Diff of the two buildlogs: -- --- b1/build.log 2025-02-14 02:04:19.317720103 +0000 +++ b2/build.log 2025-02-14 02:06:13.576581172 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Mar 18 20:24:23 -12 2026 -I: pbuilder-time-stamp: 1773908663 +I: Current time: Fri Feb 14 16:04:22 +14 2025 +I: pbuilder-time-stamp: 1739498662 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -26,52 +26,84 @@ dpkg-source: info: applying simde I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3888513/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/269166/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Feb 14 02:04 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/269166/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/269166/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='3ff728c163044573a6b421d510b36b95' - 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='3888513' - PS1='# ' - PS2='> ' + INVOCATION_ID=3c19d287fc9b44dbb400de591a74c1af + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=269166 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.lZMDkWFl/pbuilderrc_tOOm --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.lZMDkWFl/b1 --logfile b1/build.log snap-aligner_2.0.3+dfsg-2.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.lZMDkWFl/pbuilderrc_tKbd --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.lZMDkWFl/b2 --logfile b2/build.log snap-aligner_2.0.3+dfsg-2.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3888513/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/269166/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -147,7 +179,7 @@ Get: 32 http://deb.debian.org/debian trixie/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libsimde-dev all 0.8.2-2 [467 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] -Fetched 21.7 MB in 0s (106 MB/s) +Fetched 21.7 MB in 0s (145 MB/s) Preconfiguring packages ... Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19922 files and directories currently installed.) @@ -298,7 +330,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/snap-aligner-2.0.3+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 > ../snap-aligner_2.0.3+dfsg-2_source.changes +I: user script /srv/workspace/pbuilder/269166/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/269166/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/snap-aligner-2.0.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../snap-aligner_2.0.3+dfsg-2_source.changes dpkg-buildpackage: info: source package snap-aligner dpkg-buildpackage: info: source version 2.0.3+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -340,10 +376,7 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BaseAligner.o SNAPLib/BaseAligner.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BigAlloc.o SNAPLib/BigAlloc.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BufferedAsync.o SNAPLib/BufferedAsync.cpp -In file included from SNAPLib/HashTable.h:23, - from SNAPLib/GenomeIndex.h:27, - from SNAPLib/AlignmentAdjuster.h:27, - from SNAPLib/AlignmentAdjuster.cpp:26: +In file included from SNAPLib/BigAlloc.cpp:24: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -364,8 +397,10 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -In file included from SNAPLib/ApproximateCounter.h:3, - from SNAPLib/ApproximateCounter.cpp:3: +In file included from SNAPLib/HashTable.h:23, + from SNAPLib/GenomeIndex.h:27, + from SNAPLib/AlignmentAdjuster.h:27, + from SNAPLib/AlignmentAdjuster.cpp:26: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -386,7 +421,7 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -In file included from SNAPLib/BigAlloc.cpp:24: +In file included from SNAPLib/AffineGapVectorized.cpp:2: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -407,12 +442,9 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -In file included from SNAPLib/SAM.h:22, - from SNAPLib/Bam.cpp:20: -SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined - 87 | # define _MM_HINT_T0 1 - | ^~~~~~~~~~~ -In file included from SNAPLib/AffineGapVectorized.cpp:2: +In file included from SNAPLib/Genome.h:26, + from SNAPLib/AlignerOptions.h:29, + from SNAPLib/AlignerOptions.cpp:27: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -433,6 +465,11 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ +In file included from SNAPLib/ApproximateCounter.h:3, + from SNAPLib/ApproximateCounter.cpp:3: +SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined + 87 | # define _MM_HINT_T0 1 + | ^~~~~~~~~~~ In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81: /usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition @@ -447,19 +484,13 @@ SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined 89 | # define _MM_HINT_T2 3 | ^~~~~~~~~~~ -/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition - 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 - | ^~~~~~~~~~~ -In file included from SNAPLib/Genome.h:26, - from SNAPLib/AlignmentResult.h:29, - from SNAPLib/AlignmentResult.cpp:23: -SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined - 87 | # define _MM_HINT_T0 1 - | ^~~~~~~~~~~ In file included from SNAPLib/AffineGap.cpp:2: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ +/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition + 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 + | ^~~~~~~~~~~ In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81: /usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition @@ -477,9 +508,7 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -In file included from SNAPLib/Genome.h:26, - from SNAPLib/AlignerOptions.h:29, - from SNAPLib/AlignerOptions.cpp:27: +In file included from SNAPLib/BufferedAsync.cpp:21: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -500,6 +529,13 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ +In file included from SNAPLib/Genome.h:26, + from SNAPLib/AlignmentResult.h:29, + from SNAPLib/BaseAligner.h:30, + from SNAPLib/BaseAligner.cpp:29: +SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined + 87 | # define _MM_HINT_T0 1 + | ^~~~~~~~~~~ In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81: /usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition @@ -517,7 +553,8 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -In file included from SNAPLib/BufferedAsync.cpp:21: +In file included from SNAPLib/AlignerStats.h:29, + from SNAPLib/AlignerStats.cpp:27: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -538,12 +575,8 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -In file included from SNAPLib/AlignerContext.cpp:27: -SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined - 87 | # define _MM_HINT_T0 1 - | ^~~~~~~~~~~ -In file included from SNAPLib/AlignerStats.h:29, - from SNAPLib/AlignerStats.cpp:27: +In file included from SNAPLib/SAM.h:22, + from SNAPLib/Bam.cpp:20: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -552,11 +585,6 @@ /usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition 3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 | ^~~~~~~~~~~ -In file included from /usr/include/simde/x86/sse2.h:35, - from SNAPLib/Compat.h:81: -/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition - 3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 - | ^~~~~~~~~~~ SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | ^~~~~~~~~~~ @@ -569,6 +597,15 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ +In file included from SNAPLib/AlignerContext.cpp:27: +SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined + 87 | # define _MM_HINT_T0 1 + | ^~~~~~~~~~~ +In file included from /usr/include/simde/x86/sse2.h:35, + from SNAPLib/Compat.h:81: +/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition + 3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 + | ^~~~~~~~~~~ SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined 88 | # define _MM_HINT_T1 2 | ^~~~~~~~~~~ @@ -583,8 +620,7 @@ | ^~~~~~~~~~~ In file included from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, - from SNAPLib/BaseAligner.h:30, - from SNAPLib/BaseAligner.cpp:29: + from SNAPLib/AlignmentResult.cpp:23: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -608,7 +644,11 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ChimericPairedEndAligner.o SNAPLib/ChimericPairedEndAligner.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/CommandProcessor.o SNAPLib/CommandProcessor.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Compat.o SNAPLib/Compat.cpp -In file included from SNAPLib/Compat.cpp:26: +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/DataReader.o SNAPLib/DataReader.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/DataWriter.o SNAPLib/DataWriter.cpp +In file included from SNAPLib/Genome.h:26, + from SNAPLib/FASTA.h:27, + from SNAPLib/CommandProcessor.cpp:27: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -629,9 +669,6 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/DataReader.o SNAPLib/DataReader.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/DataWriter.o SNAPLib/DataWriter.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Error.o SNAPLib/Error.cpp In file included from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/PairedEndAligner.h:25, @@ -657,9 +694,8 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -In file included from SNAPLib/Genome.h:26, - from SNAPLib/FASTA.h:27, - from SNAPLib/CommandProcessor.cpp:27: +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Error.o SNAPLib/Error.cpp +In file included from SNAPLib/Compat.cpp:26: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -680,7 +716,7 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -In file included from SNAPLib/DataWriter.cpp:21: +In file included from SNAPLib/DataReader.cpp:22: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -701,7 +737,7 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -In file included from SNAPLib/DataReader.cpp:22: +In file included from SNAPLib/DataWriter.cpp:21: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -766,7 +802,6 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile.o SNAPLib/GenericFile.cpp In file included from SNAPLib/FASTQ.h:30, from SNAPLib/FASTQ.cpp:29: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined @@ -789,6 +824,7 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile.o SNAPLib/GenericFile.cpp In file included from SNAPLib/GenericFile.cpp:27: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 @@ -857,6 +893,13 @@ | | | | long long int _int64 {aka long int} | %ld +SNAPLib/Error.cpp: In function 'void WriteProgressCounter(const char*, _int64)': +SNAPLib/Error.cpp:96:49: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '_int64' {aka 'long int'} [-Wformat=] + 96 | fprintf(stderr,"reporter:counter:SNAP,%s,%lld\n", counterName, increment); + | ~~~^ ~~~~~~~~~ + | | | + | long long int _int64 {aka long int} + | %ld g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_HDFS.cpp In file included from SNAPLib/GenericFile.h:25, from SNAPLib/GenericFile_Blob.h:26, @@ -881,13 +924,6 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -SNAPLib/Error.cpp: In function 'void WriteProgressCounter(const char*, _int64)': -SNAPLib/Error.cpp:96:49: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '_int64' {aka 'long int'} [-Wformat=] - 96 | fprintf(stderr,"reporter:counter:SNAP,%s,%lld\n", counterName, increment); - | ~~~^ ~~~~~~~~~ - | | | - | long long int _int64 {aka long int} - | %ld g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_map.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_stdio.o SNAPLib/GenericFile_stdio.cpp In file included from SNAPLib/GenericFile.h:25, @@ -914,7 +950,6 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Genome.o SNAPLib/Genome.cpp In file included from SNAPLib/GenericFile_stdio.cpp:25: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 @@ -936,7 +971,9 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Genome.o SNAPLib/Genome.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenomeIndex.o SNAPLib/GenomeIndex.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GzipDataWriter.o SNAPLib/GzipDataWriter.cpp In file included from SNAPLib/Genome.h:26, from SNAPLib/Genome.cpp:26: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined @@ -959,7 +996,6 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GzipDataWriter.o SNAPLib/GzipDataWriter.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/HashTable.o SNAPLib/HashTable.cpp In file included from SNAPLib/ApproximateCounter.h:3, from SNAPLib/GenomeIndex.cpp:26: @@ -1028,6 +1064,7 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/HitDepth.o SNAPLib/HitDepth.cpp In file included from SNAPLib/Histogram.cpp:27: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 @@ -1049,7 +1086,29 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/HitDepth.o SNAPLib/HitDepth.cpp +In file included from SNAPLib/HitDepth.cpp:25: +SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined + 87 | # define _MM_HINT_T0 1 + | ^~~~~~~~~~~ +In file included from /usr/include/simde/x86/sse2.h:35, + from SNAPLib/Compat.h:81: +/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition + 3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 + | ^~~~~~~~~~~ +SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined + 88 | # define _MM_HINT_T1 2 + | ^~~~~~~~~~~ +/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition + 3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 + | ^~~~~~~~~~~ +SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined + 89 | # define _MM_HINT_T2 3 + | ^~~~~~~~~~~ +/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition + 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 + | ^~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/IntersectingPairedEndAligner.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/LandauVishkin.o SNAPLib/LandauVishkin.cpp SNAPLib/Genome.cpp: In member function 'bool Genome::saveToFile(const char*) const': SNAPLib/Genome.cpp:216:26: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'long int' [-Wformat=] 216 | fprintf(saveFile,"%lld %d %d\n",nBases, nContigs, GENOME_FLAG_ALT_CONTIGS_MARKED); @@ -1070,6 +1129,14 @@ | | | | long long int _int64 {aka long int} | %ld +In file included from SNAPLib/Genome.h:26, + from SNAPLib/AlignmentResult.h:29, + from SNAPLib/PairedEndAligner.h:25, + from SNAPLib/IntersectingPairedEndAligner.h:25, + from SNAPLib/IntersectingPairedEndAligner.cpp:24: +SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined + 87 | # define _MM_HINT_T0 1 + | ^~~~~~~~~~~ SNAPLib/Genome.cpp: In static member function 'static const Genome* Genome::loadFromFile(const char*, unsigned int, GenomeLocation, GenomeDistance, bool)': SNAPLib/Genome.cpp:356:47: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type '_int64*' {aka 'long int*'} [-Wformat=] 356 | if (7 != sscanf(contigNameBuffer, "%lld %x %d %lld %x %d %d", &contigStart, &flags, &originalContigNumber, &projContigStart, &altProjRC, &contigNameSize, &cigarLength)) { @@ -1083,45 +1150,6 @@ | | | | long long int* _int64* {aka long int*} | %ld -SNAPLib/Genome.cpp: In static member function 'static bool Genome::openFileAndGetSizes(const char*, GenericFile**, GenomeDistance*, unsigned int*, bool)': -SNAPLib/Genome.cpp:497:51: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type 'GenomeDistance*' {aka 'long int*'} [-Wformat=] - 497 | if (NULL == retval || 3 != sscanf(linebuf,"%lld %d %d\n", nBases, nContigs, &flags)) { - | ~~~^ ~~~~~~ - | | | - | | GenomeDistance* {aka long int*} - | long long int* - | %ld -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/IntersectingPairedEndAligner.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/LandauVishkin.o SNAPLib/LandauVishkin.cpp -In file included from SNAPLib/HitDepth.cpp:25: -SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined - 87 | # define _MM_HINT_T0 1 - | ^~~~~~~~~~~ -In file included from /usr/include/simde/x86/sse2.h:35, - from SNAPLib/Compat.h:81: -/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition - 3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 - | ^~~~~~~~~~~ -SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined - 88 | # define _MM_HINT_T1 2 - | ^~~~~~~~~~~ -/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition - 3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 - | ^~~~~~~~~~~ -SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined - 89 | # define _MM_HINT_T2 3 - | ^~~~~~~~~~~ -/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition - 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 - | ^~~~~~~~~~~ -In file included from SNAPLib/Genome.h:26, - from SNAPLib/AlignmentResult.h:29, - from SNAPLib/PairedEndAligner.h:25, - from SNAPLib/IntersectingPairedEndAligner.h:25, - from SNAPLib/IntersectingPairedEndAligner.cpp:24: -SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined - 87 | # define _MM_HINT_T0 1 - | ^~~~~~~~~~~ In file included from /usr/include/simde/x86/sse2.h:35, from SNAPLib/Compat.h:81: /usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition @@ -1139,7 +1167,14 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/MultiInputReadSupplier.o SNAPLib/MultiInputReadSupplier.cpp +SNAPLib/Genome.cpp: In static member function 'static bool Genome::openFileAndGetSizes(const char*, GenericFile**, GenomeDistance*, unsigned int*, bool)': +SNAPLib/Genome.cpp:497:51: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type 'GenomeDistance*' {aka 'long int*'} [-Wformat=] + 497 | if (NULL == retval || 3 != sscanf(linebuf,"%lld %d %d\n", nBases, nContigs, &flags)) { + | ~~~^ ~~~~~~ + | | | + | | GenomeDistance* {aka long int*} + | long long int* + | %ld In file included from SNAPLib/LandauVishkin.cpp:2: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 @@ -1161,7 +1196,6 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedAligner.o SNAPLib/PairedAligner.cpp SNAPLib/GenomeIndex.cpp: In static member function 'static bool GenomeIndex::BuildIndexToDirectory(const Genome*, int, double, const char*, unsigned int, unsigned int, bool, unsigned int, bool, const char*, unsigned int, bool)': SNAPLib/GenomeIndex.cpp:952:36: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 952 | fprintf(histogramFile, "%lld larger than %d with %lld total genome locations, largest seed %lld\n", countOfTooBigForHistogram, maxHistogramEntry, sumOfTooBigForHistogram, largestSeed); @@ -1218,6 +1252,9 @@ | ~~~~~~~~~~~~~~~~~~~ | | | size_t* {aka long unsigned int*} +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/MultiInputReadSupplier.o SNAPLib/MultiInputReadSupplier.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedAligner.o SNAPLib/PairedAligner.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedReadMatcher.o SNAPLib/PairedReadMatcher.cpp In file included from SNAPLib/Read.h:28, from SNAPLib/MultiInputReadSupplier.cpp:25: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined @@ -1240,6 +1277,7 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ParallelTask.o SNAPLib/ParallelTask.cpp In file included from SNAPLib/PairedAligner.cpp:34: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 @@ -1261,8 +1299,6 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedReadMatcher.o SNAPLib/PairedReadMatcher.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ParallelTask.o SNAPLib/ParallelTask.cpp In file included from SNAPLib/PairedReadMatcher.cpp:26: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 @@ -1313,9 +1349,9 @@ 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ProbabilityDistance.o SNAPLib/ProbabilityDistance.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/RangeSplitter.o SNAPLib/RangeSplitter.cpp -In file included from SNAPLib/RangeSplitter.h:29, - from SNAPLib/RangeSplitter.cpp:28: +In file included from SNAPLib/Read.h:28, + from SNAPLib/ProbabilityDistance.h:3, + from SNAPLib/ProbabilityDistance.cpp:2: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1336,9 +1372,10 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -In file included from SNAPLib/Read.h:28, - from SNAPLib/ProbabilityDistance.h:3, - from SNAPLib/ProbabilityDistance.cpp:2: +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/RangeSplitter.o SNAPLib/RangeSplitter.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Read.o SNAPLib/Read.cpp +In file included from SNAPLib/RangeSplitter.h:29, + from SNAPLib/RangeSplitter.cpp:28: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1373,8 +1410,6 @@ | | | | long long unsigned int long unsigned int | %lu -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Read.o SNAPLib/Read.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadReader.o SNAPLib/ReadReader.cpp In file included from SNAPLib/Read.h:28, from SNAPLib/Read.cpp:25: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined @@ -1397,9 +1432,9 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadReader.o SNAPLib/ReadReader.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadSupplierQueue.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadWriter.o SNAPLib/ReadWriter.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SAM.o SNAPLib/SAM.cpp In file included from SNAPLib/ReadReader.cpp:19: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 @@ -1421,8 +1456,8 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Seed.o SNAPLib/Seed.cpp -In file included from SNAPLib/ReadWriter.cpp:21: +In file included from SNAPLib/Read.h:28, + from SNAPLib/ReadSupplierQueue.cpp:25: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1443,8 +1478,7 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -In file included from SNAPLib/Read.h:28, - from SNAPLib/ReadSupplierQueue.cpp:25: +In file included from SNAPLib/ReadWriter.cpp:21: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1465,8 +1499,10 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SeedSequencer.o SNAPLib/SeedSequencer.cpp -In file included from SNAPLib/SAM.cpp:21: +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SAM.o SNAPLib/SAM.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Seed.o SNAPLib/Seed.cpp +In file included from SNAPLib/Seed.h:27, + from SNAPLib/Seed.cpp:26: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1487,8 +1523,7 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -In file included from SNAPLib/Seed.h:27, - from SNAPLib/Seed.cpp:26: +In file included from SNAPLib/SAM.cpp:21: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1509,6 +1544,9 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SeedSequencer.o SNAPLib/SeedSequencer.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SingleAligner.o SNAPLib/SingleAligner.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SortedDataWriter.o SNAPLib/SortedDataWriter.cpp In file included from SNAPLib/Seed.h:27, from SNAPLib/SeedSequencer.h:27, from SNAPLib/SeedSequencer.cpp:25: @@ -1532,7 +1570,6 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SingleAligner.o SNAPLib/SingleAligner.cpp In file included from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/BaseAligner.h:30, @@ -1557,8 +1594,57 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SortedDataWriter.o SNAPLib/SortedDataWriter.cpp +SNAPLib/ReadReader.cpp: In member function 'virtual bool SimpleReadReader::getNextRead(Read*, AlignmentResult*, unsigned int*, bool*, unsigned int*, unsigned int*, const char**)': +SNAPLib/ReadReader.cpp:44:5: warning: no return statement in function returning non-void [-Wreturn-type] + 44 | } + | ^ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Tables.o SNAPLib/Tables.cpp +In file included from SNAPLib/SortedDataWriter.cpp:21: +SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined + 87 | # define _MM_HINT_T0 1 + | ^~~~~~~~~~~ +In file included from /usr/include/simde/x86/sse2.h:35, + from SNAPLib/Compat.h:81: +/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition + 3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 + | ^~~~~~~~~~~ +SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined + 88 | # define _MM_HINT_T1 2 + | ^~~~~~~~~~~ +/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition + 3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 + | ^~~~~~~~~~~ +SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined + 89 | # define _MM_HINT_T2 3 + | ^~~~~~~~~~~ +/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition + 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 + | ^~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Util.o SNAPLib/Util.cpp +In file included from SNAPLib/Util.h:5, + from SNAPLib/Util.cpp:26: +SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined + 87 | # define _MM_HINT_T0 1 + | ^~~~~~~~~~~ +In file included from /usr/include/simde/x86/sse2.h:35, + from SNAPLib/Compat.h:81: +/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition + 3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 + | ^~~~~~~~~~~ +SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined + 88 | # define _MM_HINT_T1 2 + | ^~~~~~~~~~~ +/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition + 3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 + | ^~~~~~~~~~~ +SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined + 89 | # define _MM_HINT_T2 3 + | ^~~~~~~~~~~ +/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition + 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 + | ^~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/exit.o SNAPLib/exit.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/mapq.o SNAPLib/mapq.cpp SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeHeader(const ReaderContext&, char*, size_t, size_t*, bool, int, const char**, const char*, const char*, bool) const': SNAPLib/SAM.cpp:1292:116: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'long int' [-Wformat=] 1292 | bytesConsumed += snprintf(header + bytesConsumed, headerBufferSize - bytesConsumed, "@SQ\tSN:%s\tLN:%llu%s\n", contig->name, contig->length - context.genome->getChromosomePadding(), contig->isALT ? "\tAH:*":""); @@ -1601,10 +1687,6 @@ | ~~~~~~~~~~~~~~~~ | | | GenomeDistance {aka long int} -In file included from SNAPLib/SortedDataWriter.cpp:21: -SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined - 87 | # define _MM_HINT_T0 1 - | ^~~~~~~~~~~ SNAPLib/SAM.cpp:2076:91: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2076 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n", | ~~~^ @@ -1627,23 +1709,6 @@ | ~~~~~~~~~~~~~~ | | | _int64 {aka long int} -In file included from /usr/include/simde/x86/sse2.h:35, - from SNAPLib/Compat.h:81: -/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition - 3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 - | ^~~~~~~~~~~ -SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined - 88 | # define _MM_HINT_T1 2 - | ^~~~~~~~~~~ -/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition - 3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 - | ^~~~~~~~~~~ -SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined - 89 | # define _MM_HINT_T2 3 - | ^~~~~~~~~~~ -/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition - 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 - | ^~~~~~~~~~~ SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeRead(const ReaderContext&, AffineGapVectorizedWithCigar*, char*, size_t, size_t*, size_t, Read*, AlignmentResult, int, GenomeLocation, Direction, bool, bool, int*, int, int, bool, char*, bool, _int64, int, int, bool, bool, Read*, AlignmentResult, GenomeLocation, Direction, bool, int, int) const': SNAPLib/SAM.cpp:2312:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2312 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n", @@ -1716,13 +1781,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | GenomeLocation {aka long int} -SNAPLib/ReadReader.cpp: In member function 'virtual bool SimpleReadReader::getNextRead(Read*, AlignmentResult*, unsigned int*, bool*, unsigned int*, unsigned int*, const char**)': -SNAPLib/ReadReader.cpp:44:5: warning: no return statement in function returning non-void [-Wreturn-type] - 44 | } - | ^ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Util.o SNAPLib/Util.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/exit.o SNAPLib/exit.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/mapq.o SNAPLib/mapq.cpp In file included from SNAPLib/Error.h:25, from SNAPLib/exit.cpp:26: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined @@ -1746,28 +1804,7 @@ 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/stdafx.o SNAPLib/stdafx.cpp -In file included from SNAPLib/Util.h:5, - from SNAPLib/Util.cpp:26: -SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined - 87 | # define _MM_HINT_T0 1 - | ^~~~~~~~~~~ -In file included from /usr/include/simde/x86/sse2.h:35, - from SNAPLib/Compat.h:81: -/usr/include/simde/x86/sse.h:3486:11: note: this is the location of the previous definition - 3486 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 - | ^~~~~~~~~~~ -SNAPLib/Compat.h:88:11: warning: "_MM_HINT_T1" redefined - 88 | # define _MM_HINT_T1 2 - | ^~~~~~~~~~~ -/usr/include/simde/x86/sse.h:3488:11: note: this is the location of the previous definition - 3488 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 - | ^~~~~~~~~~~ -SNAPLib/Compat.h:89:11: warning: "_MM_HINT_T2" redefined - 89 | # define _MM_HINT_T2 3 - | ^~~~~~~~~~~ -/usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition - 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 - | ^~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/Main.o apps/snap/Main.cpp In file included from SNAPLib/mapq.cpp:25: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 @@ -1796,15 +1833,9 @@ | | | | long long unsigned int long unsigned int | %lu -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/Main.o apps/snap/Main.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/stdafx.o apps/snap/stdafx.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapTest.o tests/AffineGapTest.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapVectorizedTest.o tests/AffineGapVectorizedTest.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/EventTest.o tests/EventTest.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/LandauVishkinTest.o tests/LandauVishkinTest.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/ProbabilityDistanceTest.o tests/ProbabilityDistanceTest.cpp -In file included from SNAPLib/LandauVishkin.h:2, - from tests/EventTest.cpp:3: +In file included from SNAPLib/CommandProcessor.h:24, + from apps/snap/Main.cpp:26: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1825,8 +1856,26 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -In file included from SNAPLib/CommandProcessor.h:24, - from apps/snap/Main.cpp:26: +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapTest.o tests/AffineGapTest.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapVectorizedTest.o tests/AffineGapVectorizedTest.cpp +SNAPLib/Util.cpp: In function 'char* FormatUIntWithCommas(_uint64, char*, size_t, size_t)': +SNAPLib/Util.cpp:167:49: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] + 167 | sprintf(tempBuf, ",%03lld", x % 1000); + | ~~~~~^ ~~~~~~~~ + | | | + | | _uint64 {aka long unsigned int} + | long long int + | %03ld +SNAPLib/Util.cpp:170:46: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] + 170 | sprintf(tempBuf, "%lld", x); + | ~~~^ ~ + | | | + | | _uint64 {aka long unsigned int} + | long long int + | %ld +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/EventTest.o tests/EventTest.cpp +In file included from SNAPLib/AffineGap.h:3, + from tests/AffineGapTest.cpp:3: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1847,6 +1896,7 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/LandauVishkinTest.o tests/LandauVishkinTest.cpp In file included from SNAPLib/AffineGapVectorized.h:7, from tests/AffineGapVectorizedTest.cpp:3: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined @@ -1869,8 +1919,8 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -In file included from SNAPLib/AffineGap.h:3, - from tests/AffineGapTest.cpp:3: +In file included from SNAPLib/LandauVishkin.h:2, + from tests/EventTest.cpp:3: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1891,6 +1941,10 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/ProbabilityDistanceTest.o tests/ProbabilityDistanceTest.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/TestLib.o tests/TestLib.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/main.o tests/main.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/SNAPCommand.cpp In file included from SNAPLib/LandauVishkin.h:2, from tests/LandauVishkinTest.cpp:3: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined @@ -1913,22 +1967,6 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -SNAPLib/Util.cpp: In function 'char* FormatUIntWithCommas(_uint64, char*, size_t, size_t)': -SNAPLib/Util.cpp:167:49: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] - 167 | sprintf(tempBuf, ",%03lld", x % 1000); - | ~~~~~^ ~~~~~~~~ - | | | - | | _uint64 {aka long unsigned int} - | long long int - | %03ld -SNAPLib/Util.cpp:170:46: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] - 170 | sprintf(tempBuf, "%lld", x); - | ~~~^ ~ - | | | - | | _uint64 {aka long unsigned int} - | long long int - | %ld -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/TestLib.o tests/TestLib.cpp In file included from tests/ProbabilityDistanceTest.cpp:2: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 @@ -1950,9 +1988,6 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/main.o tests/main.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/SNAPCommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/stdafx.o apps/SNAPCommand/stdafx.cpp In file included from apps/SNAPCommand/SNAPCommand.cpp:26: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 @@ -1974,6 +2009,7 @@ /usr/include/simde/x86/sse.h:3490:11: note: this is the location of the previous definition 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/stdafx.o apps/SNAPCommand/stdafx.cpp SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': SNAPLib/SAM.cpp:2650:55: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=] 2650 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); @@ -2129,12 +2165,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/269166/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/269166/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/3888513 and its subdirectories -I: Current time: Wed Mar 18 20:27:17 -12 2026 -I: pbuilder-time-stamp: 1773908837 +I: removing directory /srv/workspace/pbuilder/269166 and its subdirectories +I: Current time: Fri Feb 14 16:06:11 +14 2025 +I: pbuilder-time-stamp: 1739498771