Diff of the two buildlogs: -- --- b1/build.log 2024-05-05 09:59:58.721295813 +0000 +++ b2/build.log 2024-05-05 10:04:26.881877142 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jun 7 04:21:30 -12 2025 -I: pbuilder-time-stamp: 1749313290 +I: Current time: Mon May 6 00:00:01 +14 2024 +I: pbuilder-time-stamp: 1714903201 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -32,52 +32,84 @@ 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/310489/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1542574/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 5 10:00 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/1542574/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1542574/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='f00acbe603a646db94afcf5d2a45759a' - 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='310489' - PS1='# ' - PS2='> ' + INVOCATION_ID=e1f8f67b0f744c128815a0897d74e50d + 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=1542574 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.M5WtZT8S/pbuilderrc_RKJt --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.M5WtZT8S/b1 --logfile b1/build.log vt_0.57721+ds-3.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://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.M5WtZT8S/pbuilderrc_oDLn --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.M5WtZT8S/b2 --logfile b2/build.log vt_0.57721+ds-3.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 5 14:46 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/310489/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 3 08:24 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1542574/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -262,7 +294,7 @@ Get: 123 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.3.2-1 [26.8 MB] Get: 125 http://deb.debian.org/debian trixie/main amd64 r-mathlib amd64 4.3.2-1 [2453 kB] -Fetched 82.4 MB in 1s (97.6 MB/s) +Fetched 82.4 MB in 2s (48.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19695 files and directories currently installed.) @@ -684,8 +716,8 @@ Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Jun 7 16:22:00 UTC 2025. -Universal Time is now: Sat Jun 7 16:22:00 UTC 2025. +Local time is now: Sun May 5 10:01:07 UTC 2024. +Universal Time is now: Sun May 5 10:01:07 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up zip (3.0-13) ... @@ -808,7 +840,11 @@ 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/1542574/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1542574/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 @@ -818,7 +854,7 @@ debian/rules clean dh clean dh_auto_clean - make -j42 clean + make -j20 clean make[1]: Entering directory '/build/reproducible-path/vt-0.57721+ds' rm -rf vt ahmm.o align.o allele.o annotate_1000g.o annotate_dbsnp_rsid.o annotate_indels.o annotate_indels2.o annotate_regions.o annotate_variants.o annotate_vntrs.o augmented_bam_record.o bcf_genotyping_buffered_reader.o bcf_single_genotyping_buffered_reader.o bam_ordered_reader.o bcf_ordered_reader.o bcf_ordered_writer.o bcf_synced_reader.o bed.o candidate_motif_picker.o candidate_region_extractor.o cat.o chmm.o complex_genotyping_record.o compute_concordance.o compute_features.o compute_features2.o compute_rl_dist.o config.o consolidate_multiallelics.o consolidate_vntrs.o consolidate.o construct_probes.o decompose.o decompose2.o decompose_blocksub.o discover.o duplicate.o estimate.o estimator.o extract_vntrs.o filter.o filter_overlap.o flank_detector.o fuzzy_aligner.o fuzzy_partition.o gencode.o genome_interval.o genotype.o genotyping_record.o ghmm.o hts_utils.o hfilter.o indel_annotator.o indel_genotyping_record.o index.o info2tab.o interval_tree.o interval.o lfhmm.o lhmm.o lhmm1.o liftover.o log_tool.o merge.o merge_candidate_variants.o merge_genotypes.o milk_filter.o motif_tree.o motif_map.o multi_partition.o multiallelics_consolidator.o needle.o normalize.o nuclear_pedigree.o ordered_bcf_overlap_matcher.o ordered_region_overlap_matcher.o partition.o paste.o paste_and_compute_features_sequential.o paste_genotypes.o pedigree.o peek.o pileup.o pregex.o profile_afs.o profile_chm1.o profile_chrom.o profile_fic_hwe.o profile_hwe.o profile_indels.o profile_len.o profile_mendelian.o profile_na12878.o profile_snps.o profile_vntrs.o program.o read_filter.o reference_sequence.o rfhmm.o rfhmm_x.o rminfo.o seq.o set_ref.o snp_genotyping_record.o sort.o subset.o sv_tree.o svm_train.o svm_predict.o tbx_ordered_reader.o test.o trio.o union_variants.o uniq.o utils.o validate.o variant.o variant_manip.o variant_filter.o view.o vntr.o vntr_annotator.o vntr_consolidator.o vntr_extractor.o vntr_genotyping_record.o vntr_tree.o vntrize.o wdp_ahmm.o main.o make[1]: Leaving directory '/build/reproducible-path/vt-0.57721+ds' @@ -829,7 +865,7 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j42 "INSTALL=install --strip-program=true" + make -j20 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/vt-0.57721+ds' 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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o ahmm.o -c ahmm.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o align.o -c align.cpp @@ -853,26 +889,6 @@ 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 -fcf-protection -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 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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o cat.o -c cat.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o chmm.o -c chmm.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o complex_genotyping_record.o -c complex_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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o compute_concordance.o -c compute_concordance.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o compute_features.o -c compute_features.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o compute_features2.o -c compute_features2.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o compute_rl_dist.o -c compute_rl_dist.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o config.o -c config.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o consolidate_multiallelics.o -c consolidate_multiallelics.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o consolidate_vntrs.o -c consolidate_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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o consolidate.o -c consolidate.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o construct_probes.o -c construct_probes.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o decompose.o -c decompose.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o decompose2.o -c decompose2.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 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", @@ -892,6 +908,22 @@ | | | int | %ld +bcf_ordered_writer.cpp: In member function 'void BCFOrderedWriter::write_hdr()': +bcf_ordered_writer.cpp:129:18: warning: ignoring return value of 'int bcf_hdr_write(htsFile*, bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 129 | bcf_hdr_write(file, hdr); + | ~~~~~~~~~~~~~^~~~~~~~~~~ +bcf_ordered_writer.cpp: In member function 'void BCFOrderedWriter::write(bcf1_t*)': +bcf_ordered_writer.cpp:195:18: warning: ignoring return value of 'int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 195 | bcf_write(file, hdr, v); + | ~~~~~~~~~^~~~~~~~~~~~~~ +bcf_ordered_writer.cpp: In member function 'void BCFOrderedWriter::flush(bool)': +bcf_ordered_writer.cpp:245:22: warning: ignoring return value of 'int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 245 | bcf_write(file, hdr, buffer.back()); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o complex_genotyping_record.o -c complex_genotyping_record.cpp ahmm.cpp: In member function 'void AHMM::collect_statistics(int32_t, int32_t, int32_t)': ahmm.cpp:687:35: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 687 | rflank_start[MODEL] = NAN; @@ -942,7 +974,6 @@ ahmm.cpp:748:17: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 748 | 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 -fcf-protection -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 ahmm.cpp:750:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 750 | rflank_start[MODEL] = NAN; | ^~~ @@ -955,21 +986,10 @@ ahmm.cpp:753:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 753 | rflank_end[READ] = NAN; | ^~~ -bcf_ordered_writer.cpp: In member function 'void BCFOrderedWriter::write_hdr()': -bcf_ordered_writer.cpp:129:18: warning: ignoring return value of 'int bcf_hdr_write(htsFile*, bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 129 | bcf_hdr_write(file, hdr); - | ~~~~~~~~~~~~~^~~~~~~~~~~ -bcf_ordered_writer.cpp: In member function 'void BCFOrderedWriter::write(bcf1_t*)': -bcf_ordered_writer.cpp:195:18: warning: ignoring return value of 'int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 195 | bcf_write(file, hdr, v); - | ~~~~~~~~~^~~~~~~~~~~~~~ -bcf_ordered_writer.cpp: In member function 'void BCFOrderedWriter::flush(bool)': -bcf_ordered_writer.cpp:245:22: warning: ignoring return value of 'int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 245 | bcf_write(file, hdr, buffer.back()); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o compute_concordance.o -c compute_concordance.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o compute_features.o -c compute_features.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o compute_features2.o -c compute_features2.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o compute_rl_dist.o -c compute_rl_dist.cpp chmm.cpp: In member function 'void CHMM::clear_statistics()': chmm.cpp:1106:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 1106 | lflank_start[MODEL] = NAN; @@ -1019,7 +1039,20 @@ chmm.cpp:1121:17: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 1121 | 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 -fcf-protection -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 +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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o config.o -c config.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o consolidate_multiallelics.o -c consolidate_multiallelics.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o consolidate_vntrs.o -c consolidate_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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o consolidate.o -c consolidate.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o construct_probes.o -c construct_probes.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o decompose.o -c decompose.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o decompose2.o -c decompose2.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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, @@ -1033,19 +1066,21 @@ | ^~~~~~~~~~~~ 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o fuzzy_partition.o -c fuzzy_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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o gencode.o -c gencode.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 -fcf-protection -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 +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 -fcf-protection -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 -fcf-protection -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 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 -fcf-protection -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 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 -fcf-protection -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 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 In file included from bam_ordered_reader.h:27, from genotype.h:27, from genotype.cpp:24: @@ -1058,28 +1093,19 @@ | ^~~~~~~~~~~~ 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}; -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 -fcf-protection -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 -fcf-protection -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 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o liftover.o -c liftover.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o log_tool.o -c log_tool.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)); - | ~^ - | | - | 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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o merge.o -c merge.cpp lfhmm.cpp: In member function 'void LFHMM::collect_statistics(int32_t, int32_t, int32_t)': lfhmm.cpp:761:33: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 761 | rflank_end[MODEL] = NAN; @@ -1133,12 +1159,20 @@ lfhmm.cpp:884:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 884 | rflank_end[READ] = 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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o liftover.o -c liftover.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o log_tool.o -c log_tool.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o merge.o -c merge.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)); + | ~^ + | | + | 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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o merge_candidate_variants.o -c merge_candidate_variants.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o merge_genotypes.o -c merge_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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o milk_filter.o -c milk_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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 milk_filter.cpp: In member function 'void {anonymous}::Igor::milk_filter()': milk_filter.cpp:456:53: warning: format '%d' expects argument of type 'int', but argument 5 has type 'hts_pos_t' {aka 'long int'} [-Wformat=] 456 | fprintf(stderr,"Processing %d variants at %s:%d\n", nread + 1, bcf_seqname(odw->hdr,nv), nv->pos); @@ -1146,11 +1180,13 @@ | | | | 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 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); | ~~~~~~~~~~~~^~~~~~~~~~ +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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 @@ -1159,6 +1195,14 @@ 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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); + | ~~~~~~~~~~~~^~~~~~~~~~ +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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 @@ -1175,23 +1219,15 @@ 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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_na12878.o -c profile_na12878.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_snps.o -c profile_snps.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_vntrs.o -c profile_vntrs.cpp +profile_mendelian.cpp: In member function 'void {anonymous}::Igor::initialize()': +profile_mendelian.cpp:191:25: warning: ignoring return value of 'int bcf_hdr_sync(bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 191 | bcf_hdr_sync(odw->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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o program.o -c program.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o read_filter.o -c read_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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o reference_sequence.o -c reference_sequence.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o rfhmm.o -c rfhmm.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 -fcf-protection -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 -fcf-protection -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 -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); - | ~~~~~~~~~~~~^~~~~~~~~~ -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 In file included from read_filter.h:30, from read_filter.cpp:24: read_filter.cpp: In member function 'bool ReadFilter::filter_read(bam_hdr_t*, bam1_t*)': @@ -1203,7 +1239,10 @@ | ^~~~~~~~~~~~ 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 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; @@ -1302,13 +1341,10 @@ 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 -fcf-protection -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 -fcf-protection -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 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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o sv_tree.o -c sv_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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o svm_train.o -c svm_train.cpp -profile_mendelian.cpp: In member function 'void {anonymous}::Igor::initialize()': -profile_mendelian.cpp:191:25: warning: ignoring return value of 'int bcf_hdr_sync(bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 191 | bcf_hdr_sync(odw->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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o svm_predict.o -c svm_predict.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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o tbx_ordered_reader.o -c tbx_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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o test.o -c test.cpp @@ -1333,7 +1369,7 @@ 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 -fcf-protection -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o vt ahmm.o align.o allele.o annotate_1000g.o annotate_dbsnp_rsid.o annotate_indels.o annotate_indels2.o annotate_regions.o annotate_variants.o annotate_vntrs.o augmented_bam_record.o bcf_genotyping_buffered_reader.o bcf_single_genotyping_buffered_reader.o bam_ordered_reader.o bcf_ordered_reader.o bcf_ordered_writer.o bcf_synced_reader.o bed.o candidate_motif_picker.o candidate_region_extractor.o cat.o chmm.o complex_genotyping_record.o compute_concordance.o compute_features.o compute_features2.o compute_rl_dist.o config.o consolidate_multiallelics.o consolidate_vntrs.o consolidate.o construct_probes.o decompose.o decompose2.o decompose_blocksub.o discover.o duplicate.o estimate.o estimator.o extract_vntrs.o filter.o filter_overlap.o flank_detector.o fuzzy_aligner.o fuzzy_partition.o gencode.o genome_interval.o genotype.o genotyping_record.o ghmm.o hts_utils.o hfilter.o indel_annotator.o indel_genotyping_record.o index.o info2tab.o interval_tree.o interval.o lfhmm.o lhmm.o lhmm1.o liftover.o log_tool.o merge.o merge_candidate_variants.o merge_genotypes.o milk_filter.o motif_tree.o motif_map.o multi_partition.o multiallelics_consolidator.o needle.o normalize.o nuclear_pedigree.o ordered_bcf_overlap_matcher.o ordered_region_overlap_matcher.o partition.o paste.o paste_and_compute_features_sequential.o paste_genotypes.o pedigree.o peek.o pileup.o pregex.o profile_afs.o profile_chm1.o profile_chrom.o profile_fic_hwe.o profile_hwe.o profile_indels.o profile_len.o profile_mendelian.o profile_na12878.o profile_snps.o profile_vntrs.o program.o read_filter.o reference_sequence.o rfhmm.o rfhmm_x.o rminfo.o seq.o set_ref.o snp_genotyping_record.o sort.o subset.o sv_tree.o svm_train.o svm_predict.o tbx_ordered_reader.o test.o trio.o union_variants.o uniq.o utils.o validate.o variant.o variant_manip.o variant_filter.o view.o vntr.o vntr_annotator.o vntr_consolidator.o vntr_extractor.o vntr_genotyping_record.o vntr_tree.o vntrize.o wdp_ahmm.o main.o -lz -lpthread -lbz2 -llzma -lcurl -lcrypto -lhts -lpcre2-8 -lsvm -lRmath -lR make[1]: Leaving directory '/build/reproducible-path/vt-0.57721+ds' dh_auto_test - make -j42 test + make -j20 test make[1]: Entering directory '/build/reproducible-path/vt-0.57721+ds' test/test.sh ++++++++++++++++++++++ @@ -1384,9 +1420,9 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'vt-examples' in '../vt-examples_0.57721+ds-3_all.deb'. -dpkg-deb: building package 'vt-dbgsym' in '../vt-dbgsym_0.57721+ds-3_amd64.deb'. dpkg-deb: building package 'vt' in '../vt_0.57721+ds-3_amd64.deb'. +dpkg-deb: building package 'vt-dbgsym' in '../vt-dbgsym_0.57721+ds-3_amd64.deb'. +dpkg-deb: building package 'vt-examples' in '../vt-examples_0.57721+ds-3_all.deb'. dpkg-genbuildinfo --build=binary -O../vt_0.57721+ds-3_amd64.buildinfo dpkg-genchanges --build=binary -O../vt_0.57721+ds-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1394,12 +1430,14 @@ 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/1542574/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1542574/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/310489 and its subdirectories -I: Current time: Sat Jun 7 04:22:58 -12 2025 -I: pbuilder-time-stamp: 1749313378 +I: removing directory /srv/workspace/pbuilder/1542574 and its subdirectories +I: Current time: Mon May 6 00:04:26 +14 2024 +I: pbuilder-time-stamp: 1714903466