Diff of the two buildlogs: -- --- b1/build.log 2025-03-07 05:39:55.442683767 +0000 +++ b2/build.log 2025-03-07 05:41:25.634615829 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Mar 6 17:33:40 -12 2025 -I: pbuilder-time-stamp: 1741325620 +I: Current time: Fri Apr 10 02:02:58 +14 2026 +I: pbuilder-time-stamp: 1775736178 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -26,52 +26,84 @@ 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/3984851/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3756556/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-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 Apr 9 12:03 /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/3756556/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3756556/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=20 ' - DISTRIBUTION='unstable' - 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=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='60f3bce74d3d40f7b8d4eb9cadd8ed92' - 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='3984851' - PS1='# ' - PS2='> ' + INVOCATION_ID=08c0e81030814b079fd6e33e478fff56 + 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=3756556 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.8hiHBqUi/pbuilderrc_kZCt --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.8hiHBqUi/b1 --logfile b1/build.log lumpy-sv_0.3.1+dfsg-7.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.8hiHBqUi/pbuilderrc_Nqw9 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.8hiHBqUi/b2 --logfile b2/build.log lumpy-sv_0.3.1+dfsg-7.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3984851/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3756556/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -247,7 +279,7 @@ Get: 116 http://deb.debian.org/debian unstable/main amd64 libsqlite3-dev amd64 3.46.1-1 [1107 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 python3-pysam amd64 0.23.0+ds-1+b1 [3665 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.21-1 [667 kB] -Fetched 52.7 MB in 2s (23.8 MB/s) +Fetched 52.7 MB in 1s (60.9 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:amd64. (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 ... 19783 files and directories currently installed.) @@ -641,8 +673,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Mar 7 05:36:34 UTC 2025. -Universal Time is now: Fri Mar 7 05:36:34 UTC 2025. +Local time is now: Thu Apr 9 12:03:33 UTC 2026. +Universal Time is now: Thu Apr 9 12:03:33 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -746,7 +778,11 @@ 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/3756556/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3756556/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 @@ -756,7 +792,7 @@ debian/rules clean dh clean --with python3 dh_auto_clean - make -j20 clean + make -j42 clean make[1]: Entering directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' Cleaning up. #rm -Rf /lib @@ -771,16 +807,16 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j20 "INSTALL=install --strip-program=true" + make -j42 "INSTALL=install --strip-program=true" 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 -[ -d obj ] || mkdir -p obj > bin/lumpyexpress.config -[ -d bin ] || mkdir -p bin Building lumpy: ========================================================= #make --no-print-directory --directory= api @@ -841,85 +877,76 @@ - Building in src/lumpy * 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 +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_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_Evidence.cpp -o ../../obj//SV_Evidence.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_Pair.cpp -o ../../obj//SV_Pair.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_Evidence.cpp -o ../../obj//SV_Evidence.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_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_Bedpe.cpp -o ../../obj//SV_Bedpe.o * compiling SV_SplitRead.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_Bedpe.cpp -o ../../obj//SV_Bedpe.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_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 * compiling SV_BedpeReader.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 * 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_BedpeReader.cpp -o ../../obj//SV_BedpeReader.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_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 +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_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 * compiling SV_Tools.cpp - * 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_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 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 log_space.cpp -o ../../obj//log_space.o In file included from SV_BreakPoint.h:19, - from SV_BreakPoint.cpp:16: + from SV_Evidence.h:22, + 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) { | ^ In file included from SV_BreakPoint.h:19, - from SV_SplitReadReader.h:22, - from SV_SplitReadReader.cpp:15: + 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_Evidence.h:22, - from SV_Evidence.cpp:15: + 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) { | ^ -In file included from SV_EvidenceReader.h:20, - from SV_EvidenceReader.cpp:15: +In file included from SV_BreakPoint.h:19, + from SV_VcfVariant.h:18, + from SV_VcfVariant.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 ../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 SV_BreakPoint.h:19, from SV_PairReader.h:22, - from SV_PairReader.cpp:15: + 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_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) { | ^ -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_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; - | ^~~~~~~~~~~~~~ -SV_BreakPoint.cpp:266:50: warning: variable ‘b_overlap_intr’ set but not used [-Wunused-but-set-variable] - 266 | struct breakpoint_interval *a_overlap_intr, *b_overlap_intr; - | ^~~~~~~~~~~~~~ In file included from SV_BreakPoint.h:19, from SV_PairReader.h:22, from SV_BamReader.cpp:15: @@ -929,88 +956,127 @@ | ^ In file included from SV_BreakPoint.h:19, from SV_SplitReadReader.h:22, - from SV_SplitRead.cpp:19: + 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 ../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_BreakPoint.h:19, - from SV_VcfVariant.h:18, - from SV_VcfVariant.cpp:15: + 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 ../utils//bedFilePE/bedFilePE.h:12, - from SV_SplitRead.h:27, - from SV_SplitReadReader.cpp:16: +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_Pair.cpp:15: + 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_Evidence.h:22, - from lumpy.cpp:24: +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 SV_Tools.h:19, + from SV_Tools.cpp:24: ../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_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_Evidence.h:22, - from SV_Bedpe.h:18, - from SV_BedpeReader.cpp:15: +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_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 SV_Tools.h:19, - from SV_Tools.cpp:24: +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 SV_BreakPoint.h:19, - from SV_PairReader.h:22, - from SV_Pair.cpp:19: + from SV_Evidence.h:22, + from lumpy.cpp:24: ../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: +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; + | ^~~~~~~~~~~~~~ +SV_BreakPoint.cpp:266:50: warning: variable ‘b_overlap_intr’ set but not used [-Wunused-but-set-variable] + 266 | struct breakpoint_interval *a_overlap_intr, *b_overlap_intr; + | ^~~~~~~~~~~~~~ +In file included from ../utils//bedFilePE/bedFilePE.h:12, + 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 SV_Tools.cpp:27: +../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_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) { + | ~~^~~~~~ +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 ../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) { + | ^ +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 ) ) { + | ~~~~~~~~~~~~~^~~~~ 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_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) { - | ^ ../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); @@ -1029,29 +1095,6 @@ ../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_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_Tools.cpp:27: -../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_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 ) ) { - | ~~~~~~~~~~~~~^~~~~ -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) { - | ^ ../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); @@ -1070,13 +1113,6 @@ ../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_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) { - | ^ 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)) @@ -1181,8 +1217,8 @@ dpkg-gencontrol: warning: package lumpy-sv: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'lumpy-sv-dbgsym' in '../lumpy-sv-dbgsym_0.3.1+dfsg-7_amd64.deb'. dpkg-deb: building package 'lumpy-sv' in '../lumpy-sv_0.3.1+dfsg-7_amd64.deb'. +dpkg-deb: building package 'lumpy-sv-dbgsym' in '../lumpy-sv-dbgsym_0.3.1+dfsg-7_amd64.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_amd64.buildinfo dpkg-genchanges --build=binary -O../lumpy-sv_0.3.1+dfsg-7_amd64.changes @@ -1191,12 +1227,14 @@ 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/3756556/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3756556/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/3984851 and its subdirectories -I: Current time: Thu Mar 6 17:39:54 -12 2025 -I: pbuilder-time-stamp: 1741325994 +I: removing directory /srv/workspace/pbuilder/3756556 and its subdirectories +I: Current time: Fri Apr 10 02:04:24 +14 2026 +I: pbuilder-time-stamp: 1775736264