Running as unit: rb-build-amd64_33-81125.service; invocation ID: 4578a130995841aa9400e47b183737c6 ==================================================================================== Sun Sep 14 23:24:10 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_33) on jenkins, called using "infom01-amd64 infom02-amd64" as arguments. Sun Sep 14 23:24:10 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-WGyIfoNT" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sun Sep 14 23:24:10 UTC 2025 - checking /var/lib/jenkins/offline_nodes if infom01-amd64.debian.net is marked as down. Sun Sep 14 23:24:10 UTC 2025 - checking via ssh if infom01-amd64.debian.net is up. removed '/tmp/read-only-fs-test-JT1alg' Sun Sep 14 23:24:10 UTC 2025 - checking /var/lib/jenkins/offline_nodes if infom02-amd64.debian.net is marked as down. Sun Sep 14 23:24:10 UTC 2025 - checking via ssh if infom02-amd64.debian.net is up. removed '/tmp/read-only-fs-test-bRJVeK' ok, let's check if rapmap is building anywhere yet… ok, rapmap is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of rapmap in unstable on amd64 on jenkins now. 1st build will be done on infom01-amd64.debian.net. 2nd build will be done on infom02-amd64.debian.net. ============================================================================= Sun Sep 14 23:24:33 UTC 2025 I: starting to build rapmap/unstable/amd64 on jenkins on '2025-09-14 23:24' Sun Sep 14 23:24:33 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_33/81125/console.log 1757892273 amd64 unstable rapmap Sun Sep 14 23:24:33 UTC 2025 I: Downloading source for unstable/rapmap=0.15.0+dfsg-4 --2025-09-14 23:24:33-- http://deb.debian.org/debian/pool/main/r/rapmap/rapmap_0.15.0%2bdfsg-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2322 (2.3K) [text/prs.lines.tag] Saving to: ‘rapmap_0.15.0+dfsg-4.dsc’ 0K .. 100% 275M=0s 2025-09-14 23:24:33 (275 MB/s) - ‘rapmap_0.15.0+dfsg-4.dsc’ saved [2322/2322] --2025-09-14 23:24:33-- http://deb.debian.org/debian/pool/main/r/rapmap/rapmap_0.15.0%2bdfsg-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2322 (2.3K) [text/prs.lines.tag] Saving to: ‘rapmap_0.15.0+dfsg-4.dsc’ 0K .. 100% 275M=0s 2025-09-14 23:24:33 (275 MB/s) - ‘rapmap_0.15.0+dfsg-4.dsc’ saved [2322/2322] Sun Sep 14 23:24:33 UTC 2025 I: rapmap_0.15.0+dfsg-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: rapmap Binary: rapmap, rapmap-example-data, rapmap-dev Architecture: any all Version: 0.15.0+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Michael R. Crusoe Homepage: https://github.com/COMBINE-lab/RapMap Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/rapmap Vcs-Git: https://salsa.debian.org/med-team/rapmap.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), cmake, zlib1g-dev, libdivsufsort-dev, libcereal-dev, libjellyfish-2.0-dev, libjemalloc-dev, libsimde-dev, libsparsehash-dev, libspdlog-dev, libtclap-dev, pkg-config, python3-markdown, python3 Package-List: rapmap deb science optional arch=any rapmap-dev deb science optional arch=all rapmap-example-data deb science optional arch=all Checksums-Sha1: 0c4a16003c0d2fe77679260ebdb6e21792f862f0 624916 rapmap_0.15.0+dfsg.orig.tar.xz 32044b4fcb178f5e7b2495f00c5253358ad9d741 15008 rapmap_0.15.0+dfsg-4.debian.tar.xz Checksums-Sha256: 17068c4f664e07bec3ade28d624e5b84ef240b116bcc39e5b495d73b2d87ede5 624916 rapmap_0.15.0+dfsg.orig.tar.xz 4267978d5484cb29f0a7993df95e6ce48006b946cb6e2d8498716db7e40138af 15008 rapmap_0.15.0+dfsg-4.debian.tar.xz Files: c52551692c7480f0c1a46478595dd24b 624916 rapmap_0.15.0+dfsg.orig.tar.xz 624fa352250052cb177e582f3d50161d 15008 rapmap_0.15.0+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmYBufUACgkQPCZ2P2xn 5uL8zRAAgxcnDWblU3dZFeCPt3A1A86+92J2q7BZTAeYdMuybryMTiNeZQyuggo/ Jd4RDWqP8bbGRig6s6wqm9cPNtELDRpjVYMUUgG3ond3b5K2mUJWk9/PaeH6HCne D+JTO0tIzi/IYSAEO3YieqCXTZHpIggqCYB7+bECk1KjV/pjF8PWMRk6NikCuVdM D07xl3IzMsL6/crI+O193JsHtdur/OnSHcnB6mkTbr6HMU/pFZ+RdAWW33RuRj8J O9W9vTQ4O3zZsLwc8kyG7S6OK1p7qM+2lbVln+H/ojvTb6nlPrqxi7+gpfSI+opt VT5ptkJV1rXTLFYTbp12Gd7spSBoZkq0Fv3pJCb0hKYj1gwqj1rgmK4xt4kvU5Sy c4Zu4s5HOGqShskfcp6QCXPmidTFUrYPdHXg2PGGWKu2eHx55DTQlZiWho4NSEMn x0lKGgnOgl/WLgRZuZrZ6mAzRUbJcz6GXmraekWLlhi5UmnFfzsj3sND1ivBbYYz erva/LDvjxPr8SUpclMbYZkw1IHcAsU680o81G3/gHmaW8+kfaKaCrm2cmJQqxRd vXZVixcM6FmKcp8VgIURtL3pedTuQXR1DyZunnmvM2lJyBPXzvN5jIW2y/dH4Gjv JRw1rOujMJDQiynxCclWKNiBXsHN9HTdlCuN5n5Cksp+f6d5uZI= =5gwA -----END PGP SIGNATURE----- Sun Sep 14 23:24:33 UTC 2025 I: Checking whether the package is not for us Sun Sep 14 23:24:33 UTC 2025 I: Starting 1st build on remote node infom01-amd64.debian.net. Sun Sep 14 23:24:33 UTC 2025 I: Preparing to do remote build '1' on infom01-amd64.debian.net. Sun Sep 14 23:24:33 UTC 2025 - checking /var/lib/jenkins/offline_nodes if infom01-amd64.debian.net is marked as down. Sun Sep 14 23:24:33 UTC 2025 - checking via ssh if infom01-amd64.debian.net is up. removed '/tmp/read-only-fs-test-tAtedD' ==================================================================================== Sun Sep 14 23:24:34 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on infom01-amd64, called using "1 rapmap unstable /srv/reproducible-results/rbuild-debian/r-b-build.JNFgRBMC 0.15.0+dfsg-4" as arguments. Sun Sep 14 23:24:34 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-CNoZxWfc" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sun Sep 14 23:24:35 UTC 2025 I: Downloading source for unstable/rapmap=0.15.0+dfsg-4 Reading package lists... NOTICE: 'rapmap' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/rapmap.git Please use: git clone https://salsa.debian.org/med-team/rapmap.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 642 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main rapmap 0.15.0+dfsg-4 (dsc) [2322 B] Get:2 http://deb.debian.org/debian unstable/main rapmap 0.15.0+dfsg-4 (tar) [625 kB] Get:3 http://deb.debian.org/debian unstable/main rapmap 0.15.0+dfsg-4 (diff) [15.0 kB] Fetched 642 kB in 0s (4428 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'rapmap' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/rapmap.git Please use: git clone https://salsa.debian.org/med-team/rapmap.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 642 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main rapmap 0.15.0+dfsg-4 (dsc) [2322 B] Get:2 http://deb.debian.org/debian unstable/main rapmap 0.15.0+dfsg-4 (tar) [625 kB] Get:3 http://deb.debian.org/debian unstable/main rapmap 0.15.0+dfsg-4 (diff) [15.0 kB] Fetched 642 kB in 0s (4428 kB/s) Download complete and in download only mode ============================================================================= Building rapmap in unstable on amd64 on infom01-amd64 now. Date: Sun Sep 14 23:24:35 UTC 2025 Date UTC: Sun Sep 14 23:24:35 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 Sep 14 11:24:35 -12 2025 I: pbuilder-time-stamp: 1757892275 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 [rapmap_0.15.0+dfsg-4.dsc] I: copying [./rapmap_0.15.0+dfsg.orig.tar.xz] I: copying [./rapmap_0.15.0+dfsg-4.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./rapmap_0.15.0+dfsg-4.dsc: no acceptable signature found dpkg-source: info: extracting rapmap in rapmap-0.15.0+dfsg dpkg-source: info: unpacking rapmap_0.15.0+dfsg.orig.tar.xz dpkg-source: info: unpacking rapmap_0.15.0+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use-debian-libs.patch dpkg-source: info: applying use_shared_libs.patch dpkg-source: info: applying avoid_privacy_breach.patch dpkg-source: info: applying spelling dpkg-source: info: applying portable_pause dpkg-source: info: applying no_gomp_needed dpkg-source: info: applying simde I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3054226/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='4eecf533f1eb4791b60b35603ac3aa92' 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='3054226' 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.JNFgRBMC/pbuilderrc_hzcB --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.JNFgRBMC/b1 --logfile b1/build.log rapmap_0.15.0+dfsg-4.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom01-amd64 6.12.43+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3054226/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: amd64 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), cmake, zlib1g-dev, libdivsufsort-dev, libcereal-dev, libjellyfish-2.0-dev, libjemalloc-dev, libsimde-dev, libsparsehash-dev, libspdlog-dev, libtclap-dev, pkg-config, python3-markdown, python3 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 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 cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libdivsufsort-dev; however: Package libdivsufsort-dev is not installed. pbuilder-satisfydepends-dummy depends on libcereal-dev; however: Package libcereal-dev is not installed. pbuilder-satisfydepends-dummy depends on libjellyfish-2.0-dev; however: Package libjellyfish-2.0-dev is not installed. pbuilder-satisfydepends-dummy depends on libjemalloc-dev; however: Package libjemalloc-dev is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev is not installed. pbuilder-satisfydepends-dummy depends on libsparsehash-dev; however: Package libsparsehash-dev is not installed. pbuilder-satisfydepends-dummy depends on libspdlog-dev; however: Package libspdlog-dev is not installed. pbuilder-satisfydepends-dummy depends on libtclap-dev; however: Package libtclap-dev is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on python3-markdown; however: Package python3-markdown is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli1{a} libcereal-dev{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libdivsufsort-dev{a} libdivsufsort3{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfmt-dev{a} libfmt10{a} libgnutls30t64{a} libgssapi-krb5-2{a} libidn2-0{a} libjellyfish-2.0-2{a} libjellyfish-2.0-dev{a} libjemalloc-dev{a} libjemalloc2{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsimde-dev{a} libsparsehash-dev{a} libspdlog-dev{a} libspdlog1.15{a} libssh2-1t64{a} libtasn1-6{a} libtclap-dev{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2-16{a} m4{a} man-db{a} media-types{a} netbase{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python3{a} python3-importlib-metadata{a} python3-markdown{a} python3-minimal{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} rapidjson-dev{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix python3-pygments python3-yaml wget 0 packages upgraded, 94 newly installed, 0 to remove and 0 not upgraded. Need to get 44.8 MB of archives. After unpacking 174 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 cmake-data all 4.1.1+really3.31.6-1 [2268 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-4+b1 [349 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 40 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.11.0-1 [73.7 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.16.0-1 [437 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-4 [89.4 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.6-1 [137 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.51.0-2 [155 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 cmake amd64 4.1.1+really3.31.6-1 [12.0 MB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 66 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.4 [98.1 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libcereal-dev amd64 1.3.2+dfsg-6 [221 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libdivsufsort3 amd64 2.0.1-6+b1 [45.9 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libdivsufsort-dev amd64 2.0.1-6+b1 [19.1 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libfmt10 amd64 10.1.1+ds1-4 [127 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libfmt-dev amd64 10.1.1+ds1-4 [177 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libjellyfish-2.0-2 amd64 2.3.1-4+b1 [67.3 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libjellyfish-2.0-dev amd64 2.3.1-4+b1 [138 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libjemalloc2 amd64 5.3.0-3 [274 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libjemalloc-dev amd64 5.3.0-3 [490 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libsimde-dev all 0.8.2-3 [467 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libspdlog1.15 amd64 1:1.15.3+ds-1 [109 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libspdlog-dev amd64 1:1.15.3+ds-1 [91.9 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libtclap-dev amd64 1.2.5-1+b2 [3359 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 pkg-config amd64 1.8.1-4 [14.0 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 python3-importlib-metadata all 8.7.0-2 [21.8 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 python3-markdown all 3.9-1 [87.4 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 44.8 MB in 1s (52.0 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Selecting previously unselected package libexpat1:amd64. (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 ... 19917 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.7-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.7-1_amd64.deb ... Unpacking python3.13-minimal (3.13.7-1) ... Setting up libpython3.13-minimal:amd64 (3.13.7-1) ... Setting up libexpat1:amd64 (2.7.1-2) ... Setting up python3.13-minimal (3.13.7-1) ... 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 ... 20251 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_amd64.deb ... Unpacking python3-minimal (3.13.7-1) ... 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) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-5_all.deb ... Unpacking tzdata (2025b-5) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../4-libffi8_3.5.2-2_amd64.deb ... Unpacking libffi8:amd64 (3.5.2-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.3-3_all.deb ... Unpacking readline-common (8.3-3) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../6-libreadline8t64_8.3-3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.7-1) ... Setting up python3-minimal (3.13.7-1) ... 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 ... 21266 files and directories currently installed.) Preparing to unpack .../00-python3_3.13.7-1_amd64.deb ... Unpacking python3 (3.13.7-1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../01-libproc2-0_2%3a4.0.4-9_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-9) ... Selecting previously unselected package procps. Preparing to unpack .../02-procps_2%3a4.0.4-9_amd64.deb ... Unpacking procps (2:4.0.4-9) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../05-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../08-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../09-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../10-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../11-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. 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Preparing to unpack .../20-libarchive13t64_3.7.4-4+b1_amd64.deb ... Unpacking libarchive13t64:amd64 (3.7.4-4+b1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../21-libbrotli1_1.1.0-2+b7_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b7) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../22-libkrb5support0_1.21.3-5_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-5) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../23-libcom-err2_1.47.2-3+b3_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2-3+b3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../24-libk5crypto3_1.21.3-5_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../25-libkeyutils1_1.6.3-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../26-libkrb5-3_1.21.3-5_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../27-libgssapi-krb5-2_1.21.3-5_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-5) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../28-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libidn2-0:amd64. Preparing to unpack .../29-libidn2-0_2.3.8-4_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.8-4) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../30-libsasl2-modules-db_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../31-libsasl2-2_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libldap2:amd64. Preparing to unpack .../32-libldap2_2.6.10+dfsg-1_amd64.deb ... Unpacking libldap2:amd64 (2.6.10+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../33-libnghttp2-14_1.64.0-1.1+b1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Selecting previously unselected package libnghttp3-9:amd64. Preparing to unpack .../34-libnghttp3-9_1.11.0-1_amd64.deb ... Unpacking libnghttp3-9:amd64 (1.11.0-1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../35-libpsl5t64_0.21.2-1.1+b1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1+b1) ... Selecting previously unselected package libp11-kit0:amd64. Preparing to unpack .../36-libp11-kit0_0.25.5-3_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:amd64. Preparing to unpack .../37-libtasn1-6_4.20.0-2_amd64.deb ... Unpacking libtasn1-6:amd64 (4.20.0-2) ... Selecting previously unselected package libgnutls30t64:amd64. Preparing to unpack .../38-libgnutls30t64_3.8.10-2_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.10-2) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../39-librtmp1_2.4+20151223.gitfa8646d.1-3_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../40-libssh2-1t64_1.11.1-1_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.1-1) ... Selecting previously unselected package libcurl4t64:amd64. Preparing to unpack .../41-libcurl4t64_8.16.0-1_amd64.deb ... Unpacking libcurl4t64:amd64 (8.16.0-1) ... Selecting previously unselected package libjsoncpp26:amd64. Preparing to unpack .../42-libjsoncpp26_1.9.6-4_amd64.deb ... Unpacking libjsoncpp26:amd64 (1.9.6-4) ... Selecting previously unselected package librhash1:amd64. Preparing to unpack .../43-librhash1_1.4.6-1_amd64.deb ... Unpacking librhash1:amd64 (1.4.6-1) ... Selecting previously unselected package libuv1t64:amd64. Preparing to unpack .../44-libuv1t64_1.51.0-2_amd64.deb ... Unpacking libuv1t64:amd64 (1.51.0-2) ... Selecting previously unselected package cmake. Preparing to unpack .../45-cmake_4.1.1+really3.31.6-1_amd64.deb ... Unpacking cmake (4.1.1+really3.31.6-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../46-libdebhelper-perl_13.26_all.deb ... Unpacking libdebhelper-perl (13.26) ... Selecting previously unselected package libtool. Preparing to unpack .../47-libtool_2.5.4-5_all.deb ... Unpacking libtool (2.5.4-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../48-dh-autoreconf_21_all.deb ... Unpacking dh-autoreconf (21) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../49-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../50-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../51-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../52-libelf1t64_0.193-3_amd64.deb ... Unpacking libelf1t64:amd64 (0.193-3) ... Selecting previously unselected package dwz. Preparing to unpack .../53-dwz_0.16-2_amd64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package gettext. Preparing to unpack .../54-gettext_0.23.1-2+b1_amd64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../55-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 .../56-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../57-debhelper_13.26_all.deb ... Unpacking debhelper (13.26) ... Selecting previously unselected package rapidjson-dev. Preparing to unpack .../58-rapidjson-dev_1.1.0+dfsg2-7.4_all.deb ... Unpacking rapidjson-dev (1.1.0+dfsg2-7.4) ... Selecting previously unselected package libcereal-dev:amd64. Preparing to unpack .../59-libcereal-dev_1.3.2+dfsg-6_amd64.deb ... Unpacking libcereal-dev:amd64 (1.3.2+dfsg-6) ... Selecting previously unselected package libdivsufsort3:amd64. Preparing to unpack .../60-libdivsufsort3_2.0.1-6+b1_amd64.deb ... Unpacking libdivsufsort3:amd64 (2.0.1-6+b1) ... Selecting previously unselected package libdivsufsort-dev:amd64. Preparing to unpack .../61-libdivsufsort-dev_2.0.1-6+b1_amd64.deb ... Unpacking libdivsufsort-dev:amd64 (2.0.1-6+b1) ... Selecting previously unselected package libfmt10:amd64. Preparing to unpack .../62-libfmt10_10.1.1+ds1-4_amd64.deb ... Unpacking libfmt10:amd64 (10.1.1+ds1-4) ... Selecting previously unselected package libfmt-dev:amd64. Preparing to unpack .../63-libfmt-dev_10.1.1+ds1-4_amd64.deb ... Unpacking libfmt-dev:amd64 (10.1.1+ds1-4) ... Selecting previously unselected package libjellyfish-2.0-2:amd64. Preparing to unpack .../64-libjellyfish-2.0-2_2.3.1-4+b1_amd64.deb ... Unpacking libjellyfish-2.0-2:amd64 (2.3.1-4+b1) ... Selecting previously unselected package libjellyfish-2.0-dev. Preparing to unpack .../65-libjellyfish-2.0-dev_2.3.1-4+b1_amd64.deb ... Unpacking libjellyfish-2.0-dev (2.3.1-4+b1) ... Selecting previously unselected package libjemalloc2:amd64. 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Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up libpython3.13-stdlib:amd64 (3.13.7-1) ... Setting up libpython3-stdlib:amd64 (3.13.7-1) ... Setting up libgnutls30t64:amd64 (3.8.10-2) ... Setting up python3.13 (3.13.7-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.7-1) ... Setting up python3-zipp (3.23.0-1) ... Setting up libspdlog-dev:amd64 (1:1.15.3+ds-1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up python3-markdown (3.9-1) ... Setting up python3-importlib-metadata (8.7.0-2) ... Setting up libcurl4t64:amd64 (8.16.0-1) ... Setting up debhelper (13.26) ... Setting up cmake (4.1.1+really3.31.6-1) ... Processing triggers for libc-bin (2.41-12) ... 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/rapmap-0.15.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../rapmap_0.15.0+dfsg-4_source.changes dpkg-buildpackage: info: source package rapmap dpkg-buildpackage: info: source version 0.15.0+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg' dh_clean README.html sample_data/sample_quasi_index/ sample_data/sample_quasi_index_ph/ sample_data/sample_quasi_map.sam sample_data/sample_quasi_map_ph.sam make[1]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg' dh_auto_configure -- -DJELLYFISH_ROOT=/usr -DNO_NATIVE_ARCH=true cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DJELLYFISH_ROOT=/usr -DNO_NATIVE_ARCH=true .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CC: gcc CC version: -- The C compiler identification is GNU 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done version: 0.6.0 -- DISABLING NATIVE ARCH. -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE Making Default build type -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") -- Found Cereal: /usr/include (Required is at least version "1.2.2") -- Cereal found (include: /usr/include) -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Found Jemalloc: /usr/lib/x86_64-linux-gnu/libjemalloc.so (found version "5.3.0-0-g54eaed1d8b56b1aa528be3bdd1877e59c56fa90c") Found Jemalloc library --- using this memory allocator CPACK_SOURCE_IGNORE_FILES = .git/ CMAKE_SYSTEM_PROCESSOR: amd64 -- Configuring done (1.2s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED JELLYFISH_ROOT -- Build files have been written to: /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg' dh_auto_build cd obj-x86_64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rapmap-0.15.0+dfsg -B/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' make -f src/CMakeFiles/ksw2pp_basic.dir/build.make src/CMakeFiles/ksw2pp_basic.dir/depend make -f src/CMakeFiles/ksw2pp_sse4.dir/build.make src/CMakeFiles/ksw2pp_sse4.dir/depend make -f src/CMakeFiles/ksw2pp_sse2.dir/build.make src/CMakeFiles/ksw2pp_sse2.dir/depend make[4]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rapmap-0.15.0+dfsg /build/reproducible-path/rapmap-0.15.0+dfsg/src /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src/CMakeFiles/ksw2pp_basic.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rapmap-0.15.0+dfsg /build/reproducible-path/rapmap-0.15.0+dfsg/src /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src/CMakeFiles/ksw2pp_sse4.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rapmap-0.15.0+dfsg /build/reproducible-path/rapmap-0.15.0+dfsg/src /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src/CMakeFiles/ksw2pp_sse2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' make -f src/CMakeFiles/ksw2pp_sse4.dir/build.make src/CMakeFiles/ksw2pp_sse4.dir/build make -f src/CMakeFiles/ksw2pp_basic.dir/build.make src/CMakeFiles/ksw2pp_basic.dir/build make[4]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' make -f src/CMakeFiles/ksw2pp_sse2.dir/build.make src/CMakeFiles/ksw2pp_sse2.dir/build make[4]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' [ 13%] Building C object src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o [ 13%] Building C object src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o [ 13%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o [ 17%] Building C object src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o [ 17%] Building C object src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o [ 24%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o [ 24%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o [ 27%] Building C object src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_gg.c [ 34%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o [ 34%] Building C object src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse2 -mno-sse4.1 -MD -MT src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extd2_sse.c cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse4.1 -MD -MT src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o -MF CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o.d -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extf2_sse.c cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_gg2.c [ 37%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse2 -mno-sse4.1 -MD -MT src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extz2_sse.c cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse4.1 -MD -MT src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -MF CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o.d -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extz2_sse.c cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extd.c cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse2 -mno-sse4.1 -MD -MT src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extf2_sse.c [ 41%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/kalloc.c cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extz.c cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse4.1 -MD -MT src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o -MF CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o.d -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extd2_sse.c cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_gg2_sse.c [ 44%] Building CXX object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/KSW2Aligner.cpp make[4]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' [ 44%] Built target ksw2pp_sse2 [ 44%] Built target ksw2pp_sse4 make[4]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' [ 44%] Built target ksw2pp_basic make -f src/CMakeFiles/ksw2pp.dir/build.make src/CMakeFiles/ksw2pp.dir/depend make[4]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rapmap-0.15.0+dfsg /build/reproducible-path/rapmap-0.15.0+dfsg/src /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src/CMakeFiles/ksw2pp.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' make -f src/CMakeFiles/ksw2pp.dir/build.make src/CMakeFiles/ksw2pp.dir/build make[4]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' [ 48%] Linking CXX static library libksw2pp.a cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/ksw2pp.dir/cmake_clean_target.cmake cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ksw2pp.dir/link.txt --verbose=1 /usr/bin/ar qc libksw2pp.a CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o /usr/bin/ranlib libksw2pp.a make[4]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' [ 48%] Built target ksw2pp make -f src/CMakeFiles/rapmap.dir/build.make src/CMakeFiles/rapmap.dir/depend make[4]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rapmap-0.15.0+dfsg /build/reproducible-path/rapmap-0.15.0+dfsg/src /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src/CMakeFiles/rapmap.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' make -f src/CMakeFiles/rapmap.dir/build.make src/CMakeFiles/rapmap.dir/build make[4]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' [ 51%] Building CXX object src/CMakeFiles/rapmap.dir/RapMap.cpp.o [ 55%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapSAIndexer.cpp.o [ 62%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o [ 62%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapUtils.cpp.o [ 65%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapFileSystem.cpp.o [ 68%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapSAMapper.cpp.o cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/RapMap.cpp.o -MF CMakeFiles/rapmap.dir/RapMap.cpp.o.d -o CMakeFiles/rapmap.dir/RapMap.cpp.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMap.cpp cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/RapMapSAIndexer.cpp.o -MF CMakeFiles/rapmap.dir/RapMapSAIndexer.cpp.o.d -o CMakeFiles/rapmap.dir/RapMapSAIndexer.cpp.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp [ 86%] Building CXX object src/CMakeFiles/rapmap.dir/HitManager.cpp.o [ 86%] Building C object src/CMakeFiles/rapmap.dir/bit_array.c.o [ 86%] Building C object src/CMakeFiles/rapmap.dir/xxhash.c.o [ 86%] Building CXX object src/CMakeFiles/rapmap.dir/stringpiece.cc.o [ 86%] Building CXX object src/CMakeFiles/rapmap.dir/rank9b.cpp.o cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/RapMapUtils.cpp.o -MF CMakeFiles/rapmap.dir/RapMapUtils.cpp.o.d -o CMakeFiles/rapmap.dir/RapMapUtils.cpp.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapUtils.cpp [ 89%] Building CXX object src/CMakeFiles/rapmap.dir/FastxParser.cpp.o cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/RapMapFileSystem.cpp.o -MF CMakeFiles/rapmap.dir/RapMapFileSystem.cpp.o.d -o CMakeFiles/rapmap.dir/RapMapFileSystem.cpp.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapFileSystem.cpp cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/RapMapSAMapper.cpp.o -MF CMakeFiles/rapmap.dir/RapMapSAMapper.cpp.o.d -o CMakeFiles/rapmap.dir/RapMapSAMapper.cpp.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o -MF CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o.d -o CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndex.cpp cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/HitManager.cpp.o -MF CMakeFiles/rapmap.dir/HitManager.cpp.o.d -o CMakeFiles/rapmap.dir/HitManager.cpp.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/HitManager.cpp cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/FastxParser.cpp.o -MF CMakeFiles/rapmap.dir/FastxParser.cpp.o.d -o CMakeFiles/rapmap.dir/FastxParser.cpp.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/FastxParser.cpp cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/rank9b.cpp.o -MF CMakeFiles/rapmap.dir/rank9b.cpp.o.d -o CMakeFiles/rapmap.dir/rank9b.cpp.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/rank9b.cpp cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/stringpiece.cc.o -MF CMakeFiles/rapmap.dir/stringpiece.cc.o.d -o CMakeFiles/rapmap.dir/stringpiece.cc.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/stringpiece.cc cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/rapmap.dir/xxhash.c.o -MF CMakeFiles/rapmap.dir/xxhash.c.o.d -o CMakeFiles/rapmap.dir/xxhash.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/xxhash.c cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/rapmap.dir/bit_array.c.o -MF CMakeFiles/rapmap.dir/bit_array.c.o.d -o CMakeFiles/rapmap.dir/bit_array.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/bit_array.c [ 93%] Building CXX object src/CMakeFiles/rapmap.dir/edlib.cpp.o cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/edlib.cpp.o -MF CMakeFiles/rapmap.dir/edlib.cpp.o.d -o CMakeFiles/rapmap.dir/edlib.cpp.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/edlib.cpp [ 96%] Building CXX object src/CMakeFiles/rapmap.dir/metro/metrohash64.cpp.o cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/metro/metrohash64.cpp.o -MF CMakeFiles/rapmap.dir/metro/metrohash64.cpp.o.d -o CMakeFiles/rapmap.dir/metro/metrohash64.cpp.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/metro/metrohash64.cpp In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooMap.hpp:4, from /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndex.cpp:22: /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:184:9: warning: inline variables are only available with '-std=c++17' or '-std=gnu++17' [-Wc++17-extensions] 184 | inline unsigned int popcount_64(uint64_t x) | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:184:41: error: 'uint64_t' was not declared in this scope 184 | inline unsigned int popcount_64(uint64_t x) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:20:1: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' 19 | #include +++ |+#include 20 | /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:202:17: error: 'uint64_t' does not name a type 202 | uint64_t done; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:202:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:203:17: error: 'uint64_t' does not name a type 203 | uint64_t todo; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:203:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:208:29: error: 'uint64_t' was not declared in this scope 208 | std::vector done_threaded; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:208:29: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:208:38: error: template argument 1 is invalid 208 | std::vector done_threaded; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:208:38: error: template argument 2 is invalid /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:212:27: error: 'uint64_t' has not been declared 212 | void init(uint64_t ntasks, const char * msg,int nthreads =1) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:212:27: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:263:26: error: 'uint64_t' has not been declared 263 | void inc(uint64_t ntasks_done) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:263:26: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:300:26: error: 'uint64_t' has not been declared 300 | void inc(uint64_t ntasks_done, int tid) //threads collaborate to this same progress bar | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:300:26: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:338:26: error: 'uint64_t' has not been declared 338 | void set(uint64_t ntasks_done) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:338:26: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::Progress::init(int, const char*, int)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:221:25: error: 'todo' was not declared in this scope 221 | todo= ntasks; | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:222:25: error: 'done' was not declared in this scope 222 | done = 0; | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:226:39: error: request for member 'resize' in '((boomphf::Progress*)this)->boomphf::Progress::done_threaded', which is of non-class type 'int' 226 | done_threaded.resize(_nthreads); | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:229:72: error: invalid types 'int[int]' for array subscript 229 | for (int ii=0; ii<_nthreads;ii++) done_threaded[ii]=0; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::Progress::finish()': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:241:29: error: 'todo' was not declared in this scope 241 | set(todo); | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:249:25: error: 'done' was not declared in this scope 249 | done = 0; | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::Progress::finish_threaded()': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:255:25: error: 'done' was not declared in this scope 255 | done = 0; | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:257:81: error: invalid types 'int[int]' for array subscript 257 | for (int ii=0; ii<_nthreads;ii++) done += (done_threaded[ii] ); | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::Progress::inc(int)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:265:25: error: 'done' was not declared in this scope 265 | done += ntasks_done; | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:277:55: error: 'todo' was not declared in this scope 277 | double rem = (todo-done) / speed; | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::Progress::inc(int, int)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:303:38: error: invalid types 'int[int]' for array subscript 303 | done_threaded[tid] += ntasks_done; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:312:41: error: 'uint64_t' was not declared in this scope 312 | uint64_t total_done = 0; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:312:41: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:313:75: error: 'total_done' was not declared in this scope 313 | for (int ii=0; ii<_nthreads;ii++) total_done += (done_threaded[ii] ); | ^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:313:103: error: invalid types 'int[int]' for array subscript 313 | for (int ii=0; ii<_nthreads;ii++) total_done += (done_threaded[ii] ); | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:315:56: error: 'total_done' was not declared in this scope 315 | double speed = total_done / elapsed; | ^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:316:55: error: 'todo' was not declared in this scope 316 | double rem = (todo-total_done) / speed; | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::Progress::set(int)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:340:42: error: 'done' was not declared in this scope 340 | if(ntasks_done > done) | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: At global scope: /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:354:28: error: 'uint64_t' was not declared in this scope 354 | typedef std::array hash_set_t; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:354:28: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:354:39: error: template argument 1 is invalid 354 | typedef std::array hash_set_t; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:355:28: error: 'uint64_t' was not declared in this scope 355 | typedef std::array hash_pair_t; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:355:28: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:355:38: error: template argument 1 is invalid 355 | typedef std::array hash_pair_t; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:374:9: error: 'uint64_t' does not name a type [-Wtemplate-body] 374 | uint64_t operator () (const Item& key, size_t idx) const { return hash64 (key, _seed_tab[idx]); } | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:374:9: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:376:9: error: 'uint64_t' does not name a type [-Wtemplate-body] 376 | uint64_t hashWithSeed(const Item& key, uint64_t seed) const { return hash64 (key, seed); } | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:376:9: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:394:31: error: 'uint64_t' does not name a type [-Wtemplate-body] 394 | inline static uint64_t hash64 (Item key, uint64_t seed) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:394:31: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:426:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 426 | uint64_t _seed_tab[MAXNBFUNC]; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:426:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:427:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 427 | uint64_t _user_seed; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:427:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In constructor 'boomphf::HashFunctors::HashFunctors()': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:369:25: error: '_user_seed' was not declared in this scope [-Wtemplate-body] 369 | _user_seed = 0; | ^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'boomphf::hash_set_t boomphf::HashFunctors::operator()(const Item&)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:386:37: error: invalid types 'boomphf::hash_set_t {aka int}[size_t {aka long unsigned int}]' for array subscript [-Wtemplate-body] 386 | hset[ii] = hash64 (key, _seed_tab[ii]); | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:386:58: error: '_seed_tab' was not declared in this scope [-Wtemplate-body] 386 | hset[ii] = hash64 (key, _seed_tab[ii]); | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::HashFunctors::generate_hash_seed()': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:412:38: error: 'uint64_t' does not name a type [-Wtemplate-body] 412 | static const uint64_t rbase[MAXNBFUNC] = | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:412:38: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:419:64: error: '_seed_tab' was not declared in this scope [-Wtemplate-body] 419 | for (size_t i=0; i'; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:468:9: error: 'uint64_t' does not name a type [-Wtemplate-body] 468 | uint64_t next(uint64_t * s) { | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:468:9: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:479:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 479 | uint64_t h0(hash_pair_t & s, const Item& key ) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:479:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:485:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 485 | uint64_t h1(hash_pair_t & s, const Item& key ) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:485:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:493:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 493 | uint64_t next(hash_pair_t & s ) { | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:493:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'boomphf::hash_set_t boomphf::XorshiftHashFunctors::operator()(const Item&)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:504:25: error: 'uint64_t' was not declared in this scope [-Wtemplate-body] 504 | uint64_t s[ 2 ]; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:504:25: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:508:17: error: invalid types 'boomphf::hash_set_t {aka int}[int]' for array subscript [-Wtemplate-body] 508 | hset[0] = singleHasher (key, 0xAAAAAAAA55555555ULL); | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:509:17: error: invalid types 'boomphf::hash_set_t {aka int}[int]' for array subscript [-Wtemplate-body] 509 | hset[1] = singleHasher (key, 0x33333333CCCCCCCCULL); | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:511:13: error: 's' was not declared in this scope [-Wtemplate-body] 511 | s[0] = hset[0]; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:511:24: error: invalid types 'boomphf::hash_set_t {aka int}[int]' for array subscript [-Wtemplate-body] 511 | s[0] = hset[0]; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:512:24: error: invalid types 'boomphf::hash_set_t {aka int}[int]' for array subscript [-Wtemplate-body] 512 | s[1] = hset[1]; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:516:21: error: invalid types 'boomphf::hash_set_t {aka int}[size_t {aka long unsigned int}]' for array subscript [-Wtemplate-body] 516 | hset[ii] = next(s); | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:516:28: error: there are no arguments to 'next' that depend on a template parameter, so a declaration of 'next' must be available [-Wtemplate-body] 516 | hset[ii] = next(s); | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:516:28: note: (if you use '-fpermissive', G++ will accept your code, but allowing the use of an undeclared name is deprecated) /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: At global scope: /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:568:35: error: expected ')' before 'n' 568 | bitVector(uint64_t n) : _size(n) | ~ ^~ | ) /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:630:29: error: 'uint64_t' has not been declared 630 | void resize(uint64_t newsize) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:630:29: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:643:17: error: 'uint64_t' does not name a type 643 | uint64_t bitSize() const {return (_nchar*64ULL + _ranks.capacity()*64ULL );} | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:643:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:652:38: error: 'uint64_t' has not been declared 652 | void clearCollisions(uint64_t start, size_t size, bitVector * cc) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:652:38: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:667:28: error: 'uint64_t' has not been declared 667 | void clear(uint64_t start, size_t size) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:667:28: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:696:17: error: 'uint64_t' does not name a type 696 | uint64_t operator[](uint64_t pos) const | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:696:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:706:17: error: 'uint64_t' does not name a type 706 | uint64_t atomic_test_and_set(uint64_t pos) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:706:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:714:17: error: 'uint64_t' does not name a type 714 | uint64_t get(uint64_t pos) const | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:714:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:719:17: error: 'uint64_t' does not name a type 719 | uint64_t get64(uint64_t cell64) const | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:719:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:725:26: error: 'uint64_t' has not been declared 725 | void set(uint64_t pos) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:725:26: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:733:28: error: 'uint64_t' has not been declared 733 | void reset(uint64_t pos) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:733:28: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:741:17: error: 'uint64_t' does not name a type 741 | uint64_t build_ranks(uint64_t offset =0) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:741:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:756:17: error: 'uint64_t' does not name a type 756 | uint64_t rank(uint64_t pos) const | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:756:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:798:17: error: 'uint64_t' does not name a type 798 | uint64_t* _bitArray; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:798:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:800:17: error: 'uint64_t' does not name a type 800 | uint64_t _size; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:800:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:801:17: error: 'uint64_t' does not name a type 801 | uint64_t _nchar; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:801:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:805:30: error: 'uint64_t' does not name a type 805 | static const uint64_t _nb_bits_per_rank_sample = 512; //512 seems ok | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:805:30: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:806:29: error: 'uint64_t' was not declared in this scope 806 | std::vector _ranks; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:806:29: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:806:37: error: template argument 1 is invalid 806 | std::vector _ranks; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:806:37: error: template argument 2 is invalid /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In constructor 'boomphf::bitVector::bitVector()': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:563:31: error: class 'boomphf::bitVector' does not have any field named '_size' 563 | bitVector() : _size(0) | ^~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:565:25: error: '_bitArray' was not declared in this scope 565 | _bitArray = nullptr; | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In destructor 'boomphf::bitVector::~bitVector()': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:576:28: error: '_bitArray' was not declared in this scope 576 | if(_bitArray != nullptr) | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In copy constructor 'boomphf::bitVector::bitVector(const boomphf::bitVector&)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:583:26: error: '_size' was not declared in this scope; did you mean 'size'? 583 | _size = r._size; | ^~~~~ | size /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:583:37: error: 'const class boomphf::bitVector' has no member named '_size'; did you mean 'size'? 583 | _size = r._size; | ^~~~~ | size /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:584:26: error: '_nchar' was not declared in this scope; did you mean 'u_char'? 584 | _nchar = r._nchar; | ^~~~~~ | u_char /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:584:37: error: 'const class boomphf::bitVector' has no member named '_nchar' 584 | _nchar = r._nchar; | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:586:26: error: '_bitArray' was not declared in this scope 586 | _bitArray = (uint64_t *) calloc (_nchar,sizeof(uint64_t)); | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:586:39: error: 'uint64_t' was not declared in this scope 586 | _bitArray = (uint64_t *) calloc (_nchar,sizeof(uint64_t)); | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:586:39: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:586:49: error: expected primary-expression before ')' token 586 | _bitArray = (uint64_t *) calloc (_nchar,sizeof(uint64_t)); | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:587:46: error: 'const class boomphf::bitVector' has no member named '_bitArray' 587 | memcpy(_bitArray, r._bitArray, _nchar*sizeof(uint64_t) ); | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'boomphf::bitVector& boomphf::bitVector::operator=(const boomphf::bitVector&)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:595:33: error: '_size' was not declared in this scope; did you mean 'size'? 595 | _size = r._size; | ^~~~~ | size /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:595:44: error: 'const class boomphf::bitVector' has no member named '_size'; did you mean 'size'? 595 | _size = r._size; | ^~~~~ | size /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:596:33: error: '_nchar' was not declared in this scope; did you mean 'u_char'? 596 | _nchar = r._nchar; | ^~~~~~ | u_char /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:596:44: error: 'const class boomphf::bitVector' has no member named '_nchar' 596 | _nchar = r._nchar; | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:598:36: error: '_bitArray' was not declared in this scope 598 | if(_bitArray != nullptr) | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:600:33: error: '_bitArray' was not declared in this scope 600 | _bitArray = (uint64_t *) calloc (_nchar,sizeof(uint64_t)); | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:600:46: error: 'uint64_t' was not declared in this scope 600 | _bitArray = (uint64_t *) calloc (_nchar,sizeof(uint64_t)); | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:600:46: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:600:56: error: expected primary-expression before ')' token 600 | _bitArray = (uint64_t *) calloc (_nchar,sizeof(uint64_t)); | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:601:53: error: 'const class boomphf::bitVector' has no member named '_bitArray' 601 | memcpy(_bitArray, r._bitArray, _nchar*sizeof(uint64_t) ); | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'boomphf::bitVector& boomphf::bitVector::operator=(boomphf::bitVector&&)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:612:36: error: '_bitArray' was not declared in this scope 612 | if(_bitArray != nullptr) | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:615:33: error: '_size' was not declared in this scope; did you mean 'size'? 615 | _size = std::move (r._size); | ^~~~~ | size /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:615:55: error: 'class boomphf::bitVector' has no member named '_size'; did you mean 'size'? 615 | _size = std::move (r._size); | ^~~~~ | size /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:616:33: error: '_nchar' was not declared in this scope; did you mean 'u_char'? 616 | _nchar = std::move (r._nchar); | ^~~~~~ | u_char /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:616:55: error: 'class boomphf::bitVector' has no member named '_nchar' 616 | _nchar = std::move (r._nchar); | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:618:33: error: '_bitArray' was not declared in this scope 618 | _bitArray = r._bitArray; | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:618:47: error: 'class boomphf::bitVector' has no member named '_bitArray' 618 | _bitArray = r._bitArray; | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:619:35: error: 'class boomphf::bitVector' has no member named '_bitArray' 619 | r._bitArray = nullptr; | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In constructor 'boomphf::bitVector::bitVector(boomphf::bitVector&&)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:624:44: error: class 'boomphf::bitVector' does not have any field named '_bitArray' 624 | bitVector(bitVector &&r) : _bitArray ( nullptr),_size(0) | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:624:65: error: class 'boomphf::bitVector' does not have any field named '_size' 624 | bitVector(bitVector &&r) : _bitArray ( nullptr),_size(0) | ^~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::bitVector::resize(int)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:633:25: error: '_nchar' was not declared in this scope; did you mean 'u_char'? 633 | _nchar = (1ULL+newsize/64ULL); | ^~~~~~ | u_char /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:634:25: error: '_bitArray' was not declared in this scope 634 | _bitArray = (uint64_t *) realloc(_bitArray,_nchar*sizeof(uint64_t)); | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:634:38: error: 'uint64_t' was not declared in this scope 634 | _bitArray = (uint64_t *) realloc(_bitArray,_nchar*sizeof(uint64_t)); | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:634:38: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:634:48: error: expected primary-expression before ')' token 634 | _bitArray = (uint64_t *) realloc(_bitArray,_nchar*sizeof(uint64_t)); | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:635:25: error: '_size' was not declared in this scope; did you mean 'size'? 635 | _size = newsize; | ^~~~~ | size /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'size_t boomphf::bitVector::size() const': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:640:32: error: '_size' was not declared in this scope; did you mean 'size'? 640 | return _size; | ^~~~~ | size /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::bitVector::clear()': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:648:32: error: '_bitArray' was not declared in this scope 648 | memset(_bitArray,0,_nchar*sizeof(uint64_t)); | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:648:44: error: '_nchar' was not declared in this scope; did you mean 'u_char'? 648 | memset(_bitArray,0,_nchar*sizeof(uint64_t)); | ^~~~~~ | u_char /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:648:58: error: 'uint64_t' was not declared in this scope 648 | memset(_bitArray,0,_nchar*sizeof(uint64_t)); | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:648:58: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::bitVector::clearCollisions(int, size_t, boomphf::bitVector*)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:656:25: error: 'uint64_t' was not declared in this scope 656 | uint64_t ids = (start/64ULL); | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:656:25: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:657:38: error: expected ';' before 'ii' 657 | for(uint64_t ii =0; ii< (size/64ULL); ii++ ) | ^~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:657:46: error: 'ii' was not declared in this scope 657 | for(uint64_t ii =0; ii< (size/64ULL); ii++ ) | ^~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:659:33: error: '_bitArray' was not declared in this scope 659 | _bitArray[ids+ii] = _bitArray[ids+ii] & (~ (cc->get64(ii)) ); | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:659:43: error: 'ids' was not declared in this scope 659 | _bitArray[ids+ii] = _bitArray[ids+ii] & (~ (cc->get64(ii)) ); | ^~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:659:82: error: 'class boomphf::bitVector' has no member named 'get64' 659 | _bitArray[ids+ii] = _bitArray[ids+ii] & (~ (cc->get64(ii)) ); | ^~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::bitVector::clear(int, size_t)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:671:32: error: '_bitArray' was not declared in this scope 671 | memset(_bitArray + (start/64ULL),0,(size/64ULL)*sizeof(uint64_t)); | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:671:80: error: 'uint64_t' was not declared in this scope 671 | memset(_bitArray + (start/64ULL),0,(size/64ULL)*sizeof(uint64_t)); | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:671:80: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::bitVector::print() const': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:677:94: error: '_size' was not declared in this scope; did you mean 'size'? 677 | printf("bit array of size %llu: \n", static_cast(_size)); | ^~~~~ | size /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:678:29: error: 'uint64_t' was not declared in this scope 678 | for(uint64_t ii = 0; ii< _size; ii++) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:678:29: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:678:46: error: 'ii' was not declared in this scope 678 | for(uint64_t ii = 0; ii< _size; ii++) | ^~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:682:44: error: '_bitArray' was not declared in this scope 682 | int val = (_bitArray[ii >> 6] >> (ii & 63 ) ) & 1; | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:687:100: error: request for member 'size' in '((const boomphf::bitVector*)this)->boomphf::bitVector::_ranks', which is of non-class type 'const int' 687 | printf("rank array : size %llu \n", static_cast(_ranks.size())); | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:688:30: error: 'uint64_t' was not declared in this scope 688 | for (uint64_t ii = 0; ii< _ranks.size(); ii++) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:688:30: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:688:47: error: 'ii' was not declared in this scope 688 | for (uint64_t ii = 0; ii< _ranks.size(); ii++) | ^~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:688:58: error: request for member 'size' in '((const boomphf::bitVector*)this)->boomphf::bitVector::_ranks', which is of non-class type 'const int' 688 | for (uint64_t ii = 0; ii< _ranks.size(); ii++) | ^~~~ In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:15: /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::bitVector::set(int)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:727:36: error: '_size' was not declared in this scope; did you mean 'size'? 727 | assert(pos<_size); | ^~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:729:46: error: '_bitArray' was not declared in this scope 729 | __sync_fetch_and_or (_bitArray + (pos >> 6ULL), (1ULL << (pos & 63)) ); | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::bitVector::reset(int)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:736:47: error: '_bitArray' was not declared in this scope 736 | __sync_fetch_and_and (_bitArray + (pos >> 6ULL), ~(1ULL << (pos & 63) )); | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::bitVector::save(std::ostream&) const': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:775:65: error: '_size' was not declared in this scope; did you mean 'size'? 775 | os.write(reinterpret_cast(&_size), sizeof(_size)); | ^~~~~ | size /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:776:65: error: '_nchar' was not declared in this scope; did you mean 'u_char'? 776 | os.write(reinterpret_cast(&_nchar), sizeof(_nchar)); | ^~~~~~ | u_char /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:777:64: error: '_bitArray' was not declared in this scope 777 | os.write(reinterpret_cast(_bitArray), (std::streamsize)(sizeof(uint64_t) * _nchar)); | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:777:101: error: 'uint64_t' was not declared in this scope 777 | os.write(reinterpret_cast(_bitArray), (std::streamsize)(sizeof(uint64_t) * _nchar)); | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:777:101: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:778:47: error: request for member 'size' in '((const boomphf::bitVector*)this)->boomphf::bitVector::_ranks', which is of non-class type 'const int' 778 | size_t sizer = _ranks.size(); | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:780:71: error: request for member 'data' in '((const boomphf::bitVector*)this)->boomphf::bitVector::_ranks', which is of non-class type 'const int' 780 | os.write(reinterpret_cast(_ranks.data()), (std::streamsize)(sizeof(_ranks[0]) * _ranks.size())); | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:780:111: error: invalid types 'const int[int]' for array subscript 780 | os.write(reinterpret_cast(_ranks.data()), (std::streamsize)(sizeof(_ranks[0]) * _ranks.size())); | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:780:125: error: request for member 'size' in '((const boomphf::bitVector*)this)->boomphf::bitVector::_ranks', which is of non-class type 'const int' 780 | os.write(reinterpret_cast(_ranks.data()), (std::streamsize)(sizeof(_ranks[0]) * _ranks.size())); | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::bitVector::load(std::istream&)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:785:58: error: '_size' was not declared in this scope; did you mean 'size'? 785 | is.read(reinterpret_cast(&_size), sizeof(_size)); | ^~~~~ | size /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:786:58: error: '_nchar' was not declared in this scope; did you mean 'u_char'? 786 | is.read(reinterpret_cast(&_nchar), sizeof(_nchar)); | ^~~~~~ | u_char /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:788:58: error: '_bitArray' was not declared in this scope 788 | is.read(reinterpret_cast(_bitArray), (std::streamsize)(sizeof(uint64_t) * _nchar)); | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:788:95: error: 'uint64_t' was not declared in this scope 788 | is.read(reinterpret_cast(_bitArray), (std::streamsize)(sizeof(uint64_t) * _nchar)); | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:788:95: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:792:32: error: request for member 'resize' in '((boomphf::bitVector*)this)->boomphf::bitVector::_ranks', which is of non-class type 'int' 792 | _ranks.resize(sizer); | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:793:64: error: request for member 'data' in '((boomphf::bitVector*)this)->boomphf::bitVector::_ranks', which is of non-class type 'int' 793 | is.read(reinterpret_cast(_ranks.data()), (std::streamsize)(sizeof(_ranks[0]) * _ranks.size())); | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:793:104: error: invalid types 'int[int]' for array subscript 793 | is.read(reinterpret_cast(_ranks.data()), (std::streamsize)(sizeof(_ranks[0]) * _ranks.size())); | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:793:118: error: request for member 'size' in '((boomphf::bitVector*)this)->boomphf::bitVector::_ranks', which is of non-class type 'int' 793 | is.read(reinterpret_cast(_ranks.data()), (std::streamsize)(sizeof(_ranks[0]) * _ranks.size())); | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: At global scope: /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:815:23: error: 'uint64_t' does not name a type 815 | static inline uint64_t fastrange64(uint64_t word, uint64_t p) { | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:815:23: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:829:17: error: 'uint64_t' does not name a type 829 | uint64_t get(uint64_t hash_raw) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:829:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:837:17: error: 'uint64_t' does not name a type 837 | uint64_t idx_begin; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:837:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:838:17: error: 'uint64_t' does not name a type 838 | uint64_t hash_domain; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:838:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:971:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 971 | uint64_t lookup(elem_t elem) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:971:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1011:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 1011 | uint64_t nbKeys() const | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1011:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1016:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 1016 | uint64_t totalBitSize() | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1016:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1318:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 1318 | uint64_t getLevel(hash_pair_t & bbhash, elem_t val,int * res_level, int maxlevel = 100, int minlevel =0) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1318:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1355:38: error: 'uint64_t' has not been declared [-Wtemplate-body] 1355 | void insertIntoLevel(uint64_t level_hash, int i) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1355:38: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1506:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 1506 | uint64_t _hash_domain; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1506:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1507:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 1507 | uint64_t _nelem; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1507:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1508:35: error: 'uint64_t' was not declared in this scope [-Wtemplate-body] 1508 | std::unordered_map _final_hash; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1508:35: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1508:52: error: template argument 2 is invalid [-Wtemplate-body] 1508 | std::unordered_map _final_hash; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1508:52: error: template argument 5 is invalid [-Wtemplate-body] /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1512:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 1512 | uint64_t _hashidx; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1512:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1514:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 1514 | uint64_t _lastbitsetrank; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1514:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1515:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 1515 | uint64_t _idxLevelsetLevelFastmode; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1515:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1516:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 1516 | uint64_t _cptLevel; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1516:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1517:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 1517 | uint64_t _cptTotalProcessed; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1517:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In constructor 'boomphf::mphf::mphf(size_t, const Range&, int, double, bool, bool, float)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:892:32: error: class 'boomphf::mphf' does not have any field named '_hash_domain' [-Wtemplate-body] 892 | _gamma(gamma), _hash_domain(size_t(ceil(double(n) * gamma))), _nelem(n), _num_thread(num_thread), _percent_elem_loaded_for_fastMode (perc_elem_loaded), _withprogress(progress) | ^~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:892:79: error: class 'boomphf::mphf' does not have any field named '_nelem' [-Wtemplate-body] 892 | _gamma(gamma), _hash_domain(size_t(ceil(double(n) * gamma))), _nelem(n), _num_thread(num_thread), _percent_elem_loaded_for_fastMode (perc_elem_loaded), _withprogress(progress) | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:932:59: error: '_nelem' was not declared in this scope [-Wtemplate-body] 932 | _progressBar.init(_nelem * total_writeEach,"Building BooPHF",num_thread); | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:935:60: error: '_nelem' was not declared in this scope [-Wtemplate-body] 935 | _progressBar.init( _nelem * total_fastmode_ram ,"Building BooPHF",num_thread); | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:937:60: error: '_nelem' was not declared in this scope [-Wtemplate-body] 937 | _progressBar.init( _nelem * _nb_levels ,"Building BooPHF",num_thread); | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:940:25: error: 'uint64_t' was not declared in this scope [-Wtemplate-body] 940 | uint64_t offset = 0; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:940:25: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:943:74: error: '__gnu_cxx::__alloc_traits, boomphf::level>::value_type' {aka 'class boomphf::level'} has no member named 'hash_domain' [-Wtemplate-body] 943 | _tempBitset = new bitVector(_levels[ii].hash_domain); // temp collision bitarray for this level | ^~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:947:84: error: '__gnu_cxx::__alloc_traits, boomphf::level>::value_type' {aka 'class boomphf::level'} has no member named 'hash_domain' [-Wtemplate-body] 947 | _levels[ii].bitset.clearCollisions(0 , _levels[ii].hash_domain , _tempBitset); | ^~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:949:33: error: 'offset' was not declared in this scope; did you mean 'off_t'? [-Wtemplate-body] 949 | offset = _levels[ii].bitset.build_ranks(offset); | ^~~~~~ | off_t /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:949:61: error: 'class boomphf::bitVector' has no member named 'build_ranks' [-Wtemplate-body] 949 | offset = _levels[ii].bitset.build_ranks(offset); | ^~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:958:25: error: '_lastbitsetrank' was not declared in this scope [-Wtemplate-body] 958 | _lastbitsetrank = offset ; | ^~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:958:43: error: 'offset' was not declared in this scope; did you mean 'off_t'? [-Wtemplate-body] 958 | _lastbitsetrank = offset ; | ^~~~~~ | off_t /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::mphf::pthread_processLevel(std::vector&, std::shared_ptr<_Yp>, std::shared_ptr<_Yp>, int)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1038:25: error: 'uint64_t' was not declared in this scope [-Wtemplate-body] 1038 | uint64_t nb_done =0; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1038:25: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1041:34: error: expected ';' before 'inbuff' [-Wtemplate-body] 1041 | uint64_t inbuff =0; | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1043:34: error: expected ';' before 'writebuff' [-Wtemplate-body] 1043 | uint64_t writebuff =0; | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1052:23: error: 'inbuff' was not declared in this scope [-Wtemplate-body] 1052 | for(; inbuff() {} | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1094:60: error: 'idxl2' was not declared in this scope [-Wtemplate-body] 1094 | if(idxl2>= setLevelFastmode.size()) | ^~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1104:66: error: expected ';' before 'hashidx' [-Wtemplate-body] 1104 | uint64_t hashidx = __sync_fetch_and_add (& _hashidx, 1); | ^~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1108:76: error: 'hashidx' was not declared in this scope [-Wtemplate-body] 1108 | _final_hash[val] = hashidx; | ^~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1119:68: error: 'writebuff' was not declared in this scope; did you mean 'myWriteBuff'? [-Wtemplate-body] 1119 | if(writebuff>=NBBUFF) | ^~~~~~~~~ | myWriteBuff /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1129:85: error: 'writebuff' was not declared in this scope; did you mean 'myWriteBuff'? [-Wtemplate-body] 1129 | myWriteBuff[writebuff++] = val; | ^~~~~~~~~ | myWriteBuff /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1141:65: error: 'level_hash' was not declared in this scope [-Wtemplate-body] 1141 | level_hash = _hasher.h0(bbhash,val); | ^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1143:65: error: 'level_hash' was not declared in this scope [-Wtemplate-body] 1143 | level_hash = _hasher.h1(bbhash,val); | ^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1146:65: error: 'level_hash' was not declared in this scope [-Wtemplate-body] 1146 | level_hash = _hasher.next(bbhash); | ^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1148:73: error: 'level_hash' was not declared in this scope [-Wtemplate-body] 1148 | insertIntoLevel(level_hash,i); //should be safe | ^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1152:41: error: 'nb_done' was not declared in this scope [-Wtemplate-body] 1152 | nb_done++; | ^~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1157:33: error: 'inbuff' was not declared in this scope [-Wtemplate-body] 1157 | inbuff = 0; | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1160:47: error: 'writebuff' was not declared in this scope; did you mean 'myWriteBuff'? [-Wtemplate-body] 1160 | if(_writeEachLevel && writebuff>0) | ^~~~~~~~~ | myWriteBuff /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::mphf::save(std::ostream&) const': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1177:65: error: '_lastbitsetrank' was not declared in this scope [-Wtemplate-body] 1177 | os.write(reinterpret_cast(&_lastbitsetrank), sizeof(_lastbitsetrank)); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/spdlog.h:192, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/RapMapUtils.hpp:33, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/HitManager.hpp:25, from /build/reproducible-path/rapmap-0.15.0+dfsg/src/HitManager.cpp:22: /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1178:65: error: '_nelem' was not declared in this scope [-Wtemplate-body] 1178 | os.write(reinterpret_cast(&_nelem), sizeof(_nelem)); | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1185:62: error: request for member 'size' in '((const boomphf::mphf*)this)->boomphf::mphf::_final_hash', which is of non-class type 'const int' [-Wtemplate-body] 1185 | size_t final_hash_size = _final_hash.size(); | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1191:52: error: request for member 'begin' in '((const boomphf::mphf*)this)->boomphf::mphf::_final_hash', which is of non-class type 'const int' [-Wtemplate-body] 1191 | for (auto it = _final_hash.begin(); it != _final_hash.end(); ++it ) | ^~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1191:79: error: request for member 'end' in '((const boomphf::mphf*)this)->boomphf::mphf::_final_hash', which is of non-class type 'const int' [-Wtemplate-body] 1191 | for (auto it = _final_hash.begin(); it != _final_hash.end(); ++it ) | ^~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1194:95: error: 'uint64_t' was not declared in this scope [-Wtemplate-body] 1194 | os.write(reinterpret_cast(&(it->second)), sizeof(uint64_t)); | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1194:95: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::mphf::load(std::istream&)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1204:58: error: '_lastbitsetrank' was not declared in this scope [-Wtemplate-body] 1204 | is.read(reinterpret_cast(&_lastbitsetrank), sizeof(_lastbitsetrank)); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/spdlog.h:192, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/IndexHeader.hpp:25, from /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMap.cpp:30: /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1205:58: error: '_nelem' was not declared in this scope [-Wtemplate-body] 1205 | is.read(reinterpret_cast(&_nelem), sizeof(_nelem)); | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1220:25: error: 'uint64_t' was not declared in this scope [-Wtemplate-body] 1220 | uint64_t previous_idx =0; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1220:25: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1221:25: error: '_hash_domain' was not declared in this scope [-Wtemplate-body] 1221 | _hash_domain = (size_t) (ceil(double(_nelem) * _gamma)) ; | ^~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1225:45: error: '__gnu_cxx::__alloc_traits, boomphf::level>::value_type' {aka 'class boomphf::level'} has no member named 'idx_begin' [-Wtemplate-body] 1225 | _levels[ii].idx_begin = previous_idx; | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1225:57: error: 'previous_idx' was not declared in this scope [-Wtemplate-body] 1225 | _levels[ii].idx_begin = previous_idx; | ^~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1226:45: error: '__gnu_cxx::__alloc_traits, boomphf::level>::value_type' {aka 'class boomphf::level'} has no member named 'hash_domain' [-Wtemplate-body] 1226 | _levels[ii].hash_domain = (( (uint64_t) (_hash_domain * pow(_proba_collision,ii)) + 63) / 64 ) * 64; | ^~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1227:48: error: '__gnu_cxx::__alloc_traits, boomphf::level>::value_type' {aka 'class boomphf::level'} has no member named 'hash_domain' [-Wtemplate-body] 1227 | if(_levels[ii].hash_domain == 0 ) | ^~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1228:53: error: '__gnu_cxx::__alloc_traits, boomphf::level>::value_type' {aka 'class boomphf::level'} has no member named 'hash_domain' [-Wtemplate-body] 1228 | _levels[ii].hash_domain = 64 ; | ^~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1229:61: error: '__gnu_cxx::__alloc_traits, boomphf::level>::value_type' {aka 'class boomphf::level'} has no member named 'hash_domain' [-Wtemplate-body] 1229 | previous_idx += _levels[ii].hash_domain; | ^~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1234:37: error: request for member 'clear' in '((boomphf::mphf*)this)->boomphf::mphf::_final_hash', which is of non-class type 'int' [-Wtemplate-body] 1234 | _final_hash.clear(); | ^~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1242:42: error: expected ';' before 'value' [-Wtemplate-body] 1242 | uint64_t value; | ^~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1245:67: error: 'value' was not declared in this scope [-Wtemplate-body] 1245 | is.read(reinterpret_cast(&value), sizeof(uint64_t)); | ^~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::mphf::setup()': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1262:25: error: '_cptTotalProcessed' was not declared in this scope [-Wtemplate-body] 1262 | _cptTotalProcessed=0; | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1267:101: error: '_nelem' was not declared in this scope [-Wtemplate-body] 1267 | setLevelFastmode.resize(_percent_elem_loaded_for_fastMode * (double)_nelem ); | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1280:72: error: '_nelem' was not declared in this scope [-Wtemplate-body] 1280 | _proba_collision = 1.0 - pow(((_gamma*(double)_nelem -1 ) / (_gamma*(double)_nelem)),_nelem-1); | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1289:25: error: 'uint64_t' was not declared in this scope [-Wtemplate-body] 1289 | uint64_t previous_idx =0; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1289:25: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1293:45: error: '__gnu_cxx::__alloc_traits, boomphf::level>::value_type' {aka 'class boomphf::level'} has no member named 'idx_begin' [-Wtemplate-body] 1293 | _levels[ii].idx_begin = previous_idx; | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1293:57: error: 'previous_idx' was not declared in this scope [-Wtemplate-body] 1293 | _levels[ii].idx_begin = previous_idx; | ^~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1296:45: error: '__gnu_cxx::__alloc_traits, boomphf::level>::value_type' {aka 'class boomphf::level'} has no member named 'hash_domain' [-Wtemplate-body] 1296 | _levels[ii].hash_domain = (( (uint64_t) (_hash_domain * pow(_proba_collision,ii)) + 63) / 64 ) * 64; | ^~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1296:75: error: '_hash_domain' was not declared in this scope [-Wtemplate-body] 1296 | _levels[ii].hash_domain = (( (uint64_t) (_hash_domain * pow(_proba_collision,ii)) + 63) / 64 ) * 64; | ^~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1297:48: error: '__gnu_cxx::__alloc_traits, boomphf::level>::value_type' {aka 'class boomphf::level'} has no member named 'hash_domain' [-Wtemplate-body] 1297 | if(_levels[ii].hash_domain == 0 ) _levels[ii].hash_domain = 64 ; | ^~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1297:79: error: '__gnu_cxx::__alloc_traits, boomphf::level>::value_type' {aka 'class boomphf::level'} has no member named 'hash_domain' [-Wtemplate-body] 1297 | if(_levels[ii].hash_domain == 0 ) _levels[ii].hash_domain = 64 ; | ^~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1298:61: error: '__gnu_cxx::__alloc_traits, boomphf::level>::value_type' {aka 'class boomphf::level'} has no member named 'hash_domain' [-Wtemplate-body] 1298 | previous_idx += _levels[ii].hash_domain; | ^~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::mphf::insertIntoLevel(int, int)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1358:25: error: 'uint64_t' was not declared in this scope [-Wtemplate-body] 1358 | uint64_t hashl = fastrange64( level_hash,_levels[i].hash_domain); | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1358:25: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1360:47: error: 'class boomphf::bitVector' has no member named 'atomic_test_and_set' [-Wtemplate-body] 1360 | if( _levels[i].bitset.atomic_test_and_set(hashl) ) | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1360:67: error: 'hashl' was not declared in this scope [-Wtemplate-body] 1360 | if( _levels[i].bitset.atomic_test_and_set(hashl) ) | ^~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1362:46: error: 'class boomphf::bitVector' has no member named 'atomic_test_and_set' [-Wtemplate-body] 1362 | _tempBitset->atomic_test_and_set(hashl); | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::mphf::processLevel(const Range&, int)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1373:67: error: '__gnu_cxx::__alloc_traits, boomphf::level>::value_type' {aka 'class boomphf::level'} has no member named 'hash_domain' [-Wtemplate-body] 1373 | _levels[i].bitset = bitVector(_levels[i].hash_domain); ; | ^~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1402:25: error: '_cptLevel' was not declared in this scope [-Wtemplate-body] 1402 | _cptLevel = 0; | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1403:25: error: '_hashidx' was not declared in this scope [-Wtemplate-body] 1403 | _hashidx = 0; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1404:25: error: '_idxLevelsetLevelFastmode' was not declared in this scope; did you mean 'setLevelFastmode'? [-Wtemplate-body] 1404 | _idxLevelsetLevelFastmode =0; | ^~~~~~~~~~~~~~~~~~~~~~~~~ | setLevelFastmode In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/spdlog.h:192, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/RapMapUtils.hpp:33, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/HitManager.hpp:25, from /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:50: /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/spdlog.h:192, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/RapMapUtils.hpp:33, from /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:50: /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/spdlog.h:192, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/RapMapUtils.hpp:33, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:5, from /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndex.cpp:23: /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h: At global scope: /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/zstr/zstr.hpp:16, from /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:62: /build/reproducible-path/rapmap-0.15.0+dfsg/include/zstr/strict_fstream.hpp: In static member function 'static void strict_fstream::detail::static_method_holder::check_peek(std::istream*, const std::string&, std::ios_base::openmode)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/zstr/strict_fstream.hpp:128:39: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] 128 | catch (std::ios_base::failure e) {} | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In instantiation of 'void boomphf::mphf::load(std::istream&) [with elem_t = long unsigned int; Hasher_t = boomphf::SingleHashFunctor; std::istream = std::basic_istream]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:234:26: required from 'void FrugalBooMap::load(const std::string&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval; std::string = std::__cxx11::basic_string]' 234 | boophf_->load(is); | ~~~~~~~~~~~~~^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndex.cpp:82:11: required from 'bool loadHashFromIndex(const std::string&, PerfectHashT >&) [with IndexT = int; std::string = std::__cxx11::basic_string; PerfectHashT > = FrugalBooMap >]' 82 | h.load(hashBase); | ~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndex.cpp:126:26: required from 'bool RapMapSAIndex::load(const std::string&) [with IndexT = int; HashT = FrugalBooMap >; std::string = std::__cxx11::basic_string]' 126 | return loadHashFromIndex(indDir, khash); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndex.cpp:213:16: required from here 213 | template class RapMapSAIndex>>; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1247:44: error: subscripted value is neither array nor pointer 1247 | _final_hash[key] = value; | ~~~~~~~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp: In instantiation of 'void processReadsSingleSA(single_parser*, RapMapIndexT&, MutexT*, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; single_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]': /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:789:37: required from 'bool spawnProcessReadsThreads(uint32_t, single_parser*, RapMapIndexT&, MutexT&, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; uint32_t = unsigned int; single_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' 789 | threads.emplace_back(processReadsSingleSA, | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 790 | parser, | ~~~~~~~ 791 | std::ref(rmi), | ~~~~~~~~~~~~~~ 792 | &iomutex, | ~~~~~~~~~ 793 | outQueue, | ~~~~~~~~~ 794 | std::ref(hctr), | ~~~~~~~~~~~~~~~ 795 | mopts); | ~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:883:31: required from 'bool mapReads(RapMapIndexT&, std::shared_ptr, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >]' 883 | spawnProcessReadsThreads(nthread, singleParserPtr.get(), rmi, iomutex, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 884 | outLog, hctrs, mopts); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:1217:29: required from here 1217 | success = mapReads(rmi, consoleLog, &mopts); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:228:28: warning: ignoring return value of 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result] 228 | read.seq.length(); | ~~~~~~~~~~~~~~~^~ In file included from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:22: /usr/include/c++/15/bits/basic_string.h:1175:7: note: declared here 1175 | length() const _GLIBCXX_NOEXCEPT | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp: In instantiation of 'void processReadsSingleSA(single_parser*, RapMapIndexT&, MutexT*, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > > >; MutexT = std::mutex; single_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]': /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:789:37: required from 'bool spawnProcessReadsThreads(uint32_t, single_parser*, RapMapIndexT&, MutexT&, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > > >; MutexT = std::mutex; uint32_t = unsigned int; single_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' 789 | threads.emplace_back(processReadsSingleSA, | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 790 | parser, | ~~~~~~~ 791 | std::ref(rmi), | ~~~~~~~~~~~~~~ 792 | &iomutex, | ~~~~~~~~~ 793 | outQueue, | ~~~~~~~~~ 794 | std::ref(hctr), | ~~~~~~~~~~~~~~~ 795 | mopts); | ~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:883:31: required from 'bool mapReads(RapMapIndexT&, std::shared_ptr, MappingOpts*) [with RapMapIndexT = RapMapSAIndex, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > > >]' 883 | spawnProcessReadsThreads(nthread, singleParserPtr.get(), rmi, iomutex, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 884 | outLog, hctrs, mopts); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:1223:29: required from here 1223 | success = mapReads(rmi, consoleLog, &mopts); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:228:28: warning: ignoring return value of 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result] 228 | read.seq.length(); | ~~~~~~~~~~~~~~~^~ /usr/include/c++/15/bits/basic_string.h:1175:7: note: declared here 1175 | length() const _GLIBCXX_NOEXCEPT | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp: In instantiation of 'void processReadsSingleSA(single_parser*, RapMapIndexT&, MutexT*, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; single_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]': /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:789:37: required from 'bool spawnProcessReadsThreads(uint32_t, single_parser*, RapMapIndexT&, MutexT&, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; uint32_t = unsigned int; single_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' 789 | threads.emplace_back(processReadsSingleSA, | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 790 | parser, | ~~~~~~~ 791 | std::ref(rmi), | ~~~~~~~~~~~~~~ 792 | &iomutex, | ~~~~~~~~~ 793 | outQueue, | ~~~~~~~~~ 794 | std::ref(hctr), | ~~~~~~~~~~~~~~~ 795 | mopts); | ~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:883:31: required from 'bool mapReads(RapMapIndexT&, std::shared_ptr, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >]' 883 | spawnProcessReadsThreads(nthread, singleParserPtr.get(), rmi, iomutex, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 884 | outLog, hctrs, mopts); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:1232:31: required from here 1232 | success = mapReads(rmi, consoleLog, &mopts); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:228:28: warning: ignoring return value of 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result] 228 | read.seq.length(); | ~~~~~~~~~~~~~~~^~ /usr/include/c++/15/bits/basic_string.h:1175:7: note: declared here 1175 | length() const _GLIBCXX_NOEXCEPT | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp: In instantiation of 'void processReadsSingleSA(single_parser*, RapMapIndexT&, MutexT*, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > > >; MutexT = std::mutex; single_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]': /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:789:37: required from 'bool spawnProcessReadsThreads(uint32_t, single_parser*, RapMapIndexT&, MutexT&, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > > >; MutexT = std::mutex; uint32_t = unsigned int; single_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' 789 | threads.emplace_back(processReadsSingleSA, | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 790 | parser, | ~~~~~~~ 791 | std::ref(rmi), | ~~~~~~~~~~~~~~ 792 | &iomutex, | ~~~~~~~~~ 793 | outQueue, | ~~~~~~~~~ 794 | std::ref(hctr), | ~~~~~~~~~~~~~~~ 795 | mopts); | ~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:883:31: required from 'bool mapReads(RapMapIndexT&, std::shared_ptr, MappingOpts*) [with RapMapIndexT = RapMapSAIndex, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > > >]' 883 | spawnProcessReadsThreads(nthread, singleParserPtr.get(), rmi, iomutex, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 884 | outLog, hctrs, mopts); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:1238:31: required from here 1238 | success = mapReads(rmi, consoleLog, &mopts); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:228:28: warning: ignoring return value of 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result] 228 | read.seq.length(); | ~~~~~~~~~~~~~~~^~ /usr/include/c++/15/bits/basic_string.h:1175:7: note: declared here 1175 | length() const _GLIBCXX_NOEXCEPT | ^~~~~~ In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/RapMapUtils.hpp:29: /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; value_type = std::pair > >; reference = std::pair > >&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; pointer = std::pair > >*; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair > >; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]' 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]' 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:652:33: required from 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]' 652 | duplicateNames[dupInfo.txId].push_back(processedName); | ~~~~~~~~~~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 | usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup > >, spp::libc_allocator > > > >::value_type' {aka 'std::pair > >'} to 'spp::sparsegroup > >, spp::libc_allocator > > > >::mutable_reference' {aka 'std::pair > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = std::vector >]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; mutable_value_type = std::pair > >; reference = std::pair > >&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]' 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; pointer = std::pair > >*; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair > >; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]' 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]' 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:652:33: required from 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]' 652 | duplicateNames[dupInfo.txId].push_back(processedName); | ~~~~~~~~~~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 | usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup > >, spp::libc_allocator > > > >::value_type' {aka 'std::pair > >'} to 'spp::sparsegroup > >, spp::libc_allocator > > > >::mutable_reference' {aka 'std::pair > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = std::vector >]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::DefaultValue; KT = long unsigned int&; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = rapmap::utils::SAInterval; HashFcn = rapmap::utils::KmerKeyHasher; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = rapmap::utils::SAInterval]' 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:319:18: required from 'bool buildHash(const std::string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&) [with IndexT = long int; std::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' 319 | khash[bits] = {start, stop}; | ~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:842:34: required from 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]' 842 | success = buildHash(outputDir, concatText, tlen, k, SA); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 | usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = rapmap::utils::SAInterval; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = rapmap::utils::SAInterval]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::DefaultValue; KT = long unsigned int&; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = rapmap::utils::SAInterval; HashFcn = rapmap::utils::KmerKeyHasher; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = rapmap::utils::SAInterval]' 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:319:18: required from 'bool buildHash(const std::string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&) [with IndexT = int; std::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' 319 | khash[bits] = {start, stop}; | ~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:863:34: required from 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]' 863 | success = buildHash(outputDir, concatText, tlen, k, SA); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 | usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = rapmap::utils::SAInterval; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = rapmap::utils::SAInterval]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; KT = long int; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long int; Key = long int; T = long int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = long int]' 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:106:22: required from 'void FrugalBooMap::add(KeyT&&, ValueT&&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval]' 106 | overflow_[v.begin()] = l; | ~~~~~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:162:24: required from 'bool buildPerfectHash(const std::string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&, uint32_t) [with IndexT = long int; std::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' 162 | intervals.add(std::move(bits), {start, stop}); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:839:41: required from 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]' 839 | success = buildPerfectHash(outputDir, concatText, tlen, k, SA, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 840 | numHashThreads); | ~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 | usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long int; _U2 = long int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long int; _T2 = long int]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::DefaultValue; KT = long unsigned int&; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = rapmap::utils::SAInterval; HashFcn = rapmap::utils::KmerKeyHasher; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = rapmap::utils::SAInterval]' 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:319:18: required from 'bool buildHash(const std::string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&) [with IndexT = long int; std::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' 319 | khash[bits] = {start, stop}; | ~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:842:34: required from 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]' 842 | success = buildHash(outputDir, concatText, tlen, k, SA); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 | usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = rapmap::utils::SAInterval; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = rapmap::utils::SAInterval]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; KT = int; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = int; Key = int; T = int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = int]' 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:106:22: required from 'void FrugalBooMap::add(KeyT&&, ValueT&&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval]' 106 | overflow_[v.begin()] = l; | ~~~~~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:162:24: required from 'bool buildPerfectHash(const std::string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&, uint32_t) [with IndexT = int; std::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' 162 | intervals.add(std::move(bits), {start, stop}); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:860:41: required from 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]' 860 | success = buildPerfectHash(outputDir, concatText, tlen, k, SA, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 861 | numHashThreads); | ~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 | usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const int; _U2 = int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = int; _T2 = int]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::DefaultValue; KT = long unsigned int&; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = rapmap::utils::SAInterval; HashFcn = rapmap::utils::KmerKeyHasher; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = rapmap::utils::SAInterval]' 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:319:18: required from 'bool buildHash(const std::string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&) [with IndexT = int; std::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' 319 | khash[bits] = {start, stop}; | ~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:863:34: required from 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]' 863 | success = buildHash(outputDir, concatText, tlen, k, SA); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 | usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = rapmap::utils::SAInterval; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = rapmap::utils::SAInterval]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; KT = long int; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long int; Key = long int; T = long int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = long int]' 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:106:22: required from 'void FrugalBooMap::add(KeyT&&, ValueT&&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval]' 106 | overflow_[v.begin()] = l; | ~~~~~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:162:24: required from 'bool buildPerfectHash(const std::string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&, uint32_t) [with IndexT = long int; std::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' 162 | intervals.add(std::move(bits), {start, stop}); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:839:41: required from 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]' 839 | success = buildPerfectHash(outputDir, concatText, tlen, k, SA, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 840 | numHashThreads); | ~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 | usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long int; _U2 = long int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long int; _T2 = long int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; KT = int; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = int; Key = int; T = int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = int]' 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:106:22: required from 'void FrugalBooMap::add(KeyT&&, ValueT&&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval]' 106 | overflow_[v.begin()] = l; | ~~~~~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:162:24: required from 'bool buildPerfectHash(const std::string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&, uint32_t) [with IndexT = int; std::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' 162 | intervals.add(std::move(bits), {start, stop}); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:860:41: required from 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]' 860 | success = buildPerfectHash(outputDir, concatText, tlen, k, SA, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 861 | numHashThreads); | ~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 | usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const int; _U2 = int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = int; _T2 = int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/RapMapUtils.hpp:29: /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:162:30: required from 'FrugalBooMap::IteratorT FrugalBooMap::find(const KeyT&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval; IteratorT = KVProxy<__gnu_cxx::__normal_iterator > >, rapmap::utils::SAInterval >]' 162 | l = overflow_[ind]; | ~~~~~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/SACollector.hpp:196:25: required from 'bool SACollector::operator()(std::string&, SASearcher&, rapmap::hit_manager::HitCollectorInfo >&) [with RapMapIndexT = RapMapSAIndex > >; std::string = std::__cxx11::basic_string; typename RapMapIndexT::IndexType = long int]' 196 | merIt = khash.find(mer.word(0));//get_bits(0, 2 * k)); | ~~~~~~~~~~^~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:472:35: required from 'void processReadsPairSA(paired_parser*, RapMapIndexT&, MutexT*, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' 472 | bool lh = hitCollector(rpair.first.seq, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 473 | saSearcher, | ~~~~~~~~~~~ 474 | leftHCInfo); | ~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:765:37: required from 'bool spawnProcessReadsThreads(uint32_t, paired_parser*, RapMapIndexT&, MutexT&, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; uint32_t = unsigned int; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' 765 | threads.emplace_back(processReadsPairSA, | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 766 | parser, | ~~~~~~~ 767 | std::ref(rmi), | ~~~~~~~~~~~~~~ 768 | &iomutex, | ~~~~~~~~~ 769 | outQueue, | ~~~~~~~~~ 770 | std::ref(hctr), | ~~~~~~~~~~~~~~~ 771 | mopts); | ~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:872:31: required from 'bool mapReads(RapMapIndexT&, std::shared_ptr, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >]' 872 | spawnProcessReadsThreads(nthread, pairParserPtr.get(), rmi, iomutex, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 873 | outLog, hctrs, mopts); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:1217:29: required from here 1217 | success = mapReads(rmi, consoleLog, &mopts); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long int; _U2 = long int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long int; _T2 = long int]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:162:30: required from 'FrugalBooMap::IteratorT FrugalBooMap::find(const KeyT&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval; IteratorT = KVProxy<__gnu_cxx::__normal_iterator >, rapmap::utils::SAInterval >]' 162 | l = overflow_[ind]; | ~~~~~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/SACollector.hpp:196:25: required from 'bool SACollector::operator()(std::string&, SASearcher&, rapmap::hit_manager::HitCollectorInfo >&) [with RapMapIndexT = RapMapSAIndex > >; std::string = std::__cxx11::basic_string; typename RapMapIndexT::IndexType = int]' 196 | merIt = khash.find(mer.word(0));//get_bits(0, 2 * k)); | ~~~~~~~~~~^~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:472:35: required from 'void processReadsPairSA(paired_parser*, RapMapIndexT&, MutexT*, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' 472 | bool lh = hitCollector(rpair.first.seq, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 473 | saSearcher, | ~~~~~~~~~~~ 474 | leftHCInfo); | ~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:765:37: required from 'bool spawnProcessReadsThreads(uint32_t, paired_parser*, RapMapIndexT&, MutexT&, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; uint32_t = unsigned int; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' 765 | threads.emplace_back(processReadsPairSA, | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 766 | parser, | ~~~~~~~ 767 | std::ref(rmi), | ~~~~~~~~~~~~~~ 768 | &iomutex, | ~~~~~~~~~ 769 | outQueue, | ~~~~~~~~~ 770 | std::ref(hctr), | ~~~~~~~~~~~~~~~ 771 | mopts); | ~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:872:31: required from 'bool mapReads(RapMapIndexT&, std::shared_ptr, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >]' 872 | spawnProcessReadsThreads(nthread, pairParserPtr.get(), rmi, iomutex, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 873 | outLog, hctrs, mopts); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:1232:31: required from here 1232 | success = mapReads(rmi, consoleLog, &mopts); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const int; _U2 = int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = int; _T2 = int]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:162:30: required from 'FrugalBooMap::IteratorT FrugalBooMap::find(const KeyT&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval; IteratorT = KVProxy<__gnu_cxx::__normal_iterator > >, rapmap::utils::SAInterval >]' 162 | l = overflow_[ind]; | ~~~~~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/SACollector.hpp:196:25: required from 'bool SACollector::operator()(std::string&, SASearcher&, rapmap::hit_manager::HitCollectorInfo >&) [with RapMapIndexT = RapMapSAIndex > >; std::string = std::__cxx11::basic_string; typename RapMapIndexT::IndexType = long int]' 196 | merIt = khash.find(mer.word(0));//get_bits(0, 2 * k)); | ~~~~~~~~~~^~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:472:35: required from 'void processReadsPairSA(paired_parser*, RapMapIndexT&, MutexT*, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' 472 | bool lh = hitCollector(rpair.first.seq, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 473 | saSearcher, | ~~~~~~~~~~~ 474 | leftHCInfo); | ~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:765:37: required from 'bool spawnProcessReadsThreads(uint32_t, paired_parser*, RapMapIndexT&, MutexT&, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; uint32_t = unsigned int; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' 765 | threads.emplace_back(processReadsPairSA, | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 766 | parser, | ~~~~~~~ 767 | std::ref(rmi), | ~~~~~~~~~~~~~~ 768 | &iomutex, | ~~~~~~~~~ 769 | outQueue, | ~~~~~~~~~ 770 | std::ref(hctr), | ~~~~~~~~~~~~~~~ 771 | mopts); | ~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:872:31: required from 'bool mapReads(RapMapIndexT&, std::shared_ptr, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >]' 872 | spawnProcessReadsThreads(nthread, pairParserPtr.get(), rmi, iomutex, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 873 | outLog, hctrs, mopts); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:1217:29: required from here 1217 | success = mapReads(rmi, consoleLog, &mopts); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long int; _U2 = long int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long int; _T2 = long int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:162:30: required from 'FrugalBooMap::IteratorT FrugalBooMap::find(const KeyT&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval; IteratorT = KVProxy<__gnu_cxx::__normal_iterator >, rapmap::utils::SAInterval >]' 162 | l = overflow_[ind]; | ~~~~~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/SACollector.hpp:196:25: required from 'bool SACollector::operator()(std::string&, SASearcher&, rapmap::hit_manager::HitCollectorInfo >&) [with RapMapIndexT = RapMapSAIndex > >; std::string = std::__cxx11::basic_string; typename RapMapIndexT::IndexType = int]' 196 | merIt = khash.find(mer.word(0));//get_bits(0, 2 * k)); | ~~~~~~~~~~^~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:472:35: required from 'void processReadsPairSA(paired_parser*, RapMapIndexT&, MutexT*, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' 472 | bool lh = hitCollector(rpair.first.seq, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 473 | saSearcher, | ~~~~~~~~~~~ 474 | leftHCInfo); | ~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:765:37: required from 'bool spawnProcessReadsThreads(uint32_t, paired_parser*, RapMapIndexT&, MutexT&, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; uint32_t = unsigned int; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' 765 | threads.emplace_back(processReadsPairSA, | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 766 | parser, | ~~~~~~~ 767 | std::ref(rmi), | ~~~~~~~~~~~~~~ 768 | &iomutex, | ~~~~~~~~~ 769 | outQueue, | ~~~~~~~~~ 770 | std::ref(hctr), | ~~~~~~~~~~~~~~~ 771 | mopts); | ~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:872:31: required from 'bool mapReads(RapMapIndexT&, std::shared_ptr, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >]' 872 | spawnProcessReadsThreads(nthread, pairParserPtr.get(), rmi, iomutex, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 873 | outLog, hctrs, mopts); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:1232:31: required from here 1232 | success = mapReads(rmi, consoleLog, &mopts); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const int; _U2 = int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = int; _T2 = int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ cc1plus: note: unrecognized command-line option '-Wno-unused-local-typedef' may have been intended to silence earlier diagnostics make[4]: *** [src/CMakeFiles/rapmap.dir/build.make:152: src/CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o] Error 1 make[4]: *** Waiting for unfinished jobs.... cc1plus: note: unrecognized command-line option '-Wno-unused-local-typedef' may have been intended to silence earlier diagnostics cc1plus: note: unrecognized command-line option '-Wno-unused-local-typedef' may have been intended to silence earlier diagnostics cc1plus: note: unrecognized command-line option '-Wno-unused-local-typedef' may have been intended to silence earlier diagnostics In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/algorithm/sha2.hpp:9, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/digestpp.hpp:6, from /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:73: In member function 'void digestpp::detail::sha2_provider::transform(const unsigned char*, size_t) [with T = long unsigned int; long unsigned int O = 0]', inlined from 'digestpp::detail::sha2_provider::update(const unsigned char*, size_t)::' at /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61, inlined from 'void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider::update(const unsigned char*, size_t)::]' at /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12, inlined from 'void digestpp::detail::sha2_provider::update(const unsigned char*, size_t) [with T = long unsigned int; long unsigned int O = 0]' at /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23, inlined from 'digestpp::hasher& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; Mixin = digestpp::mixin::null_mixin]' at /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/hasher.hpp:170:19, inlined from 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser]' at /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:581:30: /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript 'const long unsigned int[0]' is partly outside array bounds of 'unsigned char [1]' [-Warray-bounds=] 208 | M[i] = byteswap(reinterpret_cast(data)[blk * 16 + i]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/digestpp.hpp:5: /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/hasher.hpp: In function 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/hasher.hpp:169:39: note: object 'byte' of size 1 169 | unsigned char byte = *begin++; | ^~~~ In member function 'void digestpp::detail::sha2_provider::transform(const unsigned char*, size_t) [with T = long unsigned int; long unsigned int O = 0]', inlined from 'digestpp::detail::sha2_provider::update(const unsigned char*, size_t)::' at /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61, inlined from 'void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider::update(const unsigned char*, size_t)::]' at /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12, inlined from 'void digestpp::detail::sha2_provider::update(const unsigned char*, size_t) [with T = long unsigned int; long unsigned int O = 0]' at /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23, inlined from 'digestpp::hasher& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; Mixin = digestpp::mixin::null_mixin]' at /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/hasher.hpp:170:19, inlined from 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser]' at /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:671:33: /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript 'const long unsigned int[0]' is partly outside array bounds of 'unsigned char [1]' [-Warray-bounds=] 208 | M[i] = byteswap(reinterpret_cast(data)[blk * 16 + i]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/hasher.hpp: In function 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/hasher.hpp:169:39: note: object 'byte' of size 1 169 | unsigned char byte = *begin++; | ^~~~ At global scope: cc1plus: note: unrecognized command-line option '-Wno-unused-local-typedef' may have been intended to silence earlier diagnostics At global scope: cc1plus: note: unrecognized command-line option '-Wno-unused-local-typedef' may have been intended to silence earlier diagnostics make[4]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' make[3]: *** [CMakeFiles/Makefile2:154: src/CMakeFiles/rapmap.dir/all] Error 2 make[3]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' make[2]: *** [Makefile:169: all] Error 2 make[2]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2 make[1]: *** [debian/rules:23: override_dh_auto_build] Error 25 make[1]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg' make: *** [debian/rules:17: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3054226 and its subdirectories Starting cleanup. All cleanup done. Sun Sep 14 23:26:01 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-CNoZxWfc, removing. /srv/reproducible-results/rbuild-debian/r-b-build.JNFgRBMC: total 16 drwxrwxr-x 2 jenkins jenkins 4096 Sep 14 23:26 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 14 23:24 b2 -rw-rw-r-- 1 jenkins jenkins 2322 Mar 25 2024 rapmap_0.15.0+dfsg-4.dsc -rw------- 1 jenkins jenkins 3449 Sep 14 23:24 rbuildlog.Rilbvc4 /srv/reproducible-results/rbuild-debian/r-b-build.JNFgRBMC/b1: total 316 -rw-r--r-- 1 jenkins jenkins 323431 Sep 14 23:26 build.log /srv/reproducible-results/rbuild-debian/r-b-build.JNFgRBMC/b2: total 0 Sun Sep 14 23:26:02 UTC 2025 I: Deleting $TMPDIR on infom01-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Sep 14 11:24:35 -12 2025 I: pbuilder-time-stamp: 1757892275 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 [rapmap_0.15.0+dfsg-4.dsc] I: copying [./rapmap_0.15.0+dfsg.orig.tar.xz] I: copying [./rapmap_0.15.0+dfsg-4.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./rapmap_0.15.0+dfsg-4.dsc: no acceptable signature found dpkg-source: info: extracting rapmap in rapmap-0.15.0+dfsg dpkg-source: info: unpacking rapmap_0.15.0+dfsg.orig.tar.xz dpkg-source: info: unpacking rapmap_0.15.0+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use-debian-libs.patch dpkg-source: info: applying use_shared_libs.patch dpkg-source: info: applying avoid_privacy_breach.patch dpkg-source: info: applying spelling dpkg-source: info: applying portable_pause dpkg-source: info: applying no_gomp_needed dpkg-source: info: applying simde I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3054226/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='4eecf533f1eb4791b60b35603ac3aa92' 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='3054226' 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.JNFgRBMC/pbuilderrc_hzcB --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.JNFgRBMC/b1 --logfile b1/build.log rapmap_0.15.0+dfsg-4.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom01-amd64 6.12.43+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3054226/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: amd64 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), cmake, zlib1g-dev, libdivsufsort-dev, libcereal-dev, libjellyfish-2.0-dev, libjemalloc-dev, libsimde-dev, libsparsehash-dev, libspdlog-dev, libtclap-dev, pkg-config, python3-markdown, python3 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 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 cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libdivsufsort-dev; however: Package libdivsufsort-dev is not installed. pbuilder-satisfydepends-dummy depends on libcereal-dev; however: Package libcereal-dev is not installed. pbuilder-satisfydepends-dummy depends on libjellyfish-2.0-dev; however: Package libjellyfish-2.0-dev is not installed. pbuilder-satisfydepends-dummy depends on libjemalloc-dev; however: Package libjemalloc-dev is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev is not installed. pbuilder-satisfydepends-dummy depends on libsparsehash-dev; however: Package libsparsehash-dev is not installed. pbuilder-satisfydepends-dummy depends on libspdlog-dev; however: Package libspdlog-dev is not installed. pbuilder-satisfydepends-dummy depends on libtclap-dev; however: Package libtclap-dev is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on python3-markdown; however: Package python3-markdown is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli1{a} libcereal-dev{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libdivsufsort-dev{a} libdivsufsort3{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfmt-dev{a} libfmt10{a} libgnutls30t64{a} libgssapi-krb5-2{a} libidn2-0{a} libjellyfish-2.0-2{a} libjellyfish-2.0-dev{a} libjemalloc-dev{a} libjemalloc2{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsimde-dev{a} libsparsehash-dev{a} libspdlog-dev{a} libspdlog1.15{a} libssh2-1t64{a} libtasn1-6{a} libtclap-dev{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2-16{a} m4{a} man-db{a} media-types{a} netbase{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python3{a} python3-importlib-metadata{a} python3-markdown{a} python3-minimal{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} rapidjson-dev{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix python3-pygments python3-yaml wget 0 packages upgraded, 94 newly installed, 0 to remove and 0 not upgraded. Need to get 44.8 MB of archives. After unpacking 174 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 cmake-data all 4.1.1+really3.31.6-1 [2268 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-4+b1 [349 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 40 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.11.0-1 [73.7 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.16.0-1 [437 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-4 [89.4 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.6-1 [137 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.51.0-2 [155 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 cmake amd64 4.1.1+really3.31.6-1 [12.0 MB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 66 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.4 [98.1 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libcereal-dev amd64 1.3.2+dfsg-6 [221 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libdivsufsort3 amd64 2.0.1-6+b1 [45.9 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libdivsufsort-dev amd64 2.0.1-6+b1 [19.1 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libfmt10 amd64 10.1.1+ds1-4 [127 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libfmt-dev amd64 10.1.1+ds1-4 [177 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libjellyfish-2.0-2 amd64 2.3.1-4+b1 [67.3 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libjellyfish-2.0-dev amd64 2.3.1-4+b1 [138 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libjemalloc2 amd64 5.3.0-3 [274 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libjemalloc-dev amd64 5.3.0-3 [490 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libsimde-dev all 0.8.2-3 [467 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libspdlog1.15 amd64 1:1.15.3+ds-1 [109 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libspdlog-dev amd64 1:1.15.3+ds-1 [91.9 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libtclap-dev amd64 1.2.5-1+b2 [3359 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 pkg-config amd64 1.8.1-4 [14.0 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 python3-importlib-metadata all 8.7.0-2 [21.8 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 python3-markdown all 3.9-1 [87.4 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 44.8 MB in 1s (52.0 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (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 ... 19917 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.7-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.7-1_amd64.deb ... Unpacking python3.13-minimal (3.13.7-1) ... Setting up libpython3.13-minimal:amd64 (3.13.7-1) ... Setting up libexpat1:amd64 (2.7.1-2) ... Setting up python3.13-minimal (3.13.7-1) ... 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 ... 20251 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_amd64.deb ... Unpacking python3-minimal (3.13.7-1) ... 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) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-5_all.deb ... Unpacking tzdata (2025b-5) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../4-libffi8_3.5.2-2_amd64.deb ... Unpacking libffi8:amd64 (3.5.2-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.3-3_all.deb ... Unpacking readline-common (8.3-3) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../6-libreadline8t64_8.3-3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.7-1) ... Setting up python3-minimal (3.13.7-1) ... 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 ... 21266 files and directories currently installed.) Preparing to unpack .../00-python3_3.13.7-1_amd64.deb ... Unpacking python3 (3.13.7-1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../01-libproc2-0_2%3a4.0.4-9_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-9) ... Selecting previously unselected package procps. Preparing to unpack .../02-procps_2%3a4.0.4-9_amd64.deb ... Unpacking procps (2:4.0.4-9) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../05-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../08-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../09-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../10-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../11-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. 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Preparing to unpack .../20-libarchive13t64_3.7.4-4+b1_amd64.deb ... Unpacking libarchive13t64:amd64 (3.7.4-4+b1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../21-libbrotli1_1.1.0-2+b7_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b7) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../22-libkrb5support0_1.21.3-5_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-5) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../23-libcom-err2_1.47.2-3+b3_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2-3+b3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../24-libk5crypto3_1.21.3-5_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../25-libkeyutils1_1.6.3-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../26-libkrb5-3_1.21.3-5_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../27-libgssapi-krb5-2_1.21.3-5_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-5) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../28-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libidn2-0:amd64. Preparing to unpack .../29-libidn2-0_2.3.8-4_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.8-4) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../30-libsasl2-modules-db_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../31-libsasl2-2_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libldap2:amd64. Preparing to unpack .../32-libldap2_2.6.10+dfsg-1_amd64.deb ... Unpacking libldap2:amd64 (2.6.10+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../33-libnghttp2-14_1.64.0-1.1+b1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Selecting previously unselected package libnghttp3-9:amd64. Preparing to unpack .../34-libnghttp3-9_1.11.0-1_amd64.deb ... Unpacking libnghttp3-9:amd64 (1.11.0-1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../35-libpsl5t64_0.21.2-1.1+b1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1+b1) ... Selecting previously unselected package libp11-kit0:amd64. Preparing to unpack .../36-libp11-kit0_0.25.5-3_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:amd64. 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Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/rapmap-0.15.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../rapmap_0.15.0+dfsg-4_source.changes dpkg-buildpackage: info: source package rapmap dpkg-buildpackage: info: source version 0.15.0+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg' dh_clean README.html sample_data/sample_quasi_index/ sample_data/sample_quasi_index_ph/ sample_data/sample_quasi_map.sam sample_data/sample_quasi_map_ph.sam make[1]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg' dh_auto_configure -- -DJELLYFISH_ROOT=/usr -DNO_NATIVE_ARCH=true cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DJELLYFISH_ROOT=/usr -DNO_NATIVE_ARCH=true .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CC: gcc CC version: -- The C compiler identification is GNU 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done version: 0.6.0 -- DISABLING NATIVE ARCH. -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE Making Default build type -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") -- Found Cereal: /usr/include (Required is at least version "1.2.2") -- Cereal found (include: /usr/include) -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Found Jemalloc: /usr/lib/x86_64-linux-gnu/libjemalloc.so (found version "5.3.0-0-g54eaed1d8b56b1aa528be3bdd1877e59c56fa90c") Found Jemalloc library --- using this memory allocator CPACK_SOURCE_IGNORE_FILES = .git/ CMAKE_SYSTEM_PROCESSOR: amd64 -- Configuring done (1.2s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED JELLYFISH_ROOT -- Build files have been written to: /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg' dh_auto_build cd obj-x86_64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory 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/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rapmap-0.15.0+dfsg /build/reproducible-path/rapmap-0.15.0+dfsg/src /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src/CMakeFiles/ksw2pp_basic.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rapmap-0.15.0+dfsg /build/reproducible-path/rapmap-0.15.0+dfsg/src /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src/CMakeFiles/ksw2pp_sse4.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rapmap-0.15.0+dfsg /build/reproducible-path/rapmap-0.15.0+dfsg/src /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src/CMakeFiles/ksw2pp_sse2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' make -f src/CMakeFiles/ksw2pp_sse4.dir/build.make src/CMakeFiles/ksw2pp_sse4.dir/build make -f src/CMakeFiles/ksw2pp_basic.dir/build.make src/CMakeFiles/ksw2pp_basic.dir/build make[4]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' make -f src/CMakeFiles/ksw2pp_sse2.dir/build.make src/CMakeFiles/ksw2pp_sse2.dir/build make[4]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' [ 13%] Building C object src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o [ 13%] Building C object src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o [ 13%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o [ 17%] Building C object src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o [ 17%] Building C object src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o [ 24%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o [ 24%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o [ 27%] Building C object src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_gg.c [ 34%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o [ 34%] Building C object src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse2 -mno-sse4.1 -MD -MT src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extd2_sse.c cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse4.1 -MD -MT src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o -MF CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o.d -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extf2_sse.c cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_gg2.c [ 37%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse2 -mno-sse4.1 -MD -MT src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extz2_sse.c cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse4.1 -MD -MT src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -MF CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o.d -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extz2_sse.c cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extd.c cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse2 -mno-sse4.1 -MD -MT src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extf2_sse.c [ 41%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/kalloc.c cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extz.c cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse4.1 -MD -MT src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o -MF CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o.d -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extd2_sse.c cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_gg2_sse.c [ 44%] Building CXX object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/ksw2pp/KSW2Aligner.cpp make[4]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' [ 44%] Built target ksw2pp_sse2 [ 44%] Built target ksw2pp_sse4 make[4]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' [ 44%] Built target ksw2pp_basic make -f src/CMakeFiles/ksw2pp.dir/build.make src/CMakeFiles/ksw2pp.dir/depend make[4]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rapmap-0.15.0+dfsg /build/reproducible-path/rapmap-0.15.0+dfsg/src /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src/CMakeFiles/ksw2pp.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' make -f src/CMakeFiles/ksw2pp.dir/build.make src/CMakeFiles/ksw2pp.dir/build make[4]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' [ 48%] Linking CXX static library libksw2pp.a cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/ksw2pp.dir/cmake_clean_target.cmake cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ksw2pp.dir/link.txt --verbose=1 /usr/bin/ar qc libksw2pp.a CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o /usr/bin/ranlib libksw2pp.a make[4]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' [ 48%] Built target ksw2pp make -f src/CMakeFiles/rapmap.dir/build.make src/CMakeFiles/rapmap.dir/depend make[4]: Entering directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rapmap-0.15.0+dfsg /build/reproducible-path/rapmap-0.15.0+dfsg/src 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CMakeFiles/rapmap.dir/RapMap.cpp.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMap.cpp cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/RapMapSAIndexer.cpp.o -MF CMakeFiles/rapmap.dir/RapMapSAIndexer.cpp.o.d -o CMakeFiles/rapmap.dir/RapMapSAIndexer.cpp.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp [ 86%] Building CXX object src/CMakeFiles/rapmap.dir/HitManager.cpp.o [ 86%] Building C object src/CMakeFiles/rapmap.dir/bit_array.c.o [ 86%] Building C object src/CMakeFiles/rapmap.dir/xxhash.c.o [ 86%] Building CXX object src/CMakeFiles/rapmap.dir/stringpiece.cc.o [ 86%] Building CXX object src/CMakeFiles/rapmap.dir/rank9b.cpp.o cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 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/build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o -MF CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o.d -o CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndex.cpp cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ 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-DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/FastxParser.cpp.o -MF CMakeFiles/rapmap.dir/FastxParser.cpp.o.d -o CMakeFiles/rapmap.dir/FastxParser.cpp.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/FastxParser.cpp cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd 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-fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/rapmap.dir/bit_array.c.o -MF CMakeFiles/rapmap.dir/bit_array.c.o.d -o CMakeFiles/rapmap.dir/bit_array.c.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/bit_array.c [ 93%] Building CXX object src/CMakeFiles/rapmap.dir/edlib.cpp.o cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/edlib.cpp.o -MF CMakeFiles/rapmap.dir/edlib.cpp.o.d -o CMakeFiles/rapmap.dir/edlib.cpp.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/edlib.cpp [ 96%] Building CXX object src/CMakeFiles/rapmap.dir/metro/metrohash64.cpp.o cd /build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/rapmap-0.15.0+dfsg/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/digestpp -I/build/reproducible-path/rapmap-0.15.0+dfsg/external -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/cereal/include -I/build/reproducible-path/rapmap-0.15.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/reproducible-path/rapmap-0.15.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/metro/metrohash64.cpp.o -MF CMakeFiles/rapmap.dir/metro/metrohash64.cpp.o.d -o CMakeFiles/rapmap.dir/metro/metrohash64.cpp.o -c /build/reproducible-path/rapmap-0.15.0+dfsg/src/metro/metrohash64.cpp In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooMap.hpp:4, from /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndex.cpp:22: /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:184:9: warning: inline variables are only available with '-std=c++17' or '-std=gnu++17' [-Wc++17-extensions] 184 | inline unsigned int popcount_64(uint64_t x) | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:184:41: error: 'uint64_t' was not declared in this scope 184 | inline unsigned int popcount_64(uint64_t x) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:20:1: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' 19 | #include +++ |+#include 20 | /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:202:17: error: 'uint64_t' does not name a type 202 | uint64_t done; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:202:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:203:17: error: 'uint64_t' does not name a type 203 | uint64_t todo; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:203:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:208:29: error: 'uint64_t' was not declared in this scope 208 | std::vector done_threaded; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:208:29: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:208:38: error: template argument 1 is invalid 208 | std::vector done_threaded; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:208:38: error: template argument 2 is invalid /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:212:27: error: 'uint64_t' has not been declared 212 | void init(uint64_t ntasks, const char * msg,int nthreads =1) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:212:27: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:263:26: error: 'uint64_t' has not been declared 263 | void inc(uint64_t ntasks_done) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:263:26: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:300:26: error: 'uint64_t' has not been declared 300 | void inc(uint64_t ntasks_done, int tid) //threads collaborate to this same progress bar | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:300:26: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:338:26: error: 'uint64_t' has not been declared 338 | void set(uint64_t ntasks_done) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:338:26: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::Progress::init(int, const char*, int)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:221:25: error: 'todo' was not declared in this scope 221 | todo= ntasks; | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:222:25: error: 'done' was not declared in this scope 222 | done = 0; | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:226:39: error: request for member 'resize' in '((boomphf::Progress*)this)->boomphf::Progress::done_threaded', which is of non-class type 'int' 226 | done_threaded.resize(_nthreads); | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:229:72: error: invalid types 'int[int]' for array subscript 229 | for (int ii=0; ii<_nthreads;ii++) done_threaded[ii]=0; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::Progress::finish()': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:241:29: error: 'todo' was not declared in this scope 241 | set(todo); | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:249:25: error: 'done' was not declared in this scope 249 | done = 0; | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::Progress::finish_threaded()': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:255:25: error: 'done' was not declared in this scope 255 | done = 0; | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:257:81: error: invalid types 'int[int]' for array subscript 257 | for (int ii=0; ii<_nthreads;ii++) done += (done_threaded[ii] ); | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::Progress::inc(int)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:265:25: error: 'done' was not declared in this scope 265 | done += ntasks_done; | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:277:55: error: 'todo' was not declared in this scope 277 | double rem = (todo-done) / speed; | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::Progress::inc(int, int)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:303:38: error: invalid types 'int[int]' for array subscript 303 | done_threaded[tid] += ntasks_done; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:312:41: error: 'uint64_t' was not declared in this scope 312 | uint64_t total_done = 0; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:312:41: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:313:75: error: 'total_done' was not declared in this scope 313 | for (int ii=0; ii<_nthreads;ii++) total_done += (done_threaded[ii] ); | ^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:313:103: error: invalid types 'int[int]' for array subscript 313 | for (int ii=0; ii<_nthreads;ii++) total_done += (done_threaded[ii] ); | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:315:56: error: 'total_done' was not declared in this scope 315 | double speed = total_done / elapsed; | ^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:316:55: error: 'todo' was not declared in this scope 316 | double rem = (todo-total_done) / speed; | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::Progress::set(int)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:340:42: error: 'done' was not declared in this scope 340 | if(ntasks_done > done) | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: At global scope: /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:354:28: error: 'uint64_t' was not declared in this scope 354 | typedef std::array hash_set_t; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:354:28: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:354:39: error: template argument 1 is invalid 354 | typedef std::array hash_set_t; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:355:28: error: 'uint64_t' was not declared in this scope 355 | typedef std::array hash_pair_t; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:355:28: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:355:38: error: template argument 1 is invalid 355 | typedef std::array hash_pair_t; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:374:9: error: 'uint64_t' does not name a type [-Wtemplate-body] 374 | uint64_t operator () (const Item& key, size_t idx) const { return hash64 (key, _seed_tab[idx]); } | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:374:9: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:376:9: error: 'uint64_t' does not name a type [-Wtemplate-body] 376 | uint64_t hashWithSeed(const Item& key, uint64_t seed) const { return hash64 (key, seed); } | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:376:9: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:394:31: error: 'uint64_t' does not name a type [-Wtemplate-body] 394 | inline static uint64_t hash64 (Item key, uint64_t seed) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:394:31: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:426:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 426 | uint64_t _seed_tab[MAXNBFUNC]; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:426:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:427:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 427 | uint64_t _user_seed; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:427:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In constructor 'boomphf::HashFunctors::HashFunctors()': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:369:25: error: '_user_seed' was not declared in this scope [-Wtemplate-body] 369 | _user_seed = 0; | ^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'boomphf::hash_set_t boomphf::HashFunctors::operator()(const Item&)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:386:37: error: invalid types 'boomphf::hash_set_t {aka int}[size_t {aka long unsigned int}]' for array subscript [-Wtemplate-body] 386 | hset[ii] = hash64 (key, _seed_tab[ii]); | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:386:58: error: '_seed_tab' was not declared in this scope [-Wtemplate-body] 386 | hset[ii] = hash64 (key, _seed_tab[ii]); | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::HashFunctors::generate_hash_seed()': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:412:38: error: 'uint64_t' does not name a type [-Wtemplate-body] 412 | static const uint64_t rbase[MAXNBFUNC] = | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:412:38: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:419:64: error: '_seed_tab' was not declared in this scope [-Wtemplate-body] 419 | for (size_t i=0; i'; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:468:9: error: 'uint64_t' does not name a type [-Wtemplate-body] 468 | uint64_t next(uint64_t * s) { | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:468:9: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:479:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 479 | uint64_t h0(hash_pair_t & s, const Item& key ) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:479:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:485:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 485 | uint64_t h1(hash_pair_t & s, const Item& key ) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:485:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:493:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 493 | uint64_t next(hash_pair_t & s ) { | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:493:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'boomphf::hash_set_t boomphf::XorshiftHashFunctors::operator()(const Item&)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:504:25: error: 'uint64_t' was not declared in this scope [-Wtemplate-body] 504 | uint64_t s[ 2 ]; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:504:25: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:508:17: error: invalid types 'boomphf::hash_set_t {aka int}[int]' for array subscript [-Wtemplate-body] 508 | hset[0] = singleHasher (key, 0xAAAAAAAA55555555ULL); | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:509:17: error: invalid types 'boomphf::hash_set_t {aka int}[int]' for array subscript [-Wtemplate-body] 509 | hset[1] = singleHasher (key, 0x33333333CCCCCCCCULL); | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:511:13: error: 's' was not declared in this scope [-Wtemplate-body] 511 | s[0] = hset[0]; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:511:24: error: invalid types 'boomphf::hash_set_t {aka int}[int]' for array subscript [-Wtemplate-body] 511 | s[0] = hset[0]; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:512:24: error: invalid types 'boomphf::hash_set_t {aka int}[int]' for array subscript [-Wtemplate-body] 512 | s[1] = hset[1]; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:516:21: error: invalid types 'boomphf::hash_set_t {aka int}[size_t {aka long unsigned int}]' for array subscript [-Wtemplate-body] 516 | hset[ii] = next(s); | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:516:28: error: there are no arguments to 'next' that depend on a template parameter, so a declaration of 'next' must be available [-Wtemplate-body] 516 | hset[ii] = next(s); | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:516:28: note: (if you use '-fpermissive', G++ will accept your code, but allowing the use of an undeclared name is deprecated) /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: At global scope: /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:568:35: error: expected ')' before 'n' 568 | bitVector(uint64_t n) : _size(n) | ~ ^~ | ) /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:630:29: error: 'uint64_t' has not been declared 630 | void resize(uint64_t newsize) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:630:29: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:643:17: error: 'uint64_t' does not name a type 643 | uint64_t bitSize() const {return (_nchar*64ULL + _ranks.capacity()*64ULL );} | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:643:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:652:38: error: 'uint64_t' has not been declared 652 | void clearCollisions(uint64_t start, size_t size, bitVector * cc) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:652:38: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:667:28: error: 'uint64_t' has not been declared 667 | void clear(uint64_t start, size_t size) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:667:28: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:696:17: error: 'uint64_t' does not name a type 696 | uint64_t operator[](uint64_t pos) const | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:696:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:706:17: error: 'uint64_t' does not name a type 706 | uint64_t atomic_test_and_set(uint64_t pos) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:706:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:714:17: error: 'uint64_t' does not name a type 714 | uint64_t get(uint64_t pos) const | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:714:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:719:17: error: 'uint64_t' does not name a type 719 | uint64_t get64(uint64_t cell64) const | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:719:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:725:26: error: 'uint64_t' has not been declared 725 | void set(uint64_t pos) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:725:26: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:733:28: error: 'uint64_t' has not been declared 733 | void reset(uint64_t pos) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:733:28: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:741:17: error: 'uint64_t' does not name a type 741 | uint64_t build_ranks(uint64_t offset =0) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:741:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:756:17: error: 'uint64_t' does not name a type 756 | uint64_t rank(uint64_t pos) const | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:756:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:798:17: error: 'uint64_t' does not name a type 798 | uint64_t* _bitArray; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:798:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:800:17: error: 'uint64_t' does not name a type 800 | uint64_t _size; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:800:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:801:17: error: 'uint64_t' does not name a type 801 | uint64_t _nchar; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:801:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:805:30: error: 'uint64_t' does not name a type 805 | static const uint64_t _nb_bits_per_rank_sample = 512; //512 seems ok | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:805:30: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:806:29: error: 'uint64_t' was not declared in this scope 806 | std::vector _ranks; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:806:29: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:806:37: error: template argument 1 is invalid 806 | std::vector _ranks; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:806:37: error: template argument 2 is invalid /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In constructor 'boomphf::bitVector::bitVector()': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:563:31: error: class 'boomphf::bitVector' does not have any field named '_size' 563 | bitVector() : _size(0) | ^~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:565:25: error: '_bitArray' was not declared in this scope 565 | _bitArray = nullptr; | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In destructor 'boomphf::bitVector::~bitVector()': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:576:28: error: '_bitArray' was not declared in this scope 576 | if(_bitArray != nullptr) | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In copy constructor 'boomphf::bitVector::bitVector(const boomphf::bitVector&)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:583:26: error: '_size' was not declared in this scope; did you mean 'size'? 583 | _size = r._size; | ^~~~~ | size /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:583:37: error: 'const class boomphf::bitVector' has no member named '_size'; did you mean 'size'? 583 | _size = r._size; | ^~~~~ | size /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:584:26: error: '_nchar' was not declared in this scope; did you mean 'u_char'? 584 | _nchar = r._nchar; | ^~~~~~ | u_char /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:584:37: error: 'const class boomphf::bitVector' has no member named '_nchar' 584 | _nchar = r._nchar; | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:586:26: error: '_bitArray' was not declared in this scope 586 | _bitArray = (uint64_t *) calloc (_nchar,sizeof(uint64_t)); | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:586:39: error: 'uint64_t' was not declared in this scope 586 | _bitArray = (uint64_t *) calloc (_nchar,sizeof(uint64_t)); | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:586:39: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:586:49: error: expected primary-expression before ')' token 586 | _bitArray = (uint64_t *) calloc (_nchar,sizeof(uint64_t)); | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:587:46: error: 'const class boomphf::bitVector' has no member named '_bitArray' 587 | memcpy(_bitArray, r._bitArray, _nchar*sizeof(uint64_t) ); | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'boomphf::bitVector& boomphf::bitVector::operator=(const boomphf::bitVector&)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:595:33: error: '_size' was not declared in this scope; did you mean 'size'? 595 | _size = r._size; | ^~~~~ | size /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:595:44: error: 'const class boomphf::bitVector' has no member named '_size'; did you mean 'size'? 595 | _size = r._size; | ^~~~~ | size /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:596:33: error: '_nchar' was not declared in this scope; did you mean 'u_char'? 596 | _nchar = r._nchar; | ^~~~~~ | u_char /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:596:44: error: 'const class boomphf::bitVector' has no member named '_nchar' 596 | _nchar = r._nchar; | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:598:36: error: '_bitArray' was not declared in this scope 598 | if(_bitArray != nullptr) | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:600:33: error: '_bitArray' was not declared in this scope 600 | _bitArray = (uint64_t *) calloc (_nchar,sizeof(uint64_t)); | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:600:46: error: 'uint64_t' was not declared in this scope 600 | _bitArray = (uint64_t *) calloc (_nchar,sizeof(uint64_t)); | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:600:46: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:600:56: error: expected primary-expression before ')' token 600 | _bitArray = (uint64_t *) calloc (_nchar,sizeof(uint64_t)); | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:601:53: error: 'const class boomphf::bitVector' has no member named '_bitArray' 601 | memcpy(_bitArray, r._bitArray, _nchar*sizeof(uint64_t) ); | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'boomphf::bitVector& boomphf::bitVector::operator=(boomphf::bitVector&&)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:612:36: error: '_bitArray' was not declared in this scope 612 | if(_bitArray != nullptr) | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:615:33: error: '_size' was not declared in this scope; did you mean 'size'? 615 | _size = std::move (r._size); | ^~~~~ | size /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:615:55: error: 'class boomphf::bitVector' has no member named '_size'; did you mean 'size'? 615 | _size = std::move (r._size); | ^~~~~ | size /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:616:33: error: '_nchar' was not declared in this scope; did you mean 'u_char'? 616 | _nchar = std::move (r._nchar); | ^~~~~~ | u_char /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:616:55: error: 'class boomphf::bitVector' has no member named '_nchar' 616 | _nchar = std::move (r._nchar); | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:618:33: error: '_bitArray' was not declared in this scope 618 | _bitArray = r._bitArray; | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:618:47: error: 'class boomphf::bitVector' has no member named '_bitArray' 618 | _bitArray = r._bitArray; | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:619:35: error: 'class boomphf::bitVector' has no member named '_bitArray' 619 | r._bitArray = nullptr; | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In constructor 'boomphf::bitVector::bitVector(boomphf::bitVector&&)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:624:44: error: class 'boomphf::bitVector' does not have any field named '_bitArray' 624 | bitVector(bitVector &&r) : _bitArray ( nullptr),_size(0) | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:624:65: error: class 'boomphf::bitVector' does not have any field named '_size' 624 | bitVector(bitVector &&r) : _bitArray ( nullptr),_size(0) | ^~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::bitVector::resize(int)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:633:25: error: '_nchar' was not declared in this scope; did you mean 'u_char'? 633 | _nchar = (1ULL+newsize/64ULL); | ^~~~~~ | u_char /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:634:25: error: '_bitArray' was not declared in this scope 634 | _bitArray = (uint64_t *) realloc(_bitArray,_nchar*sizeof(uint64_t)); | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:634:38: error: 'uint64_t' was not declared in this scope 634 | _bitArray = (uint64_t *) realloc(_bitArray,_nchar*sizeof(uint64_t)); | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:634:38: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:634:48: error: expected primary-expression before ')' token 634 | _bitArray = (uint64_t *) realloc(_bitArray,_nchar*sizeof(uint64_t)); | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:635:25: error: '_size' was not declared in this scope; did you mean 'size'? 635 | _size = newsize; | ^~~~~ | size /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'size_t boomphf::bitVector::size() const': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:640:32: error: '_size' was not declared in this scope; did you mean 'size'? 640 | return _size; | ^~~~~ | size /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::bitVector::clear()': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:648:32: error: '_bitArray' was not declared in this scope 648 | memset(_bitArray,0,_nchar*sizeof(uint64_t)); | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:648:44: error: '_nchar' was not declared in this scope; did you mean 'u_char'? 648 | memset(_bitArray,0,_nchar*sizeof(uint64_t)); | ^~~~~~ | u_char /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:648:58: error: 'uint64_t' was not declared in this scope 648 | memset(_bitArray,0,_nchar*sizeof(uint64_t)); | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:648:58: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::bitVector::clearCollisions(int, size_t, boomphf::bitVector*)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:656:25: error: 'uint64_t' was not declared in this scope 656 | uint64_t ids = (start/64ULL); | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:656:25: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:657:38: error: expected ';' before 'ii' 657 | for(uint64_t ii =0; ii< (size/64ULL); ii++ ) | ^~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:657:46: error: 'ii' was not declared in this scope 657 | for(uint64_t ii =0; ii< (size/64ULL); ii++ ) | ^~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:659:33: error: '_bitArray' was not declared in this scope 659 | _bitArray[ids+ii] = _bitArray[ids+ii] & (~ (cc->get64(ii)) ); | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:659:43: error: 'ids' was not declared in this scope 659 | _bitArray[ids+ii] = _bitArray[ids+ii] & (~ (cc->get64(ii)) ); | ^~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:659:82: error: 'class boomphf::bitVector' has no member named 'get64' 659 | _bitArray[ids+ii] = _bitArray[ids+ii] & (~ (cc->get64(ii)) ); | ^~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::bitVector::clear(int, size_t)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:671:32: error: '_bitArray' was not declared in this scope 671 | memset(_bitArray + (start/64ULL),0,(size/64ULL)*sizeof(uint64_t)); | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:671:80: error: 'uint64_t' was not declared in this scope 671 | memset(_bitArray + (start/64ULL),0,(size/64ULL)*sizeof(uint64_t)); | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:671:80: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::bitVector::print() const': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:677:94: error: '_size' was not declared in this scope; did you mean 'size'? 677 | printf("bit array of size %llu: \n", static_cast(_size)); | ^~~~~ | size /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:678:29: error: 'uint64_t' was not declared in this scope 678 | for(uint64_t ii = 0; ii< _size; ii++) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:678:29: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:678:46: error: 'ii' was not declared in this scope 678 | for(uint64_t ii = 0; ii< _size; ii++) | ^~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:682:44: error: '_bitArray' was not declared in this scope 682 | int val = (_bitArray[ii >> 6] >> (ii & 63 ) ) & 1; | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:687:100: error: request for member 'size' in '((const boomphf::bitVector*)this)->boomphf::bitVector::_ranks', which is of non-class type 'const int' 687 | printf("rank array : size %llu \n", static_cast(_ranks.size())); | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:688:30: error: 'uint64_t' was not declared in this scope 688 | for (uint64_t ii = 0; ii< _ranks.size(); ii++) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:688:30: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:688:47: error: 'ii' was not declared in this scope 688 | for (uint64_t ii = 0; ii< _ranks.size(); ii++) | ^~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:688:58: error: request for member 'size' in '((const boomphf::bitVector*)this)->boomphf::bitVector::_ranks', which is of non-class type 'const int' 688 | for (uint64_t ii = 0; ii< _ranks.size(); ii++) | ^~~~ In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:15: /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::bitVector::set(int)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:727:36: error: '_size' was not declared in this scope; did you mean 'size'? 727 | assert(pos<_size); | ^~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:729:46: error: '_bitArray' was not declared in this scope 729 | __sync_fetch_and_or (_bitArray + (pos >> 6ULL), (1ULL << (pos & 63)) ); | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::bitVector::reset(int)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:736:47: error: '_bitArray' was not declared in this scope 736 | __sync_fetch_and_and (_bitArray + (pos >> 6ULL), ~(1ULL << (pos & 63) )); | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::bitVector::save(std::ostream&) const': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:775:65: error: '_size' was not declared in this scope; did you mean 'size'? 775 | os.write(reinterpret_cast(&_size), sizeof(_size)); | ^~~~~ | size /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:776:65: error: '_nchar' was not declared in this scope; did you mean 'u_char'? 776 | os.write(reinterpret_cast(&_nchar), sizeof(_nchar)); | ^~~~~~ | u_char /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:777:64: error: '_bitArray' was not declared in this scope 777 | os.write(reinterpret_cast(_bitArray), (std::streamsize)(sizeof(uint64_t) * _nchar)); | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:777:101: error: 'uint64_t' was not declared in this scope 777 | os.write(reinterpret_cast(_bitArray), (std::streamsize)(sizeof(uint64_t) * _nchar)); | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:777:101: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:778:47: error: request for member 'size' in '((const boomphf::bitVector*)this)->boomphf::bitVector::_ranks', which is of non-class type 'const int' 778 | size_t sizer = _ranks.size(); | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:780:71: error: request for member 'data' in '((const boomphf::bitVector*)this)->boomphf::bitVector::_ranks', which is of non-class type 'const int' 780 | os.write(reinterpret_cast(_ranks.data()), (std::streamsize)(sizeof(_ranks[0]) * _ranks.size())); | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:780:111: error: invalid types 'const int[int]' for array subscript 780 | os.write(reinterpret_cast(_ranks.data()), (std::streamsize)(sizeof(_ranks[0]) * _ranks.size())); | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:780:125: error: request for member 'size' in '((const boomphf::bitVector*)this)->boomphf::bitVector::_ranks', which is of non-class type 'const int' 780 | os.write(reinterpret_cast(_ranks.data()), (std::streamsize)(sizeof(_ranks[0]) * _ranks.size())); | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::bitVector::load(std::istream&)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:785:58: error: '_size' was not declared in this scope; did you mean 'size'? 785 | is.read(reinterpret_cast(&_size), sizeof(_size)); | ^~~~~ | size /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:786:58: error: '_nchar' was not declared in this scope; did you mean 'u_char'? 786 | is.read(reinterpret_cast(&_nchar), sizeof(_nchar)); | ^~~~~~ | u_char /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:788:58: error: '_bitArray' was not declared in this scope 788 | is.read(reinterpret_cast(_bitArray), (std::streamsize)(sizeof(uint64_t) * _nchar)); | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:788:95: error: 'uint64_t' was not declared in this scope 788 | is.read(reinterpret_cast(_bitArray), (std::streamsize)(sizeof(uint64_t) * _nchar)); | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:788:95: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:792:32: error: request for member 'resize' in '((boomphf::bitVector*)this)->boomphf::bitVector::_ranks', which is of non-class type 'int' 792 | _ranks.resize(sizer); | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:793:64: error: request for member 'data' in '((boomphf::bitVector*)this)->boomphf::bitVector::_ranks', which is of non-class type 'int' 793 | is.read(reinterpret_cast(_ranks.data()), (std::streamsize)(sizeof(_ranks[0]) * _ranks.size())); | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:793:104: error: invalid types 'int[int]' for array subscript 793 | is.read(reinterpret_cast(_ranks.data()), (std::streamsize)(sizeof(_ranks[0]) * _ranks.size())); | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:793:118: error: request for member 'size' in '((boomphf::bitVector*)this)->boomphf::bitVector::_ranks', which is of non-class type 'int' 793 | is.read(reinterpret_cast(_ranks.data()), (std::streamsize)(sizeof(_ranks[0]) * _ranks.size())); | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: At global scope: /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:815:23: error: 'uint64_t' does not name a type 815 | static inline uint64_t fastrange64(uint64_t word, uint64_t p) { | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:815:23: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:829:17: error: 'uint64_t' does not name a type 829 | uint64_t get(uint64_t hash_raw) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:829:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:837:17: error: 'uint64_t' does not name a type 837 | uint64_t idx_begin; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:837:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:838:17: error: 'uint64_t' does not name a type 838 | uint64_t hash_domain; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:838:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:971:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 971 | uint64_t lookup(elem_t elem) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:971:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1011:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 1011 | uint64_t nbKeys() const | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1011:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1016:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 1016 | uint64_t totalBitSize() | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1016:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1318:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 1318 | uint64_t getLevel(hash_pair_t & bbhash, elem_t val,int * res_level, int maxlevel = 100, int minlevel =0) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1318:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1355:38: error: 'uint64_t' has not been declared [-Wtemplate-body] 1355 | void insertIntoLevel(uint64_t level_hash, int i) | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1355:38: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1506:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 1506 | uint64_t _hash_domain; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1506:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1507:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 1507 | uint64_t _nelem; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1507:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1508:35: error: 'uint64_t' was not declared in this scope [-Wtemplate-body] 1508 | std::unordered_map _final_hash; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1508:35: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1508:52: error: template argument 2 is invalid [-Wtemplate-body] 1508 | std::unordered_map _final_hash; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1508:52: error: template argument 5 is invalid [-Wtemplate-body] /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1512:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 1512 | uint64_t _hashidx; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1512:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1514:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 1514 | uint64_t _lastbitsetrank; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1514:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1515:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 1515 | uint64_t _idxLevelsetLevelFastmode; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1515:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1516:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 1516 | uint64_t _cptLevel; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1516:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1517:17: error: 'uint64_t' does not name a type [-Wtemplate-body] 1517 | uint64_t _cptTotalProcessed; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1517:17: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In constructor 'boomphf::mphf::mphf(size_t, const Range&, int, double, bool, bool, float)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:892:32: error: class 'boomphf::mphf' does not have any field named '_hash_domain' [-Wtemplate-body] 892 | _gamma(gamma), _hash_domain(size_t(ceil(double(n) * gamma))), _nelem(n), _num_thread(num_thread), _percent_elem_loaded_for_fastMode (perc_elem_loaded), _withprogress(progress) | ^~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:892:79: error: class 'boomphf::mphf' does not have any field named '_nelem' [-Wtemplate-body] 892 | _gamma(gamma), _hash_domain(size_t(ceil(double(n) * gamma))), _nelem(n), _num_thread(num_thread), _percent_elem_loaded_for_fastMode (perc_elem_loaded), _withprogress(progress) | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:932:59: error: '_nelem' was not declared in this scope [-Wtemplate-body] 932 | _progressBar.init(_nelem * total_writeEach,"Building BooPHF",num_thread); | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:935:60: error: '_nelem' was not declared in this scope [-Wtemplate-body] 935 | _progressBar.init( _nelem * total_fastmode_ram ,"Building BooPHF",num_thread); | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:937:60: error: '_nelem' was not declared in this scope [-Wtemplate-body] 937 | _progressBar.init( _nelem * _nb_levels ,"Building BooPHF",num_thread); | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:940:25: error: 'uint64_t' was not declared in this scope [-Wtemplate-body] 940 | uint64_t offset = 0; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:940:25: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:943:74: error: '__gnu_cxx::__alloc_traits, boomphf::level>::value_type' {aka 'class boomphf::level'} has no member named 'hash_domain' [-Wtemplate-body] 943 | _tempBitset = new bitVector(_levels[ii].hash_domain); // temp collision bitarray for this level | ^~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:947:84: error: '__gnu_cxx::__alloc_traits, boomphf::level>::value_type' {aka 'class boomphf::level'} has no member named 'hash_domain' [-Wtemplate-body] 947 | _levels[ii].bitset.clearCollisions(0 , _levels[ii].hash_domain , _tempBitset); | ^~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:949:33: error: 'offset' was not declared in this scope; did you mean 'off_t'? [-Wtemplate-body] 949 | offset = _levels[ii].bitset.build_ranks(offset); | ^~~~~~ | off_t /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:949:61: error: 'class boomphf::bitVector' has no member named 'build_ranks' [-Wtemplate-body] 949 | offset = _levels[ii].bitset.build_ranks(offset); | ^~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:958:25: error: '_lastbitsetrank' was not declared in this scope [-Wtemplate-body] 958 | _lastbitsetrank = offset ; | ^~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:958:43: error: 'offset' was not declared in this scope; did you mean 'off_t'? [-Wtemplate-body] 958 | _lastbitsetrank = offset ; | ^~~~~~ | off_t /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::mphf::pthread_processLevel(std::vector&, std::shared_ptr<_Yp>, std::shared_ptr<_Yp>, int)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1038:25: error: 'uint64_t' was not declared in this scope [-Wtemplate-body] 1038 | uint64_t nb_done =0; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1038:25: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1041:34: error: expected ';' before 'inbuff' [-Wtemplate-body] 1041 | uint64_t inbuff =0; | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1043:34: error: expected ';' before 'writebuff' [-Wtemplate-body] 1043 | uint64_t writebuff =0; | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1052:23: error: 'inbuff' was not declared in this scope [-Wtemplate-body] 1052 | for(; inbuff() {} | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1094:60: error: 'idxl2' was not declared in this scope [-Wtemplate-body] 1094 | if(idxl2>= setLevelFastmode.size()) | ^~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1104:66: error: expected ';' before 'hashidx' [-Wtemplate-body] 1104 | uint64_t hashidx = __sync_fetch_and_add (& _hashidx, 1); | ^~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1108:76: error: 'hashidx' was not declared in this scope [-Wtemplate-body] 1108 | _final_hash[val] = hashidx; | ^~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1119:68: error: 'writebuff' was not declared in this scope; did you mean 'myWriteBuff'? [-Wtemplate-body] 1119 | if(writebuff>=NBBUFF) | ^~~~~~~~~ | myWriteBuff /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1129:85: error: 'writebuff' was not declared in this scope; did you mean 'myWriteBuff'? [-Wtemplate-body] 1129 | myWriteBuff[writebuff++] = val; | ^~~~~~~~~ | myWriteBuff /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1141:65: error: 'level_hash' was not declared in this scope [-Wtemplate-body] 1141 | level_hash = _hasher.h0(bbhash,val); | ^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1143:65: error: 'level_hash' was not declared in this scope [-Wtemplate-body] 1143 | level_hash = _hasher.h1(bbhash,val); | ^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1146:65: error: 'level_hash' was not declared in this scope [-Wtemplate-body] 1146 | level_hash = _hasher.next(bbhash); | ^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1148:73: error: 'level_hash' was not declared in this scope [-Wtemplate-body] 1148 | insertIntoLevel(level_hash,i); //should be safe | ^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1152:41: error: 'nb_done' was not declared in this scope [-Wtemplate-body] 1152 | nb_done++; | ^~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1157:33: error: 'inbuff' was not declared in this scope [-Wtemplate-body] 1157 | inbuff = 0; | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1160:47: error: 'writebuff' was not declared in this scope; did you mean 'myWriteBuff'? [-Wtemplate-body] 1160 | if(_writeEachLevel && writebuff>0) | ^~~~~~~~~ | myWriteBuff /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::mphf::save(std::ostream&) const': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1177:65: error: '_lastbitsetrank' was not declared in this scope [-Wtemplate-body] 1177 | os.write(reinterpret_cast(&_lastbitsetrank), sizeof(_lastbitsetrank)); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/spdlog.h:192, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/RapMapUtils.hpp:33, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/HitManager.hpp:25, from /build/reproducible-path/rapmap-0.15.0+dfsg/src/HitManager.cpp:22: /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1178:65: error: '_nelem' was not declared in this scope [-Wtemplate-body] 1178 | os.write(reinterpret_cast(&_nelem), sizeof(_nelem)); | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1185:62: error: request for member 'size' in '((const boomphf::mphf*)this)->boomphf::mphf::_final_hash', which is of non-class type 'const int' [-Wtemplate-body] 1185 | size_t final_hash_size = _final_hash.size(); | ^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1191:52: error: request for member 'begin' in '((const boomphf::mphf*)this)->boomphf::mphf::_final_hash', which is of non-class type 'const int' [-Wtemplate-body] 1191 | for (auto it = _final_hash.begin(); it != _final_hash.end(); ++it ) | ^~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1191:79: error: request for member 'end' in '((const boomphf::mphf*)this)->boomphf::mphf::_final_hash', which is of non-class type 'const int' [-Wtemplate-body] 1191 | for (auto it = _final_hash.begin(); it != _final_hash.end(); ++it ) | ^~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1194:95: error: 'uint64_t' was not declared in this scope [-Wtemplate-body] 1194 | os.write(reinterpret_cast(&(it->second)), sizeof(uint64_t)); | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1194:95: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::mphf::load(std::istream&)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1204:58: error: '_lastbitsetrank' was not declared in this scope [-Wtemplate-body] 1204 | is.read(reinterpret_cast(&_lastbitsetrank), sizeof(_lastbitsetrank)); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/spdlog.h:192, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/IndexHeader.hpp:25, from /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMap.cpp:30: /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1205:58: error: '_nelem' was not declared in this scope [-Wtemplate-body] 1205 | is.read(reinterpret_cast(&_nelem), sizeof(_nelem)); | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1220:25: error: 'uint64_t' was not declared in this scope [-Wtemplate-body] 1220 | uint64_t previous_idx =0; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1220:25: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1221:25: error: '_hash_domain' was not declared in this scope [-Wtemplate-body] 1221 | _hash_domain = (size_t) (ceil(double(_nelem) * _gamma)) ; | ^~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1225:45: error: '__gnu_cxx::__alloc_traits, boomphf::level>::value_type' {aka 'class boomphf::level'} has no member named 'idx_begin' [-Wtemplate-body] 1225 | _levels[ii].idx_begin = previous_idx; | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1225:57: error: 'previous_idx' was not declared in this scope [-Wtemplate-body] 1225 | _levels[ii].idx_begin = previous_idx; | ^~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1226:45: error: '__gnu_cxx::__alloc_traits, boomphf::level>::value_type' {aka 'class boomphf::level'} has no member named 'hash_domain' [-Wtemplate-body] 1226 | _levels[ii].hash_domain = (( (uint64_t) (_hash_domain * pow(_proba_collision,ii)) + 63) / 64 ) * 64; | ^~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1227:48: error: '__gnu_cxx::__alloc_traits, boomphf::level>::value_type' {aka 'class boomphf::level'} has no member named 'hash_domain' [-Wtemplate-body] 1227 | if(_levels[ii].hash_domain == 0 ) | ^~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1228:53: error: '__gnu_cxx::__alloc_traits, boomphf::level>::value_type' {aka 'class boomphf::level'} has no member named 'hash_domain' [-Wtemplate-body] 1228 | _levels[ii].hash_domain = 64 ; | ^~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1229:61: error: '__gnu_cxx::__alloc_traits, boomphf::level>::value_type' {aka 'class boomphf::level'} has no member named 'hash_domain' [-Wtemplate-body] 1229 | previous_idx += _levels[ii].hash_domain; | ^~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1234:37: error: request for member 'clear' in '((boomphf::mphf*)this)->boomphf::mphf::_final_hash', which is of non-class type 'int' [-Wtemplate-body] 1234 | _final_hash.clear(); | ^~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1242:42: error: expected ';' before 'value' [-Wtemplate-body] 1242 | uint64_t value; | ^~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1245:67: error: 'value' was not declared in this scope [-Wtemplate-body] 1245 | is.read(reinterpret_cast(&value), sizeof(uint64_t)); | ^~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::mphf::setup()': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1262:25: error: '_cptTotalProcessed' was not declared in this scope [-Wtemplate-body] 1262 | _cptTotalProcessed=0; | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1267:101: error: '_nelem' was not declared in this scope [-Wtemplate-body] 1267 | setLevelFastmode.resize(_percent_elem_loaded_for_fastMode * (double)_nelem ); | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1280:72: error: '_nelem' was not declared in this scope [-Wtemplate-body] 1280 | _proba_collision = 1.0 - pow(((_gamma*(double)_nelem -1 ) / (_gamma*(double)_nelem)),_nelem-1); | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1289:25: error: 'uint64_t' was not declared in this scope [-Wtemplate-body] 1289 | uint64_t previous_idx =0; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1289:25: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1293:45: error: '__gnu_cxx::__alloc_traits, boomphf::level>::value_type' {aka 'class boomphf::level'} has no member named 'idx_begin' [-Wtemplate-body] 1293 | _levels[ii].idx_begin = previous_idx; | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1293:57: error: 'previous_idx' was not declared in this scope [-Wtemplate-body] 1293 | _levels[ii].idx_begin = previous_idx; | ^~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1296:45: error: '__gnu_cxx::__alloc_traits, boomphf::level>::value_type' {aka 'class boomphf::level'} has no member named 'hash_domain' [-Wtemplate-body] 1296 | _levels[ii].hash_domain = (( (uint64_t) (_hash_domain * pow(_proba_collision,ii)) + 63) / 64 ) * 64; | ^~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1296:75: error: '_hash_domain' was not declared in this scope [-Wtemplate-body] 1296 | _levels[ii].hash_domain = (( (uint64_t) (_hash_domain * pow(_proba_collision,ii)) + 63) / 64 ) * 64; | ^~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1297:48: error: '__gnu_cxx::__alloc_traits, boomphf::level>::value_type' {aka 'class boomphf::level'} has no member named 'hash_domain' [-Wtemplate-body] 1297 | if(_levels[ii].hash_domain == 0 ) _levels[ii].hash_domain = 64 ; | ^~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1297:79: error: '__gnu_cxx::__alloc_traits, boomphf::level>::value_type' {aka 'class boomphf::level'} has no member named 'hash_domain' [-Wtemplate-body] 1297 | if(_levels[ii].hash_domain == 0 ) _levels[ii].hash_domain = 64 ; | ^~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1298:61: error: '__gnu_cxx::__alloc_traits, boomphf::level>::value_type' {aka 'class boomphf::level'} has no member named 'hash_domain' [-Wtemplate-body] 1298 | previous_idx += _levels[ii].hash_domain; | ^~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::mphf::insertIntoLevel(int, int)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1358:25: error: 'uint64_t' was not declared in this scope [-Wtemplate-body] 1358 | uint64_t hashl = fastrange64( level_hash,_levels[i].hash_domain); | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1358:25: note: 'uint64_t' is defined in header ''; this is probably fixable by adding '#include ' /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1360:47: error: 'class boomphf::bitVector' has no member named 'atomic_test_and_set' [-Wtemplate-body] 1360 | if( _levels[i].bitset.atomic_test_and_set(hashl) ) | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1360:67: error: 'hashl' was not declared in this scope [-Wtemplate-body] 1360 | if( _levels[i].bitset.atomic_test_and_set(hashl) ) | ^~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1362:46: error: 'class boomphf::bitVector' has no member named 'atomic_test_and_set' [-Wtemplate-body] 1362 | _tempBitset->atomic_test_and_set(hashl); | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In member function 'void boomphf::mphf::processLevel(const Range&, int)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1373:67: error: '__gnu_cxx::__alloc_traits, boomphf::level>::value_type' {aka 'class boomphf::level'} has no member named 'hash_domain' [-Wtemplate-body] 1373 | _levels[i].bitset = bitVector(_levels[i].hash_domain); ; | ^~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1402:25: error: '_cptLevel' was not declared in this scope [-Wtemplate-body] 1402 | _cptLevel = 0; | ^~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1403:25: error: '_hashidx' was not declared in this scope [-Wtemplate-body] 1403 | _hashidx = 0; | ^~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1404:25: error: '_idxLevelsetLevelFastmode' was not declared in this scope; did you mean 'setLevelFastmode'? [-Wtemplate-body] 1404 | _idxLevelsetLevelFastmode =0; | ^~~~~~~~~~~~~~~~~~~~~~~~~ | setLevelFastmode In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/spdlog.h:192, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/RapMapUtils.hpp:33, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/HitManager.hpp:25, from /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:50: /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/spdlog.h:192, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/RapMapUtils.hpp:33, from /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:50: /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/spdlog.h:192, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/RapMapUtils.hpp:33, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:5, from /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndex.cpp:23: /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h: At global scope: /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/zstr/zstr.hpp:16, from /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:62: /build/reproducible-path/rapmap-0.15.0+dfsg/include/zstr/strict_fstream.hpp: In static member function 'static void strict_fstream::detail::static_method_holder::check_peek(std::istream*, const std::string&, std::ios_base::openmode)': /build/reproducible-path/rapmap-0.15.0+dfsg/include/zstr/strict_fstream.hpp:128:39: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] 128 | catch (std::ios_base::failure e) {} | ^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp: In instantiation of 'void boomphf::mphf::load(std::istream&) [with elem_t = long unsigned int; Hasher_t = boomphf::SingleHashFunctor; std::istream = std::basic_istream]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:234:26: required from 'void FrugalBooMap::load(const std::string&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval; std::string = std::__cxx11::basic_string]' 234 | boophf_->load(is); | ~~~~~~~~~~~~~^~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndex.cpp:82:11: required from 'bool loadHashFromIndex(const std::string&, PerfectHashT >&) [with IndexT = int; std::string = std::__cxx11::basic_string; PerfectHashT > = FrugalBooMap >]' 82 | h.load(hashBase); | ~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndex.cpp:126:26: required from 'bool RapMapSAIndex::load(const std::string&) [with IndexT = int; HashT = FrugalBooMap >; std::string = std::__cxx11::basic_string]' 126 | return loadHashFromIndex(indDir, khash); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndex.cpp:213:16: required from here 213 | template class RapMapSAIndex>>; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1247:44: error: subscripted value is neither array nor pointer 1247 | _final_hash[key] = value; | ~~~~~~~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp: In instantiation of 'void processReadsSingleSA(single_parser*, RapMapIndexT&, MutexT*, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; single_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]': /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:789:37: required from 'bool spawnProcessReadsThreads(uint32_t, single_parser*, RapMapIndexT&, MutexT&, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; uint32_t = unsigned int; single_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' 789 | threads.emplace_back(processReadsSingleSA, | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 790 | parser, | ~~~~~~~ 791 | std::ref(rmi), | ~~~~~~~~~~~~~~ 792 | &iomutex, | ~~~~~~~~~ 793 | outQueue, | ~~~~~~~~~ 794 | std::ref(hctr), | ~~~~~~~~~~~~~~~ 795 | mopts); | ~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:883:31: required from 'bool mapReads(RapMapIndexT&, std::shared_ptr, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >]' 883 | spawnProcessReadsThreads(nthread, singleParserPtr.get(), rmi, iomutex, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 884 | outLog, hctrs, mopts); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:1217:29: required from here 1217 | success = mapReads(rmi, consoleLog, &mopts); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:228:28: warning: ignoring return value of 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result] 228 | read.seq.length(); | ~~~~~~~~~~~~~~~^~ In file included from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:22: /usr/include/c++/15/bits/basic_string.h:1175:7: note: declared here 1175 | length() const _GLIBCXX_NOEXCEPT | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp: In instantiation of 'void processReadsSingleSA(single_parser*, RapMapIndexT&, MutexT*, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > > >; MutexT = std::mutex; single_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]': /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:789:37: required from 'bool spawnProcessReadsThreads(uint32_t, single_parser*, RapMapIndexT&, MutexT&, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > > >; MutexT = std::mutex; uint32_t = unsigned int; single_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' 789 | threads.emplace_back(processReadsSingleSA, | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 790 | parser, | ~~~~~~~ 791 | std::ref(rmi), | ~~~~~~~~~~~~~~ 792 | &iomutex, | ~~~~~~~~~ 793 | outQueue, | ~~~~~~~~~ 794 | std::ref(hctr), | ~~~~~~~~~~~~~~~ 795 | mopts); | ~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:883:31: required from 'bool mapReads(RapMapIndexT&, std::shared_ptr, MappingOpts*) [with RapMapIndexT = RapMapSAIndex, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > > >]' 883 | spawnProcessReadsThreads(nthread, singleParserPtr.get(), rmi, iomutex, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 884 | outLog, hctrs, mopts); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:1223:29: required from here 1223 | success = mapReads(rmi, consoleLog, &mopts); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:228:28: warning: ignoring return value of 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result] 228 | read.seq.length(); | ~~~~~~~~~~~~~~~^~ /usr/include/c++/15/bits/basic_string.h:1175:7: note: declared here 1175 | length() const _GLIBCXX_NOEXCEPT | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp: In instantiation of 'void processReadsSingleSA(single_parser*, RapMapIndexT&, MutexT*, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; single_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]': /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:789:37: required from 'bool spawnProcessReadsThreads(uint32_t, single_parser*, RapMapIndexT&, MutexT&, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; uint32_t = unsigned int; single_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' 789 | threads.emplace_back(processReadsSingleSA, | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 790 | parser, | ~~~~~~~ 791 | std::ref(rmi), | ~~~~~~~~~~~~~~ 792 | &iomutex, | ~~~~~~~~~ 793 | outQueue, | ~~~~~~~~~ 794 | std::ref(hctr), | ~~~~~~~~~~~~~~~ 795 | mopts); | ~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:883:31: required from 'bool mapReads(RapMapIndexT&, std::shared_ptr, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >]' 883 | spawnProcessReadsThreads(nthread, singleParserPtr.get(), rmi, iomutex, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 884 | outLog, hctrs, mopts); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:1232:31: required from here 1232 | success = mapReads(rmi, consoleLog, &mopts); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:228:28: warning: ignoring return value of 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result] 228 | read.seq.length(); | ~~~~~~~~~~~~~~~^~ /usr/include/c++/15/bits/basic_string.h:1175:7: note: declared here 1175 | length() const _GLIBCXX_NOEXCEPT | ^~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp: In instantiation of 'void processReadsSingleSA(single_parser*, RapMapIndexT&, MutexT*, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > > >; MutexT = std::mutex; single_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]': /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:789:37: required from 'bool spawnProcessReadsThreads(uint32_t, single_parser*, RapMapIndexT&, MutexT&, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > > >; MutexT = std::mutex; uint32_t = unsigned int; single_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' 789 | threads.emplace_back(processReadsSingleSA, | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 790 | parser, | ~~~~~~~ 791 | std::ref(rmi), | ~~~~~~~~~~~~~~ 792 | &iomutex, | ~~~~~~~~~ 793 | outQueue, | ~~~~~~~~~ 794 | std::ref(hctr), | ~~~~~~~~~~~~~~~ 795 | mopts); | ~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:883:31: required from 'bool mapReads(RapMapIndexT&, std::shared_ptr, MappingOpts*) [with RapMapIndexT = RapMapSAIndex, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > > >]' 883 | spawnProcessReadsThreads(nthread, singleParserPtr.get(), rmi, iomutex, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 884 | outLog, hctrs, mopts); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:1238:31: required from here 1238 | success = mapReads(rmi, consoleLog, &mopts); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:228:28: warning: ignoring return value of 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result] 228 | read.seq.length(); | ~~~~~~~~~~~~~~~^~ /usr/include/c++/15/bits/basic_string.h:1175:7: note: declared here 1175 | length() const _GLIBCXX_NOEXCEPT | ^~~~~~ In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/RapMapUtils.hpp:29: /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; value_type = std::pair > >; reference = std::pair > >&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; pointer = std::pair > >*; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair > >; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]' 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]' 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:652:33: required from 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]' 652 | duplicateNames[dupInfo.txId].push_back(processedName); | ~~~~~~~~~~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 | usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup > >, spp::libc_allocator > > > >::value_type' {aka 'std::pair > >'} to 'spp::sparsegroup > >, spp::libc_allocator > > > >::mutable_reference' {aka 'std::pair > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = std::vector >]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; mutable_value_type = std::pair > >; reference = std::pair > >&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]' 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; pointer = std::pair > >*; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair > >; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]' 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]' 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:652:33: required from 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]' 652 | duplicateNames[dupInfo.txId].push_back(processedName); | ~~~~~~~~~~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 | usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup > >, spp::libc_allocator > > > >::value_type' {aka 'std::pair > >'} to 'spp::sparsegroup > >, spp::libc_allocator > > > >::mutable_reference' {aka 'std::pair > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = std::vector >]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::DefaultValue; KT = long unsigned int&; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = rapmap::utils::SAInterval; HashFcn = rapmap::utils::KmerKeyHasher; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = rapmap::utils::SAInterval]' 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:319:18: required from 'bool buildHash(const std::string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&) [with IndexT = long int; std::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' 319 | khash[bits] = {start, stop}; | ~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:842:34: required from 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]' 842 | success = buildHash(outputDir, concatText, tlen, k, SA); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 | usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = rapmap::utils::SAInterval; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = rapmap::utils::SAInterval]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::DefaultValue; KT = long unsigned int&; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = rapmap::utils::SAInterval; HashFcn = rapmap::utils::KmerKeyHasher; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = rapmap::utils::SAInterval]' 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:319:18: required from 'bool buildHash(const std::string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&) [with IndexT = int; std::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' 319 | khash[bits] = {start, stop}; | ~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:863:34: required from 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]' 863 | success = buildHash(outputDir, concatText, tlen, k, SA); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 | usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = rapmap::utils::SAInterval; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = rapmap::utils::SAInterval]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; KT = long int; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long int; Key = long int; T = long int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = long int]' 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:106:22: required from 'void FrugalBooMap::add(KeyT&&, ValueT&&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval]' 106 | overflow_[v.begin()] = l; | ~~~~~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:162:24: required from 'bool buildPerfectHash(const std::string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&, uint32_t) [with IndexT = long int; std::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' 162 | intervals.add(std::move(bits), {start, stop}); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:839:41: required from 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]' 839 | success = buildPerfectHash(outputDir, concatText, tlen, k, SA, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 840 | numHashThreads); | ~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 | usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long int; _U2 = long int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long int; _T2 = long int]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::DefaultValue; KT = long unsigned int&; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = rapmap::utils::SAInterval; HashFcn = rapmap::utils::KmerKeyHasher; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = rapmap::utils::SAInterval]' 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:319:18: required from 'bool buildHash(const std::string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&) [with IndexT = long int; std::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' 319 | khash[bits] = {start, stop}; | ~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:842:34: required from 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]' 842 | success = buildHash(outputDir, concatText, tlen, k, SA); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 | usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = rapmap::utils::SAInterval; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = rapmap::utils::SAInterval]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; KT = int; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = int; Key = int; T = int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = int]' 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:106:22: required from 'void FrugalBooMap::add(KeyT&&, ValueT&&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval]' 106 | overflow_[v.begin()] = l; | ~~~~~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:162:24: required from 'bool buildPerfectHash(const std::string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&, uint32_t) [with IndexT = int; std::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' 162 | intervals.add(std::move(bits), {start, stop}); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:860:41: required from 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]' 860 | success = buildPerfectHash(outputDir, concatText, tlen, k, SA, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 861 | numHashThreads); | ~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 | usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const int; _U2 = int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = int; _T2 = int]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::DefaultValue; KT = long unsigned int&; Value = std::pair >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SelectKey; SetKey = spp::sparse_hash_map, rapmap::utils::KmerKeyHasher, std::equal_to, spp::libc_allocator > > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = rapmap::utils::SAInterval; HashFcn = rapmap::utils::KmerKeyHasher; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = rapmap::utils::SAInterval]' 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:319:18: required from 'bool buildHash(const std::string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&) [with IndexT = int; std::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' 319 | khash[bits] = {start, stop}; | ~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:863:34: required from 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]' 863 | success = buildHash(outputDir, concatText, tlen, k, SA); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 | usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = rapmap::utils::SAInterval; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = rapmap::utils::SAInterval]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; KT = long int; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long int; Key = long int; T = long int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = long int]' 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:106:22: required from 'void FrugalBooMap::add(KeyT&&, ValueT&&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval]' 106 | overflow_[v.begin()] = l; | ~~~~~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:162:24: required from 'bool buildPerfectHash(const std::string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&, uint32_t) [with IndexT = long int; std::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' 162 | intervals.add(std::move(bits), {start, stop}); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:839:41: required from 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]' 839 | success = buildPerfectHash(outputDir, concatText, tlen, k, SA, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 840 | numHashThreads); | ~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 | usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long int; _U2 = long int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long int; _T2 = long int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; KT = int; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 3288 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3810:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = int; Key = int; T = int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = int]' 3810 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:106:22: required from 'void FrugalBooMap::add(KeyT&&, ValueT&&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval]' 106 | overflow_[v.begin()] = l; | ~~~~~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:162:24: required from 'bool buildPerfectHash(const std::string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&, uint32_t) [with IndexT = int; std::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' 162 | intervals.add(std::move(bits), {start, stop}); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:860:41: required from 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]' 860 | success = buildPerfectHash(outputDir, concatText, tlen, k, SA, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 861 | numHashThreads); | ~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:1032:21: required from here 1032 | indexTranscriptsSA(transcriptParserPtr.get(), indexDir, decoyNames, noClipPolyA, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1033 | usePerfectHash, numPerfectHashThreads, keepDuplicates, sepStr, iomutex, jointLog); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const int; _U2 = int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = int; _T2 = int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/RapMapUtils.hpp:29: /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:162:30: required from 'FrugalBooMap::IteratorT FrugalBooMap::find(const KeyT&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval; IteratorT = KVProxy<__gnu_cxx::__normal_iterator > >, rapmap::utils::SAInterval >]' 162 | l = overflow_[ind]; | ~~~~~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/SACollector.hpp:196:25: required from 'bool SACollector::operator()(std::string&, SASearcher&, rapmap::hit_manager::HitCollectorInfo >&) [with RapMapIndexT = RapMapSAIndex > >; std::string = std::__cxx11::basic_string; typename RapMapIndexT::IndexType = long int]' 196 | merIt = khash.find(mer.word(0));//get_bits(0, 2 * k)); | ~~~~~~~~~~^~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:472:35: required from 'void processReadsPairSA(paired_parser*, RapMapIndexT&, MutexT*, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' 472 | bool lh = hitCollector(rpair.first.seq, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 473 | saSearcher, | ~~~~~~~~~~~ 474 | leftHCInfo); | ~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:765:37: required from 'bool spawnProcessReadsThreads(uint32_t, paired_parser*, RapMapIndexT&, MutexT&, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; uint32_t = unsigned int; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' 765 | threads.emplace_back(processReadsPairSA, | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 766 | parser, | ~~~~~~~ 767 | std::ref(rmi), | ~~~~~~~~~~~~~~ 768 | &iomutex, | ~~~~~~~~~ 769 | outQueue, | ~~~~~~~~~ 770 | std::ref(hctr), | ~~~~~~~~~~~~~~~ 771 | mopts); | ~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:872:31: required from 'bool mapReads(RapMapIndexT&, std::shared_ptr, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >]' 872 | spawnProcessReadsThreads(nthread, pairParserPtr.get(), rmi, iomutex, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 873 | outLog, hctrs, mopts); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:1217:29: required from here 1217 | success = mapReads(rmi, consoleLog, &mopts); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long int; _U2 = long int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long int; _T2 = long int]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:162:30: required from 'FrugalBooMap::IteratorT FrugalBooMap::find(const KeyT&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval; IteratorT = KVProxy<__gnu_cxx::__normal_iterator >, rapmap::utils::SAInterval >]' 162 | l = overflow_[ind]; | ~~~~~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/SACollector.hpp:196:25: required from 'bool SACollector::operator()(std::string&, SASearcher&, rapmap::hit_manager::HitCollectorInfo >&) [with RapMapIndexT = RapMapSAIndex > >; std::string = std::__cxx11::basic_string; typename RapMapIndexT::IndexType = int]' 196 | merIt = khash.find(mer.word(0));//get_bits(0, 2 * k)); | ~~~~~~~~~~^~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:472:35: required from 'void processReadsPairSA(paired_parser*, RapMapIndexT&, MutexT*, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' 472 | bool lh = hitCollector(rpair.first.seq, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 473 | saSearcher, | ~~~~~~~~~~~ 474 | leftHCInfo); | ~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:765:37: required from 'bool spawnProcessReadsThreads(uint32_t, paired_parser*, RapMapIndexT&, MutexT&, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; uint32_t = unsigned int; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' 765 | threads.emplace_back(processReadsPairSA, | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 766 | parser, | ~~~~~~~ 767 | std::ref(rmi), | ~~~~~~~~~~~~~~ 768 | &iomutex, | ~~~~~~~~~ 769 | outQueue, | ~~~~~~~~~ 770 | std::ref(hctr), | ~~~~~~~~~~~~~~~ 771 | mopts); | ~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:872:31: required from 'bool mapReads(RapMapIndexT&, std::shared_ptr, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >]' 872 | spawnProcessReadsThreads(nthread, pairParserPtr.get(), rmi, iomutex, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 873 | outLog, hctrs, mopts); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:1232:31: required from here 1232 | success = mapReads(rmi, consoleLog, &mopts); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const int; _U2 = int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = int; _T2 = int]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:162:30: required from 'FrugalBooMap::IteratorT FrugalBooMap::find(const KeyT&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval; IteratorT = KVProxy<__gnu_cxx::__normal_iterator > >, rapmap::utils::SAInterval >]' 162 | l = overflow_[ind]; | ~~~~~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/SACollector.hpp:196:25: required from 'bool SACollector::operator()(std::string&, SASearcher&, rapmap::hit_manager::HitCollectorInfo >&) [with RapMapIndexT = RapMapSAIndex > >; std::string = std::__cxx11::basic_string; typename RapMapIndexT::IndexType = long int]' 196 | merIt = khash.find(mer.word(0));//get_bits(0, 2 * k)); | ~~~~~~~~~~^~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:472:35: required from 'void processReadsPairSA(paired_parser*, RapMapIndexT&, MutexT*, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' 472 | bool lh = hitCollector(rpair.first.seq, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 473 | saSearcher, | ~~~~~~~~~~~ 474 | leftHCInfo); | ~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:765:37: required from 'bool spawnProcessReadsThreads(uint32_t, paired_parser*, RapMapIndexT&, MutexT&, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; uint32_t = unsigned int; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' 765 | threads.emplace_back(processReadsPairSA, | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 766 | parser, | ~~~~~~~ 767 | std::ref(rmi), | ~~~~~~~~~~~~~~ 768 | &iomutex, | ~~~~~~~~~ 769 | outQueue, | ~~~~~~~~~ 770 | std::ref(hctr), | ~~~~~~~~~~~~~~~ 771 | mopts); | ~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:872:31: required from 'bool mapReads(RapMapIndexT&, std::shared_ptr, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >]' 872 | spawnProcessReadsThreads(nthread, pairParserPtr.get(), rmi, iomutex, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 873 | outLog, hctrs, mopts); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:1217:29: required from here 1217 | success = mapReads(rmi, consoleLog, &mopts); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long int; _U2 = long int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long int; _T2 = long int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2241:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 2241 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3171:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 3171 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:3288:38: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp:162:30: required from 'FrugalBooMap::IteratorT FrugalBooMap::find(const KeyT&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval; IteratorT = KVProxy<__gnu_cxx::__normal_iterator >, rapmap::utils::SAInterval >]' 162 | l = overflow_[ind]; | ~~~~~~~~~^ /build/reproducible-path/rapmap-0.15.0+dfsg/include/SACollector.hpp:196:25: required from 'bool SACollector::operator()(std::string&, SASearcher&, rapmap::hit_manager::HitCollectorInfo >&) [with RapMapIndexT = RapMapSAIndex > >; std::string = std::__cxx11::basic_string; typename RapMapIndexT::IndexType = int]' 196 | merIt = khash.find(mer.word(0));//get_bits(0, 2 * k)); | ~~~~~~~~~~^~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:472:35: required from 'void processReadsPairSA(paired_parser*, RapMapIndexT&, MutexT*, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' 472 | bool lh = hitCollector(rpair.first.seq, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 473 | saSearcher, | ~~~~~~~~~~~ 474 | leftHCInfo); | ~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:765:37: required from 'bool spawnProcessReadsThreads(uint32_t, paired_parser*, RapMapIndexT&, MutexT&, std::shared_ptr, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >; MutexT = std::mutex; uint32_t = unsigned int; paired_parser = fastx_parser::FastxParser; HitCounters = rapmap::utils::HitCounters]' 765 | threads.emplace_back(processReadsPairSA, | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 766 | parser, | ~~~~~~~ 767 | std::ref(rmi), | ~~~~~~~~~~~~~~ 768 | &iomutex, | ~~~~~~~~~ 769 | outQueue, | ~~~~~~~~~ 770 | std::ref(hctr), | ~~~~~~~~~~~~~~~ 771 | mopts); | ~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:872:31: required from 'bool mapReads(RapMapIndexT&, std::shared_ptr, MappingOpts*) [with RapMapIndexT = RapMapSAIndex > >]' 872 | spawnProcessReadsThreads(nthread, pairParserPtr.get(), rmi, iomutex, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 873 | outLog, hctrs, mopts); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:1232:31: required from here 1232 | success = mapReads(rmi, consoleLog, &mopts); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const int; _U2 = int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = int; _T2 = int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ cc1plus: note: unrecognized command-line option '-Wno-unused-local-typedef' may have been intended to silence earlier diagnostics make[4]: *** [src/CMakeFiles/rapmap.dir/build.make:152: src/CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o] Error 1 make[4]: *** Waiting for unfinished jobs.... cc1plus: note: unrecognized command-line option '-Wno-unused-local-typedef' may have been intended to silence earlier diagnostics cc1plus: note: unrecognized command-line option '-Wno-unused-local-typedef' may have been intended to silence earlier diagnostics cc1plus: note: unrecognized command-line option '-Wno-unused-local-typedef' may have been intended to silence earlier diagnostics In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/algorithm/sha2.hpp:9, from /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/digestpp.hpp:6, from /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:73: In member function 'void digestpp::detail::sha2_provider::transform(const unsigned char*, size_t) [with T = long unsigned int; long unsigned int O = 0]', inlined from 'digestpp::detail::sha2_provider::update(const unsigned char*, size_t)::' at /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61, inlined from 'void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider::update(const unsigned char*, size_t)::]' at /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12, inlined from 'void digestpp::detail::sha2_provider::update(const unsigned char*, size_t) [with T = long unsigned int; long unsigned int O = 0]' at /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23, inlined from 'digestpp::hasher& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; Mixin = digestpp::mixin::null_mixin]' at /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/hasher.hpp:170:19, inlined from 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser]' at /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:581:30: /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript 'const long unsigned int[0]' is partly outside array bounds of 'unsigned char [1]' [-Warray-bounds=] 208 | M[i] = byteswap(reinterpret_cast(data)[blk * 16 + i]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/digestpp.hpp:5: /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/hasher.hpp: In function 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/hasher.hpp:169:39: note: object 'byte' of size 1 169 | unsigned char byte = *begin++; | ^~~~ In member function 'void digestpp::detail::sha2_provider::transform(const unsigned char*, size_t) [with T = long unsigned int; long unsigned int O = 0]', inlined from 'digestpp::detail::sha2_provider::update(const unsigned char*, size_t)::' at /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61, inlined from 'void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider::update(const unsigned char*, size_t)::]' at /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12, inlined from 'void digestpp::detail::sha2_provider::update(const unsigned char*, size_t) [with T = long unsigned int; long unsigned int O = 0]' at /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23, inlined from 'digestpp::hasher& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; Mixin = digestpp::mixin::null_mixin]' at /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/hasher.hpp:170:19, inlined from 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser]' at /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:671:33: /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript 'const long unsigned int[0]' is partly outside array bounds of 'unsigned char [1]' [-Warray-bounds=] 208 | M[i] = byteswap(reinterpret_cast(data)[blk * 16 + i]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/hasher.hpp: In function 'void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser]': /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/hasher.hpp:169:39: note: object 'byte' of size 1 169 | unsigned char byte = *begin++; | ^~~~ At global scope: cc1plus: note: unrecognized command-line option '-Wno-unused-local-typedef' may have been intended to silence earlier diagnostics At global scope: cc1plus: note: unrecognized command-line option '-Wno-unused-local-typedef' may have been intended to silence earlier diagnostics make[4]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' make[3]: *** [CMakeFiles/Makefile2:154: src/CMakeFiles/rapmap.dir/all] Error 2 make[3]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' make[2]: *** [Makefile:169: all] Error 2 make[2]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu' dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2 make[1]: *** [debian/rules:23: override_dh_auto_build] Error 25 make[1]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg' make: *** [debian/rules:17: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3054226 and its subdirectories rapmap failed to build from source. removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/rapmap_0.15.0+dfsg-4.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/rapmap_0.15.0+dfsg-4.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/rapmap_0.15.0+dfsg-4.build1.log.gz' Sun Sep 14 23:26:03 UTC 2025 W: No second build log, what happened? Compressing the 1st log... b1/build.log: 91.9% -- replaced with stdout INSERT 0 1 INSERT 0 1 DELETE 1 [2025-09-14 23:26:03] INFO: Starting at 2025-09-14 23:26:03.578462 [2025-09-14 23:26:03] INFO: Generating the pages of 1 package(s) [2025-09-14 23:26:03] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/rapmap didn't produce a buildlog, even though it has been built. [2025-09-14 23:26:04] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/rapmap_0.15.0+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/rapmap_0.15.0+dfsg-4.diff.gz is missing [2025-09-14 23:26:04] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/forky/amd64/rapmap_0.15.0+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/amd64/rapmap_0.15.0+dfsg-4.diff.gz is missing [2025-09-14 23:26:04] CRITICAL: https://tests.reproducible-builds.org/debian/forky/arm64/rapmap didn't produce a buildlog, even though it has been built. [2025-09-14 23:26:04] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/rapmap_0.15.0+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/rapmap_0.15.0+dfsg-4.diff.gz is missing [2025-09-14 23:26:04] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/arm64/rapmap_0.15.0+dfsg-3.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/arm64/rapmap_0.15.0+dfsg-3.diff.gz is missing [2025-09-14 23:26:04] INFO: Finished at 2025-09-14 23:26:04.034642, took: 0:00:00.456183 Sun Sep 14 23:26:04 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/rapmap.html Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/rapmap_0.15.0+dfsg-4.rbuild.log: 91.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/rapmap_0.15.0+dfsg-4.rbuild.log.gz [2025-09-14 23:26:04] INFO: Starting at 2025-09-14 23:26:04.363063 [2025-09-14 23:26:04] INFO: Generating the pages of 1 package(s) [2025-09-14 23:26:04] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/rapmap_0.15.0+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/rapmap_0.15.0+dfsg-4.diff.gz is missing [2025-09-14 23:26:04] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/rapmap_0.15.0+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/rapmap_0.15.0+dfsg-4.diff.gz is missing [2025-09-14 23:26:04] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/forky/amd64/rapmap_0.15.0+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/amd64/rapmap_0.15.0+dfsg-4.diff.gz is missing [2025-09-14 23:26:04] CRITICAL: https://tests.reproducible-builds.org/debian/forky/arm64/rapmap didn't produce a buildlog, even though it has been built. [2025-09-14 23:26:04] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/rapmap_0.15.0+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/rapmap_0.15.0+dfsg-4.diff.gz is missing [2025-09-14 23:26:04] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/arm64/rapmap_0.15.0+dfsg-3.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/arm64/rapmap_0.15.0+dfsg-3.diff.gz is missing [2025-09-14 23:26:04] INFO: Finished at 2025-09-14 23:26:04.717138, took: 0:00:00.354078 All cleanup done. Sun Sep 14 23:26:04 UTC 2025 - total duration: 0h 1m 53s. Sun Sep 14 23:26:04 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-WGyIfoNT, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 1min 54.344s CPU time consumed: 2.795s Memory peak: 55M (swap: 0B)