Diff of the two buildlogs: -- --- b1/build.log 2025-02-07 05:19:51.035851595 +0000 +++ b2/build.log 2025-02-07 05:22:30.956598158 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Mar 11 23:39:12 -12 2026 -I: pbuilder-time-stamp: 1773315552 +I: Current time: Fri Feb 7 19:19:54 +14 2025 +I: pbuilder-time-stamp: 1738905594 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -28,52 +28,84 @@ dpkg-source: info: applying 0002-hts-1.11.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2914229/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1773495/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 Feb 7 05:20 /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/1773495/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1773495/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]="37" [3]="1" [4]="release" [5]="aarch64-unknown-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=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='31864dbb8270414b8950888cbcc00f81' - 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='2914229' - PS1='# ' - PS2='> ' + INVOCATION_ID=4a4b4909d0714fdca8408fe1c8f4906e + 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=1773495 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.U56F9uxS/pbuilderrc_IZgz --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.U56F9uxS/b1 --logfile b1/build.log vt_0.57721+ds-3.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.U56F9uxS/pbuilderrc_zLvh --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.U56F9uxS/b2 --logfile b2/build.log vt_0.57721+ds-3.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 codethink03-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2914229/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1773495/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -300,7 +332,7 @@ Get: 165 http://deb.debian.org/debian trixie/main arm64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 166 http://deb.debian.org/debian trixie/main arm64 r-base-core arm64 4.4.2-1 [28.0 MB] Get: 167 http://deb.debian.org/debian trixie/main arm64 r-mathlib arm64 4.4.2-1 [2582 kB] -Fetched 92.3 MB in 1s (134 MB/s) +Fetched 92.3 MB in 1s (106 MB/s) Preconfiguring packages ... Selecting previously unselected package tzdata. (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 ... 19956 files and directories currently installed.) @@ -855,8 +887,8 @@ Setting up tzdata (2024b-6) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Mar 12 11:39:59 UTC 2026. -Universal Time is now: Thu Mar 12 11:39:59 UTC 2026. +Local time is now: Fri Feb 7 05:20:46 UTC 2025. +Universal Time is now: Fri Feb 7 05:20:46 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up zip (3.0-14+b1) ... @@ -1011,7 +1043,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/vt-0.57721+ds/ && 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 > ../vt_0.57721+ds-3_source.changes +I: user script /srv/workspace/pbuilder/1773495/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1773495/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/vt-0.57721+ds/ && 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 > ../vt_0.57721+ds-3_source.changes dpkg-buildpackage: info: source package vt dpkg-buildpackage: info: source version 0.57721+ds-3 dpkg-buildpackage: info: source distribution unstable @@ -1112,7 +1148,6 @@ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o bam_ordered_reader.o -c bam_ordered_reader.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o bcf_ordered_reader.o -c bcf_ordered_reader.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o bcf_ordered_writer.o -c bcf_ordered_writer.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o bcf_synced_reader.o -c bcf_synced_reader.cpp bcf_ordered_writer.cpp: In member function 'void BCFOrderedWriter::write(bcf1_t*)': bcf_ordered_writer.cpp:162:114: warning: format '%d' expects argument of type 'int', but argument 8 has type 'hts_pos_t' {aka 'long int'} [-Wformat=] 162 | fprintf(stderr, "[%s:%d %s] Might not be sorted for window size %d at current record %s:%d < %d (%d [last record] - %d), please increase window size to at least %d.\n", @@ -1147,6 +1182,7 @@ bcf_ordered_writer.cpp:261:30: warning: ignoring return value of 'int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 261 | bcf_write(file, hdr, buffer.back()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o bcf_synced_reader.o -c bcf_synced_reader.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o bed.o -c bed.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o candidate_motif_picker.o -c candidate_motif_picker.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o candidate_region_extractor.o -c candidate_region_extractor.cpp @@ -1216,10 +1252,6 @@ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o decompose_blocksub.o -c decompose_blocksub.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o discover.o -c discover.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o duplicate.o -c duplicate.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o estimate.o -c estimate.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o estimator.o -c estimator.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o extract_vntrs.o -c extract_vntrs.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o filter.o -c filter.cpp In file included from bcf_ordered_reader.h:27, from program.h:32, from discover.h:27, @@ -1233,6 +1265,10 @@ | ^~~~~~~~~~~~ discover.cpp:355:95: warning: narrowing conversion of '(((s->bam1_t::core.bam1_core_t::pos + 1) + ((hts_pos_t)s->bam1_t::core.bam1_core_t::l_qseq)) - 1)' from 'hts_pos_t' {aka 'long int'} to 'int32_t' {aka 'int'} [-Wnarrowing] 355 | kh_val(reads, k) = {bam_get_pos1(s), bam_get_pos1(s)+bam_get_l_qseq(s)-1}; +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o estimate.o -c estimate.cpp +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o estimator.o -c estimator.cpp +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o extract_vntrs.o -c extract_vntrs.cpp +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o filter.o -c filter.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o filter_overlap.o -c filter_overlap.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o flank_detector.o -c flank_detector.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o fuzzy_aligner.o -c fuzzy_aligner.cpp @@ -1241,10 +1277,6 @@ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o genome_interval.o -c genome_interval.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o genotype.o -c genotype.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o genotyping_record.o -c genotyping_record.cpp -fuzzy_partition.cpp: In member function 'void {anonymous}::Igor::initialize()': -fuzzy_partition.cpp:153:21: warning: ignoring return value of 'int bcf_hdr_sync(bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 153 | bcf_hdr_sync(odr->hdr); - | ~~~~~~~~~~~~^~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o ghmm.o -c ghmm.cpp In file included from bam_ordered_reader.h:27, from genotype.h:27, @@ -1259,16 +1291,21 @@ genotype.cpp:304:95: warning: narrowing conversion of '(((s->bam1_t::core.bam1_core_t::pos + 1) + ((hts_pos_t)s->bam1_t::core.bam1_core_t::l_qseq)) - 1)' from 'hts_pos_t' {aka 'long int'} to 'int32_t' {aka 'int'} [-Wnarrowing] 304 | kh_val(reads, k) = {bam_get_pos1(s), bam_get_pos1(s)+bam_get_l_qseq(s)-1}; g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o hts_utils.o -c hts_utils.cpp +fuzzy_partition.cpp: In member function 'void {anonymous}::Igor::initialize()': +fuzzy_partition.cpp:153:21: warning: ignoring return value of 'int bcf_hdr_sync(bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 153 | bcf_hdr_sync(odr->hdr); + | ~~~~~~~~~~~~^~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o hfilter.o -c hfilter.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o indel_annotator.o -c indel_annotator.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o indel_genotyping_record.o -c indel_genotyping_record.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o index.o -c index.cpp hts_utils.cpp: In function 'void bcf_hdr_print(bcf_hdr_t*)': hts_utils.cpp:406:33: warning: ignoring return value of 'int bcf_hdr_sync(bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 406 | if ( h->dirty ) bcf_hdr_sync(h); | ~~~~~~~~~~~~^~~ +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o indel_genotyping_record.o -c indel_genotyping_record.cpp +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o index.o -c index.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o info2tab.o -c info2tab.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o interval_tree.o -c interval_tree.cpp +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o interval.o -c interval.cpp info2tab.cpp: In member function 'void {anonymous}::Igor::info2tab()': info2tab.cpp:278:32: warning: format '%d' expects argument of type 'int', but argument 4 has type 'hts_pos_t' {aka 'long int'} [-Wformat=] 278 | fprintf(out, "%s\t%d", bcf_get_chrom(h, v), bcf_get_pos1(v)); @@ -1276,7 +1313,6 @@ | | | int | %ld -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o interval.o -c interval.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o lfhmm.o -c lfhmm.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o lhmm.o -c lhmm.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o lhmm1.o -c lhmm1.cpp @@ -1342,7 +1378,6 @@ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o motif_tree.o -c motif_tree.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o motif_map.o -c motif_map.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o multi_partition.o -c multi_partition.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o multiallelics_consolidator.o -c multiallelics_consolidator.cpp merge_genotypes.cpp: In member function 'void {anonymous}::Igor::initialize()': merge_genotypes.cpp:215:21: warning: ignoring return value of 'int bcf_hdr_sync(bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | bcf_hdr_sync(odw->hdr); @@ -1354,22 +1389,23 @@ | | | | int hts_pos_t {aka long int} | %ld +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o multiallelics_consolidator.o -c multiallelics_consolidator.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o needle.o -c needle.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o normalize.o -c normalize.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o nuclear_pedigree.o -c nuclear_pedigree.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o ordered_bcf_overlap_matcher.o -c ordered_bcf_overlap_matcher.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o ordered_region_overlap_matcher.o -c ordered_region_overlap_matcher.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o partition.o -c partition.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o paste.o -c paste.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o paste_and_compute_features_sequential.o -c paste_and_compute_features_sequential.cpp ordered_bcf_overlap_matcher.cpp: In constructor 'OrderedBCFOverlapMatcher::OrderedBCFOverlapMatcher(std::string&, std::vector&)': ordered_bcf_overlap_matcher.cpp:34:17: warning: ignoring return value of 'int bcf_hdr_sync(bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 34 | bcf_hdr_sync(odr->hdr); | ~~~~~~~~~~~~^~~~~~~~~~ +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o paste.o -c paste.cpp ordered_bcf_overlap_matcher.cpp: In constructor 'OrderedBCFOverlapMatcher::OrderedBCFOverlapMatcher(std::string&, std::vector&, std::string)': ordered_bcf_overlap_matcher.cpp:52:17: warning: ignoring return value of 'int bcf_hdr_sync(bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 52 | bcf_hdr_sync(odr->hdr); | ~~~~~~~~~~~~^~~~~~~~~~ +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o paste_and_compute_features_sequential.o -c paste_and_compute_features_sequential.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o paste_genotypes.o -c paste_genotypes.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o pedigree.o -c pedigree.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o peek.o -c peek.cpp @@ -1405,6 +1441,9 @@ | ^~~~~~~~~~~~ read_filter.cpp:95:91: warning: narrowing conversion of '(((s->bam1_t::core.bam1_core_t::pos + 1) + ((hts_pos_t)s->bam1_t::core.bam1_core_t::l_qseq)) - 1)' from 'hts_pos_t' {aka 'long int'} to 'int32_t' {aka 'int'} [-Wnarrowing] 95 | kh_val(reads, k) = {bam_get_pos1(s), bam_get_pos1(s)+bam_get_l_qseq(s)-1}; +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o rfhmm_x.o -c rfhmm_x.cpp +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o rminfo.o -c rminfo.cpp +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o seq.o -c seq.cpp rfhmm.cpp: In member function 'void RFHMM::clear_statistics()': rfhmm.cpp:833:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 833 | lflank_start[MODEL] = NAN; @@ -1454,9 +1493,7 @@ rfhmm.cpp:848:17: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 848 | motif_xid = NAN; | ^~~ -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o rfhmm_x.o -c rfhmm_x.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o rminfo.o -c rminfo.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o seq.o -c seq.cpp +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o set_ref.o -c set_ref.cpp rfhmm_x.cpp: In member function 'void RFHMM_X::clear_statistics()': rfhmm_x.cpp:928:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 928 | lflank_start[MODEL] = NAN; @@ -1506,7 +1543,6 @@ rfhmm_x.cpp:943:17: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 943 | motif_xid = NAN; | ^~~ -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o set_ref.o -c set_ref.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o snp_genotyping_record.o -c snp_genotyping_record.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o sort.o -c sort.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o subset.o -c subset.cpp @@ -1601,12 +1637,14 @@ 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/1773495/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1773495/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/2914229 and its subdirectories -I: Current time: Wed Mar 11 23:42:49 -12 2026 -I: pbuilder-time-stamp: 1773315769 +I: removing directory /srv/workspace/pbuilder/1773495 and its subdirectories +I: Current time: Fri Feb 7 19:22:29 +14 2025 +I: pbuilder-time-stamp: 1738905749