Diff of the two buildlogs: -- --- b1/build.log 2025-09-09 13:29:27.491981446 +0000 +++ b2/build.log 2025-09-09 13:31:24.672126726 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Oct 12 07:50:33 -12 2026 -I: pbuilder-time-stamp: 1791834633 +I: Current time: Wed Sep 10 03:29:41 +14 2025 +I: pbuilder-time-stamp: 1757424581 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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/19138/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1789023/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 Sep 9 13:29 /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/1789023/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1789023/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]="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 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='16288fc3ff03400aa16812a4a7ff62bc' - 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='19138' - PS1='# ' - PS2='> ' + INVOCATION_ID=7663714e525d4229b11c8c09a7a9a2e3 + 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=1789023 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.FZ1rseUw/pbuilderrc_2jMz --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.FZ1rseUw/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.FZ1rseUw/pbuilderrc_FqfW --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.FZ1rseUw/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 codethink03-arm64 6.12.43+deb13-cloud-arm64 #1 SMP Debian 6.12.43-1 (2025-08-27) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-cloud-arm64 #1 SMP Debian 6.12.43-1 (2025-08-27) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/19138/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1789023/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 forky/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 33 http://deb.debian.org/debian forky/main arm64 libsimde-dev all 0.8.2-3 [467 kB] Get: 34 http://deb.debian.org/debian forky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] -Fetched 12.6 MB in 0s (86.9 MB/s) +Fetched 12.6 MB in 0s (120 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 ... 20012 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/1789023/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/1789023/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 @@ -344,7 +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: +In file included from SNAPLib/AffineGap.cpp:2: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -365,7 +401,12 @@ /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/AlignerStats.h:29, + from SNAPLib/AlignerStats.cpp:27: +SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined + 87 | # define _MM_HINT_T0 1 + | ^~~~~~~~~~~ +In file included from SNAPLib/AlignerContext.cpp:27: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -386,12 +427,6 @@ /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/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 /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 @@ -409,7 +444,8 @@ /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/BigAlloc.cpp:24: +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 | ^~~~~~~~~~~ @@ -430,7 +466,9 @@ /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/BufferedAsync.cpp:21: +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 | ^~~~~~~~~~~ @@ -451,8 +489,9 @@ /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/AlignerOptions.h:29, + from SNAPLib/AlignerOptions.cpp:27: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -473,13 +512,24 @@ /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 | ^~~~~~~~~~~ -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/AffineGapVectorized.cpp:2: +SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined + 87 | # define _MM_HINT_T0 1 + | ^~~~~~~~~~~ +In file included from SNAPLib/BigAlloc.cpp:24: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ +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 /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 + | ^~~~~~~~~~~ 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 @@ -497,15 +547,6 @@ /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/AffineGap.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 - 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 | ^~~~~~~~~~~ @@ -518,12 +559,6 @@ /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/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 - | ^~~~~~~~~~~ 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 @@ -541,8 +576,17 @@ /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 + | ^~~~~~~~~~~ +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 | ^~~~~~~~~~~ @@ -557,24 +601,17 @@ /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 | ^~~~~~~~~~~ +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: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/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 - 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 | ^~~~~~~~~~~ @@ -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/BufferedAsync.cpp:21: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -662,7 +698,7 @@ 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/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/DataReader.cpp:22: +In file included from SNAPLib/Compat.cpp:26: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -683,8 +719,7 @@ /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 -In file included from SNAPLib/Compat.cpp:26: +In file included from SNAPLib/DataReader.cpp:22: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -705,6 +740,8 @@ /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/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 In file included from SNAPLib/DataWriter.cpp:21: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 @@ -726,6 +763,8 @@ /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/FASTQ.o SNAPLib/FASTQ.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.o SNAPLib/GenericFile.cpp In file included from SNAPLib/Error.cpp:25: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 @@ -747,8 +786,6 @@ /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/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/FASTA.cpp:26: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 @@ -770,9 +807,7 @@ /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/FASTQ.h:30, - from SNAPLib/FASTQ.cpp:29: +In file included from SNAPLib/GenericFile.cpp:27: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -793,7 +828,8 @@ /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/GenericFile.cpp:27: +In file included from SNAPLib/FASTQ.h:30, + from SNAPLib/FASTQ.cpp:29: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -815,6 +851,13 @@ 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 +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 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); @@ -823,6 +866,7 @@ | | _int64 {aka long int} | long long unsigned int | %lx +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 SNAPLib/DataReader.cpp: In member function 'char* DecompressDataReader::findPointer(void*)': SNAPLib/DataReader.cpp:2105:50: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=] 2105 | sprintf(result, "compressed #%d @ %lld", i, (char*)p - e->compressed); @@ -861,13 +905,6 @@ | | | | 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 In file included from SNAPLib/GenericFile.h:25, from SNAPLib/GenericFile_Blob.h:26, from SNAPLib/GenericFile_Blob.cpp:25: @@ -891,39 +928,15 @@ /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 | ^~~~~~~~~~~ -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_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 - | ^~~~~~~~~~~ -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-2.0.5+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 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 -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 -In file included from SNAPLib/Genome.h:26, - from SNAPLib/Genome.cpp:26: +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: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -966,6 +979,7 @@ /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/HashTable.o SNAPLib/HashTable.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 @@ -1009,8 +1023,8 @@ /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/HashTable.h:23, - from SNAPLib/HashTable.cpp:20: +In file included from SNAPLib/Genome.h:26, + from SNAPLib/Genome.cpp:26: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1031,9 +1045,8 @@ /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/Histogram.o SNAPLib/Histogram.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/HitDepth.o SNAPLib/HitDepth.cpp -In file included from SNAPLib/HitDepth.cpp:25: +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 | ^~~~~~~~~~~ @@ -1054,7 +1067,7 @@ /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/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/Histogram.o SNAPLib/Histogram.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 @@ -1076,6 +1089,7 @@ /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/HitDepth.o SNAPLib/HitDepth.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); @@ -1132,31 +1146,6 @@ | ~~~~~~~~~~~~~~~~~~~ | | | size_t* {aka long unsigned int*} -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 - 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/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); @@ -1198,10 +1187,9 @@ | | 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/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 -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/LandauVishkin.cpp:2: +In file included from SNAPLib/HitDepth.cpp:25: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1222,9 +1210,7 @@ /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/PairedReadMatcher.o SNAPLib/PairedReadMatcher.cpp -In file included from SNAPLib/Read.h:28, - from SNAPLib/MultiInputReadSupplier.cpp:25: +In file included from SNAPLib/LandauVishkin.cpp:2: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1245,9 +1231,11 @@ /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 | ^~~~~~~~~~~ -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/PairedAligner.cpp:34: +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 | ^~~~~~~~~~~ @@ -1268,8 +1256,9 @@ /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/ParallelTask.h:25, - from SNAPLib/ParallelTask.cpp:18: +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/PairedAligner.cpp:34: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1291,8 +1280,7 @@ 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: + from SNAPLib/MultiInputReadSupplier.cpp:25: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1313,6 +1301,8 @@ /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/PairedReadMatcher.o SNAPLib/PairedReadMatcher.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/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 @@ -1334,16 +1324,24 @@ /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 | ^~~~~~~~~~~ +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/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 -In file included from SNAPLib/RangeSplitter.h:29, - from SNAPLib/RangeSplitter.cpp:28: +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 | ^~~~~~~~~~~ @@ -1364,15 +1362,10 @@ /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/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} }; - | ^ +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 In file included from SNAPLib/Read.h:28, - from SNAPLib/Read.cpp:25: + 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 | ^~~~~~~~~~~ @@ -1387,23 +1380,20 @@ /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/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 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-2.0.5+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 -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/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/RangeSplitter.h:29, + from SNAPLib/RangeSplitter.cpp:28: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1425,28 +1415,7 @@ 3490 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | ^~~~~~~~~~~ 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 - | ^~~~~~~~~~~ -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/ReadWriter.cpp:21: + from SNAPLib/Read.cpp:25: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1467,10 +1436,11 @@ /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 | ^~~~~~~~~~~ -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/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/ReadReader.o SNAPLib/ReadReader.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/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/Read.h:28, + from SNAPLib/ReadSupplierQueue.cpp:25: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1491,13 +1461,7 @@ /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/SingleAligner.o SNAPLib/SingleAligner.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 | } - | ^ -In file included from SNAPLib/Seed.h:27, - from SNAPLib/Seed.cpp:26: +In file included from SNAPLib/ReadReader.cpp:19: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1518,11 +1482,7 @@ /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/SortedDataWriter.o SNAPLib/SortedDataWriter.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/Tables.o SNAPLib/Tables.cpp -In file included from SNAPLib/Seed.h:27, - from SNAPLib/SeedSequencer.h:27, - from SNAPLib/SeedSequencer.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 | ^~~~~~~~~~~ @@ -1543,10 +1503,9 @@ /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/Genome.h:26, - from SNAPLib/AlignmentResult.h:29, - from SNAPLib/BaseAligner.h:30, - from SNAPLib/SingleAligner.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/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/SAM.cpp:21: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1567,7 +1526,10 @@ /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/SortedDataWriter.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/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 +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 | ^~~~~~~~~~~ @@ -1588,10 +1550,9 @@ /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/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/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 | ^~~~~~~~~~~ @@ -1612,8 +1573,10 @@ /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/Error.h:25, - from SNAPLib/exit.cpp:26: +In file included from SNAPLib/Genome.h:26, + from SNAPLib/AlignmentResult.h:29, + from SNAPLib/BaseAligner.h:30, + from SNAPLib/SingleAligner.cpp:27: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1634,6 +1597,11 @@ /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 | ^~~~~~~~~~~ +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/SortedDataWriter.o SNAPLib/SortedDataWriter.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:*":""); @@ -1641,7 +1609,6 @@ | | | | long long unsigned int long 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/mapq.o SNAPLib/mapq.cpp SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writePairs(const ReaderContext&, LandauVishkinWithCigar*, AffineGapVectorizedWithCigar*, bool, char*, size_t, size_t*, size_t*, Read**, GenomeLocation*, PairedAlignmentResult*, bool, bool, char*, bool, int*, int*, bool*, bool*) const': SNAPLib/SAM.cpp:1854:77: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 1854 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%d\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%s%s%.*s\n", @@ -1753,7 +1720,6 @@ | | | | long long unsigned int GenomeDistance {aka long 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/stdafx.o SNAPLib/stdafx.cpp SNAPLib/SAM.cpp:2749:56: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2749 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1772,7 +1738,54 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | GenomeLocation {aka long int} -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 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-2.0.5+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 +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 +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 + | ^~~~~~~~~~~ +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/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); @@ -1780,8 +1793,8 @@ | | | | long long unsigned int long unsigned int | %lu -In file included from SNAPLib/CommandProcessor.h:24, - from apps/snap/Main.cpp:26: +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 | ^~~~~~~~~~~ @@ -1802,6 +1815,7 @@ /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/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 @@ -1824,27 +1838,32 @@ 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 -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 +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 + | ^~~~~~~~~~~ +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-2.0.5+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 -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/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 | ^~~~~~~~~~~ @@ -1865,10 +1884,11 @@ /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 | ^~~~~~~~~~~ +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 +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 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 -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/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 | ^~~~~~~~~~~ @@ -1911,8 +1931,23 @@ /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.h:2, - from tests/LandauVishkinTest.cpp:3: +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/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 | ^~~~~~~~~~~ @@ -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/main.o tests/main.cpp -In file included from tests/ProbabilityDistanceTest.cpp:2: +In file included from SNAPLib/LandauVishkin.h:2, + from tests/LandauVishkinTest.cpp:3: SNAPLib/Compat.h:87:11: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | ^~~~~~~~~~~ @@ -1955,6 +1990,7 @@ /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 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 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: @@ -2133,12 +2169,14 @@ 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/1789023/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1789023/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/19138 and its subdirectories -I: Current time: Mon Oct 12 07:52:26 -12 2026 -I: pbuilder-time-stamp: 1791834746 +I: removing directory /srv/workspace/pbuilder/1789023 and its subdirectories +I: Current time: Wed Sep 10 03:31:23 +14 2025 +I: pbuilder-time-stamp: 1757424683