Diff of the two buildlogs: -- --- b1/build.log 2025-11-07 17:08:32.763895503 +0000 +++ b2/build.log 2025-11-07 17:09:19.511949821 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Nov 7 05:06:50 -12 2025 -I: pbuilder-time-stamp: 1762535210 +I: Current time: Fri Dec 11 13:31:35 +14 2026 +I: pbuilder-time-stamp: 1796945495 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -27,53 +27,85 @@ dpkg-source: info: applying spelling I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1625899/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/549312/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Dec 10 23:31 /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/549312/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/549312/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + 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]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.3.3(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 nocheck' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='9493b7c7229947429b4b86a0e434da48' - 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='1625899' - PS1='# ' - PS2='> ' + INVOCATION_ID=c369b612b58c48a1b6d1cc7ea430d353 + 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=549312 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.p86oiYAR/pbuilderrc_H6ag --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.p86oiYAR/b1 --logfile b1/build.log snap-aligner_2.0.5+dfsg-1.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' - 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.p86oiYAR/pbuilderrc_VGrz --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.p86oiYAR/b2 --logfile b2/build.log snap-aligner_2.0.5+dfsg-1.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1625899/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/549312/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -151,7 +183,7 @@ Get: 32 http://deb.debian.org/debian unstable/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libsimde-dev all 0.8.2-3 [467 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] -Fetched 12.6 MB in 0s (213 MB/s) +Fetched 12.6 MB in 0s (89.6 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 ... 19968 files and directories currently installed.) @@ -302,7 +334,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/snap-aligner-2.0.5+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_2.0.5+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/549312/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/549312/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/snap-aligner-2.0.5+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_2.0.5+dfsg-1_source.changes dpkg-buildpackage: info: source package snap-aligner dpkg-buildpackage: info: source version 2.0.5+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -344,17 +380,7 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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-2.0.5+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-2.0.5+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/AlignerContext.cpp:27: -SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined - 87 | # define _MM_HINT_T0 1 - | ^~~~~~~~~~~ -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/BufferedAsync.cpp:21: +In file included from SNAPLib/AffineGapVectorized.cpp:2: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -375,11 +401,32 @@ /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 + | ^~~~~~~~~~~ +/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/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 @@ -388,28 +435,16 @@ SNAPLib/Compat.h:88:11: warning: '_MM_HINT_T1' redefined 88 | # define _MM_HINT_T1 2 | ^~~~~~~~~~~ -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 - | ^~~~~~~~~~~ /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 | ^~~~~~~~~~~ -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 | ^~~~~~~~~~~ -/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/AffineGap.cpp:2: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -427,14 +462,15 @@ 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/ApproximateCounter.h:3, - from SNAPLib/ApproximateCounter.cpp:3: +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 | ^~~~~~~~~~~ +/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 @@ -452,9 +488,8 @@ /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/AlignerOptions.h:29, - from SNAPLib/AlignerOptions.cpp:27: +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 | ^~~~~~~~~~~ @@ -499,7 +534,7 @@ /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/AffineGap.cpp:2: +In file included from SNAPLib/BufferedAsync.cpp:21: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -520,7 +555,8 @@ /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/AffineGapVectorized.cpp:2: +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 | ^~~~~~~~~~~ @@ -565,8 +601,9 @@ /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/AlignerStats.h:29, - from SNAPLib/AlignerStats.cpp:27: +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 | ^~~~~~~~~~~ @@ -587,8 +624,7 @@ /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/SAM.h:22, - from SNAPLib/Bam.cpp:20: +In file included from SNAPLib/BigAlloc.cpp:24: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -612,8 +648,6 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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-2.0.5+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-2.0.5+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 -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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-2.0.5+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/AlignmentResult.h:29, from SNAPLib/PairedEndAligner.h:25, @@ -639,6 +673,8 @@ /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-2.0.5+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-2.0.5+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/Compat.cpp:26: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 @@ -660,6 +696,9 @@ /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-2.0.5+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 +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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/FASTA.o SNAPLib/FASTA.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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/FASTQ.o SNAPLib/FASTQ.cpp In file included from SNAPLib/Genome.h:26, from SNAPLib/FASTA.h:27, from SNAPLib/CommandProcessor.cpp:27: @@ -704,7 +743,7 @@ /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/Error.cpp:25: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -725,10 +764,7 @@ /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-2.0.5+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 -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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/FASTA.o SNAPLib/FASTA.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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/FASTQ.o SNAPLib/FASTQ.cpp -In file included from SNAPLib/Error.cpp:25: +In file included from SNAPLib/DataWriter.cpp:21: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -749,6 +785,7 @@ /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-2.0.5+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/FASTA.cpp:26: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 @@ -770,7 +807,6 @@ /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-2.0.5+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 @@ -793,6 +829,27 @@ /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/GenericFile.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 + | ^~~~~~~~~~~ +/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/DataReader.cpp: In static member function 'static bool DecompressDataReader::decompress(z_stream*, ThreadHeap*, char*, _int64, _int64*, char*, _int64, _int64*, DecompressMode)': SNAPLib/DataReader.cpp:2052:53: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] 2052 | fprintf(stderr, "\n0x%llx\t", offset); @@ -839,7 +896,12 @@ | | | | long long int _int64 {aka long int} | %ld -In file included from SNAPLib/GenericFile.cpp:27: +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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_Blob.o SNAPLib/GenericFile_Blob.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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 +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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 +In file included from SNAPLib/GenericFile.h:25, + from SNAPLib/GenericFile_Blob.h:26, + from SNAPLib/GenericFile_Blob.cpp:25: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -860,8 +922,7 @@ /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-2.0.5+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_Blob.o SNAPLib/GenericFile_Blob.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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 +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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 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); @@ -869,10 +930,10 @@ | | | | long long int _int64 {aka long int} | %ld -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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 In file included from SNAPLib/GenericFile.h:25, from SNAPLib/GenericFile_Blob.h:26, - from SNAPLib/GenericFile_Blob.cpp:25: + from SNAPLib/GenericFile_map.h:26, + from SNAPLib/GenericFile_map.cpp:25: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -893,12 +954,8 @@ /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-2.0.5+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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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.h:25, - from SNAPLib/GenericFile_Blob.h:26, - from SNAPLib/GenericFile_map.h:26, - from SNAPLib/GenericFile_map.cpp:25: +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 | ^~~~~~~~~~~ @@ -921,7 +978,8 @@ | ^~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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-2.0.5+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/GenericFile_stdio.cpp:25: +In file included from SNAPLib/ApproximateCounter.h:3, + from SNAPLib/GenomeIndex.cpp:26: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -942,6 +1000,8 @@ /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-2.0.5+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 +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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/Histogram.o SNAPLib/Histogram.cpp In file included from SNAPLib/Genome.h:26, from SNAPLib/Genome.cpp:26: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined @@ -964,8 +1024,8 @@ /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/ApproximateCounter.h:3, - from SNAPLib/GenomeIndex.cpp:26: +In file included from SNAPLib/GzipDataWriter.h:25, + from SNAPLib/GzipDataWriter.cpp:20: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -986,8 +1046,9 @@ /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/GzipDataWriter.h:25, - from SNAPLib/GzipDataWriter.cpp:20: +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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/HashTable.h:23, + from SNAPLib/HashTable.cpp:20: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1008,10 +1069,8 @@ /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-2.0.5+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 -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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/Histogram.o SNAPLib/Histogram.cpp -In file included from SNAPLib/HashTable.h:23, - from SNAPLib/HashTable.cpp:20: +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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 +In file included from SNAPLib/HitDepth.cpp:25: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1036,6 +1095,28 @@ SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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 /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/LandauVishkin.cpp:2: +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 @@ -1053,48 +1134,6 @@ /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-2.0.5+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 -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); - | ~~~^ ~~~~~~ - | | | - | | long int - | long long int - | %ld -SNAPLib/Genome.cpp:226:31: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] - 226 | fprintf(saveFile, "%lld %x %d %lld %x %d %d %s %s\n", GenomeLocationAsInt64(contigs[i].beginningLocation), (contigs[i].isALT ? GENOME_FLAG_CONTIG_IS_ALT : 0), OriginalContigNumToInt(contigs[i].originalContigNumber), GenomeLocationAsInt64(contigs[i].projBeginningLocation), - | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | long long int _int64 {aka long int} - | %ld -SNAPLib/Genome.cpp:226:42: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '_int64' {aka 'long int'} [-Wformat=] - 226 | fprintf(saveFile, "%lld %x %d %lld %x %d %d %s %s\n", GenomeLocationAsInt64(contigs[i].beginningLocation), (contigs[i].isALT ? GENOME_FLAG_CONTIG_IS_ALT : 0), OriginalContigNumToInt(contigs[i].originalContigNumber), GenomeLocationAsInt64(contigs[i].projBeginningLocation), - | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | long long int _int64 {aka long int} - | %ld -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)) { - | ~~~^ ~~~~~~~~~~~~ - | | | - | long long int* _int64* {aka long int*} - | %ld -SNAPLib/Genome.cpp:356:58: warning: format '%lld' expects argument of type 'long long int*', but argument 6 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)) { - | ~~~^ ~~~~~~~~~~~~~~~~ - | | | - | 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 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); @@ -1151,7 +1190,11 @@ | ~~~~~~~~~~~~~~~~~~~ | | | size_t* {aka long unsigned int*} -In file included from SNAPLib/HitDepth.cpp:25: +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 | ^~~~~~~~~~~ @@ -1172,15 +1215,57 @@ /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-2.0.5+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-2.0.5+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); + | ~~~^ ~~~~~~ + | | | + | | long int + | long long int + | %ld +SNAPLib/Genome.cpp:226:31: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] + 226 | fprintf(saveFile, "%lld %x %d %lld %x %d %d %s %s\n", GenomeLocationAsInt64(contigs[i].beginningLocation), (contigs[i].isALT ? GENOME_FLAG_CONTIG_IS_ALT : 0), OriginalContigNumToInt(contigs[i].originalContigNumber), GenomeLocationAsInt64(contigs[i].projBeginningLocation), + | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | long long int _int64 {aka long int} + | %ld +SNAPLib/Genome.cpp:226:42: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '_int64' {aka 'long int'} [-Wformat=] + 226 | fprintf(saveFile, "%lld %x %d %lld %x %d %d %s %s\n", GenomeLocationAsInt64(contigs[i].beginningLocation), (contigs[i].isALT ? GENOME_FLAG_CONTIG_IS_ALT : 0), OriginalContigNumToInt(contigs[i].originalContigNumber), GenomeLocationAsInt64(contigs[i].projBeginningLocation), + | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | long long int _int64 {aka long int} + | %ld +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)) { + | ~~~^ ~~~~~~~~~~~~ + | | | + | long long int* _int64* {aka long int*} + | %ld +SNAPLib/Genome.cpp:356:58: warning: format '%lld' expects argument of type 'long long int*', but argument 6 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)) { + | ~~~^ ~~~~~~~~~~~~~~~~ + | | | + | 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-2.0.5+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-2.0.5+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 -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/IntersectingPairedEndAligner.h:767:71: warning: non-static data member initializers only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions] + 767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; + | ^ +SNAPLib/IntersectingPairedEndAligner.h:767:104: warning: extended initializer lists only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions] + 767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; + | ^ +In file included from SNAPLib/Read.h:28, + from SNAPLib/MultiInputReadSupplier.cpp:25: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1201,7 +1286,7 @@ /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/LandauVishkin.cpp:2: +In file included from SNAPLib/PairedAligner.cpp:34: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1223,8 +1308,9 @@ 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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: +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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 +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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 +In file included from SNAPLib/PairedReadMatcher.cpp:26: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1245,7 +1331,8 @@ /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/PairedAligner.cpp:34: +In file included from SNAPLib/ParallelTask.h:25, + from SNAPLib/ParallelTask.cpp:18: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1266,8 +1353,9 @@ /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-2.0.5+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: +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 | ^~~~~~~~~~~ @@ -1288,39 +1376,24 @@ /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-2.0.5+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-2.0.5+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-2.0.5+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-2.0.5+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/PairedAligner.cpp:47: SNAPLib/IntersectingPairedEndAligner.h:767:71: warning: non-static data member initializers only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions] 767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; | ^ SNAPLib/IntersectingPairedEndAligner.h:767:104: warning: extended initializer lists only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions] 767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; | ^ -In file included from SNAPLib/ParallelTask.h:25, - from SNAPLib/ParallelTask.cpp:18: -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/Read.h:28, - from SNAPLib/ProbabilityDistance.h:3, - from SNAPLib/ProbabilityDistance.cpp:2: +SNAPLib/PairedAligner.cpp: In member function 'void PairedAlignerContext::runIterationThreadImpl(Read**)': +SNAPLib/PairedAligner.cpp:673:72: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 673 | fprintf(stderr, "reporter:counter:SNAP,readsAligned,%llu\n", stats->totalReads - readsWhenLastReported); + | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +In file included from SNAPLib/ReadReader.cpp:19: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1363,22 +1436,6 @@ /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 | ^~~~~~~~~~~ -In file included from SNAPLib/PairedAligner.cpp:47: -SNAPLib/IntersectingPairedEndAligner.h:767:71: warning: non-static data member initializers only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions] - 767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; - | ^ -SNAPLib/IntersectingPairedEndAligner.h:767:104: warning: extended initializer lists only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions] - 767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; - | ^ -SNAPLib/PairedAligner.cpp: In member function 'void PairedAlignerContext::runIterationThreadImpl(Read**)': -SNAPLib/PairedAligner.cpp:673:72: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 673 | fprintf(stderr, "reporter:counter:SNAP,readsAligned,%llu\n", stats->totalReads - readsWhenLastReported); - | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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-2.0.5+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 @@ -1403,7 +1460,15 @@ | ^~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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-2.0.5+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 -In file included from SNAPLib/ReadReader.cpp:19: +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-2.0.5+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-2.0.5+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 +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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/Read.h:28, + from SNAPLib/ReadSupplierQueue.cpp:25: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1424,10 +1489,7 @@ /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-2.0.5+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-2.0.5+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/Read.h:28, - from SNAPLib/ReadSupplierQueue.cpp:25: +In file included from SNAPLib/SAM.cpp:21: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1448,7 +1510,9 @@ /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.cpp:21: +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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/Seed.h:27, + from SNAPLib/Seed.cpp:26: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1469,8 +1533,7 @@ /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/ReadWriter.cpp:21: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1491,7 +1554,9 @@ /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/ReadWriter.cpp:21: +In file included from SNAPLib/Seed.h:27, + from SNAPLib/SeedSequencer.h:27, + from SNAPLib/SeedSequencer.cpp:25: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1512,12 +1577,8 @@ /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-2.0.5+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-2.0.5+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-2.0.5+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: +In file included from SNAPLib/SortedDataWriter.cpp:21: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1538,11 +1599,6 @@ /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/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-2.0.5+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/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/BaseAligner.h:30, @@ -1567,6 +1623,10 @@ /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-2.0.5+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 +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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-2.0.5+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-2.0.5+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:*":""); @@ -1703,7 +1763,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | GenomeLocation {aka long int} -In file included from SNAPLib/SortedDataWriter.cpp:21: +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 | ^~~~~~~~~~~ @@ -1724,10 +1785,8 @@ /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-2.0.5+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-2.0.5+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 -In file included from SNAPLib/Util.h:5, - from SNAPLib/Util.cpp:26: +In file included from SNAPLib/Error.h:25, + from SNAPLib/exit.cpp:26: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1748,8 +1807,7 @@ /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/Error.h:25, - from SNAPLib/exit.cpp:26: +In file included from SNAPLib/mapq.cpp:25: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1770,9 +1828,7 @@ /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-2.0.5+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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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 -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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 SNAPLib/SingleAligner.cpp: In member function 'virtual void SingleAlignerContext::runIterationThreadImpl(Read*&)': SNAPLib/SingleAligner.cpp:207:67: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 207 | fprintf(stderr,"reporter:counter:SNAP,readsAligned,%llu\n",stats->totalReads - readsWhenLastReported); @@ -1780,27 +1836,25 @@ | | | | long long unsigned int long unsigned int | %lu -In file included from SNAPLib/mapq.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 - | ^~~~~~~~~~~ +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-2.0.5+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-2.0.5+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-2.0.5+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-2.0.5+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 In file included from SNAPLib/CommandProcessor.h:24, from apps/snap/Main.cpp:26: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined @@ -1823,28 +1877,10 @@ /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-2.0.5+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-2.0.5+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-2.0.5+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-2.0.5+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 -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-2.0.5+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/AffineGap.h:3, - from tests/AffineGapTest.cpp:3: +In file included from SNAPLib/AffineGapVectorized.h:7, + from tests/AffineGapVectorizedTest.cpp:3: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1865,9 +1901,8 @@ /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-2.0.5+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/AffineGapVectorized.h:7, - from tests/AffineGapVectorizedTest.cpp:3: +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 | ^~~~~~~~~~~ @@ -1888,9 +1923,8 @@ /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-2.0.5+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 SNAPLib/LandauVishkin.h:2, - from tests/EventTest.cpp:3: + from tests/LandauVishkinTest.cpp:3: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1911,8 +1945,9 @@ /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-2.0.5+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/LandauVishkinTest.cpp:3: + from tests/EventTest.cpp:3: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1933,8 +1968,8 @@ /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-2.0.5+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-2.0.5+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-2.0.5+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 tests/ProbabilityDistanceTest.cpp:2: SNAPLib/Compat.h:87:11: warning: '_MM_HINT_T0' redefined 87 | # define _MM_HINT_T0 1 @@ -1956,6 +1991,7 @@ /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-2.0.5+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-2.0.5+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 @@ -2048,12 +2084,12 @@ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -o snap-aligner -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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 -Itests -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/HitDepth.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/snap/Main.o apps/snap/stdafx.o -lrt -lz -g++ -o unit_tests -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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 -Itests -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/HitDepth.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o tests/AffineGapTest.o tests/AffineGapVectorizedTest.o tests/EventTest.o tests/LandauVishkinTest.o tests/ProbabilityDistanceTest.o tests/TestLib.o tests/main.o -lrt -lz echo SNAPCOMMAND_OBJ is apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o SNAPCOMMAND_OBJ is apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o echo SNAP_OBJ is apps/snap/Main.o apps/snap/stdafx.o SNAP_OBJ is apps/snap/Main.o apps/snap/stdafx.o g++ -o SNAPCommand -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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 -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/HitDepth.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o -lrt -lz +g++ -o unit_tests -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.5+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 -Itests -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/HitDepth.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o tests/AffineGapTest.o tests/AffineGapVectorizedTest.o tests/EventTest.o tests/LandauVishkinTest.o tests/ProbabilityDistanceTest.o tests/TestLib.o tests/main.o -lrt -lz make[2]: Leaving directory '/build/reproducible-path/snap-aligner-2.0.5+dfsg' help2man --no-discard-stderr --no-info --version-string="2.0.5" \ --name "scalable nucleotide alignment program" \ @@ -2067,37 +2103,6 @@ --name "scalable nucleotide alignment program" \ --help-option=" " ./SNAPCommand > debian/SNAPCommand.1 make[1]: Leaving directory '/build/reproducible-path/snap-aligner-2.0.5+dfsg' - debian/rules override_dh_auto_test -make[1]: Entering directory '/build/reproducible-path/snap-aligner-2.0.5+dfsg' -dh_auto_test -./unit_tests -AffineGapTest: -- synthetic: [OK] - -AffineGapVectorizedTest: -- equal strings: [OK] -- one deletion: [OK] -- long deletion: [OK] -- long insertion: [OK] -- synthetic: [OK] - -EventTest: -- many waiters: [OK] -- single waiters: [OK] - -LandauVishkinTest: -- equal strings: [OK] -- prefixes: [OK] -- non-equal strings: [OK] -- overly distant strings: [OK] -- CIGAR strings: [OK] - -ProbabilityDistanceTest: -- basic probabilities: [OK] -- indels: [OK] - -15 / 15 tests passed. -make[1]: Leaving directory '/build/reproducible-path/snap-aligner-2.0.5+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/snap-aligner/ @@ -2133,12 +2138,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/549312/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/549312/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/1625899 and its subdirectories -I: Current time: Fri Nov 7 05:08:32 -12 2025 -I: pbuilder-time-stamp: 1762535312 +I: removing directory /srv/workspace/pbuilder/549312 and its subdirectories +I: Current time: Fri Dec 11 13:32:18 +14 2026 +I: pbuilder-time-stamp: 1796945538