Diff of the two buildlogs: -- --- b1/build.log 2023-04-23 00:19:04.015228052 +0000 +++ b2/build.log 2023-04-23 00:23:39.994998384 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri May 24 18:38:57 -12 2024 -I: pbuilder-time-stamp: 1716619137 +I: Current time: Sun Apr 23 14:19:08 +14 2023 +I: pbuilder-time-stamp: 1682209148 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./snap-aligner_2.0.2+dfsg.orig.tar.xz] I: copying [./snap-aligner_2.0.2+dfsg-1.debian.tar.xz] I: Extracting source -gpgv: Signature made Wed Feb 1 07:29:56 2023 -12 +gpgv: Signature made Thu Feb 2 09:29:56 2023 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -30,52 +30,84 @@ dpkg-source: info: applying simde I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/17708/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/5533/tmp/hooks/D01_modify_environment starting +debug: Running on codethink16-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 Apr 23 14:19 /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/5533/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/5533/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + 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=8' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='17708' - PS1='# ' - PS2='> ' + 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=5533 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.OVlMBsxY/pbuilderrc_ov7V --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.OVlMBsxY/b1 --logfile b1/build.log snap-aligner_2.0.2+dfsg-1.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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.OVlMBsxY/pbuilderrc_LMDx --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.OVlMBsxY/b2 --logfile b2/build.log --extrapackages usrmerge snap-aligner_2.0.2+dfsg-1.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink11-arm64 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 24 04:47 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/17708/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 21 00:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/5533/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 bookworm/main arm64 help2man arm64 1.49.3 [198 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 libsimde-dev all 0.7.4~rc2-2 [377 kB] Get: 34 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] -Fetched 19.8 MB in 1s (37.0 MB/s) +Fetched 19.8 MB in 0s (43.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19616 files and directories currently installed.) @@ -301,8 +333,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/snap-aligner-2.0.2+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_2.0.2+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/5533/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/5533/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/snap-aligner-2.0.2+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_2.0.2+dfsg-1_source.changes dpkg-buildpackage: info: source package snap-aligner dpkg-buildpackage: info: source version 2.0.2+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -361,7 +402,10 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | -In file included from SNAPLib/AffineGap.cpp:2: +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: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | @@ -382,10 +426,9 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #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/Genome.h:26, + from SNAPLib/AlignerOptions.h:29, + from SNAPLib/AlignerOptions.cpp:27: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | @@ -406,7 +449,7 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | -In file included from SNAPLib/AffineGapVectorized.cpp:2: +In file included from SNAPLib/AffineGap.cpp:2: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | @@ -472,8 +515,7 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #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/AffineGapVectorized.cpp:2: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | @@ -494,9 +536,8 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #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/ApproximateCounter.h:3, + from SNAPLib/ApproximateCounter.cpp:3: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | @@ -519,11 +560,8 @@ | g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Bam.o SNAPLib/Bam.cpp g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -In file included from SNAPLib/Genome.h:26, - from SNAPLib/AlignmentResult.h:29, - from SNAPLib/BaseAligner.h:30, - from SNAPLib/BaseAligner.cpp:29: +In file included from SNAPLib/SAM.h:22, + from SNAPLib/Bam.cpp:20: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | @@ -544,8 +582,11 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | -In file included from SNAPLib/SAM.h:22, - from SNAPLib/Bam.cpp:20: +g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 +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: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | @@ -566,6 +607,7 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | +g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/BigAlloc.cpp:24: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 @@ -587,8 +629,6 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | -g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 In file included from SNAPLib/BufferedAsync.cpp:21: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 @@ -610,7 +650,9 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | +g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Compat.o SNAPLib/Compat.cpp In file included from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, from SNAPLib/PairedEndAligner.h:25, @@ -659,7 +701,6 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | -g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Compat.o SNAPLib/Compat.cpp In file included from SNAPLib/Compat.cpp:26: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 @@ -683,7 +724,8 @@ | g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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: +g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/DataWriter.cpp:21: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | @@ -704,8 +746,7 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | -g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/DataWriter.cpp:21: +In file included from SNAPLib/Error.cpp:25: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | @@ -726,7 +767,7 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | -In file included from SNAPLib/Error.cpp:25: +In file included from SNAPLib/DataReader.cpp:22: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | @@ -748,6 +789,29 @@ 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/FASTQ.h:30, + from SNAPLib/FASTQ.cpp:29: +SNAPLib/Compat.h:87: 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:3344: note: this is the location of the previous definition + 3344 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 + | +SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined + 88 | # define _MM_HINT_T1 2 + | +/usr/include/simde/x86/sse.h:3346: note: this is the location of the previous definition + 3346 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 + | +SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined + 89 | # define _MM_HINT_T2 3 + | +/usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition + 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 + | In file included from SNAPLib/FASTA.cpp:26: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 @@ -769,9 +833,15 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | -g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/FASTQ.h:30, - from SNAPLib/FASTQ.cpp:29: +SNAPLib/Error.cpp: In function 'void WriteProgressCounter(const char*, _int64)': +SNAPLib/Error.cpp:96:49: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '_int64' {aka 'long int'} [-Wformat=] + 96 | fprintf(stderr,"reporter:counter:SNAP,%s,%lld\n", counterName, increment); + | ~~~^ ~~~~~~~~~ + | | | + | long long int _int64 {aka long int} + | %ld +g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile.o SNAPLib/GenericFile.cpp +In file included from SNAPLib/GenericFile.cpp:27: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | @@ -792,6 +862,7 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | +g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/DataReader.cpp: In static member function 'static bool DecompressDataReader::decompress(z_stream*, ThreadHeap*, char*, _int64, _int64*, char*, _int64, _int64*, DecompressMode)': SNAPLib/DataReader.cpp:2012:53: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] 2012 | fprintf(stderr, "\n0x%llx\t", offset); @@ -838,8 +909,9 @@ | | | | long long int _int64 {aka long int} | %ld -g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile.o SNAPLib/GenericFile.cpp -In file included from SNAPLib/GenericFile.cpp:27: +In file included from SNAPLib/GenericFile.h:25, + from SNAPLib/GenericFile_Blob.h:26, + from SNAPLib/GenericFile_Blob.cpp:25: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | @@ -860,17 +932,13 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | -SNAPLib/Error.cpp: In function 'void WriteProgressCounter(const char*, _int64)': -SNAPLib/Error.cpp:96:49: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '_int64' {aka 'long int'} [-Wformat=] - 96 | fprintf(stderr,"reporter:counter:SNAP,%s,%lld\n", counterName, increment); - | ~~~^ ~~~~~~~~~ - | | | - | long long int _int64 {aka long int} - | %ld -g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_map.cpp +g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_stdio.o SNAPLib/GenericFile_stdio.cpp In file included from SNAPLib/GenericFile.h:25, 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: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | @@ -891,12 +959,8 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | -g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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: +g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Genome.o SNAPLib/Genome.cpp +In file included from SNAPLib/GenericFile_stdio.cpp:25: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | @@ -917,10 +981,7 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | -g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GzipDataWriter.o SNAPLib/GzipDataWriter.cpp In file included from SNAPLib/Genome.h:26, from SNAPLib/Genome.cpp:26: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined @@ -943,7 +1004,8 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | -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: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | @@ -964,8 +1026,9 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | -In file included from SNAPLib/ApproximateCounter.h:3, - from SNAPLib/GenomeIndex.cpp:26: +g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/GzipDataWriter.h:25, + from SNAPLib/GzipDataWriter.cpp:20: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | @@ -986,8 +1049,9 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #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/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/HashTable.h:23, + from SNAPLib/HashTable.cpp:20: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | @@ -1008,7 +1072,47 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | -g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 +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/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 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=] @@ -1049,27 +1153,6 @@ | ~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} -g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/GenomeIndex.cpp: In static member function 'static GenomeIndex* GenomeIndex::loadFromDirectory(char*, bool, bool)': SNAPLib/GenomeIndex.cpp:1879:57: warning: format '%lld' expects argument of type 'long long int*', but argument 6 has type '_int64*' {aka 'long int*'} [-Wformat=] 1879 | if (10 != (nRead = sscanf(indexFileBuf,"%d %d %d %lld %d %d %d %lld %d %d", &majorVersion, &minorVersion, &nHashTables, &overflowTableSize, &seedLen, &chromosomePadding, @@ -1087,29 +1170,7 @@ | ~~~~~~~~~~~~~~~~~~~ | | | size_t* {aka long unsigned int*} -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 -In file included from SNAPLib/HashTable.h:23, - from SNAPLib/HashTable.cpp:20: +In file included from SNAPLib/Histogram.cpp:27: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | @@ -1130,7 +1191,8 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | -In file included from SNAPLib/Histogram.cpp:27: +g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/HitDepth.o SNAPLib/HitDepth.cpp +In file included from SNAPLib/HitDepth.cpp:25: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | @@ -1152,7 +1214,12 @@ 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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: +g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/LandauVishkin.o SNAPLib/LandauVishkin.cpp +In file included from SNAPLib/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: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | @@ -1173,11 +1240,8 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | -In file included from SNAPLib/Genome.h:26, - from SNAPLib/AlignmentResult.h:29, - from SNAPLib/PairedEndAligner.h:25, - from SNAPLib/IntersectingPairedEndAligner.h:25, - from SNAPLib/IntersectingPairedEndAligner.cpp:24: +g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 +In file included from SNAPLib/LandauVishkin.cpp:2: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | @@ -1198,9 +1262,6 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | -g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/Read.h:28, from SNAPLib/MultiInputReadSupplier.cpp:25: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined @@ -1223,7 +1284,9 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | -In file included from SNAPLib/LandauVishkin.cpp:2: +g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedAligner.o SNAPLib/PairedAligner.cpp +g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/PairedAligner.cpp:34: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | @@ -1244,7 +1307,7 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | -In file included from SNAPLib/PairedAligner.cpp:34: +In file included from SNAPLib/PairedReadMatcher.cpp:26: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | @@ -1265,15 +1328,16 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | +g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 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/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/ParallelTask.h:25, + from SNAPLib/ParallelTask.cpp:18: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | @@ -1294,8 +1358,9 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | -In file included from SNAPLib/ParallelTask.h:25, - from SNAPLib/ParallelTask.cpp:18: +In file included from SNAPLib/Read.h:28, + from SNAPLib/ProbabilityDistance.h:3, + from SNAPLib/ProbabilityDistance.cpp:2: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | @@ -1316,7 +1381,6 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | -g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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: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} }; @@ -1332,9 +1396,10 @@ | long long unsigned int long unsigned int | %lu g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/ProbabilityDistance.h:3, - from SNAPLib/ProbabilityDistance.cpp:2: + from SNAPLib/Read.cpp:25: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 | @@ -1355,7 +1420,6 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | -g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Read.o SNAPLib/Read.cpp In file included from SNAPLib/RangeSplitter.h:29, from SNAPLib/RangeSplitter.cpp:28: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined @@ -1378,29 +1442,6 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | -In file included from SNAPLib/Read.h:28, - from SNAPLib/Read.cpp:25: -SNAPLib/Compat.h:87: 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:3344: note: this is the location of the previous definition - 3344 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 - | -SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined - 88 | # define _MM_HINT_T1 2 - | -/usr/include/simde/x86/sse.h:3346: note: this is the location of the previous definition - 3346 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 - | -SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined - 89 | # define _MM_HINT_T2 3 - | -/usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition - 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 - | -g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/ReadReader.cpp:19: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 @@ -1446,6 +1487,8 @@ 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadWriter.o SNAPLib/ReadWriter.cpp +g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Seed.o SNAPLib/Seed.cpp In file included from SNAPLib/ReadWriter.cpp:21: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 @@ -1467,8 +1510,6 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | -g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 @@ -1490,7 +1531,6 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | -g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/Seed.h:27, from SNAPLib/Seed.cpp:26: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined @@ -1513,6 +1553,11 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #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/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/Seed.h:27, from SNAPLib/SeedSequencer.h:27, from SNAPLib/SeedSequencer.cpp:25: @@ -1536,10 +1581,6 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #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/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SingleAligner.o SNAPLib/SingleAligner.cpp In file included from SNAPLib/Genome.h:26, from SNAPLib/AlignmentResult.h:29, @@ -1749,6 +1790,13 @@ | g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/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); + | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu In file included from SNAPLib/Error.h:25, from SNAPLib/exit.cpp:26: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined @@ -1771,13 +1819,6 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #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); - | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu In file included from SNAPLib/mapq.cpp:25: SNAPLib/Compat.h:87: warning: "_MM_HINT_T0" redefined 87 | # define _MM_HINT_T0 1 @@ -1886,51 +1927,6 @@ /usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 | -In file included from SNAPLib/LandauVishkin.h:2, - from tests/EventTest.cpp:3: -SNAPLib/Compat.h:87: 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:3344: note: this is the location of the previous definition - 3344 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 - | -SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined - 88 | # define _MM_HINT_T1 2 - | -/usr/include/simde/x86/sse.h:3346: note: this is the location of the previous definition - 3346 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 - | -SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined - 89 | # define _MM_HINT_T2 3 - | -/usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition - 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 - | -g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/LandauVishkin.h:2, - from tests/LandauVishkinTest.cpp:3: -SNAPLib/Compat.h:87: 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:3344: note: this is the location of the previous definition - 3344 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 - | -SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined - 88 | # define _MM_HINT_T1 2 - | -/usr/include/simde/x86/sse.h:3346: note: this is the location of the previous definition - 3346 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 - | -SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined - 89 | # define _MM_HINT_T2 3 - | -/usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition - 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 - | SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': SNAPLib/SAM.cpp:2650:55: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=] 2650 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); @@ -1968,28 +1964,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 tests/ProbabilityDistanceTest.cpp:2: -SNAPLib/Compat.h:87: 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:3344: note: this is the location of the previous definition - 3344 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 - | -SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined - 88 | # define _MM_HINT_T1 2 - | -/usr/include/simde/x86/sse.h:3346: note: this is the location of the previous definition - 3346 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 - | -SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined - 89 | # define _MM_HINT_T2 3 - | -/usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition - 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 - | +g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, const char*, GenomeDistance, int, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': SNAPLib/SAM.cpp:2745:55: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=] 2745 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); @@ -2022,7 +1997,73 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +In file included from SNAPLib/LandauVishkin.h:2, + from tests/EventTest.cpp:3: +SNAPLib/Compat.h:87: 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:3344: note: this is the location of the previous definition + 3344 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 + | +SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined + 88 | # define _MM_HINT_T1 2 + | +/usr/include/simde/x86/sse.h:3346: note: this is the location of the previous definition + 3346 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 + | +SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined + 89 | # define _MM_HINT_T2 3 + | +/usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition + 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 + | +In file included from SNAPLib/LandauVishkin.h:2, + from tests/LandauVishkinTest.cpp:3: +SNAPLib/Compat.h:87: 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:3344: note: this is the location of the previous definition + 3344 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 + | +SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined + 88 | # define _MM_HINT_T1 2 + | +/usr/include/simde/x86/sse.h:3346: note: this is the location of the previous definition + 3346 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 + | +SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined + 89 | # define _MM_HINT_T2 3 + | +/usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition + 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 + | +g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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: 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:3344: note: this is the location of the previous definition + 3344 | #define _MM_HINT_T0 SIMDE_MM_HINT_T0 + | +SNAPLib/Compat.h:88: warning: "_MM_HINT_T1" redefined + 88 | # define _MM_HINT_T1 2 + | +/usr/include/simde/x86/sse.h:3346: note: this is the location of the previous definition + 3346 | #define _MM_HINT_T1 SIMDE_MM_HINT_T1 + | +SNAPLib/Compat.h:89: warning: "_MM_HINT_T2" redefined + 89 | # define _MM_HINT_T2 3 + | +/usr/include/simde/x86/sse.h:3348: note: this is the location of the previous definition + 3348 | #define _MM_HINT_T2 SIMDE_MM_HINT_T2 + | g++ -g -O2 -ffile-prefix-map=/build/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/snap-aligner-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 apps/SNAPCommand/SNAPCommand.cpp:26: @@ -2129,12 +2170,14 @@ 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/5533/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/5533/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/17708 and its subdirectories -I: Current time: Fri May 24 18:42:02 -12 2024 -I: pbuilder-time-stamp: 1716619322 +I: removing directory /srv/workspace/pbuilder/5533 and its subdirectories +I: Current time: Sun Apr 23 14:23:39 +14 2023 +I: pbuilder-time-stamp: 1682209419