Diff of the two buildlogs: -- --- b1/build.log 2025-09-15 07:58:55.472927097 +0000 +++ b2/build.log 2025-09-15 07:59:47.764994943 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Oct 18 02:21:11 -12 2026 -I: pbuilder-time-stamp: 1792333271 +I: Current time: Mon Sep 15 21:58:57 +14 2025 +I: pbuilder-time-stamp: 1757923137 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -24,53 +24,85 @@ dpkg-source: info: applying cross.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1644662/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/139500/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Sep 15 07:59 /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/139500/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/139500/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='255f36d4e32d481a88103ab39a2bd453' - 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='1644662' - PS1='# ' - PS2='> ' + INVOCATION_ID=8fae54167d784b79ab5016550f77c5d6 + 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=139500 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.cVBiH1Tm/pbuilderrc_a8jt --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.cVBiH1Tm/b1 --logfile b1/build.log survivor_1.0.7-4.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.cVBiH1Tm/pbuilderrc_EbbG --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.cVBiH1Tm/b2 --logfile b2/build.log survivor_1.0.7-4.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.12.43+deb13-cloud-arm64 #1 SMP Debian 6.12.43-1 (2025-08-27) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-cloud-arm64 #1 SMP Debian 6.12.43-1 (2025-08-27) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1644662/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/139500/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -138,7 +170,7 @@ Get: 28 http://deb.debian.org/debian forky/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian forky/main arm64 debhelper all 13.26 [939 kB] Get: 30 http://deb.debian.org/debian forky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] -Fetched 11.9 MB in 0s (190 MB/s) +Fetched 11.9 MB in 0s (103 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (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 ... 20020 files and directories currently installed.) @@ -273,7 +305,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/survivor-1.0.7/ && 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 > ../survivor_1.0.7-4_source.changes +I: user script /srv/workspace/pbuilder/139500/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/139500/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/survivor-1.0.7/ && 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 > ../survivor_1.0.7-4_source.changes dpkg-buildpackage: info: source package survivor dpkg-buildpackage: info: source version 1.0.7-4 dpkg-buildpackage: info: source distribution unstable @@ -300,60 +336,40 @@ make[1]: Entering directory '/build/reproducible-path/survivor-1.0.7/Debug' Building file: ../src/vcfs/Annotate_vcf.cpp Building file: ../src/vcfs/Combine_3_VCF.cpp +Building file: ../src/vcfs/Detect_nested.cpp Building file: ../src/vcfs/Compoverlap_VCF.cpp Invoking: Cross G++ Compiler -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Combine_3_VCF.d" -MT"src/vcfs/Combine_3_VCF.o" -o "src/vcfs/Combine_3_VCF.o" "../src/vcfs/Combine_3_VCF.cpp" +Building file: ../src/vcfs/Filter_vcf.cpp +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Annotate_vcf.d" -MT"src/vcfs/Annotate_vcf.o" -o "src/vcfs/Annotate_vcf.o" "../src/vcfs/Annotate_vcf.cpp" Invoking: Cross G++ Compiler Invoking: Cross G++ Compiler -Building file: ../src/vcfs/Detect_nested.cpp -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Annotate_vcf.d" -MT"src/vcfs/Annotate_vcf.o" -o "src/vcfs/Annotate_vcf.o" "../src/vcfs/Annotate_vcf.cpp" -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Compoverlap_VCF.d" -MT"src/vcfs/Compoverlap_VCF.o" -o "src/vcfs/Compoverlap_VCF.o" "../src/vcfs/Compoverlap_VCF.cpp" -Building file: ../src/vcfs/Filter_vcf.cpp +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Combine_3_VCF.d" -MT"src/vcfs/Combine_3_VCF.o" -o "src/vcfs/Combine_3_VCF.o" "../src/vcfs/Combine_3_VCF.cpp" Invoking: Cross G++ Compiler -Building file: ../src/vcfs/Generate_distMat.cpp g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Detect_nested.d" -MT"src/vcfs/Detect_nested.o" -o "src/vcfs/Detect_nested.o" "../src/vcfs/Detect_nested.cpp" +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Compoverlap_VCF.d" -MT"src/vcfs/Compoverlap_VCF.o" -o "src/vcfs/Compoverlap_VCF.o" "../src/vcfs/Compoverlap_VCF.cpp" Invoking: Cross G++ Compiler -Invoking: Cross G++ Compiler +Building file: ../src/vcfs/Generate_distMat.cpp g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Filter_vcf.d" -MT"src/vcfs/Filter_vcf.o" -o "src/vcfs/Filter_vcf.o" "../src/vcfs/Filter_vcf.cpp" +Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Generate_distMat.d" -MT"src/vcfs/Generate_distMat.o" -o "src/vcfs/Generate_distMat.o" "../src/vcfs/Generate_distMat.cpp" -Building file: ../src/snp_overlap/Overlap_snps.cpp -Building file: ../src/simulator/Error_scanner.cpp Building file: ../src/vcfs/Merge_VCF.cpp -Invoking: Cross G++ Compiler +Building file: ../src/snp_overlap/Overlap_snps.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Merge_VCF.d" -MT"src/vcfs/Merge_VCF.o" -o "src/vcfs/Merge_VCF.o" "../src/vcfs/Merge_VCF.cpp" Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/snp_overlap/Overlap_snps.d" -MT"src/snp_overlap/Overlap_snps.o" -o "src/snp_overlap/Overlap_snps.o" "../src/snp_overlap/Overlap_snps.cpp" -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/Error_scanner.d" -MT"src/simulator/Error_scanner.o" -o "src/simulator/Error_scanner.o" "../src/simulator/Error_scanner.cpp" +Building file: ../src/simulator/Error_scanner.cpp Building file: ../src/simulator/Eval_vcf.cpp Building file: ../src/simulator/Pac_Simulator.cpp Invoking: Cross G++ Compiler -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/Eval_vcf.d" -MT"src/simulator/Eval_vcf.o" -o "src/simulator/Eval_vcf.o" "../src/simulator/Eval_vcf.cpp" Invoking: Cross G++ Compiler -Building file: ../src/simulator/SV_Simulator.cpp +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/Error_scanner.d" -MT"src/simulator/Error_scanner.o" -o "src/simulator/Error_scanner.o" "../src/simulator/Error_scanner.cpp" Invoking: Cross G++ Compiler +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/Eval_vcf.d" -MT"src/simulator/Eval_vcf.o" -o "src/simulator/Eval_vcf.o" "../src/simulator/Eval_vcf.cpp" g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/Pac_Simulator.d" -MT"src/simulator/Pac_Simulator.o" -o "src/simulator/Pac_Simulator.o" "../src/simulator/Pac_Simulator.cpp" +Building file: ../src/simulator/SV_Simulator.cpp +Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/SV_Simulator.d" -MT"src/simulator/SV_Simulator.o" -o "src/simulator/SV_Simulator.o" "../src/simulator/SV_Simulator.cpp" -../src/simulator/Eval_vcf.cpp: In function ‘void reprotvals(const char*)’: -../src/simulator/Eval_vcf.cpp:102:15: warning: variable ‘dv’ set but not used [-Wunused-but-set-variable] - 102 | float dv = 0; //"# high-quality variant pairs" - | ^~ -../src/simulator/Eval_vcf.cpp:103:15: warning: variable ‘dr’ set but not used [-Wunused-but-set-variable] - 103 | float dr = 0; //"# high-quality reference pairs" - | ^~ -../src/simulator/Eval_vcf.cpp:104:13: warning: variable ‘gq’ set but not used [-Wunused-but-set-variable] - 104 | int gq = 0; //"Genotype Quality" - | ^~ -../src/simulator/Eval_vcf.cpp:105:13: warning: variable ‘rr’ set but not used [-Wunused-but-set-variable] - 105 | int rr = 0; - | ^~ -../src/simulator/Eval_vcf.cpp:106:13: warning: variable ‘rv’ set but not used [-Wunused-but-set-variable] - 106 | int rv = 0; - | ^~ -../src/vcfs/Filter_vcf.cpp: In function ‘void translate(const char*, int, float, int, strentry&)’: -../src/vcfs/Filter_vcf.cpp:18:13: warning: variable ‘lumpy’ set but not used [-Wunused-but-set-variable] - 18 | int lumpy = 0; - | ^~~~~ ../src/simulator/Error_scanner.cpp: In function ‘void computeAlignment(std::vector, char*, std::string, std::vector > >&, std::string)’: ../src/simulator/Error_scanner.cpp:173:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 173 | while (pos + 1 > error_mat.size()) { @@ -377,22 +393,42 @@ ../src/snp_overlap/Overlap_snps.cpp:781:61: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 781 | for (size_t pos = entries[i].start.pos; pos < entries[i].stop.pos; pos++) { | ~~~~^~~~~~~~~~~~~~~~~~~~~ -Finished building: ../src/simulator/Pac_Simulator.cpp +../src/vcfs/Filter_vcf.cpp: In function ‘void translate(const char*, int, float, int, strentry&)’: +../src/vcfs/Filter_vcf.cpp:18:13: warning: variable ‘lumpy’ set but not used [-Wunused-but-set-variable] + 18 | int lumpy = 0; + | ^~~~~ +../src/simulator/Eval_vcf.cpp: In function ‘void reprotvals(const char*)’: +../src/simulator/Eval_vcf.cpp:102:15: warning: variable ‘dv’ set but not used [-Wunused-but-set-variable] + 102 | float dv = 0; //"# high-quality variant pairs" + | ^~ +../src/simulator/Eval_vcf.cpp:103:15: warning: variable ‘dr’ set but not used [-Wunused-but-set-variable] + 103 | float dr = 0; //"# high-quality reference pairs" + | ^~ +../src/simulator/Eval_vcf.cpp:104:13: warning: variable ‘gq’ set but not used [-Wunused-but-set-variable] + 104 | int gq = 0; //"Genotype Quality" + | ^~ +../src/simulator/Eval_vcf.cpp:105:13: warning: variable ‘rr’ set but not used [-Wunused-but-set-variable] + 105 | int rr = 0; + | ^~ +../src/simulator/Eval_vcf.cpp:106:13: warning: variable ‘rv’ set but not used [-Wunused-but-set-variable] + 106 | int rv = 0; + | ^~ +Finished building: ../src/vcfs/Generate_distMat.cpp Building file: ../src/simulator/Sim_reads.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/Sim_reads.d" -MT"src/simulator/Sim_reads.o" -o "src/simulator/Sim_reads.o" "../src/simulator/Sim_reads.cpp" -Finished building: ../src/vcfs/Detect_nested.cpp +Finished building: ../src/simulator/Pac_Simulator.cpp Building file: ../src/simulator/test_cov.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/test_cov.d" -MT"src/simulator/test_cov.o" -o "src/simulator/test_cov.o" "../src/simulator/test_cov.cpp" -Finished building: ../src/vcfs/Generate_distMat.cpp +Finished building: ../src/vcfs/Detect_nested.cpp Building file: ../src/scrup_vcf/scrup_svs.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/scrup_vcf/scrup_svs.d" -MT"src/scrup_vcf/scrup_svs.o" -o "src/scrup_vcf/scrup_svs.o" "../src/scrup_vcf/scrup_svs.cpp" -Finished building: ../src/scrup_vcf/scrup_svs.cpp +Finished building: ../src/simulator/Error_scanner.cpp Building file: ../src/phasing/Phasing_vcf.cpp Invoking: Cross G++ Compiler @@ -402,12 +438,12 @@ Building file: ../src/merge_vcf/IntervallTree.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/merge_vcf/IntervallTree.d" -MT"src/merge_vcf/IntervallTree.o" -o "src/merge_vcf/IntervallTree.o" "../src/merge_vcf/IntervallTree.cpp" -Finished building: ../src/vcfs/Compoverlap_VCF.cpp +Finished building: ../src/scrup_vcf/scrup_svs.cpp Building file: ../src/merge_vcf/combine_svs.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/merge_vcf/combine_svs.d" -MT"src/merge_vcf/combine_svs.o" -o "src/merge_vcf/combine_svs.o" "../src/merge_vcf/combine_svs.cpp" -Finished building: ../src/simulator/Error_scanner.cpp +Finished building: ../src/vcfs/Compoverlap_VCF.cpp Building file: ../src/convert/ConvertMQ0Bed.cpp Invoking: Cross G++ Compiler @@ -422,26 +458,26 @@ ../src/merge_vcf/combine_svs.cpp:215:58: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 215 | if (pos < entry->caller_info.size() && i == entry->caller_info[pos]->id) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -Finished building: ../src/simulator/Sim_reads.cpp - -Building file: ../src/convert/Convert_Assemblytics.cpp -Invoking: Cross G++ Compiler -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_Assemblytics.d" -MT"src/convert/Convert_Assemblytics.o" -o "src/convert/Convert_Assemblytics.o" "../src/convert/Convert_Assemblytics.cpp" ../src/merge_vcf/combine_svs.cpp: In function ‘void combine_calls_svs(std::string, double, int, int, int, int, int, std::string)’: ../src/merge_vcf/combine_svs.cpp:688:31: warning: variable ‘type’ set but not used [-Wunused-but-set-variable] 688 | short type = (*i)->type; | ^~~~ Finished building: ../src/convert/ConvertMQ0Bed.cpp +Building file: ../src/convert/Convert_Assemblytics.cpp +Invoking: Cross G++ Compiler +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_Assemblytics.d" -MT"src/convert/Convert_Assemblytics.o" -o "src/convert/Convert_Assemblytics.o" "../src/convert/Convert_Assemblytics.cpp" +Finished building: ../src/phasing/Phasing_vcf.cpp + Building file: ../src/convert/Convert_Bionano.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_Bionano.d" -MT"src/convert/Convert_Bionano.o" -o "src/convert/Convert_Bionano.o" "../src/convert/Convert_Bionano.cpp" -Finished building: ../src/phasing/Phasing_vcf.cpp +Finished building: ../src/vcfs/Merge_VCF.cpp Building file: ../src/convert/Convert_Honey_tails.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_Honey_tails.d" -MT"src/convert/Convert_Honey_tails.o" -o "src/convert/Convert_Honey_tails.o" "../src/convert/Convert_Honey_tails.cpp" -Finished building: ../src/simulator/Eval_vcf.cpp +Finished building: ../src/simulator/Sim_reads.cpp Building file: ../src/convert/Convert_MUMmer.cpp Invoking: Cross G++ Compiler @@ -455,60 +491,63 @@ ../src/convert/Convert_Honey_tails.cpp:45:21: warning: variable ‘dist’ set but not used [-Wunused-but-set-variable] 45 | int dist=0; | ^~~~ -Finished building: ../src/convert/Convert_MUMmer.cpp +Finished building: ../src/simulator/Eval_vcf.cpp Building file: ../src/convert/Convert_VCF_to_BED.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_VCF_to_BED.d" -MT"src/convert/Convert_VCF_to_BED.o" -o "src/convert/Convert_VCF_to_BED.o" "../src/convert/Convert_VCF_to_BED.cpp" -Finished building: ../src/merge_vcf/IntervallTree.cpp +Finished building: ../src/convert/Convert_MUMmer.cpp Building file: ../src/convert/Convert_hapcut2.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_hapcut2.d" -MT"src/convert/Convert_hapcut2.o" -o "src/convert/Convert_hapcut2.o" "../src/convert/Convert_hapcut2.cpp" -Finished building: ../src/convert/Convert_Assemblytics.cpp - -Building file: ../src/convert/Process_Coverage.cpp -Invoking: Cross G++ Compiler -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Process_Coverage.d" -MT"src/convert/Process_Coverage.o" -o "src/convert/Process_Coverage.o" "../src/convert/Process_Coverage.cpp" ../src/convert/Convert_VCF_to_BED.cpp: In function ‘std::string print_entry_bed(strvcfentry&)’: ../src/convert/Convert_VCF_to_BED.cpp:348:20: warning: unknown escape sequence: ‘\/’ 348 | convert << "\tGT\t.\/."; | ^~~~~~~~~~~~ +Finished building: ../src/vcfs/Combine_3_VCF.cpp + +Building file: ../src/convert/Process_Coverage.cpp +Invoking: Cross G++ Compiler +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Process_Coverage.d" -MT"src/convert/Process_Coverage.o" -o "src/convert/Process_Coverage.o" "../src/convert/Process_Coverage.cpp" Finished building: ../src/snp_overlap/Overlap_snps.cpp Building file: ../src/convert/Process_Lumpy.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Process_Lumpy.d" -MT"src/convert/Process_Lumpy.o" -o "src/convert/Process_Lumpy.o" "../src/convert/Process_Lumpy.cpp" -Finished building: ../src/convert/Convert_Bionano.cpp +Finished building: ../src/convert/Convert_Assemblytics.cpp Building file: ../src/convert/Update_bam_pacbio.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Update_bam_pacbio.d" -MT"src/convert/Update_bam_pacbio.o" -o "src/convert/Update_bam_pacbio.o" "../src/convert/Update_bam_pacbio.cpp" -Finished building: ../src/vcfs/Merge_VCF.cpp +Finished building: ../src/merge_vcf/IntervallTree.cpp Building file: ../src/analysis_sv/GIAB_summary.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/GIAB_summary.d" -MT"src/analysis_sv/GIAB_summary.o" -o "src/analysis_sv/GIAB_summary.o" "../src/analysis_sv/GIAB_summary.cpp" -Finished building: ../src/convert/Convert_Pindel.cpp +Finished building: ../src/convert/Convert_Honey_tails.cpp Building file: ../src/analysis_sv/MT_identifier.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/MT_identifier.d" -MT"src/analysis_sv/MT_identifier.o" -o "src/analysis_sv/MT_identifier.o" "../src/analysis_sv/MT_identifier.cpp" -Finished building: ../src/convert/Convert_Honey_tails.cpp +Finished building: ../src/convert/Convert_Bionano.cpp Building file: ../src/analysis_sv/MUMmer_overlap.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/MUMmer_overlap.d" -MT"src/analysis_sv/MUMmer_overlap.o" -o "src/analysis_sv/MUMmer_overlap.o" "../src/analysis_sv/MUMmer_overlap.cpp" -Finished building: ../src/vcfs/Combine_3_VCF.cpp +Finished building: ../src/convert/Process_Coverage.cpp Building file: ../src/analysis_sv/Select_samples.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/Select_samples.d" -MT"src/analysis_sv/Select_samples.o" -o "src/analysis_sv/Select_samples.o" "../src/analysis_sv/Select_samples.cpp" -Finished building: ../src/convert/Process_Coverage.cpp +Finished building: ../src/merge_vcf/combine_svs.cpp Building file: ../src/analysis_sv/Simplify_SVs.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/Simplify_SVs.d" -MT"src/analysis_sv/Simplify_SVs.o" -o "src/analysis_sv/Simplify_SVs.o" "../src/analysis_sv/Simplify_SVs.cpp" +Finished building: ../src/convert/Convert_Pindel.cpp + +Building file: ../src/analysis_sv/Summ_mat.cpp ../src/analysis_sv/MUMmer_overlap.cpp: In function ‘void comp_entries_mummer(std::vector&, std::string, int)’: ../src/analysis_sv/MUMmer_overlap.cpp:60:21: warning: variable ‘stop’ set but not used [-Wunused-but-set-variable] 60 | int stop = 0; @@ -516,53 +555,48 @@ ../src/analysis_sv/MUMmer_overlap.cpp:61:21: warning: variable ‘len’ set but not used [-Wunused-but-set-variable] 61 | int len = 0; | ^~~ -Finished building: ../src/analysis_sv/MT_identifier.cpp - -Building file: ../src/analysis_sv/Summ_mat.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/Summ_mat.d" -MT"src/analysis_sv/Summ_mat.o" -o "src/analysis_sv/Summ_mat.o" "../src/analysis_sv/Summ_mat.cpp" -Finished building: ../src/convert/Update_bam_pacbio.cpp +Finished building: ../src/convert/Convert_VCF_to_BED.cpp Building file: ../src/CorrectAllele.cpp -../src/analysis_sv/Simplify_SVs.cpp: In function ‘sv_simple_str parse_line_sv(char*, int, std::vector >, std::string&)’: -../src/analysis_sv/Simplify_SVs.cpp:54:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 54 | for (size_t i = 0; i < buffer_size && buffer[i] != '\0' && buffer[i] != '\n'; i++) { - | ~~^~~~~~~~~~~~~ Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/CorrectAllele.d" -MT"src/CorrectAllele.o" -o "src/CorrectAllele.o" "../src/CorrectAllele.cpp" -../src/analysis_sv/Simplify_SVs.cpp: In function ‘void print_gene_sv(std::string, sv_simple_str, FILE*&, int, std::map, std::vector > >)’: -../src/analysis_sv/Simplify_SVs.cpp:118:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map, bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 118 | if (count + 1 < entry.accessions.size()) { - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -Finished building: ../src/convert/Process_Lumpy.cpp +Finished building: ../src/simulator/SV_Simulator.cpp Building file: ../src/DetectDif.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/DetectDif.d" -MT"src/DetectDif.o" -o "src/DetectDif.o" "../src/DetectDif.cpp" -Finished building: ../src/convert/Convert_hapcut2.cpp +Finished building: ../src/analysis_sv/MT_identifier.cpp Building file: ../src/Extract_Seq.cpp Invoking: Cross G++ Compiler +../src/analysis_sv/Simplify_SVs.cpp: In function ‘sv_simple_str parse_line_sv(char*, int, std::vector >, std::string&)’: +../src/analysis_sv/Simplify_SVs.cpp:54:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 54 | for (size_t i = 0; i < buffer_size && buffer[i] != '\0' && buffer[i] != '\n'; i++) { + | ~~^~~~~~~~~~~~~ g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Extract_Seq.d" -MT"src/Extract_Seq.o" -o "src/Extract_Seq.o" "../src/Extract_Seq.cpp" -Finished building: ../src/vcfs/Annotate_vcf.cpp +../src/analysis_sv/Simplify_SVs.cpp: In function ‘void print_gene_sv(std::string, sv_simple_str, FILE*&, int, std::map, std::vector > >)’: +../src/analysis_sv/Simplify_SVs.cpp:118:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map, bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 118 | if (count + 1 < entry.accessions.size()) { + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +Finished building: ../src/convert/Update_bam_pacbio.cpp Building file: ../src/SURVIVOR.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/SURVIVOR.d" -MT"src/SURVIVOR.o" -o "src/SURVIVOR.o" "../src/SURVIVOR.cpp" -Finished building: ../src/analysis_sv/Select_samples.cpp +Finished building: ../src/convert/Convert_hapcut2.cpp Building file: ../src/Summarize_SV.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Summarize_SV.d" -MT"src/Summarize_SV.o" -o "src/Summarize_SV.o" "../src/Summarize_SV.cpp" -Finished building: ../src/DetectDif.cpp +Finished building: ../src/convert/Process_Lumpy.cpp -Finished building: ../src/convert/Convert_VCF_to_BED.cpp +Finished building: ../src/vcfs/Annotate_vcf.cpp Finished building: ../src/analysis_sv/MUMmer_overlap.cpp -Finished building: ../src/merge_vcf/combine_svs.cpp - -Finished building: ../src/CorrectAllele.cpp +Finished building: ../src/analysis_sv/Select_samples.cpp ../src/Summarize_SV.cpp: In function ‘void summary_venn(std::string, bool, std::string)’: ../src/Summarize_SV.cpp:608:65: warning: format ‘%e’ expects argument of type ‘double’, but argument 3 has type ‘int’ [-Wformat=] @@ -572,15 +606,15 @@ | | int | double | %d -Finished building: ../src/simulator/SV_Simulator.cpp +Finished building: ../src/DetectDif.cpp Finished building: ../src/analysis_sv/Summ_mat.cpp Finished building: ../src/SURVIVOR.cpp -Finished building: ../src/analysis_sv/Simplify_SVs.cpp +Finished building: ../src/CorrectAllele.cpp -Finished building: ../src/analysis_sv/GIAB_summary.cpp +Finished building: ../src/analysis_sv/Simplify_SVs.cpp ../src/Summarize_SV.cpp: In function ‘void summary_SV_stream(int, int, std::string)’: ../src/Summarize_SV.cpp:302:70: warning: ‘type’ may be used uninitialized [-Wmaybe-uninitialized] @@ -589,6 +623,8 @@ ../src/Summarize_SV.cpp:281:39: note: ‘type’ was declared here 281 | short type; | ^~~~ +Finished building: ../src/analysis_sv/GIAB_summary.cpp + Finished building: ../src/Extract_Seq.cpp Finished building: ../src/Summarize_SV.cpp @@ -623,8 +659,8 @@ dh_gencontrol -O--sourcedirectory=Debug dh_md5sums -O--sourcedirectory=Debug dh_builddeb -O--sourcedirectory=Debug -dpkg-deb: building package 'survivor-dbgsym' in '../survivor-dbgsym_1.0.7-4_arm64.deb'. dpkg-deb: building package 'survivor' in '../survivor_1.0.7-4_arm64.deb'. +dpkg-deb: building package 'survivor-dbgsym' in '../survivor-dbgsym_1.0.7-4_arm64.deb'. dpkg-genbuildinfo --build=binary -O../survivor_1.0.7-4_arm64.buildinfo dpkg-genchanges --build=binary -O../survivor_1.0.7-4_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -632,12 +668,14 @@ 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/139500/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/139500/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/1644662 and its subdirectories -I: Current time: Sun Oct 18 02:21:53 -12 2026 -I: pbuilder-time-stamp: 1792333313 +I: removing directory /srv/workspace/pbuilder/139500 and its subdirectories +I: Current time: Mon Sep 15 21:59:47 +14 2025 +I: pbuilder-time-stamp: 1757923187