Diff of the two buildlogs: -- --- b1/build.log 2024-10-27 14:10:20.344833348 +0000 +++ b2/build.log 2024-10-27 14:12:35.640034336 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Oct 27 02:08:47 -12 2024 -I: pbuilder-time-stamp: 1730038127 +I: Current time: Mon Oct 28 04:10:25 +14 2024 +I: pbuilder-time-stamp: 1730038225 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying fix_shebang.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/397323/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3777741/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Oct 27 14:10 /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/3777741/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3777741/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='c7378a222dd243c49d4766a021962540' - 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='397323' - PS1='# ' - PS2='> ' + INVOCATION_ID=f013e47e7e5b49aea027a96706db960a + 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=3777741 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.FBIcVvAV/pbuilderrc_0cm9 --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.FBIcVvAV/b1 --logfile b1/build.log lumpy-sv_0.3.1+dfsg-7.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.FBIcVvAV/pbuilderrc_L2kw --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.FBIcVvAV/b2 --logfile b2/build.log lumpy-sv_0.3.1+dfsg-7.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink02-arm64 6.1.0-26-cloud-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-26-cloud-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/397323/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/3777741/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -249,7 +281,7 @@ Get: 114 http://deb.debian.org/debian trixie/main arm64 libsqlite3-dev arm64 3.46.1-1 [1058 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 python3-pysam arm64 0.22.1+ds-2+b1 [3244 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 samtools arm64 1.20-3 [624 kB] -Fetched 48.7 MB in 0s (142 MB/s) +Fetched 48.7 MB in 0s (166 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:arm64. (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 ... 20057 files and directories currently installed.) @@ -643,8 +675,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Oct 27 14:09:23 UTC 2024. -Universal Time is now: Sun Oct 27 14:09:23 UTC 2024. +Local time is now: Sun Oct 27 14:10:55 UTC 2024. +Universal Time is now: Sun Oct 27 14:10:55 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -742,7 +774,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/lumpy-sv-0.3.1+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 > ../lumpy-sv_0.3.1+dfsg-7_source.changes +I: user script /srv/workspace/pbuilder/3777741/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3777741/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/lumpy-sv-0.3.1+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 > ../lumpy-sv_0.3.1+dfsg-7_source.changes dpkg-buildpackage: info: source package lumpy-sv dpkg-buildpackage: info: source version 0.3.1+dfsg-7 dpkg-buildpackage: info: source distribution unstable @@ -771,12 +807,12 @@ make[1]: Entering directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' [ -d bin ] || mkdir -p bin [ -d bin ] || mkdir -p bin -[ -d obj ] || mkdir -p obj make --no-print-directory -C src/filter/ -cp scripts/lumpyexpress bin/lumpyexpress -[ -d bin ] || mkdir -p bin cc -g -I/usr/include/htslib -o lumpy_filter filter.c -lhts -lcrypto -lcurl -lpthread -lz +cp scripts/lumpyexpress bin/lumpyexpress +[ -d obj ] || mkdir -p obj > bin/lumpyexpress.config +[ -d bin ] || mkdir -p bin Building lumpy: ========================================================= #make --no-print-directory --directory= api @@ -839,16 +875,16 @@ * compiling lumpy.cpp g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack lumpy.cpp -o ../../obj//lumpy.o * compiling SV_Pair.cpp -g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Pair.cpp -o ../../obj//SV_Pair.o * compiling SV_Evidence.cpp +g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Pair.cpp -o ../../obj//SV_Pair.o g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Evidence.cpp -o ../../obj//SV_Evidence.o * compiling SV_BreakPoint.cpp -g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BreakPoint.cpp -o ../../obj//SV_BreakPoint.o * compiling SV_Bedpe.cpp +g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BreakPoint.cpp -o ../../obj//SV_BreakPoint.o g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Bedpe.cpp -o ../../obj//SV_Bedpe.o * compiling SV_SplitRead.cpp - * compiling SV_SplitReadReader.cpp g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_SplitRead.cpp -o ../../obj//SV_SplitRead.o + * compiling SV_SplitReadReader.cpp g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_SplitReadReader.cpp -o ../../obj//SV_SplitReadReader.o * compiling SV_PairReader.cpp g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_PairReader.cpp -o ../../obj//SV_PairReader.o @@ -857,49 +893,56 @@ * compiling SV_BamReader.cpp g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BamReader.cpp -o ../../obj//SV_BamReader.o * compiling SV_InterChromBamReader.cpp -g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_InterChromBamReader.cpp -o ../../obj//SV_InterChromBamReader.o * compiling SV_EvidenceReader.cpp +g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_InterChromBamReader.cpp -o ../../obj//SV_InterChromBamReader.o g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_EvidenceReader.cpp -o ../../obj//SV_EvidenceReader.o +In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, + from SV_Pair.cpp:15: +../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: +../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] + 321 | for (register short i = 0; i < _binLevels; ++i) { + | ^ +In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, + from SV_SplitRead.cpp:15: +../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: +../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] + 321 | for (register short i = 0; i < _binLevels; ++i) { + | ^ +In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, + from SV_Bedpe.cpp:14: +../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: +../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] + 321 | for (register short i = 0; i < _binLevels; ++i) { + | ^ In file included from SV_BreakPoint.h:19, - from SV_SplitReadReader.h:22, - from SV_SplitReadReader.cpp:15: + from SV_PairReader.h:22, + from SV_Pair.cpp:19: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, - from SV_BreakPoint.cpp:16: + from SV_Evidence.h:22, + from SV_Evidence.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ -In file included from SV_BreakPoint.h:19, - from SV_PairReader.h:22, - from SV_BamReader.cpp:15: +In file included from SV_BedpeReader.h:21, + from SV_Bedpe.cpp:17: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ -In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, - from lumpy.cpp:20: -../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: -../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] - 321 | for (register short i = 0; i < _binLevels; ++i) { - | ^ -In file included from SV_EvidenceReader.h:20, - from SV_EvidenceReader.cpp:15: +In file included from SV_BreakPoint.h:19, + from SV_SplitReadReader.h:22, + from SV_SplitRead.cpp:19: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, - from SV_Bedpe.cpp:14: -../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: -../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] - 321 | for (register short i = 0; i < _binLevels; ++i) { - | ^ -In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, - from SV_SplitRead.cpp:15: + from lumpy.cpp:20: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { @@ -912,40 +955,70 @@ 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, - from SV_Evidence.h:22, - from SV_Bedpe.h:18, - from SV_BedpeReader.cpp:15: + from SV_SplitReadReader.h:22, + from SV_SplitReadReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ -In file included from SV_BedpeReader.h:21, - from SV_Bedpe.cpp:17: +In file included from SV_BreakPoint.h:19, + from SV_BreakPoint.cpp:16: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, - from SV_SplitReadReader.h:22, - from SV_SplitRead.cpp:19: + from SV_PairReader.h:22, + from SV_InterChromBamReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_PairReader.h:22, - from SV_InterChromBamReader.cpp:15: + from SV_BamReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_Evidence.h:22, - from SV_Evidence.cpp:15: + from SV_Bedpe.h:18, + from SV_BedpeReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ +SV_SplitRead.cpp: In member function ‘bool SV_SplitRead::is_sane()’: +SV_SplitRead.cpp:538:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] + 538 | if ( min_mapping_quality < reader->min_mapping_threshold ) + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from SV_EvidenceReader.h:20, + from SV_EvidenceReader.cpp:15: +../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: +../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] + 253 | for (register short i = 0; i < kBinLevels; ++i) { + | ^ +In file included from SV_BreakPoint.h:19, + from SV_PairReader.h:22, + from SV_PairReader.cpp:15: +../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: +../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] + 253 | for (register short i = 0; i < kBinLevels; ++i) { + | ^ +SV_Evidence.cpp: In member function ‘virtual void SV_Evidence::set_bp_interval_probability(breakpoint_interval*)’: +SV_Evidence.cpp:81:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] + 81 | for (j = 0; j < size; ++j) { + | ~~^~~~~~ + * compiling SV_Tools.cpp +g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Tools.cpp -o ../../obj//SV_Tools.o +In file included from ../utils//bedFilePE/bedFilePE.h:12, + from SV_SplitRead.h:27, + from SV_InterChromBamReader.cpp:19: +../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: +../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] + 321 | for (register short i = 0; i < _binLevels; ++i) { + | ^ SV_BreakPoint.cpp: In member function ‘bool SV_BreakPoint::merge(SV_BreakPoint*)’: SV_BreakPoint.cpp:266:33: warning: variable ‘a_overlap_intr’ set but not used [-Wunused-but-set-variable] 266 | struct breakpoint_interval *a_overlap_intr, *b_overlap_intr; @@ -954,36 +1027,30 @@ 266 | struct breakpoint_interval *a_overlap_intr, *b_overlap_intr; | ^~~~~~~~~~~~~~ In file included from ../utils//bedFilePE/bedFilePE.h:12, - from SV_SplitRead.h:27, - from SV_SplitReadReader.cpp:16: + from SV_BedpeReader.h:23, + from SV_Bedpe.h:19: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ -In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, - from SV_Pair.cpp:15: +In file included from ../utils//bedFilePE/bedFilePE.h:12, + from SV_SplitRead.h:27, + from SV_SplitReadReader.cpp:16: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from ../utils//bedFilePE/bedFilePE.h:12, - from SV_BedpeReader.h:23, - from SV_Bedpe.h:19: + from SV_SplitRead.h:27, + from SV_BamReader.cpp:19: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ -In file included from SV_BreakPoint.h:19, - from SV_PairReader.h:22, - from SV_Pair.cpp:19: -../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: -../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] - 253 | for (register short i = 0; i < kBinLevels; ++i) { - | ^ -SV_SplitRead.cpp: In member function ‘bool SV_SplitRead::is_sane()’: -SV_SplitRead.cpp:538:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] - 538 | if ( min_mapping_quality < reader->min_mapping_threshold ) - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +SV_BamReader.cpp: In member function ‘virtual void SV_BamReader::process_input_chr_pos(std::string, CHR_POS, UCSCBins&)’: +SV_BamReader.cpp:208:28: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘CHR_POS’ {aka ‘long unsigned int’} [-Wsign-compare] + 208 | ( bam.Position < pos ) ) { + | ~~~~~~~~~~~~~^~~~~ ../utils//UCSCBins/ucsc_bins.hpp: In instantiation of ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS) [with T = SV_BreakPoint*; BIN = unsigned int; CHR_POS = long unsigned int]’: ../utils//UCSCBins/ucsc_bins.hpp:238:18: required from ‘void UCSCBins::add(std::string, CHR_POS, CHR_POS, char, T) [with T = SV_BreakPoint*; std::string = std::__cxx11::basic_string; CHR_POS = long unsigned int]’ 238 | BIN bin = getBin(start, end); @@ -1002,37 +1069,6 @@ ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ -In file included from ../utils//bedFilePE/bedFilePE.h:12, - from SV_SplitRead.h:27, - from SV_InterChromBamReader.cpp:19: -../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: -../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] - 321 | for (register short i = 0; i < _binLevels; ++i) { - | ^ -In file included from ../utils//bedFilePE/bedFilePE.h:12, - from SV_SplitRead.h:27, - from SV_BamReader.cpp:19: -../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: -../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] - 321 | for (register short i = 0; i < _binLevels; ++i) { - | ^ -In file included from SV_BreakPoint.h:19, - from SV_PairReader.h:22, - from SV_PairReader.cpp:15: -../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: -../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] - 253 | for (register short i = 0; i < kBinLevels; ++i) { - | ^ -SV_Evidence.cpp: In member function ‘virtual void SV_Evidence::set_bp_interval_probability(breakpoint_interval*)’: -SV_Evidence.cpp:81:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] - 81 | for (j = 0; j < size; ++j) { - | ~~^~~~~~ -SV_BamReader.cpp: In member function ‘virtual void SV_BamReader::process_input_chr_pos(std::string, CHR_POS, UCSCBins&)’: -SV_BamReader.cpp:208:28: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘CHR_POS’ {aka ‘long unsigned int’} [-Wsign-compare] - 208 | ( bam.Position < pos ) ) { - | ~~~~~~~~~~~~~^~~~~ - * compiling SV_Tools.cpp -g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Tools.cpp -o ../../obj//SV_Tools.o * compiling SV_VcfVariant.cpp g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_VcfVariant.cpp -o ../../obj//SV_VcfVariant.o * compiling log_space.cpp @@ -1055,6 +1091,31 @@ ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ +../utils//UCSCBins/ucsc_bins.hpp: In instantiation of ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS) [with T = int; BIN = unsigned int; CHR_POS = long unsigned int]’: +../utils//UCSCBins/ucsc_bins.hpp:238:18: required from ‘void UCSCBins::add(std::string, CHR_POS, CHR_POS, char, T) [with T = int; std::string = std::__cxx11::basic_string; CHR_POS = long unsigned int]’ + 238 | BIN bin = getBin(start, end); + | ~~~~~~^~~~~~~~~~~~ +SV_Tools.cpp:541:32: required from here + 541 | exclude_regions.add(bed.chrom, + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ + 542 | bed.start, + | ~~~~~~~~~~ + 543 | bed.end, + | ~~~~~~~~ + 544 | '+', + | ~~~~ + 545 | 1); + | ~~ +../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] + 253 | for (register short i = 0; i < kBinLevels; ++i) { + | ^ +SV_SplitRead.cpp: In static member function ‘static void SV_SplitRead::process_split(const BamTools::BamAlignment&, BamTools::RefVector, std::map, BamTools::BamAlignment>&, UCSCBins&, int, int, SV_SplitReadReader*)’: +SV_SplitRead.cpp:653:25: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 653 | free(new_split_read); + | ~~~~^~~~~~~~~~~~~~~~ +SV_SplitRead.cpp:641:41: note: returned from ‘void* operator new(std::size_t)’ + 641 | _reader); + | ^ SV_BreakPoint.cpp: In static member function ‘static void SV_BreakPoint::trim_interval(log_space*, unsigned int, int*, int*)’: SV_BreakPoint.cpp:704:24: warning: ‘max_i’ may be used uninitialized [-Wmaybe-uninitialized] 704 | if ((l == r) && (l == max_i)) @@ -1075,24 +1136,6 @@ SV_BreakPoint.cpp:1643:34: note: ‘r_max_i’ was declared here 1643 | unsigned int i, l_max_i, r_max_i; | ^~~~~~~ -../utils//UCSCBins/ucsc_bins.hpp: In instantiation of ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS) [with T = int; BIN = unsigned int; CHR_POS = long unsigned int]’: -../utils//UCSCBins/ucsc_bins.hpp:238:18: required from ‘void UCSCBins::add(std::string, CHR_POS, CHR_POS, char, T) [with T = int; std::string = std::__cxx11::basic_string; CHR_POS = long unsigned int]’ - 238 | BIN bin = getBin(start, end); - | ~~~~~~^~~~~~~~~~~~ -SV_Tools.cpp:541:32: required from here - 541 | exclude_regions.add(bed.chrom, - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ - 542 | bed.start, - | ~~~~~~~~~~ - 543 | bed.end, - | ~~~~~~~~ - 544 | '+', - | ~~~~ - 545 | 1); - | ~~ -../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] - 253 | for (register short i = 0; i < kBinLevels; ++i) { - | ^ SV_BreakPoint.cpp: In member function ‘void SV_BreakPoint::get_mixture(breakpoint_interval**, breakpoint_interval**)’: SV_BreakPoint.cpp:1379:39: warning: argument 1 value ‘18446744039349813264’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1379 | log_space *l = (log_space *)malloc((end_l-start_l+1)*sizeof(log_space)); @@ -1110,13 +1153,6 @@ /usr/include/stdlib.h:672:14: note: in a call to allocation function ‘void* malloc(size_t)’ declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ -SV_SplitRead.cpp: In static member function ‘static void SV_SplitRead::process_split(const BamTools::BamAlignment&, BamTools::RefVector, std::map, BamTools::BamAlignment>&, UCSCBins&, int, int, SV_SplitReadReader*)’: -SV_SplitRead.cpp:653:25: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 653 | free(new_split_read); - | ~~~~^~~~~~~~~~~~~~~~ -SV_SplitRead.cpp:641:41: note: returned from ‘void* operator new(std::size_t)’ - 641 | _reader); - | ^ SV_Tools.cpp: In function ‘int read_distro_file(std::string, double**, int*, int*)’: SV_Tools.cpp:156:14: warning: ‘last’ may be used uninitialized [-Wmaybe-uninitialized] 156 | *end = last; @@ -1177,9 +1213,9 @@ dpkg-gencontrol: warning: package lumpy-sv: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb +dpkg-deb: building package 'lumpy-sv-examples' in '../lumpy-sv-examples_0.3.1+dfsg-7_all.deb'. dpkg-deb: building package 'lumpy-sv' in '../lumpy-sv_0.3.1+dfsg-7_arm64.deb'. dpkg-deb: building package 'lumpy-sv-dbgsym' in '../lumpy-sv-dbgsym_0.3.1+dfsg-7_arm64.deb'. -dpkg-deb: building package 'lumpy-sv-examples' in '../lumpy-sv-examples_0.3.1+dfsg-7_all.deb'. dpkg-genbuildinfo --build=binary -O../lumpy-sv_0.3.1+dfsg-7_arm64.buildinfo dpkg-genchanges --build=binary -O../lumpy-sv_0.3.1+dfsg-7_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1187,12 +1223,14 @@ 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/3777741/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3777741/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/397323 and its subdirectories -I: Current time: Sun Oct 27 02:10:19 -12 2024 -I: pbuilder-time-stamp: 1730038219 +I: removing directory /srv/workspace/pbuilder/3777741 and its subdirectories +I: Current time: Mon Oct 28 04:12:34 +14 2024 +I: pbuilder-time-stamp: 1730038354