | ~~~~~~ 1519 | ref, | ~~~~ 1520 | sa, | ~~~ 1521 | hit_, | ~~~~~ 1522 | (index_t)range, | ~~~~~~~~~~~~~~~ 1523 | false, | ~~~~~~ 1524 | NULL, | ~~~~~ 1525 | st_, | ~~~~ 1526 | gws, | ~~~~ 1527 | met, | ~~~~ 1528 | prm); | ~~~~ hi_aligner.h:5901:34: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 5901 | _gws_local.advanceElement( | ~~~~~~~~~~~~~~~~~~~~~~~~~^ 5902 | off, | ~~~~ 5903 | gfm, // forward Bowtie index for walking left | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5904 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5905 | _sas_local, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5906 | _gwstate_local, // GroupWalk state; scratch space | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5907 | wr, // put the result here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5908 | met, // metrics | ~~~~~~~~~~~~~~~~~~~~~~~~ 5909 | prm); // per-read metrics | ~~~~ hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 5664 | getGenomeCoords_local( | ^~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ group_walk.h:1147:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1147 | if(new_node_bot - new_node_top < gws.map.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ group_walk.h:1158:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1158 | for(index_t j = 0; j + 1 < gws.map.size(); j++) { | ~~~~~~^~~~~~~~~~~~~~~~ group_walk.h:1213:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1213 | if(node_range.second - node_range.first < st.back().map_.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1224:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1224 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’: hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ 718 | alts, | ~~~~~ 719 | haplotypes, | ~~~~~~~~~~~ 720 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 721 | joinedOff, | ~~~~~~~~~~ 722 | rdseq, | ~~~~~~ 723 | rdoff - base_rdoff, | ~~~~~~~~~~~~~~~~~~~ 724 | rdoff, | ~~~~~~ 725 | rdlen, | ~~~~~~ 726 | ref, | ~~~~ 727 | sharedVar.raw_refbufs, | ~~~~~~~~~~~~~~~~~~~~~~ 728 | ASSERT_ONLY(sharedVar.destU32,) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 729 | alt_edits, | ~~~~~~~~~~ 730 | best_rdoff, | ~~~~~~~~~~~ 731 | NULL, /* rfseq */ | ~~~~~~~~~~~~~~~~~ 732 | tidx, | ~~~~~ 733 | rfoff, | ~~~~~~ 734 | rflen, | ~~~~~~ 735 | left, | ~~~~~ 736 | edits, | ~~~~~~ 737 | mm, | ~~~ 738 | ht_llist, | ~~~~~~~~~ 739 | cmp_ht, | ~~~~~~~ 740 | candidate_edits, | ~~~~~~~~~~~~~~~~ 741 | 0, /* tmp_numNs */ | ~~~~~~~~~~~~~~~~~~ 742 | numNs, | ~~~~~~ 743 | 0, /* dep */ | ~~~~~~~~~~~~~~~ 744 | gpol, | ~~~~~ 745 | numALTsTried); | ~~~~~~~~~~~~~ hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long unsigned int]’ 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, | ~~~~~ 2339 | altdb.haplotypes(), | ~~~~~~~~~~~~~~~~~~~ 2340 | altdb.haplotype_maxrights(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2341 | genomeHit._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~ 2342 | seq, | ~~~~ 2343 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2344 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2345 | genomeHit._len, | ~~~~~~~~~~~~~~~ 2346 | ref, | ~~~~ 2347 | sharedVars, | ~~~~~~~~~~~ 2348 | genomeHit._tidx, | ~~~~~~~~~~~~~~~~ 2349 | (int)genomeHit._toff, | ~~~~~~~~~~~~~~~~~~~~~ 2350 | reflen, | ~~~~~~~ 2351 | false, /* left? */ | ~~~~~~~~~~~~~~~~~~ 2352 | gpol, | ~~~~~ 2353 | *genomeHit._edits, | ~~~~~~~~~~~~~~~~~~ 2354 | sharedVars.ht_llist, | ~~~~~~~~~~~~~~~~~~~~ 2355 | *genomeHit._ht_list, | ~~~~~~~~~~~~~~~~~~~~ 2356 | sharedVars.cmp_ht, | ~~~~~~~~~~~~~~~~~~ 2357 | &candidate_edits); | ~~~~~~~~~~~~~~~~~ hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:2801:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2801 | if(rfoff >= contig_len) return 0; | ~~~~~~^~~~~~~~~~~~~ hi_aligner.h:2879:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2879 | if(alt_range.first >= alts.size()) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:3044:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 3044 | for(int i = 0; i < alt.len; i++) { | ~~^~~~~~~~~ hi_aligner.h:3085:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 3085 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { | ~~~~~^~~~~~~~ hi_aligner.h:3161:31: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 3161 | if(alignedLen == next_rdlen) return rdlen; | ~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3197:32: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 3197 | if(mm_max_rd_i + rdoff > best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:3202:39: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 3202 | } else if(mm_max_rd_i + rdoff == best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3454:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 3454 | if(best_rdoff < rdoff + rd_i) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ group_walk.h: In instantiation of ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:494:14: required from ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’ 494 | return init(gfm, ref, sa, sts, hit, range, reportList, res, met); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1453:18: required from ‘void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ 1453 | st_.back().init( | ~~~~~~~~~~~~~~~^ 1454 | gfmFw, // Bowtie index | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1455 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1456 | sa, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1457 | st_, // EList | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1458 | hit_, // GWHit | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1459 | 0, // range 0 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1460 | false, // put resolved elements into res_? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1461 | NULL, // put resolved elements here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1462 | top, // GBW row at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1463 | bot, // GBW row at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1464 | node_top, // node at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1465 | node_bot, // node at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1466 | sa.node_iedge_count, | ~~~~~~~~~~~~~~~~~~~~ 1467 | 0, // # steps taken | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1468 | met); // update metrics here | ~~~~ hi_aligner.h:5896:20: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 5896 | _gws_local.init(gfm, ref, _sas_local, rnd, met); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 5664 | getGenomeCoords_local( | ^~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ group_walk.h:785:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 785 | if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) { | ~~~~~~^~~~~~~~~~~~~~~~~~ group_walk.h:789:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 789 | if(new_top - top == tmp_gbwt_to_node.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:795:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 795 | if(i + 1 < tmp_zOffs.size()) { | ~~~~~~^~~~~~~~~~~~~~~~~~ group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 801 | if(new_bot - top < tmp_gbwt_to_node.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = long unsigned int]’: hi_aligner.h:2915:39: required from ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ 2915 | add_haplotypes(alts, | ~~~~~~~~~~~~~~^~~~~~ 2916 | haplotypes, | ~~~~~~~~~~~ 2917 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 2918 | cmp_ht, | ~~~~~~~ 2919 | ht_list, | ~~~~~~~~ 2920 | rdlen); | ~~~~~~ hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ 718 | alts, | ~~~~~ 719 | haplotypes, | ~~~~~~~~~~~ 720 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 721 | joinedOff, | ~~~~~~~~~~ 722 | rdseq, | ~~~~~~ 723 | rdoff - base_rdoff, | ~~~~~~~~~~~~~~~~~~~ 724 | rdoff, | ~~~~~~ 725 | rdlen, | ~~~~~~ 726 | ref, | ~~~~ 727 | sharedVar.raw_refbufs, | ~~~~~~~~~~~~~~~~~~~~~~ 728 | ASSERT_ONLY(sharedVar.destU32,) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 729 | alt_edits, | ~~~~~~~~~~ 730 | best_rdoff, | ~~~~~~~~~~~ 731 | NULL, /* rfseq */ | ~~~~~~~~~~~~~~~~~ 732 | tidx, | ~~~~~ 733 | rfoff, | ~~~~~~ 734 | rflen, | ~~~~~~ 735 | left, | ~~~~~ 736 | edits, | ~~~~~~ 737 | mm, | ~~~ 738 | ht_llist, | ~~~~~~~~~ 739 | cmp_ht, | ~~~~~~~ 740 | candidate_edits, | ~~~~~~~~~~~~~~~~ 741 | 0, /* tmp_numNs */ | ~~~~~~~~~~~~~~~~~~ 742 | numNs, | ~~~~~~ 743 | 0, /* dep */ | ~~~~~~~~~~~~~~~ 744 | gpol, | ~~~~~ 745 | numALTsTried); | ~~~~~~~~~~~~~ hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long unsigned int]’ 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, | ~~~~~ 2339 | altdb.haplotypes(), | ~~~~~~~~~~~~~~~~~~~ 2340 | altdb.haplotype_maxrights(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2341 | genomeHit._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~ 2342 | seq, | ~~~~ 2343 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2344 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2345 | genomeHit._len, | ~~~~~~~~~~~~~~~ 2346 | ref, | ~~~~ 2347 | sharedVars, | ~~~~~~~~~~~ 2348 | genomeHit._tidx, | ~~~~~~~~~~~~~~~~ 2349 | (int)genomeHit._toff, | ~~~~~~~~~~~~~~~~~~~~~ 2350 | reflen, | ~~~~~~~ 2351 | false, /* left? */ | ~~~~~~~~~~~~~~~~~~ 2352 | gpol, | ~~~~~ 2353 | *genomeHit._edits, | ~~~~~~~~~~~~~~~~~~ 2354 | sharedVars.ht_llist, | ~~~~~~~~~~~~~~~~~~~~ 2355 | *genomeHit._ht_list, | ~~~~~~~~~~~~~~~~~~~~ 2356 | sharedVars.cmp_ht, | ~~~~~~~~~~~~~~~~~~ 2357 | &candidate_edits); | ~~~~~~~~~~~~~~~~~ hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:2660:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2660 | if(ht_range.first >= haplotypes.size()) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ hi_aligner.h:2675:37: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 2675 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2713:41: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 2713 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2737:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2737 | for(; ht_range.second < haplotypes.size(); ht_range.second++) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ hi_aligner.h:2744:41: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 2744 | if(ht_list[h].first == ht_range.second) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int; int64_t = long int]’: spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:408:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] 408 | bool another_spliced = false; | ^~~~~~~~~~~~~~~ spliced_aligner.h:782:65: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 782 | tempHit.score() + sc.sc(0) * hit.rdoff() >= hit.score()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ spliced_aligner.h:1465:105: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 1465 | combinedHit.score() + sc.sc(0) * (rdlen - hit.rdoff() - hit.len() - hit.trim5()) >= hit.score()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h: In instantiation of ‘index_t HI_Aligner::globalGFMSearch(const GFM&, const Read&, const Scoring&, const ReportingParams&, bool, index_t, index_t&, index_t&, index_t&, index_t&, index_t&, EList >&, RandomSource&, bool&, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’: spliced_aligner.h:1086:53: required from ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int; int64_t = long int]’ 1086 | index_t nelt = this->globalGFMSearch( | ~~~~~~~~~~~~~~~~~~~~~^ 1087 | gfm, // GFM index | ~~~~~~~~~~~~~~~~~~~~ 1088 | rd, // read to align | ~~~~~~~~~~~~~~~~~~~~~~~~ 1089 | sc, // scoring scheme | ~~~~~~~~~~~~~~~~~~~~~~~~~ 1090 | sink.reportingParams(), | ~~~~~~~~~~~~~~~~~~~~~~~ 1091 | hit.fw(), | ~~~~~~~~~ 1092 | extoff, | ~~~~~~~ 1093 | extlen, | ~~~~~~~ 1094 | top, | ~~~~ 1095 | bot, | ~~~~ 1096 | node_top, | ~~~~~~~~~ 1097 | node_bot, | ~~~~~~~~~ 1098 | this->_node_iedge_count, | ~~~~~~~~~~~~~~~~~~~~~~~~ 1099 | rnd, | ~~~~ 1100 | uniqueStop); | ~~~~~~~~~~~ spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:6719:85: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 6719 | if(node_range.first < node_range.second && node_range.second - node_range.first <= rp.kseeds) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from edit.h:26, from edit.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from edit.h:26, from edit.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^~~~~~~~~~~~~~ In file included from alphabet.h:27, from gfm.h:40, from gfm.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from alphabet.h:27, from gfm.h:40, from gfm.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_sw.cpp:25: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from sequence_io.h:30, from hisat2_build.cpp:28: In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:768:29: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:764:24: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:766:29: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:764:24: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In file included from sequence_io.h:30, from hisat2_build.cpp:28: In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]’ at rfm.h:768:29: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]’ at rfm.h:764:24: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]’ at rfm.h:766:29: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]’ at rfm.h:764:24: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2259:41: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2257:41: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_ee_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2259:41: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2257:41: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_ee_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^~~~~~~~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_loc_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_loc_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from bit_packed_array.cpp:24: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from repeat_builder.cpp:26: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ repeat_builder.cpp: In function ‘std::string reverse_complement(const std::string&)’: repeat_builder.cpp:88:30: warning: array subscript has type ‘char’ [-Wchar-subscripts] 88 | rev[i] = asc2dnacomp[nt]; | ^~ repeat_builder.cpp: In function ‘std::string reverseComplement(const std::string&)’: repeat_builder.cpp:200:53: warning: array subscript has type ‘char’ [-Wchar-subscripts] 200 | rc.push_back(asc2dnacomp[str[si - 1]]); | ^ repeat_builder.cpp: In member function ‘int CoordHelper::mapJoinedOffToSeq(TIndexOffU)’: repeat_builder.cpp:403:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 403 | for(size_t i = 0; i < num_cached_; i++) { | ~~^~~~~~~~~~~~~ repeat_builder.cpp: In function ‘size_t extract_kmer(const std::string&, size_t, size_t)’: repeat_builder.cpp:1217:53: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1217 | kmer = (kmer << 2) | asc2dna[seq[offset + i]]; | ^ repeat_builder.cpp: In function ‘size_t next_kmer(size_t, char, size_t)’: repeat_builder.cpp:1225:34: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1225 | kmer = (kmer << 2) | asc2dna[base]; | ^~~~ repeat_builder.cpp: In function ‘void find_gap_pos(const std::string&, const std::string&, EList&, EList&, bool, size_t, size_t, size_t&, size_t&, bool)’: repeat_builder.cpp:1275:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1275 | for(int i = seq_len - 1; i >= gap_len; i--) { | ~~^~~~~~~~~~ repeat_builder.cpp:1277:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1277 | if(i == seq_len - 1) ed2[i] = add; | ~~^~~~~~~~~~~~~~ repeat_builder.cpp: In member function ‘void RB_SWAligner::makePadString(const std::string&, const std::string&, std::string&, size_t)’: repeat_builder.cpp:2915:39: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2915 | pad[i] = "CGTA"[asc2dna[ref[i]]]; | ^ repeat_builder.cpp:2919:43: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2919 | pad[i] = "CGTA"[asc2dna[pad[i]]]; | ^ repeat_builder.cpp:2926:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2926 | for(size_t i = 0; i < head_len; i++) { | ~~^~~~~~~~~~ repeat_builder.cpp:2929:67: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2929 | pad[pad_start + i] = "CGTA"[asc2dna[pad[pad_start + i]]]; | ^ repeat_builder.cpp: In member function ‘int RB_SWAligner::alignStrings(const std::string&, const std::string&, EList&, Coord&)’: repeat_builder.cpp:3065:13: warning: variable ‘max_match_len’ set but not used [-Wunused-but-set-variable] 3065 | int max_match_len = 0; | ^~~~~~~~~~~~~ In file included from repeat_builder.cpp:31: repeat_builder.cpp: In instantiation of ‘RepeatBuilder::RepeatBuilder(TStr&, const EList&, const EList >&, bool, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’: repeat_builder.cpp:4753:16: required from here 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.h:947:17: warning: ‘RepeatBuilder >::coordHelper_’ will be initialized after [-Wreorder] 947 | CoordHelper coordHelper_; | ^~~~~~~~~~~~ repeat_builder.h:940:10: warning: ‘bool RepeatBuilder >::forward_only_’ [-Wreorder] 940 | bool forward_only_; | ^~~~~~~~~~~~~ repeat_builder.cpp:3167:1: warning: when initialized here [-Wreorder] 3167 | RepeatBuilder::RepeatBuilder(TStr& s, | ^~~~~~~~~~~~~~~~~~~ repeat_builder.cpp: In instantiation of ‘void RepeatBuilder::build(const RepeatParameter&) [with TStr = SString]’: repeat_builder.cpp:4753:16: required from here 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:3396:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 3396 | if(spos != string::npos) { | ~~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp:3426:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 3426 | if(spos != string::npos) { | ~~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp:3553:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 3553 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp:3563:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 3563 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp: In instantiation of ‘void RepeatBuilder::saveConsensus(const RepeatParameter&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’: repeat_builder.cpp:4753:16: required from here 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:4114:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 4114 | if((oskip + out_len) == output_width) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp: In instantiation of ‘void dump_tstr(const TStr&) [with TStr = SString]’: repeat_builder.cpp:4754:46: required from here 4754 | template void dump_tstr(const SString& ); | ^ repeat_builder.cpp:309:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 309 | for(size_t j = 0; (j < print_width) && (i + j < s_len); j++) { | ~~~^~~~~~~~~~~~~~ repeat_builder.cpp:310:46: warning: array subscript has type ‘char’ [-Wchar-subscripts] 310 | buf.push_back("ACGTN"[s[i + j]]); | ~~~~~~~^ repeat_builder.cpp: In instantiation of ‘std::string getString(const TStr&, TIndexOffU, size_t) [with TStr = SString; std::string = std::__cxx11::basic_string; TIndexOffU = long unsigned int; size_t = long unsigned int]’: repeat_builder.cpp:3312:30: required from ‘void RepeatBuilder::build(const RepeatParameter&) [with TStr = SString]’ 3312 | query = getString(s_, i, rp.min_repeat_len); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:4753:16: required from here 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:272:33: warning: array subscript has type ‘char’ [-Wchar-subscripts] 272 | char nt = "ACGT"[ref[start + i]]; | ~~~~~~^ repeat_builder.cpp: In instantiation of ‘void getString(const TStr&, TIndexOffU, size_t, std::string&) [with TStr = SString; TIndexOffU = long unsigned int; size_t = long unsigned int; std::string = std::__cxx11::basic_string]’: repeat_builder.cpp:3545:22: required from ‘void RepeatBuilder::build(const RepeatParameter&) [with TStr = SString]’ 3545 | getString(s_, saElt, rp.min_repeat_len, query); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:4753:16: required from here 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:286:25: warning: array subscript has type ‘char’ [-Wchar-subscripts] 286 | char nt = "ACGT"[ref[start + i]]; | ~~~~~~^ In file included from /usr/include/c++/14/iostream:41, from repeat_builder.cpp:21: In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void RepeatBuilder::writeAllele(TIndexOffU, TIndexOffU, Range, const std::string&, TIndexOffU, const EList&, std::ostream&) [with TStr = SString]’ at repeat_builder.cpp:3678:31: /usr/include/c++/14/ostream:179:25: warning: ‘pos_in_chr’ may be used uninitialized [-Wmaybe-uninitialized] 179 | { return _M_insert(__n); } | ~~~~~~~~~^~~~~ repeat_builder.cpp: In member function ‘void RepeatBuilder::writeAllele(TIndexOffU, TIndexOffU, Range, const std::string&, TIndexOffU, const EList&, std::ostream&) [with TStr = SString]’: repeat_builder.cpp:3664:20: note: ‘pos_in_chr’ was declared here 3664 | TIndexOffU pos_in_chr; | ^~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_sw.cpp:25: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_sw.cpp:25: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_loc_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_loc_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_ee_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_ee_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_loc_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_loc_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_ee_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_ee_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ splice_site.cpp: In member function ‘void SpliceSiteDB::read(const GFM&, const EList >&)’: splice_site.cpp:717:59: warning: ‘?:’ using integer constants in boolean context, the expression will always evaluate to ‘true’ [-Wint-in-bool-context] 717 | exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from edit.h:29: ds.h: In instantiation of ‘void EList::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = long unsigned int]’: splice_site.cpp:722:31: required from here 722 | _exons.push_back_array(exons.begin(), exons.size()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ds.h:663:28: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class Exon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 663 | std::memcpy(list_ + cur_, l, bytes); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ splice_site.h:377:7: note: ‘class Exon’ declared here 377 | class Exon { | ^~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ splice_site.cpp: In member function ‘void SpliceSiteDB::read(const GFM&, const EList >&)’: splice_site.cpp:717:59: warning: ‘?:’ using integer constants in boolean context, the expression will always evaluate to ‘true’ [-Wint-in-bool-context] 717 | exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from edit.h:29: ds.h: In instantiation of ‘void EList::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = long unsigned int]’: splice_site.cpp:722:31: required from here 722 | _exons.push_back_array(exons.begin(), exons.size()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ds.h:663:28: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class Exon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 663 | std::memcpy(list_ + cur_, l, bytes); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ splice_site.h:377:7: note: ‘class Exon’ declared here 377 | class Exon { | ^~~~ make[2]: Leaving directory '/build/reproducible-path/hisat2-2.2.1' help2man ./hisat2 --no-info --name \ 'graph-based alignment of short nucleotide reads to many genomes, wrapper script' \ > debian/hisat2.1 help2man ./hisat2-align-l --name 'HISAT2 graph-based alignment of short nucleotide reads to many genomes, large index binary' \ --no-info > debian/hisat2-align-l.1 help2man ./hisat2-align-s --name 'HISAT2 graph-based alignment of short nucleotide reads to many genomes, small index binary' \ --no-info > debian/hisat2-align-s.1 help2man ./hisat2-build --name 'HISAT2 indexer, wrapper script' \ --no-info > debian/hisat2-build.1 #rm hisat2-buildc help2man ./hisat2-build-l --name 'HISAT2 indexer, large index binary' \ --no-info > debian/hisat2-build-l.1 help2man ./hisat2-build-s --name 'HISAT2 indexer, small index binary' \ --no-info > debian/hisat2-build-s.1 help2man ./hisat2-inspect --name 'HISAT2 index inspector, wrapper script' \ --no-info > debian/hisat2-inspect.1 help2man ./hisat2-inspect-l --name 'HISAT2 index inspector, large index binary' \ --no-info > debian/hisat2-inspect-l.1 help2man ./hisat2-inspect-s --name 'HISAT2 index inspector, small index binary' \ --no-info > debian/hisat2-inspect-s.1 make[1]: Leaving directory '/build/reproducible-path/hisat2-2.2.1' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/hisat2-2.2.1' dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/reproducible-path/hisat2-2.2.1' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/build/reproducible-path/hisat2-2.2.1' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.8.2-3), " make[1]: Leaving directory '/build/reproducible-path/hisat2-2.2.1' dh_md5sums dh_builddeb dpkg-deb: building package 'python3-hisat2' in '../python3-hisat2_2.2.1-5_all.deb'. dpkg-deb: building package 'hisat2-dbgsym' in '../hisat2-dbgsym_2.2.1-5_arm64.deb'. dpkg-deb: building package 'hisat2' in '../hisat2_2.2.1-5_arm64.deb'. dpkg-genbuildinfo --build=binary -O../hisat2_2.2.1-5_arm64.buildinfo dpkg-genchanges --build=binary -O../hisat2_2.2.1-5_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/966878 and its subdirectories I: Current time: Sun Apr 27 07:31:57 -12 2025 I: pbuilder-time-stamp: 1745782317 Sun Apr 27 19:31:57 UTC 2025 I: Signing ./b1/hisat2_2.2.1-5_arm64.buildinfo as hisat2_2.2.1-5_arm64.buildinfo.asc Sun Apr 27 19:31:57 UTC 2025 I: Signed ./b1/hisat2_2.2.1-5_arm64.buildinfo as ./b1/hisat2_2.2.1-5_arm64.buildinfo.asc Sun Apr 27 19:31:57 UTC 2025 - build #1 for hisat2/unstable/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Sun Apr 27 19:31:57 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-0nYkl0yb, removing. /srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Apr 27 19:31 b1 drwxr-xr-x 2 jenkins jenkins 4096 Apr 27 19:26 b2 -rw-r--r-- 1 jenkins jenkins 2104 Jul 9 2024 hisat2_2.2.1-5.dsc -rw------- 1 jenkins jenkins 3207 Apr 27 19:26 rbuildlog.TzSGPoE /srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL/b1: total 15700 -rw-r--r-- 1 jenkins jenkins 326927 Apr 27 19:31 build.log -rw-r--r-- 1 jenkins jenkins 12094096 Apr 27 19:31 hisat2-dbgsym_2.2.1-5_arm64.deb -rw-r--r-- 1 jenkins jenkins 29576 Apr 27 19:31 hisat2_2.2.1-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2104 Apr 27 19:31 hisat2_2.2.1-5.dsc -rw-r--r-- 1 jenkins jenkins 5750 Apr 27 19:31 hisat2_2.2.1-5_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6632 Apr 27 19:31 hisat2_2.2.1-5_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1718 Apr 27 19:31 hisat2_2.2.1-5_arm64.changes -rw-r--r-- 1 jenkins jenkins 3574404 Apr 27 19:31 hisat2_2.2.1-5_arm64.deb -rw-r--r-- 1 jenkins jenkins 1215 Apr 27 19:31 hisat2_2.2.1-5_source.changes -rw-r--r-- 1 jenkins jenkins 13996 Apr 27 19:31 python3-hisat2_2.2.1-5_all.deb /srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL/b2: total 0 Sun Apr 27 19:31:58 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Apr 27 07:26:32 -12 2025 I: pbuilder-time-stamp: 1745781992 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 [hisat2_2.2.1-5.dsc] I: copying [./hisat2_2.2.1.orig.tar.gz] I: copying [./hisat2_2.2.1-5.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./hisat2_2.2.1-5.dsc: unsupported subcommand dpkg-source: info: extracting hisat2 in hisat2-2.2.1 dpkg-source: info: unpacking hisat2_2.2.1.orig.tar.gz dpkg-source: info: unpacking hisat2_2.2.1-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_imp dpkg-source: info: applying hardening dpkg-source: info: applying reproducibile dpkg-source: info: applying fix-freebsd dpkg-source: info: applying compilerflags dpkg-source: info: applying simde dpkg-source: info: applying python3 dpkg-source: info: applying fix-manual dpkg-source: info: applying riscv5 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/966878/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='a8df00f6df85426e9e404fa7e51a5354' 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='966878' 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.8bp91aLL/pbuilderrc_PHmI --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.8bp91aLL/b1 --logfile b1/build.log hisat2_2.2.1-5.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 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/966878/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), libsimde-dev, help2man, pandoc, python3:any dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19953 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 libsimde-dev; however: Package libsimde-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on pandoc; however: Package pandoc is not installed. pbuilder-satisfydepends-dummy depends on python3:any. 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} 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} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} liblocale-gettext-perl{a} liblua5.4-0{a} libmagic-mgc{a} libmagic1t64{a} libnuma1{a} libpipeline1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libsimde-dev{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} netbase{a} pandoc{a} pandoc-data{a} po-debconf{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 51 newly installed, 0 to remove and 0 not upgraded. Need to get 44.7 MB of archives. After unpacking 296 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 3.13.3-2 [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 3.13.3-2 [1998 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.3-1 [27.2 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-2 [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 3.13.3-2 [1890 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.3-2 [751 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.3-1 [10.2 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.3-1 [28.2 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2 [241 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41-4 [93.9 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-4 [862 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 37 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.4 [629 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2 [1611 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.2 [919 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 liblua5.4-0 arm64 5.4.7-1+b2 [134 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libnuma1 arm64 2.0.19-1 [21.6 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libsimde-dev all 0.8.2-3 [467 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-2 [49.2 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 pandoc-data all 3.1.11.1-3 [459 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 pandoc arm64 3.1.11.1+ds-2 [26.2 MB] Fetched 44.7 MB in 0s (125 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 ... 19953 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_3.13.3-2_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.3-2) ... 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_3.13.3-2_arm64.deb ... Unpacking python3.13-minimal (3.13.3-2) ... Setting up libpython3.13-minimal:arm64 (3.13.3-2) ... Setting up libexpat1:arm64 (2.7.1-1) ... Setting up python3.13-minimal (3.13.3-2) ... Selecting previously unselected package python3-minimal. (Reading database ... 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Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-2_all.deb ... Unpacking tzdata (2025b-2) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../4-libffi8_3.4.8-2_arm64.deb ... Unpacking libffi8:arm64 (3.4.8-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../6-libreadline8t64_8.2-6_arm64.deb ... 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_3.13.3-2_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.3-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.3-2_arm64.deb ... Unpacking python3.13 (3.13.3-2) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../9-libpython3-stdlib_3.13.3-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.13.3-1) ... Setting up python3-minimal (3.13.3-1) ... 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 ... 21314 files and directories currently installed.) Preparing to unpack .../00-python3_3.13.3-1_arm64.deb ... Unpacking python3 (3.13.3-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../03-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.23.1-2_arm64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. 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Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../22-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../24-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.4_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.4) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-2_arm64.deb ... Unpacking gettext (0.23.1-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Selecting previously unselected package help2man. Preparing to unpack .../30-help2man_1.49.3+b1_arm64.deb ... Unpacking help2man (1.49.3+b1) ... Selecting previously unselected package liblua5.4-0:arm64. Preparing to unpack .../31-liblua5.4-0_5.4.7-1+b2_arm64.deb ... Unpacking liblua5.4-0:arm64 (5.4.7-1+b2) ... Selecting previously unselected package libnuma1:arm64. Preparing to unpack .../32-libnuma1_2.0.19-1_arm64.deb ... Unpacking libnuma1:arm64 (2.0.19-1) ... Selecting previously unselected package libsimde-dev. Preparing to unpack .../33-libsimde-dev_0.8.2-3_all.deb ... Unpacking libsimde-dev (0.8.2-3) ... Selecting previously unselected package libyaml-0-2:arm64. Preparing to unpack .../34-libyaml-0-2_0.2.5-2_arm64.deb ... Unpacking libyaml-0-2:arm64 (0.2.5-2) ... Selecting previously unselected package pandoc-data. Preparing to unpack .../35-pandoc-data_3.1.11.1-3_all.deb ... Unpacking pandoc-data (3.1.11.1-3) ... Selecting previously unselected package pandoc. Preparing to unpack .../36-pandoc_3.1.11.1+ds-2_arm64.deb ... Unpacking pandoc (3.1.11.1+ds-2) ... Setting up media-types (13.0.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libsimde-dev (0.8.2-3) ... Setting up bsdextrautils (2.41-4) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:arm64 (0.2.5-2) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up tzdata (2025b-2) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Apr 27 19:26:59 UTC 2025. Universal Time is now: Sun Apr 27 19:26:59 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up libffi8:arm64 (3.4.8-2) ... Setting up libnuma1:arm64 (2.0.19-1) ... 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 liblua5.4-0:arm64 (5.4.7-1+b2) ... Setting up netbase (6.5) ... Setting up pandoc-data (3.1.11.1-3) ... Setting up readline-common (8.2-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2) ... Setting up libtool (2.5.4-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3+b1) ... Setting up dh-autoreconf (20) ... Setting up pandoc (3.1.11.1+ds-2) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up libpython3.13-stdlib:arm64 (3.13.3-2) ... Setting up libpython3-stdlib:arm64 (3.13.3-1) ... Setting up python3.13 (3.13.3-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.3-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.2) ... Processing triggers for libc-bin (2.41-7) ... Reading package lists... Building dependency tree... Reading state information... 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/hisat2-2.2.1/ && 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 > ../hisat2_2.2.1-5_source.changes dpkg-buildpackage: info: source package hisat2 dpkg-buildpackage: info: source version 2.2.1-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/hisat2-2.2.1' rm -f hisat2-build-s hisat2-build-l hisat2-align-s hisat2-align-l hisat2-inspect-s hisat2-inspect-l hisat2-repeat hisat2-build-s-debug hisat2-build-l-debug hisat2-align-s-debug hisat2-align-l-debug hisat2-inspect-s-debug hisat2-inspect-l-debug hisat2-repeat-debug \ hisat2-build-s.exe hisat2-build-l.exe hisat2-align-s.exe hisat2-align-l.exe hisat2-inspect-s.exe hisat2-inspect-l.exe hisat2-repeat.exe hisat2-build-s-debug.exe hisat2-build-l-debug.exe hisat2-align-s-debug.exe hisat2-align-l-debug.exe hisat2-inspect-s-debug.exe hisat2-inspect-l-debug.exe hisat2-repeat-debug.exe \ hisat2-src.zip hisat2-bin.zip rm -f core.* .tmp.head rm -rf *.dSYM rm -rf .ht2lib-obj* rm -f libhisat2lib*.a libhisat2lib*.so make[1]: Leaving directory '/build/reproducible-path/hisat2-2.2.1' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/hisat2-2.2.1' dh_auto_build -- BUILD_HOST='Debian' BUILD_TIME="09 July 2024" all doc make -j12 "INSTALL=install --strip-program=true" BUILD_HOST=Debian "BUILD_TIME=09 July 2024" all doc make[2]: Entering directory '/build/reproducible-path/hisat2-2.2.1' /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/reproducible-path/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \ -I. -I third_party \ -o hisat2-build-s hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/reproducible-path/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-build-l hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/reproducible-path/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-align-s hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/reproducible-path/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-align-l hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \ -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/reproducible-path/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DHISAT2_INSPECT_MAIN -Wall \ -I. -I third_party -I . \ -o hisat2-inspect-s hisat2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \ -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/reproducible-path/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN -Wall \ -I. -I third_party -I . \ -o hisat2-inspect-l hisat2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/reproducible-path/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-repeat hisat2_repeat.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp mask.cpp qual.cpp aligner_bt.cpp scoring.cpp simple_func.cpp dp_framer.cpp aligner_result.cpp aligner_sw_driver.cpp aligner_sw.cpp aligner_swsse_ee_i16.cpp aligner_swsse_ee_u8.cpp aligner_swsse_loc_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse.cpp bit_packed_array.cpp repeat_builder.cpp diff_sample.cpp hisat2_repeat_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now make[2]: Nothing to be done for 'doc'. In file included from hisat2_build.cpp:35: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h: In instantiation of ‘void GFM::initFromVector(TStr&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::string&, bool, index_t, index_t, index_t, int, EList*, EList >*, uint32_t, bool) [with TStr = SString; index_t = long unsigned int; std::string = std::__cxx11::basic_string; std::ofstream = std::basic_ofstream; uint32_t = unsigned int]’: gfm.h:1039:23: required from ‘GFM::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, index_t, index_t, index_t, int, EList&, EList&, index_t, const RefReadInParams&, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ 1039 | initFromVector( | ~~~~~~~~~~~~~~~~~~~~^ 1040 | s, | ~~ 1041 | snpfile, | ~~~~~~~~ 1042 | htfile, | ~~~~~~~ 1043 | ssfile, | ~~~~~~~ 1044 | exonfile, | ~~~~~~~~~ 1045 | svfile, | ~~~~~~~ 1046 | repeatfile, | ~~~~~~~~~~~ 1047 | is, | ~~~ 1048 | szs, | ~~~~ 1049 | sztot, | ~~~~~~ 1050 | refparams, | ~~~~~~~~~~ 1051 | fout1, | ~~~~~~ 1052 | fout2, | ~~~~~~ 1053 | outfile, | ~~~~~~~~ 1054 | useBlockwise, | ~~~~~~~~~~~~~ 1055 | bmax, | ~~~~~ 1056 | bmaxSqrtMult, | ~~~~~~~~~~~~~ 1057 | bmaxDivN, | ~~~~~~~~~ 1058 | dcv, | ~~~~ 1059 | parent_szs, | ~~~~~~~~~~~ 1060 | parent_refnames, | ~~~~~~~~~~~~~~~~ 1061 | seed, | ~~~~~ 1062 | verbose); | ~~~~~~~~ hgfm.h:1989:14: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long unsigned int; uint32_t = unsigned int]’ 1989 | _in6(NULL) | ^ hisat2_build.cpp:535:15: required from ‘void driver(const std::string&, EList >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::string = std::__cxx11::basic_string]’ 535 | gfm = new HGFM( | ^~~~~~~~~~~~~~~~~~~~~ 536 | s, | ~~ 537 | packed, | ~~~~~~~ 538 | 1, // TODO: maybe not? | ~~~~~~~~~~~~~~~~~~~~~~~ 539 | lineRate, | ~~~~~~~~~ 540 | offRate, // suffix-array sampling rate | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 541 | ftabChars, // number of chars in initial arrow-pair calc | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 542 | localOffRate, | ~~~~~~~~~~~~~ 543 | localFtabChars, | ~~~~~~~~~~~~~~~ 544 | nthreads, | ~~~~~~~~~ 545 | snpfile, | ~~~~~~~~ 546 | htfile, | ~~~~~~~ 547 | ssfile, | ~~~~~~~ 548 | exonfile, | ~~~~~~~~~ 549 | svfile, | ~~~~~~~ 550 | repeatfile, | ~~~~~~~~~~~ 551 | outfile, // basename for .?.ht2 files | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 552 | reverse == 0, // fw | ~~~~~~~~~~~~~~~~~~~ 553 | !entireSA, // useBlockwise | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 554 | bmax, // block size for blockwise SA builder | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 555 | bmaxMultSqrt, // block size as multiplier of sqrt(len) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 556 | bmaxDivN, // block size as divisor of len | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 557 | noDc? 0 : dcv,// difference-cover period | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 558 | is, // list of input streams | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 559 | szs, // list of reference sizes | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 560 | (TIndexOffU)sztot.first, // total size of all unambiguous ref chars | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 561 | refparams, // reference read-in parameters | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 562 | localindex, // create local indexes? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 563 | parent_szs, // parent szs | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 564 | parent_refnames, // parent refence names | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 565 | seed, // pseudo-random number generator seed | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 566 | -1, // override offRate | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 567 | verbose, // be talkative | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 568 | autoMem, // pass exceptions up to the toplevel so that we can adjust memory settings automatically | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 569 | sanityCheck); // verify results and internal consistency | ~~~~~~~~~~~~ hisat2_build.cpp:786:39: required from here 786 | driver >(infile, | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ 787 | infiles, | ~~~~~~~~ 788 | snp_fname, | ~~~~~~~~~~ 789 | ht_fname, | ~~~~~~~~~ 790 | ss_fname, | ~~~~~~~~~ 791 | exon_fname, | ~~~~~~~~~~~ 792 | sv_fname, | ~~~~~~~~~ 793 | dummy_fname, | ~~~~~~~~~~~~ 794 | outfile, | ~~~~~~~~ 795 | false, | ~~~~~~ 796 | REF_READ_FORWARD, | ~~~~~~~~~~~~~~~~~ 797 | true, // create local indexes | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 798 | NULL, // no parent szs | ~~~~~~~~~~~~~~~~~~~~~~ 799 | NULL, // no parent refnames | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 800 | &parent_szs, // get parent szs | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 801 | &parent_refnames); // get parent refnames | ~~~~~~~~~~~~~~~~~ gfm.h:2167:33: warning: variable ‘template_len’ set but not used [-Wunused-but-set-variable] 2167 | index_t template_len = 0; | ^~~~~~~~~~~~ In file included from hisat2_build.cpp:35: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76, from aligner_sw_driver.h:86, from hi_aligner.h:42, from spliced_aligner.h:23, from hisat2.cpp:46: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void parseOptions(int, const char**)’: hisat2.cpp:1823:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1823 | auto_ptr presets(new PresetsV0()); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h: In instantiation of ‘void GFM::initFromVector(TStr&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::string&, bool, index_t, index_t, index_t, int, EList*, EList >*, uint32_t, bool) [with TStr = SString; index_t = unsigned int; std::string = std::__cxx11::basic_string; std::ofstream = std::basic_ofstream; uint32_t = unsigned int]’: gfm.h:1039:23: required from ‘GFM::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, index_t, index_t, index_t, int, EList&, EList&, index_t, const RefReadInParams&, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ 1039 | initFromVector( | ~~~~~~~~~~~~~~~~~~~~^ 1040 | s, | ~~ 1041 | snpfile, | ~~~~~~~~ 1042 | htfile, | ~~~~~~~ 1043 | ssfile, | ~~~~~~~ 1044 | exonfile, | ~~~~~~~~~ 1045 | svfile, | ~~~~~~~ 1046 | repeatfile, | ~~~~~~~~~~~ 1047 | is, | ~~~ 1048 | szs, | ~~~~ 1049 | sztot, | ~~~~~~ 1050 | refparams, | ~~~~~~~~~~ 1051 | fout1, | ~~~~~~ 1052 | fout2, | ~~~~~~ 1053 | outfile, | ~~~~~~~~ 1054 | useBlockwise, | ~~~~~~~~~~~~~ 1055 | bmax, | ~~~~~ 1056 | bmaxSqrtMult, | ~~~~~~~~~~~~~ 1057 | bmaxDivN, | ~~~~~~~~~ 1058 | dcv, | ~~~~ 1059 | parent_szs, | ~~~~~~~~~~~ 1060 | parent_refnames, | ~~~~~~~~~~~~~~~~ 1061 | seed, | ~~~~~ 1062 | verbose); | ~~~~~~~~ hgfm.h:1989:14: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = unsigned int; uint32_t = unsigned int]’ 1989 | _in6(NULL) | ^ hisat2_build.cpp:535:15: required from ‘void driver(const std::string&, EList >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::string = std::__cxx11::basic_string]’ 535 | gfm = new HGFM( | ^~~~~~~~~~~~~~~~~~~~~ 536 | s, | ~~ 537 | packed, | ~~~~~~~ 538 | 1, // TODO: maybe not? | ~~~~~~~~~~~~~~~~~~~~~~~ 539 | lineRate, | ~~~~~~~~~ 540 | offRate, // suffix-array sampling rate | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 541 | ftabChars, // number of chars in initial arrow-pair calc | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 542 | localOffRate, | ~~~~~~~~~~~~~ 543 | localFtabChars, | ~~~~~~~~~~~~~~~ 544 | nthreads, | ~~~~~~~~~ 545 | snpfile, | ~~~~~~~~ 546 | htfile, | ~~~~~~~ 547 | ssfile, | ~~~~~~~ 548 | exonfile, | ~~~~~~~~~ 549 | svfile, | ~~~~~~~ 550 | repeatfile, | ~~~~~~~~~~~ 551 | outfile, // basename for .?.ht2 files | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 552 | reverse == 0, // fw | ~~~~~~~~~~~~~~~~~~~ 553 | !entireSA, // useBlockwise | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 554 | bmax, // block size for blockwise SA builder | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 555 | bmaxMultSqrt, // block size as multiplier of sqrt(len) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 556 | bmaxDivN, // block size as divisor of len | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 557 | noDc? 0 : dcv,// difference-cover period | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 558 | is, // list of input streams | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 559 | szs, // list of reference sizes | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 560 | (TIndexOffU)sztot.first, // total size of all unambiguous ref chars | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 561 | refparams, // reference read-in parameters | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 562 | localindex, // create local indexes? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 563 | parent_szs, // parent szs | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 564 | parent_refnames, // parent refence names | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 565 | seed, // pseudo-random number generator seed | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 566 | -1, // override offRate | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 567 | verbose, // be talkative | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 568 | autoMem, // pass exceptions up to the toplevel so that we can adjust memory settings automatically | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 569 | sanityCheck); // verify results and internal consistency | ~~~~~~~~~~~~ hisat2_build.cpp:786:39: required from here 786 | driver >(infile, | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ 787 | infiles, | ~~~~~~~~ 788 | snp_fname, | ~~~~~~~~~~ 789 | ht_fname, | ~~~~~~~~~ 790 | ss_fname, | ~~~~~~~~~ 791 | exon_fname, | ~~~~~~~~~~~ 792 | sv_fname, | ~~~~~~~~~ 793 | dummy_fname, | ~~~~~~~~~~~~ 794 | outfile, | ~~~~~~~~ 795 | false, | ~~~~~~ 796 | REF_READ_FORWARD, | ~~~~~~~~~~~~~~~~~ 797 | true, // create local indexes | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 798 | NULL, // no parent szs | ~~~~~~~~~~~~~~~~~~~~~~ 799 | NULL, // no parent refnames | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 800 | &parent_szs, // get parent szs | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 801 | &parent_refnames); // get parent refnames | ~~~~~~~~~~~~~~~~~ gfm.h:2167:33: warning: variable ‘template_len’ set but not used [-Wunused-but-set-variable] 2167 | index_t template_len = 0; | ^~~~~~~~~~~~ In file included from hisat2_inspect.cpp:25: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from hisat2_repeat.cpp:36: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’: hisat2.cpp:3167:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3167 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3168:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3168 | auto_ptr ps(patsrcFact->create()); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3189:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3189 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void driver(const char*, const std::string&, const std::string&)’: hisat2.cpp:4035:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 4035 | auto_ptr refs( | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hi_aligner.h: In instantiation of ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’: hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:5688:105: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] 5688 | if(coord.off() + pepol.maxFragLen() * 2 < toff || toff + pepol.maxFragLen() * 2 < coord.off()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gfm.h: In instantiation of ‘void GFM::checkOrigs(const EList >&, bool) const [with index_t = unsigned int]’: hisat2.cpp:3815:17: required from ‘void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’ 3815 | gfm.checkOrigs(os, false); | ~~~~~~~~~~~~~~^~~~~~~~~~~ hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ gfm.h:6935:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^~~~~~~~ In file included from hisat2_inspect.cpp:25: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41: group_walk.h: In instantiation of ‘std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:1517:14: required from ‘bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ 1517 | st.advance( | ~~~~~~~~~~^ 1518 | gfmFw, | ~~~~~~ 1519 | ref, | ~~~~ 1520 | sa, | ~~~ 1521 | hit_, | ~~~~~ 1522 | (index_t)range, | ~~~~~~~~~~~~~~~ 1523 | false, | ~~~~~~ 1524 | NULL, | ~~~~~ 1525 | st_, | ~~~~ 1526 | gws, | ~~~~ 1527 | met, | ~~~~ 1528 | prm); | ~~~~ hi_aligner.h:5901:34: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’ 5901 | _gws_local.advanceElement( | ~~~~~~~~~~~~~~~~~~~~~~~~~^ 5902 | off, | ~~~~ 5903 | gfm, // forward Bowtie index for walking left | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5904 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5905 | _sas_local, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5906 | _gwstate_local, // GroupWalk state; scratch space | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5907 | wr, // put the result here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5908 | met, // metrics | ~~~~~~~~~~~~~~~~~~~~~~~~ 5909 | prm); // per-read metrics | ~~~~ hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ 5664 | getGenomeCoords_local( | ^~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ group_walk.h:1147:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1147 | if(new_node_bot - new_node_top < gws.map.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ group_walk.h:1158:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1158 | for(index_t j = 0; j + 1 < gws.map.size(); j++) { | ~~~~~~^~~~~~~~~~~~~~~~ group_walk.h:1213:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1213 | if(node_range.second - node_range.first < st.back().map_.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1224:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1224 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’: hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ 718 | alts, | ~~~~~ 719 | haplotypes, | ~~~~~~~~~~~ 720 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 721 | joinedOff, | ~~~~~~~~~~ 722 | rdseq, | ~~~~~~ 723 | rdoff - base_rdoff, | ~~~~~~~~~~~~~~~~~~~ 724 | rdoff, | ~~~~~~ 725 | rdlen, | ~~~~~~ 726 | ref, | ~~~~ 727 | sharedVar.raw_refbufs, | ~~~~~~~~~~~~~~~~~~~~~~ 728 | ASSERT_ONLY(sharedVar.destU32,) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 729 | alt_edits, | ~~~~~~~~~~ 730 | best_rdoff, | ~~~~~~~~~~~ 731 | NULL, /* rfseq */ | ~~~~~~~~~~~~~~~~~ 732 | tidx, | ~~~~~ 733 | rfoff, | ~~~~~~ 734 | rflen, | ~~~~~~ 735 | left, | ~~~~~ 736 | edits, | ~~~~~~ 737 | mm, | ~~~ 738 | ht_llist, | ~~~~~~~~~ 739 | cmp_ht, | ~~~~~~~ 740 | candidate_edits, | ~~~~~~~~~~~~~~~~ 741 | 0, /* tmp_numNs */ | ~~~~~~~~~~~~~~~~~~ 742 | numNs, | ~~~~~~ 743 | 0, /* dep */ | ~~~~~~~~~~~~~~~ 744 | gpol, | ~~~~~ 745 | numALTsTried); | ~~~~~~~~~~~~~ hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’ 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, | ~~~~~ 2339 | altdb.haplotypes(), | ~~~~~~~~~~~~~~~~~~~ 2340 | altdb.haplotype_maxrights(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2341 | genomeHit._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~ 2342 | seq, | ~~~~ 2343 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2344 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2345 | genomeHit._len, | ~~~~~~~~~~~~~~~ 2346 | ref, | ~~~~ 2347 | sharedVars, | ~~~~~~~~~~~ 2348 | genomeHit._tidx, | ~~~~~~~~~~~~~~~~ 2349 | (int)genomeHit._toff, | ~~~~~~~~~~~~~~~~~~~~~ 2350 | reflen, | ~~~~~~~ 2351 | false, /* left? */ | ~~~~~~~~~~~~~~~~~~ 2352 | gpol, | ~~~~~ 2353 | *genomeHit._edits, | ~~~~~~~~~~~~~~~~~~ 2354 | sharedVars.ht_llist, | ~~~~~~~~~~~~~~~~~~~~ 2355 | *genomeHit._ht_list, | ~~~~~~~~~~~~~~~~~~~~ 2356 | sharedVars.cmp_ht, | ~~~~~~~~~~~~~~~~~~ 2357 | &candidate_edits); | ~~~~~~~~~~~~~~~~~ hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:2801:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2801 | if(rfoff >= contig_len) return 0; | ~~~~~~^~~~~~~~~~~~~ hi_aligner.h:2879:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2879 | if(alt_range.first >= alts.size()) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:3044:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 3044 | for(int i = 0; i < alt.len; i++) { | ~~^~~~~~~~~ hi_aligner.h:3085:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 3085 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { | ~~~~~^~~~~~~~ hi_aligner.h:3161:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 3161 | if(alignedLen == next_rdlen) return rdlen; | ~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3197:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 3197 | if(mm_max_rd_i + rdoff > best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:3202:39: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 3202 | } else if(mm_max_rd_i + rdoff == best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3454:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 3454 | if(best_rdoff < rdoff + rd_i) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ group_walk.h: In instantiation of ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:494:14: required from ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’ 494 | return init(gfm, ref, sa, sts, hit, range, reportList, res, met); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1453:18: required from ‘void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ 1453 | st_.back().init( | ~~~~~~~~~~~~~~~^ 1454 | gfmFw, // Bowtie index | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1455 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1456 | sa, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1457 | st_, // EList | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1458 | hit_, // GWHit | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1459 | 0, // range 0 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1460 | false, // put resolved elements into res_? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1461 | NULL, // put resolved elements here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1462 | top, // GBW row at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1463 | bot, // GBW row at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1464 | node_top, // node at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1465 | node_bot, // node at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1466 | sa.node_iedge_count, | ~~~~~~~~~~~~~~~~~~~~ 1467 | 0, // # steps taken | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1468 | met); // update metrics here | ~~~~ hi_aligner.h:5896:20: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’ 5896 | _gws_local.init(gfm, ref, _sas_local, rnd, met); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ 5664 | getGenomeCoords_local( | ^~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ group_walk.h:785:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 785 | if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) { | ~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ group_walk.h:789:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 789 | if(new_top - top == tmp_gbwt_to_node.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:795:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 795 | if(i + 1 < tmp_zOffs.size()) { | ~~~~~~^~~~~~~~~~~~~~~~~~ group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 801 | if(new_bot - top < tmp_gbwt_to_node.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = unsigned int]’: hi_aligner.h:2915:39: required from ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ 2915 | add_haplotypes(alts, | ~~~~~~~~~~~~~~^~~~~~ 2916 | haplotypes, | ~~~~~~~~~~~ 2917 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 2918 | cmp_ht, | ~~~~~~~ 2919 | ht_list, | ~~~~~~~~ 2920 | rdlen); | ~~~~~~ hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ 718 | alts, | ~~~~~ 719 | haplotypes, | ~~~~~~~~~~~ 720 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 721 | joinedOff, | ~~~~~~~~~~ 722 | rdseq, | ~~~~~~ 723 | rdoff - base_rdoff, | ~~~~~~~~~~~~~~~~~~~ 724 | rdoff, | ~~~~~~ 725 | rdlen, | ~~~~~~ 726 | ref, | ~~~~ 727 | sharedVar.raw_refbufs, | ~~~~~~~~~~~~~~~~~~~~~~ 728 | ASSERT_ONLY(sharedVar.destU32,) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 729 | alt_edits, | ~~~~~~~~~~ 730 | best_rdoff, | ~~~~~~~~~~~ 731 | NULL, /* rfseq */ | ~~~~~~~~~~~~~~~~~ 732 | tidx, | ~~~~~ 733 | rfoff, | ~~~~~~ 734 | rflen, | ~~~~~~ 735 | left, | ~~~~~ 736 | edits, | ~~~~~~ 737 | mm, | ~~~ 738 | ht_llist, | ~~~~~~~~~ 739 | cmp_ht, | ~~~~~~~ 740 | candidate_edits, | ~~~~~~~~~~~~~~~~ 741 | 0, /* tmp_numNs */ | ~~~~~~~~~~~~~~~~~~ 742 | numNs, | ~~~~~~ 743 | 0, /* dep */ | ~~~~~~~~~~~~~~~ 744 | gpol, | ~~~~~ 745 | numALTsTried); | ~~~~~~~~~~~~~ hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’ 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, | ~~~~~ 2339 | altdb.haplotypes(), | ~~~~~~~~~~~~~~~~~~~ 2340 | altdb.haplotype_maxrights(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2341 | genomeHit._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~ 2342 | seq, | ~~~~ 2343 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2344 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2345 | genomeHit._len, | ~~~~~~~~~~~~~~~ 2346 | ref, | ~~~~ 2347 | sharedVars, | ~~~~~~~~~~~ 2348 | genomeHit._tidx, | ~~~~~~~~~~~~~~~~ 2349 | (int)genomeHit._toff, | ~~~~~~~~~~~~~~~~~~~~~ 2350 | reflen, | ~~~~~~~ 2351 | false, /* left? */ | ~~~~~~~~~~~~~~~~~~ 2352 | gpol, | ~~~~~ 2353 | *genomeHit._edits, | ~~~~~~~~~~~~~~~~~~ 2354 | sharedVars.ht_llist, | ~~~~~~~~~~~~~~~~~~~~ 2355 | *genomeHit._ht_list, | ~~~~~~~~~~~~~~~~~~~~ 2356 | sharedVars.cmp_ht, | ~~~~~~~~~~~~~~~~~~ 2357 | &candidate_edits); | ~~~~~~~~~~~~~~~~~ hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:2660:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2660 | if(ht_range.first >= haplotypes.size()) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ hi_aligner.h:2675:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2675 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2713:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2713 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2737:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2737 | for(; ht_range.second < haplotypes.size(); ht_range.second++) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ hi_aligner.h:2744:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2744 | if(ht_list[h].first == ht_range.second) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long int]’: spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:408:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] 408 | bool another_spliced = false; | ^~~~~~~~~~~~~~~ In file included from aligner_sw.h:76, from aligner_sw_driver.h:86, from hi_aligner.h:42, from spliced_aligner.h:23, from hisat2.cpp:46: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void parseOptions(int, const char**)’: hisat2.cpp:1823:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1823 | auto_ptr presets(new PresetsV0()); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’: hisat2.cpp:3167:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3167 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3168:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3168 | auto_ptr ps(patsrcFact->create()); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3189:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3189 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void driver(const char*, const std::string&, const std::string&)’: hisat2.cpp:4035:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 4035 | auto_ptr refs( | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76, from hisat2_repeat.cpp:37: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ hi_aligner.h: In instantiation of ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’: hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:4385:84: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4385 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:4404:55: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefId’ {aka ‘long int’} [-Wsign-compare] 4404 | if(positions[p].first.tid != res.refid()) continue; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:4405:63: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] 4405 | if(positions[p].first.toff + 1000 < res.refoff() || | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:4406:52: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] 4406 | res.refoff() + 1000 < positions[p].first.toff) continue; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:4407:88: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4407 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:4489:92: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4489 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:4578:69: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4578 | align2repeat = (numBestPair == 0 || numBestPair > rp.khits); | ~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:4584:83: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4584 | align2repeat = (rs->size() == 0 || sink.numBestUnp(rdi).first > rp.khits); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:4614:55: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4614 | if(sink.numBestUnp(rdi).first > rp.khits) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h: In instantiation of ‘bool HI_Aligner::pairReads(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, WalkMetrics&, PerReadMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’: hi_aligner.h:4088:17: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 4088 | pairReads(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, wlm, prm, him, rnd, sink); | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:5990:51: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] 5990 | if(_repeatConcordant[r].first == left.off() && | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:5991:52: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] 5991 | _repeatConcordant[r].second == left2.off()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h: In instantiation of ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’: hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:5661:33: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 5661 | if(nelt > 0 && nelt <= rp.kseeds && hitlen > max_hitlen) { | ~~~~~^~~~~~~~~~~~ hi_aligner.h:5688:105: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] 5688 | if(coord.off() + pepol.maxFragLen() * 2 < toff || toff + pepol.maxFragLen() * 2 < coord.off()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gfm.h: In instantiation of ‘void GFM::checkOrigs(const EList >&, bool) const [with index_t = long unsigned int]’: hisat2.cpp:3815:17: required from ‘void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’ 3815 | gfm.checkOrigs(os, false); | ~~~~~~~~~~~~~~^~~~~~~~~~~ hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ gfm.h:6935:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^~~~~~~~ hi_aligner.h: In instantiation of ‘index_t HI_Aligner::getAnchorHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const BitPairReference&, RandomSource&, index_t, bool, EList >&, index_t, SharedTempVars&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool) [with index_t = long unsigned int; local_index_t = short unsigned int]’: hi_aligner.h:5525:23: required from ‘bool HI_Aligner::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 5525 | index_t numHits = getAnchorHits(gfm, | ^~~~~~~~~~~~~ hi_aligner.h:4080:31: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 4080 | found[rdi][fwi] = align(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, swa, ssdb, rdi, fw, wlm, prm, swm, him, rnd, sink); | ^~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:5150:32: warning: comparison of integer expressions of different signedness: ‘TRefId’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] 5150 | if(coord.ref() == numeric_limits::max()) | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long unsigned int]’: hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:2267:47: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] 2267 | findSSOffs(gfm, altdb, (coord.joinedOff() >= width ? (index_t)(coord.joinedOff() - width) : 0), (index_t)(coord.joinedOff() + width), ssOffs); | ~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41: group_walk.h: In instantiation of ‘std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:1517:14: required from ‘bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ 1517 | st.advance( | ~~~~~~~~~~^ 1518 | gfmFw, | ~~~~~~ 1519 | ref, | ~~~~ 1520 | sa, | ~~~ 1521 | hit_, | ~~~~~ 1522 | (index_t)range, | ~~~~~~~~~~~~~~~ 1523 | false, | ~~~~~~ 1524 | NULL, | ~~~~~ 1525 | st_, | ~~~~ 1526 | gws, | ~~~~ 1527 | met, | ~~~~ 1528 | prm); | ~~~~ hi_aligner.h:5901:34: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 5901 | _gws_local.advanceElement( | ~~~~~~~~~~~~~~~~~~~~~~~~~^ 5902 | off, | ~~~~ 5903 | gfm, // forward Bowtie index for walking left | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5904 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5905 | _sas_local, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5906 | _gwstate_local, // GroupWalk state; scratch space | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5907 | wr, // put the result here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5908 | met, // metrics | ~~~~~~~~~~~~~~~~~~~~~~~~ 5909 | prm); // per-read metrics | ~~~~ hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 5664 | getGenomeCoords_local( | ^~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ group_walk.h:1147:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1147 | if(new_node_bot - new_node_top < gws.map.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ group_walk.h:1158:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1158 | for(index_t j = 0; j + 1 < gws.map.size(); j++) { | ~~~~~~^~~~~~~~~~~~~~~~ group_walk.h:1213:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1213 | if(node_range.second - node_range.first < st.back().map_.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1224:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1224 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’: hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ 718 | alts, | ~~~~~ 719 | haplotypes, | ~~~~~~~~~~~ 720 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 721 | joinedOff, | ~~~~~~~~~~ 722 | rdseq, | ~~~~~~ 723 | rdoff - base_rdoff, | ~~~~~~~~~~~~~~~~~~~ 724 | rdoff, | ~~~~~~ 725 | rdlen, | ~~~~~~ 726 | ref, | ~~~~ 727 | sharedVar.raw_refbufs, | ~~~~~~~~~~~~~~~~~~~~~~ 728 | ASSERT_ONLY(sharedVar.destU32,) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 729 | alt_edits, | ~~~~~~~~~~ 730 | best_rdoff, | ~~~~~~~~~~~ 731 | NULL, /* rfseq */ | ~~~~~~~~~~~~~~~~~ 732 | tidx, | ~~~~~ 733 | rfoff, | ~~~~~~ 734 | rflen, | ~~~~~~ 735 | left, | ~~~~~ 736 | edits, | ~~~~~~ 737 | mm, | ~~~ 738 | ht_llist, | ~~~~~~~~~ 739 | cmp_ht, | ~~~~~~~ 740 | candidate_edits, | ~~~~~~~~~~~~~~~~ 741 | 0, /* tmp_numNs */ | ~~~~~~~~~~~~~~~~~~ 742 | numNs, | ~~~~~~ 743 | 0, /* dep */ | ~~~~~~~~~~~~~~~ 744 | gpol, | ~~~~~ 745 | numALTsTried); | ~~~~~~~~~~~~~ hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long unsigned int]’ 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, | ~~~~~ 2339 | altdb.haplotypes(), | ~~~~~~~~~~~~~~~~~~~ 2340 | altdb.haplotype_maxrights(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2341 | genomeHit._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~ 2342 | seq, | ~~~~ 2343 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2344 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2345 | genomeHit._len, | ~~~~~~~~~~~~~~~ 2346 | ref, | ~~~~ 2347 | sharedVars, | ~~~~~~~~~~~ 2348 | genomeHit._tidx, | ~~~~~~~~~~~~~~~~ 2349 | (int)genomeHit._toff, | ~~~~~~~~~~~~~~~~~~~~~ 2350 | reflen, | ~~~~~~~ 2351 | false, /* left? */ | ~~~~~~~~~~~~~~~~~~ 2352 | gpol, | ~~~~~ 2353 | *genomeHit._edits, | ~~~~~~~~~~~~~~~~~~ 2354 | sharedVars.ht_llist, | ~~~~~~~~~~~~~~~~~~~~ 2355 | *genomeHit._ht_list, | ~~~~~~~~~~~~~~~~~~~~ 2356 | sharedVars.cmp_ht, | ~~~~~~~~~~~~~~~~~~ 2357 | &candidate_edits); | ~~~~~~~~~~~~~~~~~ hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:2801:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2801 | if(rfoff >= contig_len) return 0; | ~~~~~~^~~~~~~~~~~~~ hi_aligner.h:2879:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2879 | if(alt_range.first >= alts.size()) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:3044:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 3044 | for(int i = 0; i < alt.len; i++) { | ~~^~~~~~~~~ hi_aligner.h:3085:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 3085 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { | ~~~~~^~~~~~~~ hi_aligner.h:3161:31: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 3161 | if(alignedLen == next_rdlen) return rdlen; | ~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3197:32: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 3197 | if(mm_max_rd_i + rdoff > best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:3202:39: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 3202 | } else if(mm_max_rd_i + rdoff == best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3454:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 3454 | if(best_rdoff < rdoff + rd_i) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ group_walk.h: In instantiation of ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:494:14: required from ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’ 494 | return init(gfm, ref, sa, sts, hit, range, reportList, res, met); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1453:18: required from ‘void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ 1453 | st_.back().init( | ~~~~~~~~~~~~~~~^ 1454 | gfmFw, // Bowtie index | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1455 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1456 | sa, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1457 | st_, // EList | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1458 | hit_, // GWHit | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1459 | 0, // range 0 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1460 | false, // put resolved elements into res_? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1461 | NULL, // put resolved elements here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1462 | top, // GBW row at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1463 | bot, // GBW row at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1464 | node_top, // node at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1465 | node_bot, // node at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1466 | sa.node_iedge_count, | ~~~~~~~~~~~~~~~~~~~~ 1467 | 0, // # steps taken | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1468 | met); // update metrics here | ~~~~ hi_aligner.h:5896:20: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 5896 | _gws_local.init(gfm, ref, _sas_local, rnd, met); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 5664 | getGenomeCoords_local( | ^~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ group_walk.h:785:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 785 | if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) { | ~~~~~~^~~~~~~~~~~~~~~~~~ group_walk.h:789:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 789 | if(new_top - top == tmp_gbwt_to_node.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:795:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 795 | if(i + 1 < tmp_zOffs.size()) { | ~~~~~~^~~~~~~~~~~~~~~~~~ group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 801 | if(new_bot - top < tmp_gbwt_to_node.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = long unsigned int]’: hi_aligner.h:2915:39: required from ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ 2915 | add_haplotypes(alts, | ~~~~~~~~~~~~~~^~~~~~ 2916 | haplotypes, | ~~~~~~~~~~~ 2917 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 2918 | cmp_ht, | ~~~~~~~ 2919 | ht_list, | ~~~~~~~~ 2920 | rdlen); | ~~~~~~ hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ 718 | alts, | ~~~~~ 719 | haplotypes, | ~~~~~~~~~~~ 720 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 721 | joinedOff, | ~~~~~~~~~~ 722 | rdseq, | ~~~~~~ 723 | rdoff - base_rdoff, | ~~~~~~~~~~~~~~~~~~~ 724 | rdoff, | ~~~~~~ 725 | rdlen, | ~~~~~~ 726 | ref, | ~~~~ 727 | sharedVar.raw_refbufs, | ~~~~~~~~~~~~~~~~~~~~~~ 728 | ASSERT_ONLY(sharedVar.destU32,) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 729 | alt_edits, | ~~~~~~~~~~ 730 | best_rdoff, | ~~~~~~~~~~~ 731 | NULL, /* rfseq */ | ~~~~~~~~~~~~~~~~~ 732 | tidx, | ~~~~~ 733 | rfoff, | ~~~~~~ 734 | rflen, | ~~~~~~ 735 | left, | ~~~~~ 736 | edits, | ~~~~~~ 737 | mm, | ~~~ 738 | ht_llist, | ~~~~~~~~~ 739 | cmp_ht, | ~~~~~~~ 740 | candidate_edits, | ~~~~~~~~~~~~~~~~ 741 | 0, /* tmp_numNs */ | ~~~~~~~~~~~~~~~~~~ 742 | numNs, | ~~~~~~ 743 | 0, /* dep */ | ~~~~~~~~~~~~~~~ 744 | gpol, | ~~~~~ 745 | numALTsTried); | ~~~~~~~~~~~~~ hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long unsigned int]’ 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, | ~~~~~ 2339 | altdb.haplotypes(), | ~~~~~~~~~~~~~~~~~~~ 2340 | altdb.haplotype_maxrights(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2341 | genomeHit._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~ 2342 | seq, | ~~~~ 2343 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2344 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2345 | genomeHit._len, | ~~~~~~~~~~~~~~~ 2346 | ref, | ~~~~ 2347 | sharedVars, | ~~~~~~~~~~~ 2348 | genomeHit._tidx, | ~~~~~~~~~~~~~~~~ 2349 | (int)genomeHit._toff, | ~~~~~~~~~~~~~~~~~~~~~ 2350 | reflen, | ~~~~~~~ 2351 | false, /* left? */ | ~~~~~~~~~~~~~~~~~~ 2352 | gpol, | ~~~~~ 2353 | *genomeHit._edits, | ~~~~~~~~~~~~~~~~~~ 2354 | sharedVars.ht_llist, | ~~~~~~~~~~~~~~~~~~~~ 2355 | *genomeHit._ht_list, | ~~~~~~~~~~~~~~~~~~~~ 2356 | sharedVars.cmp_ht, | ~~~~~~~~~~~~~~~~~~ 2357 | &candidate_edits); | ~~~~~~~~~~~~~~~~~ hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:2660:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2660 | if(ht_range.first >= haplotypes.size()) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ hi_aligner.h:2675:37: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 2675 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2713:41: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 2713 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2737:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2737 | for(; ht_range.second < haplotypes.size(); ht_range.second++) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ hi_aligner.h:2744:41: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 2744 | if(ht_list[h].first == ht_range.second) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int; int64_t = long int]’: spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:408:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] 408 | bool another_spliced = false; | ^~~~~~~~~~~~~~~ spliced_aligner.h:782:65: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 782 | tempHit.score() + sc.sc(0) * hit.rdoff() >= hit.score()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ spliced_aligner.h:1465:105: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 1465 | combinedHit.score() + sc.sc(0) * (rdlen - hit.rdoff() - hit.len() - hit.trim5()) >= hit.score()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h: In instantiation of ‘index_t HI_Aligner::globalGFMSearch(const GFM&, const Read&, const Scoring&, const ReportingParams&, bool, index_t, index_t&, index_t&, index_t&, index_t&, index_t&, EList >&, RandomSource&, bool&, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’: spliced_aligner.h:1086:53: required from ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int; int64_t = long int]’ 1086 | index_t nelt = this->globalGFMSearch( | ~~~~~~~~~~~~~~~~~~~~~^ 1087 | gfm, // GFM index | ~~~~~~~~~~~~~~~~~~~~ 1088 | rd, // read to align | ~~~~~~~~~~~~~~~~~~~~~~~~ 1089 | sc, // scoring scheme | ~~~~~~~~~~~~~~~~~~~~~~~~~ 1090 | sink.reportingParams(), | ~~~~~~~~~~~~~~~~~~~~~~~ 1091 | hit.fw(), | ~~~~~~~~~ 1092 | extoff, | ~~~~~~~ 1093 | extlen, | ~~~~~~~ 1094 | top, | ~~~~ 1095 | bot, | ~~~~ 1096 | node_top, | ~~~~~~~~~ 1097 | node_bot, | ~~~~~~~~~ 1098 | this->_node_iedge_count, | ~~~~~~~~~~~~~~~~~~~~~~~~ 1099 | rnd, | ~~~~ 1100 | uniqueStop); | ~~~~~~~~~~~ spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:6719:85: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 6719 | if(node_range.first < node_range.second && node_range.second - node_range.first <= rp.kseeds) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from edit.h:26, from edit.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from edit.h:26, from edit.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^~~~~~~~~~~~~~ In file included from alphabet.h:27, from gfm.h:40, from gfm.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from alphabet.h:27, from gfm.h:40, from gfm.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_sw.cpp:25: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from sequence_io.h:30, from hisat2_build.cpp:28: In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:768:29: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:764:24: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:766:29: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:764:24: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In file included from sequence_io.h:30, from hisat2_build.cpp:28: In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]’ at rfm.h:768:29: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]’ at rfm.h:764:24: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]’ at rfm.h:766:29: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]’ at rfm.h:764:24: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2259:41: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2257:41: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_ee_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2259:41: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2257:41: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_ee_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^~~~~~~~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_loc_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_loc_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from bit_packed_array.cpp:24: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from repeat_builder.cpp:26: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ repeat_builder.cpp: In function ‘std::string reverse_complement(const std::string&)’: repeat_builder.cpp:88:30: warning: array subscript has type ‘char’ [-Wchar-subscripts] 88 | rev[i] = asc2dnacomp[nt]; | ^~ repeat_builder.cpp: In function ‘std::string reverseComplement(const std::string&)’: repeat_builder.cpp:200:53: warning: array subscript has type ‘char’ [-Wchar-subscripts] 200 | rc.push_back(asc2dnacomp[str[si - 1]]); | ^ repeat_builder.cpp: In member function ‘int CoordHelper::mapJoinedOffToSeq(TIndexOffU)’: repeat_builder.cpp:403:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 403 | for(size_t i = 0; i < num_cached_; i++) { | ~~^~~~~~~~~~~~~ repeat_builder.cpp: In function ‘size_t extract_kmer(const std::string&, size_t, size_t)’: repeat_builder.cpp:1217:53: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1217 | kmer = (kmer << 2) | asc2dna[seq[offset + i]]; | ^ repeat_builder.cpp: In function ‘size_t next_kmer(size_t, char, size_t)’: repeat_builder.cpp:1225:34: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1225 | kmer = (kmer << 2) | asc2dna[base]; | ^~~~ repeat_builder.cpp: In function ‘void find_gap_pos(const std::string&, const std::string&, EList&, EList&, bool, size_t, size_t, size_t&, size_t&, bool)’: repeat_builder.cpp:1275:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1275 | for(int i = seq_len - 1; i >= gap_len; i--) { | ~~^~~~~~~~~~ repeat_builder.cpp:1277:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1277 | if(i == seq_len - 1) ed2[i] = add; | ~~^~~~~~~~~~~~~~ repeat_builder.cpp: In member function ‘void RB_SWAligner::makePadString(const std::string&, const std::string&, std::string&, size_t)’: repeat_builder.cpp:2915:39: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2915 | pad[i] = "CGTA"[asc2dna[ref[i]]]; | ^ repeat_builder.cpp:2919:43: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2919 | pad[i] = "CGTA"[asc2dna[pad[i]]]; | ^ repeat_builder.cpp:2926:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2926 | for(size_t i = 0; i < head_len; i++) { | ~~^~~~~~~~~~ repeat_builder.cpp:2929:67: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2929 | pad[pad_start + i] = "CGTA"[asc2dna[pad[pad_start + i]]]; | ^ repeat_builder.cpp: In member function ‘int RB_SWAligner::alignStrings(const std::string&, const std::string&, EList&, Coord&)’: repeat_builder.cpp:3065:13: warning: variable ‘max_match_len’ set but not used [-Wunused-but-set-variable] 3065 | int max_match_len = 0; | ^~~~~~~~~~~~~ In file included from repeat_builder.cpp:31: repeat_builder.cpp: In instantiation of ‘RepeatBuilder::RepeatBuilder(TStr&, const EList&, const EList >&, bool, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’: repeat_builder.cpp:4753:16: required from here 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.h:947:17: warning: ‘RepeatBuilder >::coordHelper_’ will be initialized after [-Wreorder] 947 | CoordHelper coordHelper_; | ^~~~~~~~~~~~ repeat_builder.h:940:10: warning: ‘bool RepeatBuilder >::forward_only_’ [-Wreorder] 940 | bool forward_only_; | ^~~~~~~~~~~~~ repeat_builder.cpp:3167:1: warning: when initialized here [-Wreorder] 3167 | RepeatBuilder::RepeatBuilder(TStr& s, | ^~~~~~~~~~~~~~~~~~~ repeat_builder.cpp: In instantiation of ‘void RepeatBuilder::build(const RepeatParameter&) [with TStr = SString]’: repeat_builder.cpp:4753:16: required from here 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:3396:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 3396 | if(spos != string::npos) { | ~~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp:3426:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 3426 | if(spos != string::npos) { | ~~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp:3553:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 3553 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp:3563:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 3563 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp: In instantiation of ‘void RepeatBuilder::saveConsensus(const RepeatParameter&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’: repeat_builder.cpp:4753:16: required from here 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:4114:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 4114 | if((oskip + out_len) == output_width) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp: In instantiation of ‘void dump_tstr(const TStr&) [with TStr = SString]’: repeat_builder.cpp:4754:46: required from here 4754 | template void dump_tstr(const SString& ); | ^ repeat_builder.cpp:309:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 309 | for(size_t j = 0; (j < print_width) && (i + j < s_len); j++) { | ~~~^~~~~~~~~~~~~~ repeat_builder.cpp:310:46: warning: array subscript has type ‘char’ [-Wchar-subscripts] 310 | buf.push_back("ACGTN"[s[i + j]]); | ~~~~~~~^ repeat_builder.cpp: In instantiation of ‘std::string getString(const TStr&, TIndexOffU, size_t) [with TStr = SString; std::string = std::__cxx11::basic_string; TIndexOffU = long unsigned int; size_t = long unsigned int]’: repeat_builder.cpp:3312:30: required from ‘void RepeatBuilder::build(const RepeatParameter&) [with TStr = SString]’ 3312 | query = getString(s_, i, rp.min_repeat_len); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:4753:16: required from here 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:272:33: warning: array subscript has type ‘char’ [-Wchar-subscripts] 272 | char nt = "ACGT"[ref[start + i]]; | ~~~~~~^ repeat_builder.cpp: In instantiation of ‘void getString(const TStr&, TIndexOffU, size_t, std::string&) [with TStr = SString; TIndexOffU = long unsigned int; size_t = long unsigned int; std::string = std::__cxx11::basic_string]’: repeat_builder.cpp:3545:22: required from ‘void RepeatBuilder::build(const RepeatParameter&) [with TStr = SString]’ 3545 | getString(s_, saElt, rp.min_repeat_len, query); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:4753:16: required from here 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:286:25: warning: array subscript has type ‘char’ [-Wchar-subscripts] 286 | char nt = "ACGT"[ref[start + i]]; | ~~~~~~^ In file included from /usr/include/c++/14/iostream:41, from repeat_builder.cpp:21: In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void RepeatBuilder::writeAllele(TIndexOffU, TIndexOffU, Range, const std::string&, TIndexOffU, const EList&, std::ostream&) [with TStr = SString]’ at repeat_builder.cpp:3678:31: /usr/include/c++/14/ostream:179:25: warning: ‘pos_in_chr’ may be used uninitialized [-Wmaybe-uninitialized] 179 | { return _M_insert(__n); } | ~~~~~~~~~^~~~~ repeat_builder.cpp: In member function ‘void RepeatBuilder::writeAllele(TIndexOffU, TIndexOffU, Range, const std::string&, TIndexOffU, const EList&, std::ostream&) [with TStr = SString]’: repeat_builder.cpp:3664:20: note: ‘pos_in_chr’ was declared here 3664 | TIndexOffU pos_in_chr; | ^~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_sw.cpp:25: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_sw.cpp:25: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_loc_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_loc_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_ee_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_ee_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_loc_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_loc_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_ee_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_ee_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ splice_site.cpp: In member function ‘void SpliceSiteDB::read(const GFM&, const EList >&)’: splice_site.cpp:717:59: warning: ‘?:’ using integer constants in boolean context, the expression will always evaluate to ‘true’ [-Wint-in-bool-context] 717 | exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from edit.h:29: ds.h: In instantiation of ‘void EList::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = long unsigned int]’: splice_site.cpp:722:31: required from here 722 | _exons.push_back_array(exons.begin(), exons.size()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ds.h:663:28: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class Exon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 663 | std::memcpy(list_ + cur_, l, bytes); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ splice_site.h:377:7: note: ‘class Exon’ declared here 377 | class Exon { | ^~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ splice_site.cpp: In member function ‘void SpliceSiteDB::read(const GFM&, const EList >&)’: splice_site.cpp:717:59: warning: ‘?:’ using integer constants in boolean context, the expression will always evaluate to ‘true’ [-Wint-in-bool-context] 717 | exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from edit.h:29: ds.h: In instantiation of ‘void EList::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = long unsigned int]’: splice_site.cpp:722:31: required from here 722 | _exons.push_back_array(exons.begin(), exons.size()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ds.h:663:28: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class Exon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 663 | std::memcpy(list_ + cur_, l, bytes); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ splice_site.h:377:7: note: ‘class Exon’ declared here 377 | class Exon { | ^~~~ make[2]: Leaving directory '/build/reproducible-path/hisat2-2.2.1' help2man ./hisat2 --no-info --name \ 'graph-based alignment of short nucleotide reads to many genomes, wrapper script' \ > debian/hisat2.1 help2man ./hisat2-align-l --name 'HISAT2 graph-based alignment of short nucleotide reads to many genomes, large index binary' \ --no-info > debian/hisat2-align-l.1 help2man ./hisat2-align-s --name 'HISAT2 graph-based alignment of short nucleotide reads to many genomes, small index binary' \ --no-info > debian/hisat2-align-s.1 help2man ./hisat2-build --name 'HISAT2 indexer, wrapper script' \ --no-info > debian/hisat2-build.1 #rm hisat2-buildc help2man ./hisat2-build-l --name 'HISAT2 indexer, large index binary' \ --no-info > debian/hisat2-build-l.1 help2man ./hisat2-build-s --name 'HISAT2 indexer, small index binary' \ --no-info > debian/hisat2-build-s.1 help2man ./hisat2-inspect --name 'HISAT2 index inspector, wrapper script' \ --no-info > debian/hisat2-inspect.1 help2man ./hisat2-inspect-l --name 'HISAT2 index inspector, large index binary' \ --no-info > debian/hisat2-inspect-l.1 help2man ./hisat2-inspect-s --name 'HISAT2 index inspector, small index binary' \ --no-info > debian/hisat2-inspect-s.1 make[1]: Leaving directory '/build/reproducible-path/hisat2-2.2.1' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/hisat2-2.2.1' dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/reproducible-path/hisat2-2.2.1' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/build/reproducible-path/hisat2-2.2.1' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.8.2-3), " make[1]: Leaving directory '/build/reproducible-path/hisat2-2.2.1' dh_md5sums dh_builddeb dpkg-deb: building package 'python3-hisat2' in '../python3-hisat2_2.2.1-5_all.deb'. dpkg-deb: building package 'hisat2-dbgsym' in '../hisat2-dbgsym_2.2.1-5_arm64.deb'. dpkg-deb: building package 'hisat2' in '../hisat2_2.2.1-5_arm64.deb'. dpkg-genbuildinfo --build=binary -O../hisat2_2.2.1-5_arm64.buildinfo dpkg-genchanges --build=binary -O../hisat2_2.2.1-5_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/966878 and its subdirectories I: Current time: Sun Apr 27 07:31:57 -12 2025 I: pbuilder-time-stamp: 1745782317 Sun Apr 27 19:31:59 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Sun Apr 27 19:31:59 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Sun Apr 27 19:31:59 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Sun Apr 27 19:31:59 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-26UfpQ' ==================================================================================== Sun May 31 01:55:00 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink03-arm64, called using "2 hisat2 unstable /srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL 2.2.1-5" as arguments. Sun May 31 01:55:00 UTC 2026 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-RcVNNfQi" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sun May 31 01:55:00 UTC 2026 I: Downloading source for unstable/hisat2=2.2.1-5 Reading package lists... NOTICE: 'hisat2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/hisat2.git Please use: git clone https://salsa.debian.org/med-team/hisat2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 6793 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main hisat2 2.2.1-5 (dsc) [2104 B] Get:2 http://deb.debian.org/debian unstable/main hisat2 2.2.1-5 (tar) [6761 kB] Get:3 http://deb.debian.org/debian unstable/main hisat2 2.2.1-5 (diff) [29.6 kB] Fetched 6793 kB in 0s (55.9 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'hisat2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/hisat2.git Please use: git clone https://salsa.debian.org/med-team/hisat2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 6793 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main hisat2 2.2.1-5 (dsc) [2104 B] Get:2 http://deb.debian.org/debian unstable/main hisat2 2.2.1-5 (tar) [6761 kB] Get:3 http://deb.debian.org/debian unstable/main hisat2 2.2.1-5 (diff) [29.6 kB] Fetched 6793 kB in 0s (55.9 MB/s) Download complete and in download only mode ============================================================================= Re-Building hisat2 in unstable on arm64 on codethink03-arm64 now. Date: Sun May 31 02:55:01 BST 2026 Date UTC: Sun May 31 01:55:01 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL/pbuilderrc_aHjJ + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' hisat2 = debian-installer -o hisat2 = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' hisat2 = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL/pbuilderrc_aHjJ --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL/b2 --logfile b2/build.log hisat2_2.2.1-5.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Sun May 31 15:55:01 +14 2026 I: pbuilder-time-stamp: 1780192501 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 [hisat2_2.2.1-5.dsc] I: copying [./hisat2_2.2.1.orig.tar.gz] I: copying [./hisat2_2.2.1-5.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./hisat2_2.2.1-5.dsc: unsupported subcommand dpkg-source: info: extracting hisat2 in hisat2-2.2.1 dpkg-source: info: unpacking hisat2_2.2.1.orig.tar.gz dpkg-source: info: unpacking hisat2_2.2.1-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_imp dpkg-source: info: applying hardening dpkg-source: info: applying reproducibile dpkg-source: info: applying fix-freebsd dpkg-source: info: applying compilerflags dpkg-source: info: applying simde dpkg-source: info: applying python3 dpkg-source: info: applying fix-manual dpkg-source: info: applying riscv5 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3594855/tmp/hooks/D01_modify_environment starting debug: Running on codethink03-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 31 01:55 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/3594855/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3594855/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=4d01c1b79d3a4e59b3e71baf4ae97ec1 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3594855 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL/pbuilderrc_aHjJ --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL/b2 --logfile b2/build.log hisat2_2.2.1-5.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3594855/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), libsimde-dev, help2man, pandoc, python3:any dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19953 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 libsimde-dev; however: Package libsimde-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on pandoc; however: Package pandoc is not installed. pbuilder-satisfydepends-dummy depends on python3:any. 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} 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} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} liblocale-gettext-perl{a} liblua5.4-0{a} libmagic-mgc{a} libmagic1t64{a} libnuma1{a} libpipeline1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libsimde-dev{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} netbase{a} pandoc{a} pandoc-data{a} po-debconf{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 51 newly installed, 0 to remove and 0 not upgraded. Need to get 44.7 MB of archives. After unpacking 296 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 3.13.3-2 [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 3.13.3-2 [1998 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.3-1 [27.2 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-2 [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 3.13.3-2 [1890 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.3-2 [751 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.3-1 [10.2 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.3-1 [28.2 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2 [241 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41-4 [93.9 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-4 [862 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 37 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.4 [629 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2 [1611 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.2 [919 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 liblua5.4-0 arm64 5.4.7-1+b2 [134 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libnuma1 arm64 2.0.19-1 [21.6 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libsimde-dev all 0.8.2-3 [467 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-2 [49.2 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 pandoc-data all 3.1.11.1-3 [459 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 pandoc arm64 3.1.11.1+ds-2 [26.2 MB] Fetched 44.7 MB in 0s (127 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 ... 19953 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_3.13.3-2_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.3-2) ... 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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_3.13.3-2_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.3-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.3-2_arm64.deb ... Unpacking python3.13 (3.13.3-2) ... 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Setting up libdebhelper-perl (13.24.2) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up tzdata (2025b-2) ... Current default time zone: 'Etc/UTC' Local time is now: Sun May 31 01:55:20 UTC 2026. Universal Time is now: Sun May 31 01:55:20 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up libffi8:arm64 (3.4.8-2) ... Setting up libnuma1:arm64 (2.0.19-1) ... 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 liblua5.4-0:arm64 (5.4.7-1+b2) ... Setting up netbase (6.5) ... Setting up pandoc-data (3.1.11.1-3) ... Setting up readline-common (8.2-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2) ... Setting up libtool (2.5.4-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3+b1) ... Setting up dh-autoreconf (20) ... Setting up pandoc (3.1.11.1+ds-2) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up libpython3.13-stdlib:arm64 (3.13.3-2) ... Setting up libpython3-stdlib:arm64 (3.13.3-1) ... Setting up python3.13 (3.13.3-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.3-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.2) ... Processing triggers for libc-bin (2.41-7) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/3594855/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/3594855/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/hisat2-2.2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../hisat2_2.2.1-5_source.changes dpkg-buildpackage: info: source package hisat2 dpkg-buildpackage: info: source version 2.2.1-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/hisat2-2.2.1' rm -f hisat2-build-s hisat2-build-l hisat2-align-s hisat2-align-l hisat2-inspect-s hisat2-inspect-l hisat2-repeat hisat2-build-s-debug hisat2-build-l-debug hisat2-align-s-debug hisat2-align-l-debug hisat2-inspect-s-debug hisat2-inspect-l-debug hisat2-repeat-debug \ hisat2-build-s.exe hisat2-build-l.exe hisat2-align-s.exe hisat2-align-l.exe hisat2-inspect-s.exe hisat2-inspect-l.exe hisat2-repeat.exe hisat2-build-s-debug.exe hisat2-build-l-debug.exe hisat2-align-s-debug.exe hisat2-align-l-debug.exe hisat2-inspect-s-debug.exe hisat2-inspect-l-debug.exe hisat2-repeat-debug.exe \ hisat2-src.zip hisat2-bin.zip rm -f core.* .tmp.head rm -rf *.dSYM rm -rf .ht2lib-obj* rm -f libhisat2lib*.a libhisat2lib*.so make[1]: Leaving directory '/build/reproducible-path/hisat2-2.2.1' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/hisat2-2.2.1' dh_auto_build -- BUILD_HOST='Debian' BUILD_TIME="09 July 2024" all doc make -j12 "INSTALL=install --strip-program=true" BUILD_HOST=Debian "BUILD_TIME=09 July 2024" all doc make[2]: Entering directory '/build/reproducible-path/hisat2-2.2.1' /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/reproducible-path/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \ -I. -I third_party \ -o hisat2-build-s hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/reproducible-path/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-build-l hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/reproducible-path/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-align-s hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/reproducible-path/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-align-l hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \ -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/reproducible-path/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DHISAT2_INSPECT_MAIN -Wall \ -I. -I third_party -I . \ -o hisat2-inspect-s hisat2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \ -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/reproducible-path/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN -Wall \ -I. -I third_party -I . \ -o hisat2-inspect-l hisat2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/reproducible-path/hisat2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-repeat hisat2_repeat.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp mask.cpp qual.cpp aligner_bt.cpp scoring.cpp simple_func.cpp dp_framer.cpp aligner_result.cpp aligner_sw_driver.cpp aligner_sw.cpp aligner_swsse_ee_i16.cpp aligner_swsse_ee_u8.cpp aligner_swsse_loc_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse.cpp bit_packed_array.cpp repeat_builder.cpp diff_sample.cpp hisat2_repeat_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now make[2]: Nothing to be done for 'doc'. In file included from hisat2_build.cpp:35: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from hisat2_build.cpp:35: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from hisat2_repeat.cpp:36: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from hisat2_inspect.cpp:25: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from hisat2_inspect.cpp:25: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ gfm.h: In instantiation of ‘void GFM::initFromVector(TStr&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::string&, bool, index_t, index_t, index_t, int, EList*, EList >*, uint32_t, bool) [with TStr = SString; index_t = unsigned int; std::string = std::__cxx11::basic_string; std::ofstream = std::basic_ofstream; uint32_t = unsigned int]’: gfm.h:1039:23: required from ‘GFM::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, index_t, index_t, index_t, int, EList&, EList&, index_t, const RefReadInParams&, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ 1039 | initFromVector( | ~~~~~~~~~~~~~~~~~~~~^ 1040 | s, | ~~ 1041 | snpfile, | ~~~~~~~~ 1042 | htfile, | ~~~~~~~ 1043 | ssfile, | ~~~~~~~ 1044 | exonfile, | ~~~~~~~~~ 1045 | svfile, | ~~~~~~~ 1046 | repeatfile, | ~~~~~~~~~~~ 1047 | is, | ~~~ 1048 | szs, | ~~~~ 1049 | sztot, | ~~~~~~ 1050 | refparams, | ~~~~~~~~~~ 1051 | fout1, | ~~~~~~ 1052 | fout2, | ~~~~~~ 1053 | outfile, | ~~~~~~~~ 1054 | useBlockwise, | ~~~~~~~~~~~~~ 1055 | bmax, | ~~~~~ 1056 | bmaxSqrtMult, | ~~~~~~~~~~~~~ 1057 | bmaxDivN, | ~~~~~~~~~ 1058 | dcv, | ~~~~ 1059 | parent_szs, | ~~~~~~~~~~~ 1060 | parent_refnames, | ~~~~~~~~~~~~~~~~ 1061 | seed, | ~~~~~ 1062 | verbose); | ~~~~~~~~ hgfm.h:1989:14: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = unsigned int; uint32_t = unsigned int]’ 1989 | _in6(NULL) | ^ hisat2_build.cpp:535:15: required from ‘void driver(const std::string&, EList >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::string = std::__cxx11::basic_string]’ 535 | gfm = new HGFM( | ^~~~~~~~~~~~~~~~~~~~~ 536 | s, | ~~ 537 | packed, | ~~~~~~~ 538 | 1, // TODO: maybe not? | ~~~~~~~~~~~~~~~~~~~~~~~ 539 | lineRate, | ~~~~~~~~~ 540 | offRate, // suffix-array sampling rate | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 541 | ftabChars, // number of chars in initial arrow-pair calc | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 542 | localOffRate, | ~~~~~~~~~~~~~ 543 | localFtabChars, | ~~~~~~~~~~~~~~~ 544 | nthreads, | ~~~~~~~~~ 545 | snpfile, | ~~~~~~~~ 546 | htfile, | ~~~~~~~ 547 | ssfile, | ~~~~~~~ 548 | exonfile, | ~~~~~~~~~ 549 | svfile, | ~~~~~~~ 550 | repeatfile, | ~~~~~~~~~~~ 551 | outfile, // basename for .?.ht2 files | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 552 | reverse == 0, // fw | ~~~~~~~~~~~~~~~~~~~ 553 | !entireSA, // useBlockwise | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 554 | bmax, // block size for blockwise SA builder | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 555 | bmaxMultSqrt, // block size as multiplier of sqrt(len) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 556 | bmaxDivN, // block size as divisor of len | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 557 | noDc? 0 : dcv,// difference-cover period | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 558 | is, // list of input streams | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 559 | szs, // list of reference sizes | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 560 | (TIndexOffU)sztot.first, // total size of all unambiguous ref chars | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 561 | refparams, // reference read-in parameters | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 562 | localindex, // create local indexes? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 563 | parent_szs, // parent szs | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 564 | parent_refnames, // parent refence names | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 565 | seed, // pseudo-random number generator seed | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 566 | -1, // override offRate | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 567 | verbose, // be talkative | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 568 | autoMem, // pass exceptions up to the toplevel so that we can adjust memory settings automatically | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 569 | sanityCheck); // verify results and internal consistency | ~~~~~~~~~~~~ hisat2_build.cpp:786:39: required from here 786 | driver >(infile, | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ 787 | infiles, | ~~~~~~~~ 788 | snp_fname, | ~~~~~~~~~~ 789 | ht_fname, | ~~~~~~~~~ 790 | ss_fname, | ~~~~~~~~~ 791 | exon_fname, | ~~~~~~~~~~~ 792 | sv_fname, | ~~~~~~~~~ 793 | dummy_fname, | ~~~~~~~~~~~~ 794 | outfile, | ~~~~~~~~ 795 | false, | ~~~~~~ 796 | REF_READ_FORWARD, | ~~~~~~~~~~~~~~~~~ 797 | true, // create local indexes | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 798 | NULL, // no parent szs | ~~~~~~~~~~~~~~~~~~~~~~ 799 | NULL, // no parent refnames | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 800 | &parent_szs, // get parent szs | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 801 | &parent_refnames); // get parent refnames | ~~~~~~~~~~~~~~~~~ gfm.h:2167:33: warning: variable ‘template_len’ set but not used [-Wunused-but-set-variable] 2167 | index_t template_len = 0; | ^~~~~~~~~~~~ gfm.h: In instantiation of ‘void GFM::initFromVector(TStr&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::string&, bool, index_t, index_t, index_t, int, EList*, EList >*, uint32_t, bool) [with TStr = SString; index_t = long unsigned int; std::string = std::__cxx11::basic_string; std::ofstream = std::basic_ofstream; uint32_t = unsigned int]’: gfm.h:1039:23: required from ‘GFM::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, index_t, index_t, index_t, int, EList&, EList&, index_t, const RefReadInParams&, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ 1039 | initFromVector( | ~~~~~~~~~~~~~~~~~~~~^ 1040 | s, | ~~ 1041 | snpfile, | ~~~~~~~~ 1042 | htfile, | ~~~~~~~ 1043 | ssfile, | ~~~~~~~ 1044 | exonfile, | ~~~~~~~~~ 1045 | svfile, | ~~~~~~~ 1046 | repeatfile, | ~~~~~~~~~~~ 1047 | is, | ~~~ 1048 | szs, | ~~~~ 1049 | sztot, | ~~~~~~ 1050 | refparams, | ~~~~~~~~~~ 1051 | fout1, | ~~~~~~ 1052 | fout2, | ~~~~~~ 1053 | outfile, | ~~~~~~~~ 1054 | useBlockwise, | ~~~~~~~~~~~~~ 1055 | bmax, | ~~~~~ 1056 | bmaxSqrtMult, | ~~~~~~~~~~~~~ 1057 | bmaxDivN, | ~~~~~~~~~ 1058 | dcv, | ~~~~ 1059 | parent_szs, | ~~~~~~~~~~~ 1060 | parent_refnames, | ~~~~~~~~~~~~~~~~ 1061 | seed, | ~~~~~ 1062 | verbose); | ~~~~~~~~ hgfm.h:1989:14: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long unsigned int; uint32_t = unsigned int]’ 1989 | _in6(NULL) | ^ hisat2_build.cpp:535:15: required from ‘void driver(const std::string&, EList >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::string = std::__cxx11::basic_string]’ 535 | gfm = new HGFM( | ^~~~~~~~~~~~~~~~~~~~~ 536 | s, | ~~ 537 | packed, | ~~~~~~~ 538 | 1, // TODO: maybe not? | ~~~~~~~~~~~~~~~~~~~~~~~ 539 | lineRate, | ~~~~~~~~~ 540 | offRate, // suffix-array sampling rate | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 541 | ftabChars, // number of chars in initial arrow-pair calc | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 542 | localOffRate, | ~~~~~~~~~~~~~ 543 | localFtabChars, | ~~~~~~~~~~~~~~~ 544 | nthreads, | ~~~~~~~~~ 545 | snpfile, | ~~~~~~~~ 546 | htfile, | ~~~~~~~ 547 | ssfile, | ~~~~~~~ 548 | exonfile, | ~~~~~~~~~ 549 | svfile, | ~~~~~~~ 550 | repeatfile, | ~~~~~~~~~~~ 551 | outfile, // basename for .?.ht2 files | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 552 | reverse == 0, // fw | ~~~~~~~~~~~~~~~~~~~ 553 | !entireSA, // useBlockwise | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 554 | bmax, // block size for blockwise SA builder | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 555 | bmaxMultSqrt, // block size as multiplier of sqrt(len) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 556 | bmaxDivN, // block size as divisor of len | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 557 | noDc? 0 : dcv,// difference-cover period | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 558 | is, // list of input streams | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 559 | szs, // list of reference sizes | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 560 | (TIndexOffU)sztot.first, // total size of all unambiguous ref chars | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 561 | refparams, // reference read-in parameters | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 562 | localindex, // create local indexes? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 563 | parent_szs, // parent szs | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 564 | parent_refnames, // parent refence names | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 565 | seed, // pseudo-random number generator seed | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 566 | -1, // override offRate | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 567 | verbose, // be talkative | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 568 | autoMem, // pass exceptions up to the toplevel so that we can adjust memory settings automatically | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 569 | sanityCheck); // verify results and internal consistency | ~~~~~~~~~~~~ hisat2_build.cpp:786:39: required from here 786 | driver >(infile, | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ 787 | infiles, | ~~~~~~~~ 788 | snp_fname, | ~~~~~~~~~~ 789 | ht_fname, | ~~~~~~~~~ 790 | ss_fname, | ~~~~~~~~~ 791 | exon_fname, | ~~~~~~~~~~~ 792 | sv_fname, | ~~~~~~~~~ 793 | dummy_fname, | ~~~~~~~~~~~~ 794 | outfile, | ~~~~~~~~ 795 | false, | ~~~~~~ 796 | REF_READ_FORWARD, | ~~~~~~~~~~~~~~~~~ 797 | true, // create local indexes | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 798 | NULL, // no parent szs | ~~~~~~~~~~~~~~~~~~~~~~ 799 | NULL, // no parent refnames | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 800 | &parent_szs, // get parent szs | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 801 | &parent_refnames); // get parent refnames | ~~~~~~~~~~~~~~~~~ gfm.h:2167:33: warning: variable ‘template_len’ set but not used [-Wunused-but-set-variable] 2167 | index_t template_len = 0; | ^~~~~~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76, from hisat2_repeat.cpp:37: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from aligner_sw.h:76, from aligner_sw_driver.h:86, from hi_aligner.h:42, from spliced_aligner.h:23, from hisat2.cpp:46: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from aligner_sw.h:76, from aligner_sw_driver.h:86, from hi_aligner.h:42, from spliced_aligner.h:23, from hisat2.cpp:46: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ hisat2.cpp: In function ‘void parseOptions(int, const char**)’: hisat2.cpp:1823:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1823 | auto_ptr presets(new PresetsV0()); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void parseOptions(int, const char**)’: hisat2.cpp:1823:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1823 | auto_ptr presets(new PresetsV0()); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’: hisat2.cpp:3167:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3167 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3168:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3168 | auto_ptr ps(patsrcFact->create()); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3189:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3189 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’: hisat2.cpp:3167:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3167 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3168:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3168 | auto_ptr ps(patsrcFact->create()); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3189:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3189 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void driver(const char*, const std::string&, const std::string&)’: hisat2.cpp:4035:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 4035 | auto_ptr refs( | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void driver(const char*, const std::string&, const std::string&)’: hisat2.cpp:4035:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 4035 | auto_ptr refs( | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hi_aligner.h: In instantiation of ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’: hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:4385:84: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4385 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:4404:55: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefId’ {aka ‘long int’} [-Wsign-compare] 4404 | if(positions[p].first.tid != res.refid()) continue; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:4405:63: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] 4405 | if(positions[p].first.toff + 1000 < res.refoff() || | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:4406:52: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] 4406 | res.refoff() + 1000 < positions[p].first.toff) continue; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:4407:88: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4407 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:4489:92: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4489 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:4578:69: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4578 | align2repeat = (numBestPair == 0 || numBestPair > rp.khits); | ~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:4584:83: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4584 | align2repeat = (rs->size() == 0 || sink.numBestUnp(rdi).first > rp.khits); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:4614:55: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4614 | if(sink.numBestUnp(rdi).first > rp.khits) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h: In instantiation of ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’: hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:5688:105: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] 5688 | if(coord.off() + pepol.maxFragLen() * 2 < toff || toff + pepol.maxFragLen() * 2 < coord.off()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gfm.h: In instantiation of ‘void GFM::checkOrigs(const EList >&, bool) const [with index_t = unsigned int]’: hisat2.cpp:3815:17: required from ‘void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’ 3815 | gfm.checkOrigs(os, false); | ~~~~~~~~~~~~~~^~~~~~~~~~~ hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ gfm.h:6935:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^~~~~~~~ hi_aligner.h: In instantiation of ‘bool HI_Aligner::pairReads(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, WalkMetrics&, PerReadMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’: hi_aligner.h:4088:17: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 4088 | pairReads(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, wlm, prm, him, rnd, sink); | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:5990:51: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] 5990 | if(_repeatConcordant[r].first == left.off() && | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:5991:52: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] 5991 | _repeatConcordant[r].second == left2.off()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h: In instantiation of ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’: hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:5661:33: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 5661 | if(nelt > 0 && nelt <= rp.kseeds && hitlen > max_hitlen) { | ~~~~~^~~~~~~~~~~~ hi_aligner.h:5688:105: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] 5688 | if(coord.off() + pepol.maxFragLen() * 2 < toff || toff + pepol.maxFragLen() * 2 < coord.off()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gfm.h: In instantiation of ‘void GFM::checkOrigs(const EList >&, bool) const [with index_t = long unsigned int]’: hisat2.cpp:3815:17: required from ‘void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’ 3815 | gfm.checkOrigs(os, false); | ~~~~~~~~~~~~~~^~~~~~~~~~~ hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ gfm.h:6935:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^~~~~~~~ hi_aligner.h: In instantiation of ‘index_t HI_Aligner::getAnchorHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const BitPairReference&, RandomSource&, index_t, bool, EList >&, index_t, SharedTempVars&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool) [with index_t = long unsigned int; local_index_t = short unsigned int]’: hi_aligner.h:5525:23: required from ‘bool HI_Aligner::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 5525 | index_t numHits = getAnchorHits(gfm, | ^~~~~~~~~~~~~ hi_aligner.h:4080:31: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 4080 | found[rdi][fwi] = align(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, swa, ssdb, rdi, fw, wlm, prm, swm, him, rnd, sink); | ^~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:5150:32: warning: comparison of integer expressions of different signedness: ‘TRefId’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] 5150 | if(coord.ref() == numeric_limits::max()) | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long unsigned int]’: hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:2267:47: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] 2267 | findSSOffs(gfm, altdb, (coord.joinedOff() >= width ? (index_t)(coord.joinedOff() - width) : 0), (index_t)(coord.joinedOff() + width), ssOffs); | ~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41: group_walk.h: In instantiation of ‘std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:1517:14: required from ‘bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ 1517 | st.advance( | ~~~~~~~~~~^ 1518 | gfmFw, | ~~~~~~ 1519 | ref, | ~~~~ 1520 | sa, | ~~~ 1521 | hit_, | ~~~~~ 1522 | (index_t)range, | ~~~~~~~~~~~~~~~ 1523 | false, | ~~~~~~ 1524 | NULL, | ~~~~~ 1525 | st_, | ~~~~ 1526 | gws, | ~~~~ 1527 | met, | ~~~~ 1528 | prm); | ~~~~ hi_aligner.h:5901:34: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’ 5901 | _gws_local.advanceElement( | ~~~~~~~~~~~~~~~~~~~~~~~~~^ 5902 | off, | ~~~~ 5903 | gfm, // forward Bowtie index for walking left | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5904 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5905 | _sas_local, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5906 | _gwstate_local, // GroupWalk state; scratch space | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5907 | wr, // put the result here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5908 | met, // metrics | ~~~~~~~~~~~~~~~~~~~~~~~~ 5909 | prm); // per-read metrics | ~~~~ hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ 5664 | getGenomeCoords_local( | ^~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ group_walk.h:1147:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1147 | if(new_node_bot - new_node_top < gws.map.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ group_walk.h:1158:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1158 | for(index_t j = 0; j + 1 < gws.map.size(); j++) { | ~~~~~~^~~~~~~~~~~~~~~~ group_walk.h:1213:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1213 | if(node_range.second - node_range.first < st.back().map_.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1224:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1224 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’: hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ 718 | alts, | ~~~~~ 719 | haplotypes, | ~~~~~~~~~~~ 720 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 721 | joinedOff, | ~~~~~~~~~~ 722 | rdseq, | ~~~~~~ 723 | rdoff - base_rdoff, | ~~~~~~~~~~~~~~~~~~~ 724 | rdoff, | ~~~~~~ 725 | rdlen, | ~~~~~~ 726 | ref, | ~~~~ 727 | sharedVar.raw_refbufs, | ~~~~~~~~~~~~~~~~~~~~~~ 728 | ASSERT_ONLY(sharedVar.destU32,) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 729 | alt_edits, | ~~~~~~~~~~ 730 | best_rdoff, | ~~~~~~~~~~~ 731 | NULL, /* rfseq */ | ~~~~~~~~~~~~~~~~~ 732 | tidx, | ~~~~~ 733 | rfoff, | ~~~~~~ 734 | rflen, | ~~~~~~ 735 | left, | ~~~~~ 736 | edits, | ~~~~~~ 737 | mm, | ~~~ 738 | ht_llist, | ~~~~~~~~~ 739 | cmp_ht, | ~~~~~~~ 740 | candidate_edits, | ~~~~~~~~~~~~~~~~ 741 | 0, /* tmp_numNs */ | ~~~~~~~~~~~~~~~~~~ 742 | numNs, | ~~~~~~ 743 | 0, /* dep */ | ~~~~~~~~~~~~~~~ 744 | gpol, | ~~~~~ 745 | numALTsTried); | ~~~~~~~~~~~~~ hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’ 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, | ~~~~~ 2339 | altdb.haplotypes(), | ~~~~~~~~~~~~~~~~~~~ 2340 | altdb.haplotype_maxrights(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2341 | genomeHit._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~ 2342 | seq, | ~~~~ 2343 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2344 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2345 | genomeHit._len, | ~~~~~~~~~~~~~~~ 2346 | ref, | ~~~~ 2347 | sharedVars, | ~~~~~~~~~~~ 2348 | genomeHit._tidx, | ~~~~~~~~~~~~~~~~ 2349 | (int)genomeHit._toff, | ~~~~~~~~~~~~~~~~~~~~~ 2350 | reflen, | ~~~~~~~ 2351 | false, /* left? */ | ~~~~~~~~~~~~~~~~~~ 2352 | gpol, | ~~~~~ 2353 | *genomeHit._edits, | ~~~~~~~~~~~~~~~~~~ 2354 | sharedVars.ht_llist, | ~~~~~~~~~~~~~~~~~~~~ 2355 | *genomeHit._ht_list, | ~~~~~~~~~~~~~~~~~~~~ 2356 | sharedVars.cmp_ht, | ~~~~~~~~~~~~~~~~~~ 2357 | &candidate_edits); | ~~~~~~~~~~~~~~~~~ hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:2801:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2801 | if(rfoff >= contig_len) return 0; | ~~~~~~^~~~~~~~~~~~~ hi_aligner.h:2879:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2879 | if(alt_range.first >= alts.size()) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:3044:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 3044 | for(int i = 0; i < alt.len; i++) { | ~~^~~~~~~~~ hi_aligner.h:3085:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 3085 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { | ~~~~~^~~~~~~~ hi_aligner.h:3161:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 3161 | if(alignedLen == next_rdlen) return rdlen; | ~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3197:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 3197 | if(mm_max_rd_i + rdoff > best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:3202:39: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 3202 | } else if(mm_max_rd_i + rdoff == best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3454:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 3454 | if(best_rdoff < rdoff + rd_i) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41: group_walk.h: In instantiation of ‘std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:1517:14: required from ‘bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ 1517 | st.advance( | ~~~~~~~~~~^ 1518 | gfmFw, | ~~~~~~ 1519 | ref, | ~~~~ 1520 | sa, | ~~~ 1521 | hit_, | ~~~~~ 1522 | (index_t)range, | ~~~~~~~~~~~~~~~ 1523 | false, | ~~~~~~ 1524 | NULL, | ~~~~~ 1525 | st_, | ~~~~ 1526 | gws, | ~~~~ 1527 | met, | ~~~~ 1528 | prm); | ~~~~ hi_aligner.h:5901:34: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 5901 | _gws_local.advanceElement( | ~~~~~~~~~~~~~~~~~~~~~~~~~^ 5902 | off, | ~~~~ 5903 | gfm, // forward Bowtie index for walking left | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5904 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5905 | _sas_local, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5906 | _gwstate_local, // GroupWalk state; scratch space | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5907 | wr, // put the result here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5908 | met, // metrics | ~~~~~~~~~~~~~~~~~~~~~~~~ 5909 | prm); // per-read metrics | ~~~~ hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 5664 | getGenomeCoords_local( | ^~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ group_walk.h:1147:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1147 | if(new_node_bot - new_node_top < gws.map.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ group_walk.h:1158:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1158 | for(index_t j = 0; j + 1 < gws.map.size(); j++) { | ~~~~~~^~~~~~~~~~~~~~~~ group_walk.h:1213:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1213 | if(node_range.second - node_range.first < st.back().map_.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1224:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1224 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’: hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ 718 | alts, | ~~~~~ 719 | haplotypes, | ~~~~~~~~~~~ 720 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 721 | joinedOff, | ~~~~~~~~~~ 722 | rdseq, | ~~~~~~ 723 | rdoff - base_rdoff, | ~~~~~~~~~~~~~~~~~~~ 724 | rdoff, | ~~~~~~ 725 | rdlen, | ~~~~~~ 726 | ref, | ~~~~ 727 | sharedVar.raw_refbufs, | ~~~~~~~~~~~~~~~~~~~~~~ 728 | ASSERT_ONLY(sharedVar.destU32,) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 729 | alt_edits, | ~~~~~~~~~~ 730 | best_rdoff, | ~~~~~~~~~~~ 731 | NULL, /* rfseq */ | ~~~~~~~~~~~~~~~~~ 732 | tidx, | ~~~~~ 733 | rfoff, | ~~~~~~ 734 | rflen, | ~~~~~~ 735 | left, | ~~~~~ 736 | edits, | ~~~~~~ 737 | mm, | ~~~ 738 | ht_llist, | ~~~~~~~~~ 739 | cmp_ht, | ~~~~~~~ 740 | candidate_edits, | ~~~~~~~~~~~~~~~~ 741 | 0, /* tmp_numNs */ | ~~~~~~~~~~~~~~~~~~ 742 | numNs, | ~~~~~~ 743 | 0, /* dep */ | ~~~~~~~~~~~~~~~ 744 | gpol, | ~~~~~ 745 | numALTsTried); | ~~~~~~~~~~~~~ hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long unsigned int]’ 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, | ~~~~~ 2339 | altdb.haplotypes(), | ~~~~~~~~~~~~~~~~~~~ 2340 | altdb.haplotype_maxrights(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2341 | genomeHit._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~ 2342 | seq, | ~~~~ 2343 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2344 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2345 | genomeHit._len, | ~~~~~~~~~~~~~~~ 2346 | ref, | ~~~~ 2347 | sharedVars, | ~~~~~~~~~~~ 2348 | genomeHit._tidx, | ~~~~~~~~~~~~~~~~ 2349 | (int)genomeHit._toff, | ~~~~~~~~~~~~~~~~~~~~~ 2350 | reflen, | ~~~~~~~ 2351 | false, /* left? */ | ~~~~~~~~~~~~~~~~~~ 2352 | gpol, | ~~~~~ 2353 | *genomeHit._edits, | ~~~~~~~~~~~~~~~~~~ 2354 | sharedVars.ht_llist, | ~~~~~~~~~~~~~~~~~~~~ 2355 | *genomeHit._ht_list, | ~~~~~~~~~~~~~~~~~~~~ 2356 | sharedVars.cmp_ht, | ~~~~~~~~~~~~~~~~~~ 2357 | &candidate_edits); | ~~~~~~~~~~~~~~~~~ hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:2801:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2801 | if(rfoff >= contig_len) return 0; | ~~~~~~^~~~~~~~~~~~~ hi_aligner.h:2879:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2879 | if(alt_range.first >= alts.size()) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:3044:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 3044 | for(int i = 0; i < alt.len; i++) { | ~~^~~~~~~~~ hi_aligner.h:3085:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 3085 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { | ~~~~~^~~~~~~~ hi_aligner.h:3161:31: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 3161 | if(alignedLen == next_rdlen) return rdlen; | ~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3197:32: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 3197 | if(mm_max_rd_i + rdoff > best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:3202:39: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 3202 | } else if(mm_max_rd_i + rdoff == best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3454:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 3454 | if(best_rdoff < rdoff + rd_i) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ group_walk.h: In instantiation of ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:494:14: required from ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’ 494 | return init(gfm, ref, sa, sts, hit, range, reportList, res, met); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1453:18: required from ‘void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ 1453 | st_.back().init( | ~~~~~~~~~~~~~~~^ 1454 | gfmFw, // Bowtie index | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1455 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1456 | sa, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1457 | st_, // EList | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1458 | hit_, // GWHit | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1459 | 0, // range 0 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1460 | false, // put resolved elements into res_? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1461 | NULL, // put resolved elements here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1462 | top, // GBW row at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1463 | bot, // GBW row at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1464 | node_top, // node at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1465 | node_bot, // node at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1466 | sa.node_iedge_count, | ~~~~~~~~~~~~~~~~~~~~ 1467 | 0, // # steps taken | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1468 | met); // update metrics here | ~~~~ hi_aligner.h:5896:20: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’ 5896 | _gws_local.init(gfm, ref, _sas_local, rnd, met); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ 5664 | getGenomeCoords_local( | ^~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ group_walk.h:785:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 785 | if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) { | ~~~~~~^~~~~~~~~~~~~~~~~~ group_walk.h:789:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 789 | if(new_top - top == tmp_gbwt_to_node.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:795:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 795 | if(i + 1 < tmp_zOffs.size()) { | ~~~~~~^~~~~~~~~~~~~~~~~~ group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 801 | if(new_bot - top < tmp_gbwt_to_node.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = unsigned int]’: hi_aligner.h:2915:39: required from ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ 2915 | add_haplotypes(alts, | ~~~~~~~~~~~~~~^~~~~~ 2916 | haplotypes, | ~~~~~~~~~~~ 2917 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 2918 | cmp_ht, | ~~~~~~~ 2919 | ht_list, | ~~~~~~~~ 2920 | rdlen); | ~~~~~~ hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ 718 | alts, | ~~~~~ 719 | haplotypes, | ~~~~~~~~~~~ 720 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 721 | joinedOff, | ~~~~~~~~~~ 722 | rdseq, | ~~~~~~ 723 | rdoff - base_rdoff, | ~~~~~~~~~~~~~~~~~~~ 724 | rdoff, | ~~~~~~ 725 | rdlen, | ~~~~~~ 726 | ref, | ~~~~ 727 | sharedVar.raw_refbufs, | ~~~~~~~~~~~~~~~~~~~~~~ 728 | ASSERT_ONLY(sharedVar.destU32,) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 729 | alt_edits, | ~~~~~~~~~~ 730 | best_rdoff, | ~~~~~~~~~~~ 731 | NULL, /* rfseq */ | ~~~~~~~~~~~~~~~~~ 732 | tidx, | ~~~~~ 733 | rfoff, | ~~~~~~ 734 | rflen, | ~~~~~~ 735 | left, | ~~~~~ 736 | edits, | ~~~~~~ 737 | mm, | ~~~ 738 | ht_llist, | ~~~~~~~~~ 739 | cmp_ht, | ~~~~~~~ 740 | candidate_edits, | ~~~~~~~~~~~~~~~~ 741 | 0, /* tmp_numNs */ | ~~~~~~~~~~~~~~~~~~ 742 | numNs, | ~~~~~~ 743 | 0, /* dep */ | ~~~~~~~~~~~~~~~ 744 | gpol, | ~~~~~ 745 | numALTsTried); | ~~~~~~~~~~~~~ hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’ 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, | ~~~~~ 2339 | altdb.haplotypes(), | ~~~~~~~~~~~~~~~~~~~ 2340 | altdb.haplotype_maxrights(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2341 | genomeHit._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~ 2342 | seq, | ~~~~ 2343 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2344 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2345 | genomeHit._len, | ~~~~~~~~~~~~~~~ 2346 | ref, | ~~~~ 2347 | sharedVars, | ~~~~~~~~~~~ 2348 | genomeHit._tidx, | ~~~~~~~~~~~~~~~~ 2349 | (int)genomeHit._toff, | ~~~~~~~~~~~~~~~~~~~~~ 2350 | reflen, | ~~~~~~~ 2351 | false, /* left? */ | ~~~~~~~~~~~~~~~~~~ 2352 | gpol, | ~~~~~ 2353 | *genomeHit._edits, | ~~~~~~~~~~~~~~~~~~ 2354 | sharedVars.ht_llist, | ~~~~~~~~~~~~~~~~~~~~ 2355 | *genomeHit._ht_list, | ~~~~~~~~~~~~~~~~~~~~ 2356 | sharedVars.cmp_ht, | ~~~~~~~~~~~~~~~~~~ 2357 | &candidate_edits); | ~~~~~~~~~~~~~~~~~ hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:2660:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2660 | if(ht_range.first >= haplotypes.size()) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ hi_aligner.h:2675:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2675 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2713:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2713 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2737:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2737 | for(; ht_range.second < haplotypes.size(); ht_range.second++) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ hi_aligner.h:2744:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2744 | if(ht_list[h].first == ht_range.second) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ group_walk.h: In instantiation of ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:494:14: required from ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’ 494 | return init(gfm, ref, sa, sts, hit, range, reportList, res, met); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1453:18: required from ‘void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ 1453 | st_.back().init( | ~~~~~~~~~~~~~~~^ 1454 | gfmFw, // Bowtie index | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1455 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1456 | sa, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1457 | st_, // EList | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1458 | hit_, // GWHit | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1459 | 0, // range 0 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1460 | false, // put resolved elements into res_? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1461 | NULL, // put resolved elements here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1462 | top, // GBW row at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1463 | bot, // GBW row at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1464 | node_top, // node at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1465 | node_bot, // node at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1466 | sa.node_iedge_count, | ~~~~~~~~~~~~~~~~~~~~ 1467 | 0, // # steps taken | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1468 | met); // update metrics here | ~~~~ hi_aligner.h:5896:20: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 5896 | _gws_local.init(gfm, ref, _sas_local, rnd, met); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 5664 | getGenomeCoords_local( | ^~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ group_walk.h:785:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 785 | if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) { | ~~~~~~^~~~~~~~~~~~~~~~~~ group_walk.h:789:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 789 | if(new_top - top == tmp_gbwt_to_node.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:795:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 795 | if(i + 1 < tmp_zOffs.size()) { | ~~~~~~^~~~~~~~~~~~~~~~~~ group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 801 | if(new_bot - top < tmp_gbwt_to_node.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = long unsigned int]’: hi_aligner.h:2915:39: required from ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ 2915 | add_haplotypes(alts, | ~~~~~~~~~~~~~~^~~~~~ 2916 | haplotypes, | ~~~~~~~~~~~ 2917 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 2918 | cmp_ht, | ~~~~~~~ 2919 | ht_list, | ~~~~~~~~ 2920 | rdlen); | ~~~~~~ hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ 718 | alts, | ~~~~~ 719 | haplotypes, | ~~~~~~~~~~~ 720 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 721 | joinedOff, | ~~~~~~~~~~ 722 | rdseq, | ~~~~~~ 723 | rdoff - base_rdoff, | ~~~~~~~~~~~~~~~~~~~ 724 | rdoff, | ~~~~~~ 725 | rdlen, | ~~~~~~ 726 | ref, | ~~~~ 727 | sharedVar.raw_refbufs, | ~~~~~~~~~~~~~~~~~~~~~~ 728 | ASSERT_ONLY(sharedVar.destU32,) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 729 | alt_edits, | ~~~~~~~~~~ 730 | best_rdoff, | ~~~~~~~~~~~ 731 | NULL, /* rfseq */ | ~~~~~~~~~~~~~~~~~ 732 | tidx, | ~~~~~ 733 | rfoff, | ~~~~~~ 734 | rflen, | ~~~~~~ 735 | left, | ~~~~~ 736 | edits, | ~~~~~~ 737 | mm, | ~~~ 738 | ht_llist, | ~~~~~~~~~ 739 | cmp_ht, | ~~~~~~~ 740 | candidate_edits, | ~~~~~~~~~~~~~~~~ 741 | 0, /* tmp_numNs */ | ~~~~~~~~~~~~~~~~~~ 742 | numNs, | ~~~~~~ 743 | 0, /* dep */ | ~~~~~~~~~~~~~~~ 744 | gpol, | ~~~~~ 745 | numALTsTried); | ~~~~~~~~~~~~~ hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long unsigned int]’ 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, | ~~~~~ 2339 | altdb.haplotypes(), | ~~~~~~~~~~~~~~~~~~~ 2340 | altdb.haplotype_maxrights(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2341 | genomeHit._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~ 2342 | seq, | ~~~~ 2343 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2344 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2345 | genomeHit._len, | ~~~~~~~~~~~~~~~ 2346 | ref, | ~~~~ 2347 | sharedVars, | ~~~~~~~~~~~ 2348 | genomeHit._tidx, | ~~~~~~~~~~~~~~~~ 2349 | (int)genomeHit._toff, | ~~~~~~~~~~~~~~~~~~~~~ 2350 | reflen, | ~~~~~~~ 2351 | false, /* left? */ | ~~~~~~~~~~~~~~~~~~ 2352 | gpol, | ~~~~~ 2353 | *genomeHit._edits, | ~~~~~~~~~~~~~~~~~~ 2354 | sharedVars.ht_llist, | ~~~~~~~~~~~~~~~~~~~~ 2355 | *genomeHit._ht_list, | ~~~~~~~~~~~~~~~~~~~~ 2356 | sharedVars.cmp_ht, | ~~~~~~~~~~~~~~~~~~ 2357 | &candidate_edits); | ~~~~~~~~~~~~~~~~~ hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:2660:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2660 | if(ht_range.first >= haplotypes.size()) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ hi_aligner.h:2675:37: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 2675 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2713:41: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 2713 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2737:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2737 | for(; ht_range.second < haplotypes.size(); ht_range.second++) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ hi_aligner.h:2744:41: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 2744 | if(ht_list[h].first == ht_range.second) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long int]’: spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:408:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] 408 | bool another_spliced = false; | ^~~~~~~~~~~~~~~ spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int; int64_t = long int]’: spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:408:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] 408 | bool another_spliced = false; | ^~~~~~~~~~~~~~~ spliced_aligner.h:782:65: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 782 | tempHit.score() + sc.sc(0) * hit.rdoff() >= hit.score()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ spliced_aligner.h:1465:105: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 1465 | combinedHit.score() + sc.sc(0) * (rdlen - hit.rdoff() - hit.len() - hit.trim5()) >= hit.score()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h: In instantiation of ‘index_t HI_Aligner::globalGFMSearch(const GFM&, const Read&, const Scoring&, const ReportingParams&, bool, index_t, index_t&, index_t&, index_t&, index_t&, index_t&, EList >&, RandomSource&, bool&, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’: spliced_aligner.h:1086:53: required from ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int; int64_t = long int]’ 1086 | index_t nelt = this->globalGFMSearch( | ~~~~~~~~~~~~~~~~~~~~~^ 1087 | gfm, // GFM index | ~~~~~~~~~~~~~~~~~~~~ 1088 | rd, // read to align | ~~~~~~~~~~~~~~~~~~~~~~~~ 1089 | sc, // scoring scheme | ~~~~~~~~~~~~~~~~~~~~~~~~~ 1090 | sink.reportingParams(), | ~~~~~~~~~~~~~~~~~~~~~~~ 1091 | hit.fw(), | ~~~~~~~~~ 1092 | extoff, | ~~~~~~~ 1093 | extlen, | ~~~~~~~ 1094 | top, | ~~~~ 1095 | bot, | ~~~~ 1096 | node_top, | ~~~~~~~~~ 1097 | node_bot, | ~~~~~~~~~ 1098 | this->_node_iedge_count, | ~~~~~~~~~~~~~~~~~~~~~~~~ 1099 | rnd, | ~~~~ 1100 | uniqueStop); | ~~~~~~~~~~~ spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:6719:85: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 6719 | if(node_range.first < node_range.second && node_range.second - node_range.first <= rp.kseeds) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from edit.h:26, from edit.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from edit.h:26, from edit.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from alphabet.h:27, from gfm.h:40, from gfm.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from alphabet.h:27, from gfm.h:40, from gfm.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_sw.cpp:25: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from sequence_io.h:30, from hisat2_build.cpp:28: In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:768:29: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:764:24: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:766:29: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:764:24: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_ee_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2259:41: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2257:41: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In file included from sequence_io.h:30, from hisat2_build.cpp:28: In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]’ at rfm.h:768:29: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]’ at rfm.h:764:24: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]’ at rfm.h:766:29: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]’ at rfm.h:764:24: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2259:41: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2257:41: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_ee_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_loc_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_loc_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from bit_packed_array.cpp:24: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from repeat_builder.cpp:26: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ repeat_builder.cpp: In function ‘std::string reverse_complement(const std::string&)’: repeat_builder.cpp:88:30: warning: array subscript has type ‘char’ [-Wchar-subscripts] 88 | rev[i] = asc2dnacomp[nt]; | ^~ repeat_builder.cpp: In function ‘std::string reverseComplement(const std::string&)’: repeat_builder.cpp:200:53: warning: array subscript has type ‘char’ [-Wchar-subscripts] 200 | rc.push_back(asc2dnacomp[str[si - 1]]); | ^ repeat_builder.cpp: In member function ‘int CoordHelper::mapJoinedOffToSeq(TIndexOffU)’: repeat_builder.cpp:403:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 403 | for(size_t i = 0; i < num_cached_; i++) { | ~~^~~~~~~~~~~~~ repeat_builder.cpp: In function ‘size_t extract_kmer(const std::string&, size_t, size_t)’: repeat_builder.cpp:1217:53: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1217 | kmer = (kmer << 2) | asc2dna[seq[offset + i]]; | ^ repeat_builder.cpp: In function ‘size_t next_kmer(size_t, char, size_t)’: repeat_builder.cpp:1225:34: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1225 | kmer = (kmer << 2) | asc2dna[base]; | ^~~~ repeat_builder.cpp: In function ‘void find_gap_pos(const std::string&, const std::string&, EList&, EList&, bool, size_t, size_t, size_t&, size_t&, bool)’: repeat_builder.cpp:1275:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1275 | for(int i = seq_len - 1; i >= gap_len; i--) { | ~~^~~~~~~~~~ repeat_builder.cpp:1277:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1277 | if(i == seq_len - 1) ed2[i] = add; | ~~^~~~~~~~~~~~~~ repeat_builder.cpp: In member function ‘void RB_SWAligner::makePadString(const std::string&, const std::string&, std::string&, size_t)’: repeat_builder.cpp:2915:39: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2915 | pad[i] = "CGTA"[asc2dna[ref[i]]]; | ^ repeat_builder.cpp:2919:43: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2919 | pad[i] = "CGTA"[asc2dna[pad[i]]]; | ^ repeat_builder.cpp:2926:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2926 | for(size_t i = 0; i < head_len; i++) { | ~~^~~~~~~~~~ repeat_builder.cpp:2929:67: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2929 | pad[pad_start + i] = "CGTA"[asc2dna[pad[pad_start + i]]]; | ^ repeat_builder.cpp: In member function ‘int RB_SWAligner::alignStrings(const std::string&, const std::string&, EList&, Coord&)’: repeat_builder.cpp:3065:13: warning: variable ‘max_match_len’ set but not used [-Wunused-but-set-variable] 3065 | int max_match_len = 0; | ^~~~~~~~~~~~~ In file included from repeat_builder.cpp:31: repeat_builder.cpp: In instantiation of ‘RepeatBuilder::RepeatBuilder(TStr&, const EList&, const EList >&, bool, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’: repeat_builder.cpp:4753:16: required from here 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.h:947:17: warning: ‘RepeatBuilder >::coordHelper_’ will be initialized after [-Wreorder] 947 | CoordHelper coordHelper_; | ^~~~~~~~~~~~ repeat_builder.h:940:10: warning: ‘bool RepeatBuilder >::forward_only_’ [-Wreorder] 940 | bool forward_only_; | ^~~~~~~~~~~~~ repeat_builder.cpp:3167:1: warning: when initialized here [-Wreorder] 3167 | RepeatBuilder::RepeatBuilder(TStr& s, | ^~~~~~~~~~~~~~~~~~~ repeat_builder.cpp: In instantiation of ‘void RepeatBuilder::build(const RepeatParameter&) [with TStr = SString]’: repeat_builder.cpp:4753:16: required from here 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:3396:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 3396 | if(spos != string::npos) { | ~~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp:3426:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 3426 | if(spos != string::npos) { | ~~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp:3553:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 3553 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp:3563:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 3563 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp: In instantiation of ‘void RepeatBuilder::saveConsensus(const RepeatParameter&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’: repeat_builder.cpp:4753:16: required from here 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:4114:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 4114 | if((oskip + out_len) == output_width) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp: In instantiation of ‘void dump_tstr(const TStr&) [with TStr = SString]’: repeat_builder.cpp:4754:46: required from here 4754 | template void dump_tstr(const SString& ); | ^ repeat_builder.cpp:309:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 309 | for(size_t j = 0; (j < print_width) && (i + j < s_len); j++) { | ~~~^~~~~~~~~~~~~~ repeat_builder.cpp:310:46: warning: array subscript has type ‘char’ [-Wchar-subscripts] 310 | buf.push_back("ACGTN"[s[i + j]]); | ~~~~~~~^ repeat_builder.cpp: In instantiation of ‘std::string getString(const TStr&, TIndexOffU, size_t) [with TStr = SString; std::string = std::__cxx11::basic_string; TIndexOffU = long unsigned int; size_t = long unsigned int]’: repeat_builder.cpp:3312:30: required from ‘void RepeatBuilder::build(const RepeatParameter&) [with TStr = SString]’ 3312 | query = getString(s_, i, rp.min_repeat_len); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:4753:16: required from here 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:272:33: warning: array subscript has type ‘char’ [-Wchar-subscripts] 272 | char nt = "ACGT"[ref[start + i]]; | ~~~~~~^ repeat_builder.cpp: In instantiation of ‘void getString(const TStr&, TIndexOffU, size_t, std::string&) [with TStr = SString; TIndexOffU = long unsigned int; size_t = long unsigned int; std::string = std::__cxx11::basic_string]’: repeat_builder.cpp:3545:22: required from ‘void RepeatBuilder::build(const RepeatParameter&) [with TStr = SString]’ 3545 | getString(s_, saElt, rp.min_repeat_len, query); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:4753:16: required from here 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:286:25: warning: array subscript has type ‘char’ [-Wchar-subscripts] 286 | char nt = "ACGT"[ref[start + i]]; | ~~~~~~^ In file included from /usr/include/c++/14/iostream:41, from repeat_builder.cpp:21: In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void RepeatBuilder::writeAllele(TIndexOffU, TIndexOffU, Range, const std::string&, TIndexOffU, const EList&, std::ostream&) [with TStr = SString]’ at repeat_builder.cpp:3678:31: /usr/include/c++/14/ostream:179:25: warning: ‘pos_in_chr’ may be used uninitialized [-Wmaybe-uninitialized] 179 | { return _M_insert(__n); } | ~~~~~~~~~^~~~~ repeat_builder.cpp: In member function ‘void RepeatBuilder::writeAllele(TIndexOffU, TIndexOffU, Range, const std::string&, TIndexOffU, const EList&, std::ostream&) [with TStr = SString]’: repeat_builder.cpp:3664:20: note: ‘pos_in_chr’ was declared here 3664 | TIndexOffU pos_in_chr; | ^~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_sw.cpp:25: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_sw.cpp:25: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_loc_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_loc_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_ee_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_ee_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_loc_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_loc_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_ee_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, from aligner_swsse_ee_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ splice_site.cpp: In member function ‘void SpliceSiteDB::read(const GFM&, const EList >&)’: splice_site.cpp:717:59: warning: ‘?:’ using integer constants in boolean context, the expression will always evaluate to ‘true’ [-Wint-in-bool-context] 717 | exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from edit.h:29: ds.h: In instantiation of ‘void EList::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = long unsigned int]’: splice_site.cpp:722:31: required from here 722 | _exons.push_back_array(exons.begin(), exons.size()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ds.h:663:28: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class Exon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 663 | std::memcpy(list_ + cur_, l, bytes); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ splice_site.h:377:7: note: ‘class Exon’ declared here 377 | class Exon { | ^~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from gfm.h:28: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ splice_site.cpp: In member function ‘void SpliceSiteDB::read(const GFM&, const EList >&)’: splice_site.cpp:717:59: warning: ‘?:’ using integer constants in boolean context, the expression will always evaluate to ‘true’ [-Wint-in-bool-context] 717 | exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from edit.h:29: ds.h: In instantiation of ‘void EList::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = long unsigned int]’: splice_site.cpp:722:31: required from here 722 | _exons.push_back_array(exons.begin(), exons.size()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ds.h:663:28: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class Exon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 663 | std::memcpy(list_ + cur_, l, bytes); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ splice_site.h:377:7: note: ‘class Exon’ declared here 377 | class Exon { | ^~~~ make[2]: Leaving directory '/build/reproducible-path/hisat2-2.2.1' help2man ./hisat2 --no-info --name \ 'graph-based alignment of short nucleotide reads to many genomes, wrapper script' \ > debian/hisat2.1 help2man ./hisat2-align-l --name 'HISAT2 graph-based alignment of short nucleotide reads to many genomes, large index binary' \ --no-info > debian/hisat2-align-l.1 help2man ./hisat2-align-s --name 'HISAT2 graph-based alignment of short nucleotide reads to many genomes, small index binary' \ --no-info > debian/hisat2-align-s.1 help2man ./hisat2-build --name 'HISAT2 indexer, wrapper script' \ --no-info > debian/hisat2-build.1 #rm hisat2-buildc help2man ./hisat2-build-l --name 'HISAT2 indexer, large index binary' \ --no-info > debian/hisat2-build-l.1 help2man ./hisat2-build-s --name 'HISAT2 indexer, small index binary' \ --no-info > debian/hisat2-build-s.1 help2man ./hisat2-inspect --name 'HISAT2 index inspector, wrapper script' \ --no-info > debian/hisat2-inspect.1 help2man ./hisat2-inspect-l --name 'HISAT2 index inspector, large index binary' \ --no-info > debian/hisat2-inspect-l.1 help2man ./hisat2-inspect-s --name 'HISAT2 index inspector, small index binary' \ --no-info > debian/hisat2-inspect-s.1 make[1]: Leaving directory '/build/reproducible-path/hisat2-2.2.1' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/hisat2-2.2.1' dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/reproducible-path/hisat2-2.2.1' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/build/reproducible-path/hisat2-2.2.1' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.8.2-3), " make[1]: Leaving directory '/build/reproducible-path/hisat2-2.2.1' dh_md5sums dh_builddeb dpkg-deb: building package 'hisat2' in '../hisat2_2.2.1-5_arm64.deb'. dpkg-deb: building package 'hisat2-dbgsym' in '../hisat2-dbgsym_2.2.1-5_arm64.deb'. dpkg-deb: building package 'python3-hisat2' in '../python3-hisat2_2.2.1-5_all.deb'. dpkg-genbuildinfo --build=binary -O../hisat2_2.2.1-5_arm64.buildinfo dpkg-genchanges --build=binary -O../hisat2_2.2.1-5_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3594855/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3594855/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3594855 and its subdirectories I: Current time: Sun May 31 15:58:44 +14 2026 I: pbuilder-time-stamp: 1780192724 + false + set +x Sun May 31 01:58:44 UTC 2026 I: Signing ./b2/hisat2_2.2.1-5_arm64.buildinfo as hisat2_2.2.1-5_arm64.buildinfo.asc Sun May 31 01:58:44 UTC 2026 I: Signed ./b2/hisat2_2.2.1-5_arm64.buildinfo as ./b2/hisat2_2.2.1-5_arm64.buildinfo.asc Sun May 31 01:58:44 UTC 2026 - build #2 for hisat2/unstable/arm64 on codethink03-arm64 done. Starting cleanup. All cleanup done. Sun May 31 01:58:44 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-RcVNNfQi, removing. /srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL: total 340 drwxr-xr-x 2 jenkins jenkins 4096 Apr 27 19:31 b1 drwxr-xr-x 2 jenkins jenkins 4096 Apr 27 19:35 b2 -rw-r--r-- 1 jenkins jenkins 2104 Jul 9 2024 hisat2_2.2.1-5.dsc -rw------- 1 jenkins jenkins 330435 Apr 27 19:31 rbuildlog.TzSGPoE /srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL/b1: total 15724 -rw-r--r-- 1 jenkins jenkins 326927 Apr 27 19:31 build.log -rw-r--r-- 1 jenkins jenkins 12094096 Apr 27 19:31 hisat2-dbgsym_2.2.1-5_arm64.deb -rw-r--r-- 1 jenkins jenkins 29576 Apr 27 19:31 hisat2_2.2.1-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2104 Apr 27 19:31 hisat2_2.2.1-5.dsc -rw-r--r-- 1 jenkins jenkins 5750 Apr 27 19:31 hisat2_2.2.1-5_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6632 Apr 27 19:31 hisat2_2.2.1-5_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1718 Apr 27 19:31 hisat2_2.2.1-5_arm64.changes -rw-r--r-- 1 jenkins jenkins 3574404 Apr 27 19:31 hisat2_2.2.1-5_arm64.deb -rw-r--r-- 1 jenkins jenkins 1215 Apr 27 19:31 hisat2_2.2.1-5_source.changes -rw-r--r-- 1 jenkins jenkins 13996 Apr 27 19:31 python3-hisat2_2.2.1-5_all.deb /srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL/b2: total 15704 -rw-r--r-- 1 jenkins jenkins 328876 Apr 27 19:35 build.log -rw-r--r-- 1 jenkins jenkins 12094096 Apr 27 19:35 hisat2-dbgsym_2.2.1-5_arm64.deb -rw-r--r-- 1 jenkins jenkins 29576 Apr 27 19:35 hisat2_2.2.1-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2104 Apr 27 19:35 hisat2_2.2.1-5.dsc -rw-r--r-- 1 jenkins jenkins 5750 Apr 27 19:35 hisat2_2.2.1-5_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6632 Apr 27 19:35 hisat2_2.2.1-5_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1718 Apr 27 19:35 hisat2_2.2.1-5_arm64.changes -rw-r--r-- 1 jenkins jenkins 3574404 Apr 27 19:35 hisat2_2.2.1-5_arm64.deb -rw-r--r-- 1 jenkins jenkins 1215 Apr 27 19:35 hisat2_2.2.1-5_source.changes -rw-r--r-- 1 jenkins jenkins 13996 Apr 27 19:35 python3-hisat2_2.2.1-5_all.deb Sun Apr 27 19:35:46 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Sun Apr 27 19:35:46 UTC 2025 I: hisat2_2.2.1-5_arm64.changes: Format: 1.8 Date: Tue, 09 Jul 2024 12:26:53 +0200 Source: hisat2 Binary: hisat2 hisat2-dbgsym python3-hisat2 Architecture: arm64 all Version: 2.2.1-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: hisat2 - graph-based alignment of short nucleotide reads to many genomes python3-hisat2 - Python scripts accompanying hisat2 Closes: 1074739 Changes: hisat2 (2.2.1-5) unstable; urgency=medium . * d/patches/no_imp: add Python3.12 support. Closes: #1074739 Checksums-Sha1: 51b5683e886505096cfe94cdb74fb0c7b1caa0ee 12094096 hisat2-dbgsym_2.2.1-5_arm64.deb 7e38ea997b06bdf25e24ed7de5355e9b787a1c1f 5750 hisat2_2.2.1-5_arm64.buildinfo 9127985317a88f838cf80a7b5fcace92147e38f0 3574404 hisat2_2.2.1-5_arm64.deb ff0c6fba4fb37f8225daa7a1da8b30e94c2c7673 13996 python3-hisat2_2.2.1-5_all.deb Checksums-Sha256: 905c26c8289d0c9846df87104ca8fd268cccd37500d789a98a6bc24adbdf2838 12094096 hisat2-dbgsym_2.2.1-5_arm64.deb 0e86dc82e7dfa45b982033255e7c63036de9881de9c22dfa662ff49560ac94b9 5750 hisat2_2.2.1-5_arm64.buildinfo 136f7b0279270d1ca0eea9244d22c611fdccf7ca9cae9df28ebe6878ef10f74c 3574404 hisat2_2.2.1-5_arm64.deb 6df8ccf1d5fbd1c0a96e173573ebd68c021dc52c02d93f2ea600861fb6af45f1 13996 python3-hisat2_2.2.1-5_all.deb Files: 985166d0f566b137673cf334548490bd 12094096 debug optional hisat2-dbgsym_2.2.1-5_arm64.deb c08560489c3910e9f587846219db3882 5750 science optional hisat2_2.2.1-5_arm64.buildinfo 1633fe8758f2dae83d29edbdf15794d0 3574404 science optional hisat2_2.2.1-5_arm64.deb bffc89fb767d5bc384f947b9a286c1b1 13996 python optional python3-hisat2_2.2.1-5_all.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/hisat2_2.2.1-5.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/hisat2_2.2.1-5.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/hisat2_2.2.1-5.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/hisat2_2.2.1-5.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/arm64/hisat2_2.2.1-5_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/hisat2_2.2.1-5.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-04-27 19:31:58.279684057 +0000 +++ b2/build.log 2025-04-27 19:35:45.794839373 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Apr 27 07:26:32 -12 2025 -I: pbuilder-time-stamp: 1745781992 +I: Current time: Sun May 31 15:55:01 +14 2026 +I: pbuilder-time-stamp: 1780192501 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -32,52 +32,84 @@ dpkg-source: info: applying riscv5 I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/966878/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3594855/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 31 01:55 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3594855/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3594855/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' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='a8df00f6df85426e9e404fa7e51a5354' - 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='966878' - PS1='# ' - PS2='> ' + INVOCATION_ID=4d01c1b79d3a4e59b3e71baf4ae97ec1 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3594855 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.8bp91aLL/pbuilderrc_PHmI --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.8bp91aLL/b1 --logfile b1/build.log hisat2_2.2.1-5.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' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL/pbuilderrc_aHjJ --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL/b2 --logfile b2/build.log hisat2_2.2.1-5.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/966878/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3594855/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -171,7 +203,7 @@ Get: 49 http://deb.debian.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-2 [49.2 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 pandoc-data all 3.1.11.1-3 [459 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 pandoc arm64 3.1.11.1+ds-2 [26.2 MB] -Fetched 44.7 MB in 0s (125 MB/s) +Fetched 44.7 MB in 0s (127 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 ... 19953 files and directories currently installed.) @@ -353,8 +385,8 @@ Setting up tzdata (2025b-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Apr 27 19:26:59 UTC 2025. -Universal Time is now: Sun Apr 27 19:26:59 UTC 2025. +Local time is now: Sun May 31 01:55:20 UTC 2026. +Universal Time is now: Sun May 31 01:55:20 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... @@ -402,7 +434,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/hisat2-2.2.1/ && 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 > ../hisat2_2.2.1-5_source.changes +I: user script /srv/workspace/pbuilder/3594855/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3594855/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/hisat2-2.2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../hisat2_2.2.1-5_source.changes dpkg-buildpackage: info: source package hisat2 dpkg-buildpackage: info: source version 2.2.1-5 dpkg-buildpackage: info: source distribution unstable @@ -494,6 +530,38 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ +In file included from hisat2_build.cpp:35: +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +In file included from hisat2_repeat.cpp:36: +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: @@ -511,8 +579,41 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -gfm.h: In instantiation of ‘void GFM::initFromVector(TStr&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::string&, bool, index_t, index_t, index_t, int, EList*, EList >*, uint32_t, bool) [with TStr = SString; index_t = long unsigned int; std::string = std::__cxx11::basic_string; std::ofstream = std::basic_ofstream; uint32_t = unsigned int]’: -gfm.h:1039:23: required from ‘GFM::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, index_t, index_t, index_t, int, EList&, EList&, index_t, const RefReadInParams&, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ +In file included from hgfm.h:24, + from hisat2.cpp:33: +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +In file included from hisat2_inspect.cpp:25: +alt.h: In member function ‘bool ALT::repOk() const’: +assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] + 227 | if(!((a) <= (b))) { \ + | ~~~~^~~~~~ +alt.h:180:13: note: in expansion of macro ‘assert_leq’ + 180 | assert_leq(fw, 1); + | ^~~~~~~~~~ +In file included from hisat2_inspect.cpp:25: +alt.h: In member function ‘bool ALT::repOk() const’: +assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] + 227 | if(!((a) <= (b))) { \ + | ~~~~^~~~~~ +alt.h:180:13: note: in expansion of macro ‘assert_leq’ + 180 | assert_leq(fw, 1); + | ^~~~~~~~~~ +gfm.h: In instantiation of ‘void GFM::initFromVector(TStr&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::string&, bool, index_t, index_t, index_t, int, EList*, EList >*, uint32_t, bool) [with TStr = SString; index_t = unsigned int; std::string = std::__cxx11::basic_string; std::ofstream = std::basic_ofstream; uint32_t = unsigned int]’: +gfm.h:1039:23: required from ‘GFM::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, index_t, index_t, index_t, int, EList&, EList&, index_t, const RefReadInParams&, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ 1039 | initFromVector( | ~~~~~~~~~~~~~~~~~~~~^ 1040 | s, @@ -561,7 +662,7 @@ | ~~~~~ 1062 | verbose); | ~~~~~~~~ -hgfm.h:1989:14: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long unsigned int; uint32_t = unsigned int]’ +hgfm.h:1989:14: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = unsigned int; uint32_t = unsigned int]’ 1989 | _in6(NULL) | ^ hisat2_build.cpp:535:15: required from ‘void driver(const std::string&, EList >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::string = std::__cxx11::basic_string]’ @@ -671,58 +772,8 @@ gfm.h:2167:33: warning: variable ‘template_len’ set but not used [-Wunused-but-set-variable] 2167 | index_t template_len = 0; | ^~~~~~~~~~~~ -In file included from hisat2_build.cpp:35: -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -In file included from aligner_sw.h:76, - from aligner_sw_driver.h:86, - from hi_aligner.h:42, - from spliced_aligner.h:23, - from hisat2.cpp:46: -aligner_sw_nuc.h: At global scope: -aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 191 | NBest() { nelt_ = nbest_ = n_ = 0; } - | ^ -aligner_sw_nuc.h:191:17: note: remove the ‘< >’ -In file included from hgfm.h:24, - from hisat2.cpp:33: -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -hisat2.cpp: In function ‘void parseOptions(int, const char**)’: -hisat2.cpp:1823:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1823 | auto_ptr presets(new PresetsV0()); - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -gfm.h: In instantiation of ‘void GFM::initFromVector(TStr&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::string&, bool, index_t, index_t, index_t, int, EList*, EList >*, uint32_t, bool) [with TStr = SString; index_t = unsigned int; std::string = std::__cxx11::basic_string; std::ofstream = std::basic_ofstream; uint32_t = unsigned int]’: -gfm.h:1039:23: required from ‘GFM::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, index_t, index_t, index_t, int, EList&, EList&, index_t, const RefReadInParams&, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ +gfm.h: In instantiation of ‘void GFM::initFromVector(TStr&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::string&, bool, index_t, index_t, index_t, int, EList*, EList >*, uint32_t, bool) [with TStr = SString; index_t = long unsigned int; std::string = std::__cxx11::basic_string; std::ofstream = std::basic_ofstream; uint32_t = unsigned int]’: +gfm.h:1039:23: required from ‘GFM::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, index_t, index_t, index_t, int, EList&, EList&, index_t, const RefReadInParams&, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ 1039 | initFromVector( | ~~~~~~~~~~~~~~~~~~~~^ 1040 | s, @@ -771,7 +822,7 @@ | ~~~~~ 1062 | verbose); | ~~~~~~~~ -hgfm.h:1989:14: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = unsigned int; uint32_t = unsigned int]’ +hgfm.h:1989:14: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long unsigned int; uint32_t = unsigned int]’ 1989 | _in6(NULL) | ^ hisat2_build.cpp:535:15: required from ‘void driver(const std::string&, EList >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::string = std::__cxx11::basic_string]’ @@ -881,15 +932,8 @@ gfm.h:2167:33: warning: variable ‘template_len’ set but not used [-Wunused-but-set-variable] 2167 | index_t template_len = 0; | ^~~~~~~~~~~~ -In file included from hisat2_inspect.cpp:25: -alt.h: In member function ‘bool ALT::repOk() const’: -assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] - 227 | if(!((a) <= (b))) { \ - | ~~~~^~~~~~ -alt.h:180:13: note: in expansion of macro ‘assert_leq’ - 180 | assert_leq(fw, 1); - | ^~~~~~~~~~ -In file included from hisat2_repeat.cpp:36: +In file included from hgfm.h:24, + from hisat2_inspect.cpp:27: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -905,6 +949,64 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ +In file included from hgfm.h:24, + from hisat2_inspect.cpp:27: +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +In file included from aligner_sw.h:76, + from hisat2_repeat.cpp:37: +aligner_sw_nuc.h: At global scope: +aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 191 | NBest() { nelt_ = nbest_ = n_ = 0; } + | ^ +aligner_sw_nuc.h:191:17: note: remove the ‘< >’ +In file included from aligner_sw.h:76, + from aligner_sw_driver.h:86, + from hi_aligner.h:42, + from spliced_aligner.h:23, + from hisat2.cpp:46: +aligner_sw_nuc.h: At global scope: +aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 191 | NBest() { nelt_ = nbest_ = n_ = 0; } + | ^ +aligner_sw_nuc.h:191:17: note: remove the ‘< >’ +In file included from aligner_sw.h:76, + from aligner_sw_driver.h:86, + from hi_aligner.h:42, + from spliced_aligner.h:23, + from hisat2.cpp:46: +aligner_sw_nuc.h: At global scope: +aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 191 | NBest() { nelt_ = nbest_ = n_ = 0; } + | ^ +aligner_sw_nuc.h:191:17: note: remove the ‘< >’ +hisat2.cpp: In function ‘void parseOptions(int, const char**)’: +hisat2.cpp:1823:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1823 | auto_ptr presets(new PresetsV0()); + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +hisat2.cpp: In function ‘void parseOptions(int, const char**)’: +hisat2.cpp:1823:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1823 | auto_ptr presets(new PresetsV0()); + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’: hisat2.cpp:3167:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3167 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); @@ -924,6 +1026,32 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ +hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’: +hisat2.cpp:3167:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 3167 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +hisat2.cpp:3168:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 3168 | auto_ptr ps(patsrcFact->create()); + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +hisat2.cpp:3189:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 3189 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +hisat2.cpp: In function ‘void driver(const char*, const std::string&, const std::string&)’: +hisat2.cpp:4035:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 4035 | auto_ptr refs( + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ hisat2.cpp: In function ‘void driver(const char*, const std::string&, const std::string&)’: hisat2.cpp:4035:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 4035 | auto_ptr refs( @@ -931,6 +1059,75 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ +hi_aligner.h: In instantiation of ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’: +hisat2.cpp:3537:48: required from here + 3537 | int ret = splicedAligner.go( + | ~~~~~~~~~~~~~~~~~^ + 3538 | sc, + | ~~~ + 3539 | pepol, + | ~~~~~~ + 3540 | *multiseed_tpol, + | ~~~~~~~~~~~~~~~~ + 3541 | *gpol, + | ~~~~~~ + 3542 | gfm, + | ~~~~ + 3543 | rgfm, + | ~~~~~ + 3544 | *altdb, + | ~~~~~~~ + 3545 | *repeatdb, + | ~~~~~~~~~~ + 3546 | *raltdb, + | ~~~~~~~~ + 3547 | ref, + | ~~~~ + 3548 | rref, + | ~~~~~ + 3549 | sw, + | ~~~ + 3550 | *ssdb, + | ~~~~~~ + 3551 | wlm, + | ~~~~ + 3552 | prm, + | ~~~~ + 3553 | swmSeed, + | ~~~~~~~~ + 3554 | him, + | ~~~~ + 3555 | rnd, + | ~~~~ + 3556 | msinkwrap); + | ~~~~~~~~~~ +hi_aligner.h:4385:84: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] + 4385 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +hi_aligner.h:4404:55: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefId’ {aka ‘long int’} [-Wsign-compare] + 4404 | if(positions[p].first.tid != res.refid()) continue; + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +hi_aligner.h:4405:63: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] + 4405 | if(positions[p].first.toff + 1000 < res.refoff() || + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +hi_aligner.h:4406:52: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] + 4406 | res.refoff() + 1000 < positions[p].first.toff) continue; + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +hi_aligner.h:4407:88: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] + 4407 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +hi_aligner.h:4489:92: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] + 4489 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +hi_aligner.h:4578:69: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] + 4578 | align2repeat = (numBestPair == 0 || numBestPair > rp.khits); + | ~~~~~~~~~~~~^~~~~~~~~~ +hi_aligner.h:4584:83: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] + 4584 | align2repeat = (rs->size() == 0 || sink.numBestUnp(rdi).first > rp.khits); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +hi_aligner.h:4614:55: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] + 4614 | if(sink.numBestUnp(rdi).first > rp.khits) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h: In instantiation of ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’: hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( @@ -989,14 +1186,240 @@ gfm.h:6935:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^~~~~~~~ -In file included from hisat2_inspect.cpp:25: -alt.h: In member function ‘bool ALT::repOk() const’: -assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] - 227 | if(!((a) <= (b))) { \ - | ~~~~^~~~~~ -alt.h:180:13: note: in expansion of macro ‘assert_leq’ - 180 | assert_leq(fw, 1); - | ^~~~~~~~~~ +hi_aligner.h: In instantiation of ‘bool HI_Aligner::pairReads(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, WalkMetrics&, PerReadMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’: +hi_aligner.h:4088:17: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ + 4088 | pairReads(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, wlm, prm, him, rnd, sink); + | ^~~~~~~~~ +hisat2.cpp:3537:48: required from here + 3537 | int ret = splicedAligner.go( + | ~~~~~~~~~~~~~~~~~^ + 3538 | sc, + | ~~~ + 3539 | pepol, + | ~~~~~~ + 3540 | *multiseed_tpol, + | ~~~~~~~~~~~~~~~~ + 3541 | *gpol, + | ~~~~~~ + 3542 | gfm, + | ~~~~ + 3543 | rgfm, + | ~~~~~ + 3544 | *altdb, + | ~~~~~~~ + 3545 | *repeatdb, + | ~~~~~~~~~~ + 3546 | *raltdb, + | ~~~~~~~~ + 3547 | ref, + | ~~~~ + 3548 | rref, + | ~~~~~ + 3549 | sw, + | ~~~ + 3550 | *ssdb, + | ~~~~~~ + 3551 | wlm, + | ~~~~ + 3552 | prm, + | ~~~~ + 3553 | swmSeed, + | ~~~~~~~~ + 3554 | him, + | ~~~~ + 3555 | rnd, + | ~~~~ + 3556 | msinkwrap); + | ~~~~~~~~~~ +hi_aligner.h:5990:51: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] + 5990 | if(_repeatConcordant[r].first == left.off() && + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +hi_aligner.h:5991:52: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] + 5991 | _repeatConcordant[r].second == left2.off()) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +hi_aligner.h: In instantiation of ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’: +hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ + 4107 | mate_found |= alignMate( + | ^~~~~~~~~ +hisat2.cpp:3537:48: required from here + 3537 | int ret = splicedAligner.go( + | ~~~~~~~~~~~~~~~~~^ + 3538 | sc, + | ~~~ + 3539 | pepol, + | ~~~~~~ + 3540 | *multiseed_tpol, + | ~~~~~~~~~~~~~~~~ + 3541 | *gpol, + | ~~~~~~ + 3542 | gfm, + | ~~~~ + 3543 | rgfm, + | ~~~~~ + 3544 | *altdb, + | ~~~~~~~ + 3545 | *repeatdb, + | ~~~~~~~~~~ + 3546 | *raltdb, + | ~~~~~~~~ + 3547 | ref, + | ~~~~ + 3548 | rref, + | ~~~~~ + 3549 | sw, + | ~~~ + 3550 | *ssdb, + | ~~~~~~ + 3551 | wlm, + | ~~~~ + 3552 | prm, + | ~~~~ + 3553 | swmSeed, + | ~~~~~~~~ + 3554 | him, + | ~~~~ + 3555 | rnd, + | ~~~~ + 3556 | msinkwrap); + | ~~~~~~~~~~ +hi_aligner.h:5661:33: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] + 5661 | if(nelt > 0 && nelt <= rp.kseeds && hitlen > max_hitlen) { + | ~~~~~^~~~~~~~~~~~ +hi_aligner.h:5688:105: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] + 5688 | if(coord.off() + pepol.maxFragLen() * 2 < toff || toff + pepol.maxFragLen() * 2 < coord.off()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +gfm.h: In instantiation of ‘void GFM::checkOrigs(const EList >&, bool) const [with index_t = long unsigned int]’: +hisat2.cpp:3815:17: required from ‘void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’ + 3815 | gfm.checkOrigs(os, false); + | ~~~~~~~~~~~~~~^~~~~~~~~~~ +hisat2.cpp:4351:26: required from here + 4351 | driver >("DNA", bt2index, outfile); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +gfm.h:6935:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] + 6935 | int lastorig = -1; + | ^~~~~~~~ +hi_aligner.h: In instantiation of ‘index_t HI_Aligner::getAnchorHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const BitPairReference&, RandomSource&, index_t, bool, EList >&, index_t, SharedTempVars&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool) [with index_t = long unsigned int; local_index_t = short unsigned int]’: +hi_aligner.h:5525:23: required from ‘bool HI_Aligner::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ + 5525 | index_t numHits = getAnchorHits(gfm, + | ^~~~~~~~~~~~~ +hi_aligner.h:4080:31: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ + 4080 | found[rdi][fwi] = align(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, swa, ssdb, rdi, fw, wlm, prm, swm, him, rnd, sink); + | ^~~~~ +hisat2.cpp:3537:48: required from here + 3537 | int ret = splicedAligner.go( + | ~~~~~~~~~~~~~~~~~^ + 3538 | sc, + | ~~~ + 3539 | pepol, + | ~~~~~~ + 3540 | *multiseed_tpol, + | ~~~~~~~~~~~~~~~~ + 3541 | *gpol, + | ~~~~~~ + 3542 | gfm, + | ~~~~ + 3543 | rgfm, + | ~~~~~ + 3544 | *altdb, + | ~~~~~~~ + 3545 | *repeatdb, + | ~~~~~~~~~~ + 3546 | *raltdb, + | ~~~~~~~~ + 3547 | ref, + | ~~~~ + 3548 | rref, + | ~~~~~ + 3549 | sw, + | ~~~ + 3550 | *ssdb, + | ~~~~~~ + 3551 | wlm, + | ~~~~ + 3552 | prm, + | ~~~~ + 3553 | swmSeed, + | ~~~~~~~~ + 3554 | him, + | ~~~~ + 3555 | rnd, + | ~~~~ + 3556 | msinkwrap); + | ~~~~~~~~~~ +hi_aligner.h:5150:32: warning: comparison of integer expressions of different signedness: ‘TRefId’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] + 5150 | if(coord.ref() == numeric_limits::max()) + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +hi_aligner.h: In instantiation of ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long unsigned int]’: +hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ + 5692 | GenomeHit::adjustWithALT( + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ + 5693 | hitoff - hitlen + 1, + | ~~~~~~~~~~~~~~~~~~~~ + 5694 | hitlen, + | ~~~~~~~ + 5695 | coord, + | ~~~~~~ + 5696 | _sharedVars, + | ~~~~~~~~~~~~ + 5697 | _genomeHits, + | ~~~~~~~~~~~~ + 5698 | *this->_rds[ordi], + | ~~~~~~~~~~~~~~~~~~ + 5699 | gfm, + | ~~~~ + 5700 | altdb, + | ~~~~~~ + 5701 | ref, + | ~~~~ + 5702 | gpol); + | ~~~~~ +hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ + 4107 | mate_found |= alignMate( + | ^~~~~~~~~ +hisat2.cpp:3537:48: required from here + 3537 | int ret = splicedAligner.go( + | ~~~~~~~~~~~~~~~~~^ + 3538 | sc, + | ~~~ + 3539 | pepol, + | ~~~~~~ + 3540 | *multiseed_tpol, + | ~~~~~~~~~~~~~~~~ + 3541 | *gpol, + | ~~~~~~ + 3542 | gfm, + | ~~~~ + 3543 | rgfm, + | ~~~~~ + 3544 | *altdb, + | ~~~~~~~ + 3545 | *repeatdb, + | ~~~~~~~~~~ + 3546 | *raltdb, + | ~~~~~~~~ + 3547 | ref, + | ~~~~ + 3548 | rref, + | ~~~~~ + 3549 | sw, + | ~~~ + 3550 | *ssdb, + | ~~~~~~ + 3551 | wlm, + | ~~~~ + 3552 | prm, + | ~~~~ + 3553 | swmSeed, + | ~~~~~~~~ + 3554 | him, + | ~~~~ + 3555 | rnd, + | ~~~~ + 3556 | msinkwrap); + | ~~~~~~~~~~ +hi_aligner.h:2267:47: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] + 2267 | findSSOffs(gfm, altdb, (coord.joinedOff() >= width ? (index_t)(coord.joinedOff() - width) : 0), (index_t)(coord.joinedOff() + width), ssOffs); + | ~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41: @@ -1298,64 +1721,58 @@ hi_aligner.h:3454:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 3454 | if(best_rdoff < rdoff + rd_i) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ -In file included from hgfm.h:24, - from hisat2_inspect.cpp:27: -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -group_walk.h: In instantiation of ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: -group_walk.h:494:14: required from ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’ - 494 | return init(gfm, ref, sa, sts, hit, range, reportList, res, met); - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -group_walk.h:1453:18: required from ‘void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ - 1453 | st_.back().init( - | ~~~~~~~~~~~~~~~^ - 1454 | gfmFw, // Bowtie index - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1455 | ref, // bitpair-encoded reference - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1456 | sa, // SA range with offsets - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1457 | st_, // EList - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1458 | hit_, // GWHit - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1459 | 0, // range 0 - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1460 | false, // put resolved elements into res_? - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1461 | NULL, // put resolved elements here - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1462 | top, // GBW row at top - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1463 | bot, // GBW row at bot - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1464 | node_top, // node at top - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1465 | node_bot, // node at bot - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1466 | sa.node_iedge_count, - | ~~~~~~~~~~~~~~~~~~~~ - 1467 | 0, // # steps taken - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1468 | met); // update metrics here - | ~~~~ -hi_aligner.h:5896:20: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’ - 5896 | _gws_local.init(gfm, ref, _sas_local, rnd, met); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ +In file included from aligner_seed2.h:109, + from aligner_driver.h:78, + from hi_aligner.h:41: +group_walk.h: In instantiation of ‘std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: +group_walk.h:1517:14: required from ‘bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ + 1517 | st.advance( + | ~~~~~~~~~~^ + 1518 | gfmFw, + | ~~~~~~ + 1519 | ref, + | ~~~~ + 1520 | sa, + | ~~~ + 1521 | hit_, + | ~~~~~ + 1522 | (index_t)range, + | ~~~~~~~~~~~~~~~ + 1523 | false, + | ~~~~~~ + 1524 | NULL, + | ~~~~~ + 1525 | st_, + | ~~~~ + 1526 | gws, + | ~~~~ + 1527 | met, + | ~~~~ + 1528 | prm); + | ~~~~ +hi_aligner.h:5901:34: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ + 5901 | _gws_local.advanceElement( + | ~~~~~~~~~~~~~~~~~~~~~~~~~^ + 5902 | off, + | ~~~~ + 5903 | gfm, // forward Bowtie index for walking left + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 5904 | ref, // bitpair-encoded reference + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 5905 | _sas_local, // SA range with offsets + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 5906 | _gwstate_local, // GroupWalk state; scratch space + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 5907 | wr, // put the result here + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 5908 | met, // metrics + | ~~~~~~~~~~~~~~~~~~~~~~~~ + 5909 | prm); // per-read metrics + | ~~~~ +hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 5664 | getGenomeCoords_local( | ^~~~~~~~~~~~~~~~~~~~~ -hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here @@ -1399,36 +1816,20 @@ | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ -group_walk.h:785:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 785 | if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) { - | ~~~~~~^~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -group_walk.h:789:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 789 | if(new_top - top == tmp_gbwt_to_node.size()) { - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -group_walk.h:795:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 795 | if(i + 1 < tmp_zOffs.size()) { - | ~~~~~~^~~~~~~~~~~~~~~~~~ -group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 801 | if(new_bot - top < tmp_gbwt_to_node.size()) { - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = unsigned int]’: -hi_aligner.h:2915:39: required from ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ - 2915 | add_haplotypes(alts, - | ~~~~~~~~~~~~~~^~~~~~ - 2916 | haplotypes, - | ~~~~~~~~~~~ - 2917 | haplotype_maxrights, - | ~~~~~~~~~~~~~~~~~~~~ - 2918 | cmp_ht, - | ~~~~~~~ - 2919 | ht_list, - | ~~~~~~~~ - 2920 | rdlen); - | ~~~~~~ -hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ +group_walk.h:1147:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 1147 | if(new_node_bot - new_node_top < gws.map.size()) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ +group_walk.h:1158:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 1158 | for(index_t j = 0; j + 1 < gws.map.size(); j++) { + | ~~~~~~^~~~~~~~~~~~~~~~ +group_walk.h:1213:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 1213 | if(node_range.second - node_range.first < st.back().map_.size()) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +group_walk.h:1224:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 1224 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +hi_aligner.h: In instantiation of ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’: +hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ 718 | alts, @@ -1487,7 +1888,7 @@ | ~~~~~ 745 | numALTsTried); | ~~~~~~~~~~~~~ -hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’ +hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long unsigned int]’ 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, @@ -1530,395 +1931,6 @@ | ~~~~~~~~~~~~~~~~~~ 2357 | &candidate_edits); | ~~~~~~~~~~~~~~~~~ -hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ - 5692 | GenomeHit::adjustWithALT( - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ - 5693 | hitoff - hitlen + 1, - | ~~~~~~~~~~~~~~~~~~~~ - 5694 | hitlen, - | ~~~~~~~ - 5695 | coord, - | ~~~~~~ - 5696 | _sharedVars, - | ~~~~~~~~~~~~ - 5697 | _genomeHits, - | ~~~~~~~~~~~~ - 5698 | *this->_rds[ordi], - | ~~~~~~~~~~~~~~~~~~ - 5699 | gfm, - | ~~~~ - 5700 | altdb, - | ~~~~~~ - 5701 | ref, - | ~~~~ - 5702 | gpol); - | ~~~~~ -hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ - 4107 | mate_found |= alignMate( - | ^~~~~~~~~ -hisat2.cpp:3537:48: required from here - 3537 | int ret = splicedAligner.go( - | ~~~~~~~~~~~~~~~~~^ - 3538 | sc, - | ~~~ - 3539 | pepol, - | ~~~~~~ - 3540 | *multiseed_tpol, - | ~~~~~~~~~~~~~~~~ - 3541 | *gpol, - | ~~~~~~ - 3542 | gfm, - | ~~~~ - 3543 | rgfm, - | ~~~~~ - 3544 | *altdb, - | ~~~~~~~ - 3545 | *repeatdb, - | ~~~~~~~~~~ - 3546 | *raltdb, - | ~~~~~~~~ - 3547 | ref, - | ~~~~ - 3548 | rref, - | ~~~~~ - 3549 | sw, - | ~~~ - 3550 | *ssdb, - | ~~~~~~ - 3551 | wlm, - | ~~~~ - 3552 | prm, - | ~~~~ - 3553 | swmSeed, - | ~~~~~~~~ - 3554 | him, - | ~~~~ - 3555 | rnd, - | ~~~~ - 3556 | msinkwrap); - | ~~~~~~~~~~ -hi_aligner.h:2660:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 2660 | if(ht_range.first >= haplotypes.size()) - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ -hi_aligner.h:2675:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] - 2675 | if(ht_list[h].first == ht_range.first) { - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -hi_aligner.h:2713:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] - 2713 | if(ht_list[h].first == ht_range.first) { - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -hi_aligner.h:2737:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 2737 | for(; ht_range.second < haplotypes.size(); ht_range.second++) { - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -hi_aligner.h:2744:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] - 2744 | if(ht_list[h].first == ht_range.second) { - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long int]’: -spliced_aligner.h:331:9: required from here - 331 | int64_t SplicedAligner::hybridSearch_recur( - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -spliced_aligner.h:408:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] - 408 | bool another_spliced = false; - | ^~~~~~~~~~~~~~~ -In file included from aligner_sw.h:76, - from aligner_sw_driver.h:86, - from hi_aligner.h:42, - from spliced_aligner.h:23, - from hisat2.cpp:46: -aligner_sw_nuc.h: At global scope: -aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 191 | NBest() { nelt_ = nbest_ = n_ = 0; } - | ^ -aligner_sw_nuc.h:191:17: note: remove the ‘< >’ -In file included from hgfm.h:24, - from hisat2_inspect.cpp:27: -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -hisat2.cpp: In function ‘void parseOptions(int, const char**)’: -hisat2.cpp:1823:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1823 | auto_ptr presets(new PresetsV0()); - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’: -hisat2.cpp:3167:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 3167 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -hisat2.cpp:3168:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 3168 | auto_ptr ps(patsrcFact->create()); - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -hisat2.cpp:3189:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 3189 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -hisat2.cpp: In function ‘void driver(const char*, const std::string&, const std::string&)’: -hisat2.cpp:4035:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 4035 | auto_ptr refs( - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -In file included from aligner_sw.h:76, - from hisat2_repeat.cpp:37: -aligner_sw_nuc.h: At global scope: -aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 191 | NBest() { nelt_ = nbest_ = n_ = 0; } - | ^ -aligner_sw_nuc.h:191:17: note: remove the ‘< >’ -hi_aligner.h: In instantiation of ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’: -hisat2.cpp:3537:48: required from here - 3537 | int ret = splicedAligner.go( - | ~~~~~~~~~~~~~~~~~^ - 3538 | sc, - | ~~~ - 3539 | pepol, - | ~~~~~~ - 3540 | *multiseed_tpol, - | ~~~~~~~~~~~~~~~~ - 3541 | *gpol, - | ~~~~~~ - 3542 | gfm, - | ~~~~ - 3543 | rgfm, - | ~~~~~ - 3544 | *altdb, - | ~~~~~~~ - 3545 | *repeatdb, - | ~~~~~~~~~~ - 3546 | *raltdb, - | ~~~~~~~~ - 3547 | ref, - | ~~~~ - 3548 | rref, - | ~~~~~ - 3549 | sw, - | ~~~ - 3550 | *ssdb, - | ~~~~~~ - 3551 | wlm, - | ~~~~ - 3552 | prm, - | ~~~~ - 3553 | swmSeed, - | ~~~~~~~~ - 3554 | him, - | ~~~~ - 3555 | rnd, - | ~~~~ - 3556 | msinkwrap); - | ~~~~~~~~~~ -hi_aligner.h:4385:84: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] - 4385 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -hi_aligner.h:4404:55: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefId’ {aka ‘long int’} [-Wsign-compare] - 4404 | if(positions[p].first.tid != res.refid()) continue; - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -hi_aligner.h:4405:63: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] - 4405 | if(positions[p].first.toff + 1000 < res.refoff() || - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -hi_aligner.h:4406:52: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] - 4406 | res.refoff() + 1000 < positions[p].first.toff) continue; - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -hi_aligner.h:4407:88: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] - 4407 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -hi_aligner.h:4489:92: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] - 4489 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -hi_aligner.h:4578:69: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] - 4578 | align2repeat = (numBestPair == 0 || numBestPair > rp.khits); - | ~~~~~~~~~~~~^~~~~~~~~~ -hi_aligner.h:4584:83: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] - 4584 | align2repeat = (rs->size() == 0 || sink.numBestUnp(rdi).first > rp.khits); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -hi_aligner.h:4614:55: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] - 4614 | if(sink.numBestUnp(rdi).first > rp.khits) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -hi_aligner.h: In instantiation of ‘bool HI_Aligner::pairReads(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, WalkMetrics&, PerReadMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’: -hi_aligner.h:4088:17: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ - 4088 | pairReads(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, wlm, prm, him, rnd, sink); - | ^~~~~~~~~ -hisat2.cpp:3537:48: required from here - 3537 | int ret = splicedAligner.go( - | ~~~~~~~~~~~~~~~~~^ - 3538 | sc, - | ~~~ - 3539 | pepol, - | ~~~~~~ - 3540 | *multiseed_tpol, - | ~~~~~~~~~~~~~~~~ - 3541 | *gpol, - | ~~~~~~ - 3542 | gfm, - | ~~~~ - 3543 | rgfm, - | ~~~~~ - 3544 | *altdb, - | ~~~~~~~ - 3545 | *repeatdb, - | ~~~~~~~~~~ - 3546 | *raltdb, - | ~~~~~~~~ - 3547 | ref, - | ~~~~ - 3548 | rref, - | ~~~~~ - 3549 | sw, - | ~~~ - 3550 | *ssdb, - | ~~~~~~ - 3551 | wlm, - | ~~~~ - 3552 | prm, - | ~~~~ - 3553 | swmSeed, - | ~~~~~~~~ - 3554 | him, - | ~~~~ - 3555 | rnd, - | ~~~~ - 3556 | msinkwrap); - | ~~~~~~~~~~ -hi_aligner.h:5990:51: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] - 5990 | if(_repeatConcordant[r].first == left.off() && - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -hi_aligner.h:5991:52: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] - 5991 | _repeatConcordant[r].second == left2.off()) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -hi_aligner.h: In instantiation of ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’: -hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ - 4107 | mate_found |= alignMate( - | ^~~~~~~~~ -hisat2.cpp:3537:48: required from here - 3537 | int ret = splicedAligner.go( - | ~~~~~~~~~~~~~~~~~^ - 3538 | sc, - | ~~~ - 3539 | pepol, - | ~~~~~~ - 3540 | *multiseed_tpol, - | ~~~~~~~~~~~~~~~~ - 3541 | *gpol, - | ~~~~~~ - 3542 | gfm, - | ~~~~ - 3543 | rgfm, - | ~~~~~ - 3544 | *altdb, - | ~~~~~~~ - 3545 | *repeatdb, - | ~~~~~~~~~~ - 3546 | *raltdb, - | ~~~~~~~~ - 3547 | ref, - | ~~~~ - 3548 | rref, - | ~~~~~ - 3549 | sw, - | ~~~ - 3550 | *ssdb, - | ~~~~~~ - 3551 | wlm, - | ~~~~ - 3552 | prm, - | ~~~~ - 3553 | swmSeed, - | ~~~~~~~~ - 3554 | him, - | ~~~~ - 3555 | rnd, - | ~~~~ - 3556 | msinkwrap); - | ~~~~~~~~~~ -hi_aligner.h:5661:33: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] - 5661 | if(nelt > 0 && nelt <= rp.kseeds && hitlen > max_hitlen) { - | ~~~~~^~~~~~~~~~~~ -hi_aligner.h:5688:105: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] - 5688 | if(coord.off() + pepol.maxFragLen() * 2 < toff || toff + pepol.maxFragLen() * 2 < coord.off()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -gfm.h: In instantiation of ‘void GFM::checkOrigs(const EList >&, bool) const [with index_t = long unsigned int]’: -hisat2.cpp:3815:17: required from ‘void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’ - 3815 | gfm.checkOrigs(os, false); - | ~~~~~~~~~~~~~~^~~~~~~~~~~ -hisat2.cpp:4351:26: required from here - 4351 | driver >("DNA", bt2index, outfile); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -gfm.h:6935:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] - 6935 | int lastorig = -1; - | ^~~~~~~~ -hi_aligner.h: In instantiation of ‘index_t HI_Aligner::getAnchorHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const BitPairReference&, RandomSource&, index_t, bool, EList >&, index_t, SharedTempVars&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool) [with index_t = long unsigned int; local_index_t = short unsigned int]’: -hi_aligner.h:5525:23: required from ‘bool HI_Aligner::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ - 5525 | index_t numHits = getAnchorHits(gfm, - | ^~~~~~~~~~~~~ -hi_aligner.h:4080:31: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ - 4080 | found[rdi][fwi] = align(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, swa, ssdb, rdi, fw, wlm, prm, swm, him, rnd, sink); - | ^~~~~ -hisat2.cpp:3537:48: required from here - 3537 | int ret = splicedAligner.go( - | ~~~~~~~~~~~~~~~~~^ - 3538 | sc, - | ~~~ - 3539 | pepol, - | ~~~~~~ - 3540 | *multiseed_tpol, - | ~~~~~~~~~~~~~~~~ - 3541 | *gpol, - | ~~~~~~ - 3542 | gfm, - | ~~~~ - 3543 | rgfm, - | ~~~~~ - 3544 | *altdb, - | ~~~~~~~ - 3545 | *repeatdb, - | ~~~~~~~~~~ - 3546 | *raltdb, - | ~~~~~~~~ - 3547 | ref, - | ~~~~ - 3548 | rref, - | ~~~~~ - 3549 | sw, - | ~~~ - 3550 | *ssdb, - | ~~~~~~ - 3551 | wlm, - | ~~~~ - 3552 | prm, - | ~~~~ - 3553 | swmSeed, - | ~~~~~~~~ - 3554 | him, - | ~~~~ - 3555 | rnd, - | ~~~~ - 3556 | msinkwrap); - | ~~~~~~~~~~ -hi_aligner.h:5150:32: warning: comparison of integer expressions of different signedness: ‘TRefId’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] - 5150 | if(coord.ref() == numeric_limits::max()) - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -hi_aligner.h: In instantiation of ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long unsigned int]’: hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ @@ -1986,61 +1998,74 @@ | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ -hi_aligner.h:2267:47: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] - 2267 | findSSOffs(gfm, altdb, (coord.joinedOff() >= width ? (index_t)(coord.joinedOff() - width) : 0), (index_t)(coord.joinedOff() + width), ssOffs); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~ -In file included from aligner_seed2.h:109, - from aligner_driver.h:78, - from hi_aligner.h:41: -group_walk.h: In instantiation of ‘std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: -group_walk.h:1517:14: required from ‘bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ - 1517 | st.advance( - | ~~~~~~~~~~^ - 1518 | gfmFw, - | ~~~~~~ - 1519 | ref, - | ~~~~ - 1520 | sa, - | ~~~ - 1521 | hit_, - | ~~~~~ - 1522 | (index_t)range, - | ~~~~~~~~~~~~~~~ - 1523 | false, - | ~~~~~~ - 1524 | NULL, - | ~~~~~ - 1525 | st_, - | ~~~~ - 1526 | gws, - | ~~~~ - 1527 | met, - | ~~~~ - 1528 | prm); - | ~~~~ -hi_aligner.h:5901:34: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ - 5901 | _gws_local.advanceElement( - | ~~~~~~~~~~~~~~~~~~~~~~~~~^ - 5902 | off, - | ~~~~ - 5903 | gfm, // forward Bowtie index for walking left - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 5904 | ref, // bitpair-encoded reference - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 5905 | _sas_local, // SA range with offsets - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 5906 | _gwstate_local, // GroupWalk state; scratch space - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 5907 | wr, // put the result here - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 5908 | met, // metrics - | ~~~~~~~~~~~~~~~~~~~~~~~~ - 5909 | prm); // per-read metrics - | ~~~~ -hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h:2801:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 2801 | if(rfoff >= contig_len) return 0; + | ~~~~~~^~~~~~~~~~~~~ +hi_aligner.h:2879:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 2879 | if(alt_range.first >= alts.size()) { + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +hi_aligner.h:3044:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] + 3044 | for(int i = 0; i < alt.len; i++) { + | ~~^~~~~~~~~ +hi_aligner.h:3085:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] + 3085 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { + | ~~~~~^~~~~~~~ +hi_aligner.h:3161:31: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] + 3161 | if(alignedLen == next_rdlen) return rdlen; + | ~~~~~~~~~~~^~~~~~~~~~~~~ +hi_aligner.h:3197:32: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] + 3197 | if(mm_max_rd_i + rdoff > best_rdoff) { + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +hi_aligner.h:3202:39: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] + 3202 | } else if(mm_max_rd_i + rdoff == best_rdoff) { + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +hi_aligner.h:3454:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] + 3454 | if(best_rdoff < rdoff + rd_i) { + | ~~~~~~~~~~~^~~~~~~~~~~~~~ +group_walk.h: In instantiation of ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: +group_walk.h:494:14: required from ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’ + 494 | return init(gfm, ref, sa, sts, hit, range, reportList, res, met); + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +group_walk.h:1453:18: required from ‘void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ + 1453 | st_.back().init( + | ~~~~~~~~~~~~~~~^ + 1454 | gfmFw, // Bowtie index + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1455 | ref, // bitpair-encoded reference + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1456 | sa, // SA range with offsets + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1457 | st_, // EList + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1458 | hit_, // GWHit + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1459 | 0, // range 0 + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1460 | false, // put resolved elements into res_? + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1461 | NULL, // put resolved elements here + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1462 | top, // GBW row at top + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1463 | bot, // GBW row at bot + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1464 | node_top, // node at top + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1465 | node_bot, // node at bot + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1466 | sa.node_iedge_count, + | ~~~~~~~~~~~~~~~~~~~~ + 1467 | 0, // # steps taken + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1468 | met); // update metrics here + | ~~~~ +hi_aligner.h:5896:20: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’ + 5896 | _gws_local.init(gfm, ref, _sas_local, rnd, met); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ 5664 | getGenomeCoords_local( | ^~~~~~~~~~~~~~~~~~~~~ -hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here @@ -2084,20 +2109,33 @@ | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ -group_walk.h:1147:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 1147 | if(new_node_bot - new_node_top < gws.map.size()) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -group_walk.h:1158:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 1158 | for(index_t j = 0; j + 1 < gws.map.size(); j++) { - | ~~~~~~^~~~~~~~~~~~~~~~ -group_walk.h:1213:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 1213 | if(node_range.second - node_range.first < st.back().map_.size()) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -group_walk.h:1224:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 1224 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -hi_aligner.h: In instantiation of ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’: -hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ +group_walk.h:785:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 785 | if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) { + | ~~~~~~^~~~~~~~~~~~~~~~~~ +group_walk.h:789:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 789 | if(new_top - top == tmp_gbwt_to_node.size()) { + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +group_walk.h:795:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 795 | if(i + 1 < tmp_zOffs.size()) { + | ~~~~~~^~~~~~~~~~~~~~~~~~ +group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 801 | if(new_bot - top < tmp_gbwt_to_node.size()) { + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = unsigned int]’: +hi_aligner.h:2915:39: required from ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ + 2915 | add_haplotypes(alts, + | ~~~~~~~~~~~~~~^~~~~~ + 2916 | haplotypes, + | ~~~~~~~~~~~ + 2917 | haplotype_maxrights, + | ~~~~~~~~~~~~~~~~~~~~ + 2918 | cmp_ht, + | ~~~~~~~ + 2919 | ht_list, + | ~~~~~~~~ + 2920 | rdlen); + | ~~~~~~ +hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ 718 | alts, @@ -2156,7 +2194,7 @@ | ~~~~~ 745 | numALTsTried); | ~~~~~~~~~~~~~ -hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long unsigned int]’ +hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’ 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, @@ -2199,7 +2237,7 @@ | ~~~~~~~~~~~~~~~~~~ 2357 | &candidate_edits); | ~~~~~~~~~~~~~~~~~ -hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, @@ -2222,7 +2260,7 @@ | ~~~~ 5702 | gpol); | ~~~~~ -hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here @@ -2266,30 +2304,21 @@ | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ -hi_aligner.h:2801:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 2801 | if(rfoff >= contig_len) return 0; - | ~~~~~~^~~~~~~~~~~~~ -hi_aligner.h:2879:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 2879 | if(alt_range.first >= alts.size()) { - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -hi_aligner.h:3044:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] - 3044 | for(int i = 0; i < alt.len; i++) { - | ~~^~~~~~~~~ -hi_aligner.h:3085:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] - 3085 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { - | ~~~~~^~~~~~~~ -hi_aligner.h:3161:31: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] - 3161 | if(alignedLen == next_rdlen) return rdlen; - | ~~~~~~~~~~~^~~~~~~~~~~~~ -hi_aligner.h:3197:32: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] - 3197 | if(mm_max_rd_i + rdoff > best_rdoff) { - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -hi_aligner.h:3202:39: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] - 3202 | } else if(mm_max_rd_i + rdoff == best_rdoff) { - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -hi_aligner.h:3454:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] - 3454 | if(best_rdoff < rdoff + rd_i) { - | ~~~~~~~~~~~^~~~~~~~~~~~~~ +hi_aligner.h:2660:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 2660 | if(ht_range.first >= haplotypes.size()) + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ +hi_aligner.h:2675:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] + 2675 | if(ht_list[h].first == ht_range.first) { + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +hi_aligner.h:2713:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] + 2713 | if(ht_list[h].first == ht_range.first) { + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +hi_aligner.h:2737:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 2737 | for(; ht_range.second < haplotypes.size(); ht_range.second++) { + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +hi_aligner.h:2744:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] + 2744 | if(ht_list[h].first == ht_range.second) { + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ group_walk.h: In instantiation of ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:494:14: required from ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’ 494 | return init(gfm, ref, sa, sts, hit, range, reportList, res, met); @@ -2587,6 +2616,13 @@ hi_aligner.h:2744:41: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 2744 | if(ht_list[h].first == ht_range.second) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long int]’: +spliced_aligner.h:331:9: required from here + 331 | int64_t SplicedAligner::hybridSearch_recur( + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +spliced_aligner.h:408:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] + 408 | bool another_spliced = false; + | ^~~~~~~~~~~~~~~ spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int; int64_t = long int]’: spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( @@ -2689,8 +2725,7 @@ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ -In file included from splice_site.h:34, - from edit.h:30: +In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -2706,7 +2741,8 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -In file included from gfm.cpp:21: +In file included from splice_site.h:34, + from edit.h:30: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -2731,6 +2767,13 @@ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ +reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: +reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] + 522 | uint64_t origBufOff = bufOff; + | ^~~~~~~~~~ +reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] + 516 | bool binarySearched = false; + | ^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: @@ -2748,13 +2791,6 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: -reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] - 522 | uint64_t origBufOff = bufOff; - | ^~~~~~~~~~ -reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] - 516 | bool binarySearched = false; - | ^~~~~~~~~~~~~~ In file included from alphabet.h:27, from gfm.h:40, from gfm.cpp:21: @@ -2898,77 +2934,83 @@ sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ -In file included from sequence_io.h:30, - from hisat2_build.cpp:28: +In file included from splice_site.h:34, + from edit.h:30, + from aligner_result.h:30, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_ee_i16.cpp:56: +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +In file included from aligner_sw.h:76: +aligner_sw_nuc.h: At global scope: +aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 191 | NBest() { nelt_ = nbest_ = n_ = 0; } + | ^ +aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, - inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]’ at rfm.h:768:29: + inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2259:41: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]’ at rfm.h:764:24: + inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, - inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]’ at rfm.h:766:29: + inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2257:41: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]’ at rfm.h:764:24: + inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ +In file included from sequence_io.h:30, + from hisat2_build.cpp:28: In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, - inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2259:41: + inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]’ at rfm.h:768:29: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: + inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]’ at rfm.h:764:24: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, - inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2257:41: + inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]’ at rfm.h:766:29: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: + inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]’ at rfm.h:764:24: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ -In file included from splice_site.h:34, - from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_ee_i16.cpp:56: -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, @@ -2993,20 +3035,6 @@ sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ -In file included from aligner_sw.h:76: -aligner_sw_nuc.h: At global scope: -aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 191 | NBest() { nelt_ = nbest_ = n_ = 0; } - | ^ -aligner_sw_nuc.h:191:17: note: remove the ‘< >’ -ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: -ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 367 | if(i + 1 >= recs.size() || recs[i+1].first) { - | ~~~~~~^~~~~~~~~~~~~~ -ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: -ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 440 | if(i + 1 >= recs.size() || recs[i+1].first) { - | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { @@ -3060,9 +3088,15 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -In file included from splice_site.h:34, - from edit.h:30, - from edit.cpp:21: +ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: +ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 367 | if(i + 1 >= recs.size() || recs[i+1].first) { + | ~~~~~~^~~~~~~~~~~~~~ +ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: +ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 440 | if(i + 1 >= recs.size() || recs[i+1].first) { + | ~~~~~~^~~~~~~~~~~~~~ +In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -3078,7 +3112,12 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -In file included from gfm.cpp:21: +In file included from splice_site.h:34, + from edit.h:30, + from aligner_result.h:30, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_loc_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -3094,6 +3133,12 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ +In file included from aligner_sw.h:76: +aligner_sw_nuc.h: At global scope: +aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 191 | NBest() { nelt_ = nbest_ = n_ = 0; } + | ^ +aligner_sw_nuc.h:191:17: note: remove the ‘< >’ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; @@ -3101,7 +3146,9 @@ reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^~~~~~~~~~~~~~ -In file included from gfm.cpp:21: +In file included from splice_site.h:34, + from edit.h:30, + from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -3125,12 +3172,7 @@ ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ -In file included from splice_site.h:34, - from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_loc_i16.cpp:56: +In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -3146,12 +3188,6 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -In file included from aligner_sw.h:76: -aligner_sw_nuc.h: At global scope: -aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 191 | NBest() { nelt_ = nbest_ = n_ = 0; } - | ^ -aligner_sw_nuc.h:191:17: note: remove the ‘< >’ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; @@ -3177,15 +3213,12 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: -ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 367 | if(i + 1 >= recs.size() || recs[i+1].first) { - | ~~~~~~^~~~~~~~~~~~~~ -ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: -ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 440 | if(i + 1 >= recs.size() || recs[i+1].first) { - | ~~~~~~^~~~~~~~~~~~~~ -In file included from gfm.cpp:21: +In file included from splice_site.h:34, + from edit.h:30, + from aligner_result.h:30, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_loc_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -3201,12 +3234,21 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -In file included from splice_site.h:34, - from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_loc_u8.cpp:56: +ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: +ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 367 | if(i + 1 >= recs.size() || recs[i+1].first) { + | ~~~~~~^~~~~~~~~~~~~~ +ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: +ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 440 | if(i + 1 >= recs.size() || recs[i+1].first) { + | ~~~~~~^~~~~~~~~~~~~~ +In file included from aligner_sw.h:76: +aligner_sw_nuc.h: At global scope: +aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 191 | NBest() { nelt_ = nbest_ = n_ = 0; } + | ^ +aligner_sw_nuc.h:191:17: note: remove the ‘< >’ +In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -3222,12 +3264,6 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -In file included from aligner_sw.h:76: -aligner_sw_nuc.h: At global scope: -aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 191 | NBest() { nelt_ = nbest_ = n_ = 0; } - | ^ -aligner_sw_nuc.h:191:17: note: remove the ‘< >’ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; @@ -3269,13 +3305,6 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: -reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] - 522 | uint64_t origBufOff = bufOff; - | ^~~~~~~~~~ -reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] - 516 | bool binarySearched = false; - | ^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, @@ -3296,6 +3325,13 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ +reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: +reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] + 522 | uint64_t origBufOff = bufOff; + | ^~~~~~~~~~ +reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] + 516 | bool binarySearched = false; + | ^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, @@ -4189,9 +4225,9 @@ make[1]: Leaving directory '/build/reproducible-path/hisat2-2.2.1' dh_md5sums dh_builddeb -dpkg-deb: building package 'python3-hisat2' in '../python3-hisat2_2.2.1-5_all.deb'. -dpkg-deb: building package 'hisat2-dbgsym' in '../hisat2-dbgsym_2.2.1-5_arm64.deb'. dpkg-deb: building package 'hisat2' in '../hisat2_2.2.1-5_arm64.deb'. +dpkg-deb: building package 'hisat2-dbgsym' in '../hisat2-dbgsym_2.2.1-5_arm64.deb'. +dpkg-deb: building package 'python3-hisat2' in '../python3-hisat2_2.2.1-5_all.deb'. dpkg-genbuildinfo --build=binary -O../hisat2_2.2.1-5_arm64.buildinfo dpkg-genchanges --build=binary -O../hisat2_2.2.1-5_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -4199,12 +4235,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3594855/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3594855/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/966878 and its subdirectories -I: Current time: Sun Apr 27 07:31:57 -12 2025 -I: pbuilder-time-stamp: 1745782317 +I: removing directory /srv/workspace/pbuilder/3594855 and its subdirectories +I: Current time: Sun May 31 15:58:44 +14 2026 +I: pbuilder-time-stamp: 1780192724 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/hisat2_2.2.1-5.diff: 90.8% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/hisat2_2.2.1-5.diff.gz b2/build.log: 93.1% -- replaced with stdout Compressing the 1st log... b1/build.log: 92.3% -- replaced with stdout Sun Apr 27 19:35:47 UTC 2025 I: diffoscope 294 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_hisat2_unstable_arm64_1745782547 + touch /var/log/reproducible-builds/diffoscope_stamp_hisat2_unstable_arm64_1745782547 + RESULT=0 + systemd-run '--description=diffoscope on hisat2/2.2.1-5 in unstable/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_12-92900 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL --run-session -c jenkins-reproducible-unstable-diffoscope-9ca09e4f-28f6-4d5a-81fe-36e77e2d70e6 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL/dbd-tmp-rTZMUVj ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL/hisat2_2.2.1-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL/hisat2_2.2.1-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL/hisat2_2.2.1-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL/b1/hisat2_2.2.1-5_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL/b2/hisat2_2.2.1-5_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_12-92900.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL/hisat2_2.2.1-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL/hisat2_2.2.1-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL/hisat2_2.2.1-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL/b1/hisat2_2.2.1-5_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.8bp91aLL/b2/hisat2_2.2.1-5_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 233ms CPU time consumed: 232ms _ _ _ ____ | |__ (_)___ __ _| |_|___ \ | '_ \| / __|/ _` | __| __) | | | | | \__ \ (_| | |_ / __/ |_| |_|_|___/\__,_|\__|_____| Sun Apr 27 19:35:48 UTC 2025 I: diffoscope 294 found no differences in the changes files, and a .buildinfo file also exists. Sun Apr 27 19:35:48 UTC 2025 I: hisat2 from unstable built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-04-27 19:35:49] INFO: Starting at 2025-04-27 19:35:49.053226 [2025-04-27 19:35:49] INFO: Generating the pages of 1 package(s) [2025-04-27 19:35:49] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/arm64/hisat2 didn't produce a buildlog, even though it has been built. [2025-04-27 19:35:49] INFO: Finished at 2025-04-27 19:35:49.529023, took: 0:00:00.475804 Sun Apr 27 19:35:49 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/hisat2.html Sun Apr 27 19:35:49 UTC 2025 I: Submitting .buildinfo files to external archives: Sun Apr 27 19:35:49 UTC 2025 I: Submitting 8.0K b1/hisat2_2.2.1-5_arm64.buildinfo.asc https://buildinfo.debian.net/7e38ea997b06bdf25e24ed7de5355e9b787a1c1f/hisat2_2.2.1-5_all Sun Apr 27 19:36:09 UTC 2025 I: Submitting 8.0K b2/hisat2_2.2.1-5_arm64.buildinfo.asc https://buildinfo.debian.net/1539f8f0e325897bb6d0ccb8c9d74843b70ec066/hisat2_2.2.1-5_all Sun Apr 27 19:36:30 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Apr 27 19:36:30 UTC 2025 I: Done submitting .buildinfo files. Sun Apr 27 19:36:30 UTC 2025 I: Removing signed hisat2_2.2.1-5_arm64.buildinfo.asc files: removed './b1/hisat2_2.2.1-5_arm64.buildinfo.asc' removed './b2/hisat2_2.2.1-5_arm64.buildinfo.asc' 1745782590 arm64 unstable hisat2 Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/hisat2_2.2.1-5.rbuild.log: 91.5% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/hisat2_2.2.1-5.rbuild.log.gz [2025-04-27 19:36:30] INFO: Starting at 2025-04-27 19:36:30.725919 [2025-04-27 19:36:30] INFO: Generating the pages of 1 package(s) [2025-04-27 19:36:31] INFO: Finished at 2025-04-27 19:36:31.297893, took: 0:00:00.571983 All cleanup done. Sun Apr 27 19:36:31 UTC 2025 - total duration: 0h 9m 43s. Sun Apr 27 19:36:31 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-16b1VTol, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 10min 26.080s CPU time consumed: 7.673s