Diff of the two buildlogs: -- --- b1/build.log 2025-03-05 08:00:17.762813533 +0000 +++ b2/build.log 2025-03-05 08:03:39.785684337 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Apr 7 02:21:37 -12 2026 -I: pbuilder-time-stamp: 1775571697 +I: Current time: Wed Mar 5 22:00:20 +14 2025 +I: pbuilder-time-stamp: 1741161620 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -26,52 +26,84 @@ dpkg-source: info: applying simde I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3179887/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3620927/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +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 Mar 5 08:00 /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/3620927/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3620927/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='99168ca494d243398c16477e8a1c4f02' - 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='3179887' - PS1='# ' - PS2='> ' + INVOCATION_ID=5a32346c965a4fb08658fa1c00a2708b + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-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=3620927 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.NGHlf9DV/pbuilderrc_ezWJ --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.NGHlf9DV/b1 --logfile b1/build.log snap-aligner_2.0.3+dfsg-2.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.NGHlf9DV/pbuilderrc_w5H2 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.NGHlf9DV/b2 --logfile b2/build.log snap-aligner_2.0.3+dfsg-2.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3179887/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3620927/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -147,7 +179,7 @@ Get: 32 http://deb.debian.org/debian trixie/main amd64 help2man amd64 1.49.3 [198 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libsimde-dev all 0.8.2-2 [467 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 22.2 MB in 3s (6637 kB/s) +Fetched 22.2 MB in 3s (8120 kB/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 ... 19802 files and directories currently installed.) @@ -298,7 +330,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/snap-aligner-2.0.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../snap-aligner_2.0.3+dfsg-2_source.changes +I: user script /srv/workspace/pbuilder/3620927/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3620927/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/snap-aligner-2.0.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../snap-aligner_2.0.3+dfsg-2_source.changes dpkg-buildpackage: info: source package snap-aligner dpkg-buildpackage: info: source version 2.0.3+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -310,7 +346,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' dh_auto_clean - make -j42 clean + make -j20 clean make[2]: Entering directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' rm -f SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/HitDepth.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/snap/Main.o apps/snap/stdafx.o tests/AffineGapTest.o tests/AffineGapVectorizedTest.o tests/EventTest.o tests/LandauVishkinTest.o tests/ProbabilityDistanceTest.o tests/TestLib.o tests/main.o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o snap-aligner unit_tests SNAPCommand snap SNAP make[2]: Leaving directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' @@ -326,7 +362,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' dh_auto_build - make -j42 "INSTALL=install --strip-program=true" + make -j20 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AffineGap.o SNAPLib/AffineGap.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AffineGapVectorized.o SNAPLib/AffineGapVectorized.cpp @@ -352,25 +388,64 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_Blob.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +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); + | ~~~^ ~~~~~~ + | | | + | | _int64 {aka long int} + | long long unsigned int + | %lx +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); + | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | long long int long int + | %ld +SNAPLib/DataReader.cpp:2109:50: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=] + 2109 | sprintf(result, "decompressed #%d %lld", i, (char*) p - e->decompressed); + | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | long long int long int + | %ld +SNAPLib/DataReader.cpp:2113:43: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=] + 2113 | sprintf(result, "extra #%d %lld", i, (char*) p - e->decompressed - extraBytes); + | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | long long int long int + | %ld +SNAPLib/DataReader.cpp: In static member function 'static void DecompressDataReader::decompressThread(void*)': +SNAPLib/DataReader.cpp:2261:174: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] + 2261 | fprintf(stderr, "Bug in DecompressDataReader::decompressThread(); don't have enough decompress buffer when we thought we'd assured it. Existing size %lld, needed (at least) %lld, entry @0x%p\n", entry->decompressedSize, output, entry); + | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | long long int _int64 {aka long int} + | %ld +SNAPLib/DataReader.cpp:2261:198: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '_int64' {aka 'long int'} [-Wformat=] + 2261 | fprintf(stderr, "Bug in DecompressDataReader::decompressThread(); don't have enough decompress buffer when we thought we'd assured it. Existing size %lld, needed (at least) %lld, entry @0x%p\n", entry->decompressedSize, output, entry); + | ~~~^ ~~~~~~ + | | | + | long long int _int64 {aka long int} + | %ld +SNAPLib/DataReader.cpp:2265:74: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] + 2265 | fprintf(stderr, "error reading BAM file at offset %lld\n", reader->getFileOffset()); + | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | long long int _int64 {aka long int} + | %ld g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Genome.o SNAPLib/Genome.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenomeIndex.o SNAPLib/GenomeIndex.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GzipDataWriter.o SNAPLib/GzipDataWriter.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/HashTable.o SNAPLib/HashTable.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/IntersectingPairedEndAligner.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/MultiInputReadSupplier.o SNAPLib/MultiInputReadSupplier.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedAligner.o SNAPLib/PairedAligner.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedReadMatcher.o SNAPLib/PairedReadMatcher.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ProbabilityDistance.o SNAPLib/ProbabilityDistance.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/RangeSplitter.o SNAPLib/RangeSplitter.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Read.o SNAPLib/Read.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadReader.o SNAPLib/ReadReader.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadSupplierQueue.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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); @@ -412,10 +487,11 @@ | | GenomeDistance* {aka long int*} | long long int* | %ld -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SAM.o SNAPLib/SAM.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SeedSequencer.o SNAPLib/SeedSequencer.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SingleAligner.o SNAPLib/SingleAligner.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/IntersectingPairedEndAligner.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/MultiInputReadSupplier.o SNAPLib/MultiInputReadSupplier.cpp SNAPLib/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); @@ -455,15 +531,6 @@ | ~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SortedDataWriter.o SNAPLib/SortedDataWriter.cpp -In file included from SNAPLib/IntersectingPairedEndAligner.cpp:24: -SNAPLib/IntersectingPairedEndAligner.h:767:71: warning: non-static data member initializers only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions] - 767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; - | ^ -SNAPLib/IntersectingPairedEndAligner.h:767:104: warning: extended initializer lists only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions] - 767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; - | ^ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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, @@ -481,52 +548,10 @@ | ~~~~~~~~~~~~~~~~~~~ | | | size_t* {aka long unsigned int*} -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); - | ~~~^ ~~~~~~ - | | | - | | _int64 {aka long int} - | long long unsigned int - | %lx -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); - | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | long long int long int - | %ld -SNAPLib/DataReader.cpp:2109:50: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=] - 2109 | sprintf(result, "decompressed #%d %lld", i, (char*) p - e->decompressed); - | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | long long int long int - | %ld -SNAPLib/DataReader.cpp:2113:43: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=] - 2113 | sprintf(result, "extra #%d %lld", i, (char*) p - e->decompressed - extraBytes); - | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | long long int long int - | %ld -SNAPLib/DataReader.cpp: In static member function 'static void DecompressDataReader::decompressThread(void*)': -SNAPLib/DataReader.cpp:2261:174: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] - 2261 | fprintf(stderr, "Bug in DecompressDataReader::decompressThread(); don't have enough decompress buffer when we thought we'd assured it. Existing size %lld, needed (at least) %lld, entry @0x%p\n", entry->decompressedSize, output, entry); - | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | long long int _int64 {aka long int} - | %ld -SNAPLib/DataReader.cpp:2261:198: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '_int64' {aka 'long int'} [-Wformat=] - 2261 | fprintf(stderr, "Bug in DecompressDataReader::decompressThread(); don't have enough decompress buffer when we thought we'd assured it. Existing size %lld, needed (at least) %lld, entry @0x%p\n", entry->decompressedSize, output, entry); - | ~~~^ ~~~~~~ - | | | - | long long int _int64 {aka long int} - | %ld -SNAPLib/DataReader.cpp:2265:74: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] - 2265 | fprintf(stderr, "error reading BAM file at offset %lld\n", reader->getFileOffset()); - | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | long long int _int64 {aka long int} - | %ld +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedAligner.o SNAPLib/PairedAligner.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedReadMatcher.o SNAPLib/PairedReadMatcher.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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} }; @@ -534,8 +559,6 @@ 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-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Util.o SNAPLib/Util.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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); @@ -543,30 +566,28 @@ | | | | long long unsigned int long unsigned int | %lu +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/RangeSplitter.o SNAPLib/RangeSplitter.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Read.o SNAPLib/Read.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadReader.o SNAPLib/ReadReader.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +In file included from SNAPLib/IntersectingPairedEndAligner.cpp:24: +SNAPLib/IntersectingPairedEndAligner.h:767:71: warning: non-static data member initializers only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions] + 767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; + | ^ +SNAPLib/IntersectingPairedEndAligner.h:767:104: warning: extended initializer lists only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions] + 767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; + | ^ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadWriter.o SNAPLib/ReadWriter.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SAM.o SNAPLib/SAM.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SeedSequencer.o SNAPLib/SeedSequencer.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SingleAligner.o SNAPLib/SingleAligner.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Tables.o SNAPLib/Tables.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Util.o SNAPLib/Util.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/exit.o SNAPLib/exit.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/stdafx.o SNAPLib/stdafx.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/Main.o apps/snap/Main.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/Error.cpp: In function 'void WriteProgressCounter(const char*, _int64)': -SNAPLib/Error.cpp:96:49: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '_int64' {aka 'long int'} [-Wformat=] - 96 | fprintf(stderr,"reporter:counter:SNAP,%s,%lld\n", counterName, increment); - | ~~~^ ~~~~~~~~~ - | | | - | long long int _int64 {aka long int} - | %ld -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapTest.o tests/AffineGapTest.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapVectorizedTest.o tests/AffineGapVectorizedTest.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/EventTest.o tests/EventTest.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/LandauVishkinTest.o tests/LandauVishkinTest.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/ProbabilityDistanceTest.o tests/ProbabilityDistanceTest.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/TestLib.o tests/TestLib.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/main.o tests/main.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -SNAPLib/ReadReader.cpp: In member function 'virtual bool SimpleReadReader::getNextRead(Read*, AlignmentResult*, unsigned int*, bool*, unsigned int*, unsigned int*, const char**)': -SNAPLib/ReadReader.cpp:44:5: warning: no return statement in function returning non-void [-Wreturn-type] - 44 | } - | ^ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/stdafx.o apps/SNAPCommand/stdafx.cpp SNAPLib/SAM.cpp: In 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:*":""); @@ -703,13 +724,15 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | GenomeLocation {aka long int} -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 +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/Main.o apps/snap/Main.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/ReadReader.cpp: In member function 'virtual bool SimpleReadReader::getNextRead(Read*, AlignmentResult*, unsigned int*, bool*, unsigned int*, unsigned int*, const char**)': +SNAPLib/ReadReader.cpp:44:5: warning: no return statement in function returning non-void [-Wreturn-type] + 44 | } + | ^ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapTest.o tests/AffineGapTest.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapVectorizedTest.o tests/AffineGapVectorizedTest.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/EventTest.o tests/EventTest.cpp SNAPLib/Util.cpp: In function 'char* FormatUIntWithCommas(_uint64, char*, size_t, size_t)': SNAPLib/Util.cpp:167:49: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 167 | sprintf(tempBuf, ",%03lld", x % 1000); @@ -725,6 +748,19 @@ | | _uint64 {aka long unsigned int} | long long int | %ld +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/LandauVishkinTest.o tests/LandauVishkinTest.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/ProbabilityDistanceTest.o tests/ProbabilityDistanceTest.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +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 +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/main.o tests/main.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/SNAPCommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/stdafx.o apps/SNAPCommand/stdafx.cpp SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': SNAPLib/SAM.cpp:2650:55: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=] 2650 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); @@ -867,8 +903,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'snap-aligner' in '../snap-aligner_2.0.3+dfsg-2_amd64.deb'. dpkg-deb: building package 'snap-aligner-dbgsym' in '../snap-aligner-dbgsym_2.0.3+dfsg-2_amd64.deb'. +dpkg-deb: building package 'snap-aligner' in '../snap-aligner_2.0.3+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../snap-aligner_2.0.3+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../snap-aligner_2.0.3+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -876,12 +912,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3620927/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3620927/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/3179887 and its subdirectories -I: Current time: Tue Apr 7 02:23:16 -12 2026 -I: pbuilder-time-stamp: 1775571796 +I: removing directory /srv/workspace/pbuilder/3620927 and its subdirectories +I: Current time: Wed Mar 5 22:03:38 +14 2025 +I: pbuilder-time-stamp: 1741161818