Diff of the two buildlogs: -- --- b1/build.log 2024-12-18 00:20:13.978688682 +0000 +++ b2/build.log 2024-12-18 00:32:18.421856022 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jan 19 18:31:41 -12 2026 -I: pbuilder-time-stamp: 1768890701 +I: Current time: Wed Dec 18 14:20:17 +14 2024 +I: pbuilder-time-stamp: 1734481217 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -33,52 +33,84 @@ dpkg-source: info: applying intersphinx I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2443124/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/763732/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 Dec 18 00:20 /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/763732/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/763732/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='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='f9d6e7b2944b48019f326e104e977f65' - 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='2443124' - PS1='# ' - PS2='> ' + INVOCATION_ID=18ae585f0b604fb1b348a08fde9ffd9c + 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=763732 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.fmJPQiwf/pbuilderrc_D3aW --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.fmJPQiwf/b1 --logfile b1/build.log bedops_2.4.41+dfsg-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.fmJPQiwf/pbuilderrc_3Uq5 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.fmJPQiwf/b2 --logfile b2/build.log bedops_2.4.41+dfsg-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 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2443124/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/763732/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -228,7 +260,7 @@ Get: 94 http://deb.debian.org/debian unstable/main arm64 python3-sphinx all 8.1.3-2 [468 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 tcsh arm64 6.24.13-2+b1 [439 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] -Fetched 47.3 MB in 0s (198 MB/s) +Fetched 47.3 MB in 1s (67.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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 ... 20085 files and directories currently installed.) @@ -553,8 +585,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Jan 20 06:32:09 UTC 2026. -Universal Time is now: Tue Jan 20 06:32:09 UTC 2026. +Local time is now: Wed Dec 18 00:21:22 UTC 2024. +Universal Time is now: Wed Dec 18 00:21:22 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -653,7 +685,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/bedops-2.4.41+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../bedops_2.4.41+dfsg-3_source.changes +I: user script /srv/workspace/pbuilder/763732/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/763732/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/bedops-2.4.41+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../bedops_2.4.41+dfsg-3_source.changes dpkg-buildpackage: info: source package bedops dpkg-buildpackage: info: source version 2.4.41+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -679,36 +715,36 @@ rm -rf objects_typical rm -rf ../bin make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedmap/src' +rm -rf objects_typical make -C applications/bed/bedops/src -f Makefile clean +rm -rf ../bin make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedextract/src' -rm -rf objects_typical make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedops/src' rm -rf objects_typical -rm -rf ../bin make -C applications/bed/closestfeats/src -f Makefile clean -rm -rf ../bin make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedmap/src' -make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/closestfeats/src' +rm -rf ../bin make -C applications/bed/conversion/src -f Makefile clean +make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/closestfeats/src' rm -rf objects_typical -make -C applications/bed/sort-bed/src -f Makefile clean make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/conversion/src' +make -C applications/bed/sort-bed/src -f Makefile clean rm -rf ../bin -rm -rf objects -rm -rf *.so *~ -make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedops/src' rm -rf ../bin -make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/closestfeats/src' +make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedops/src' make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/sort-bed/src' make -C applications/bed/starch/src -f Makefile clean -make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/conversion/src' -rm -rf objects-typical -rm -rf ../bin -make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/sort-bed/src' make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/starch/src' rm -rf ../lib +rm -rf objects +rm -rf objects-typical +make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/closestfeats/src' +rm -rf ../bin rm -f ../lib/libstarch_debug.a +rm -rf *.so *~ rm -f ../lib/libstarch_gprof.a +make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/sort-bed/src' +make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/conversion/src' rm -rf objects rm -rf ../bin make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/starch/src' @@ -746,27 +782,39 @@ make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedextract/src' make -C applications/bed/bedmap/src -f Makefile build mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedmap/src' make -C applications/bed/bedops/src -f Makefile build mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedops/src' make -C applications/bed/closestfeats/src -f Makefile build +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/closestfeats/src' make -C applications/bed/conversion/src -f Makefile build mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/conversion/src' mkdir -p ../bin && cc -Wall -Wextra -pedantic -std=c99 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -iquote"/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/conversion/src" -iquote"../../../../interfaces/general-headers" convert2bed.c -o ../bin/convert2bed-typical -lpthread mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers +convert2bed.c: In function 'c2b_line_convert_rmsk_to_bed_unsorted': +convert2bed.c:3780:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] + 3780 | fprintf(stderr, "Error: Invalid query coordinates at line [%llu]\n", c2b_globals.rmsk->line); + | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~ + | | | + | long long unsigned int uint64_t {aka long unsigned int} + | %lu +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, Boolean, Boolean, char*, Bed::LineLengthType)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] 311 | strncpy(iter->filename, fn, strlen(fn) + 1); @@ -780,29 +828,7 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers -convert2bed.c: In function 'c2b_line_convert_rmsk_to_bed_unsorted': -convert2bed.c:3780:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] - 3780 | fprintf(stderr, "Error: Invalid query coordinates at line [%llu]\n", c2b_globals.rmsk->line); - | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~ - | | | - | long long unsigned int uint64_t {aka long unsigned int} - | %lu -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)': -../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here - 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); - | ~~~~~~^~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(Metadata**, const FILE*, CompressionType, const char*, const char*)': -../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here - 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - | ~~~~~~^~~~~~~~~~~~ +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, Boolean, Boolean, char*, Bed::LineLengthType)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] 311 | strncpy(iter->filename, fn, strlen(fn) + 1); @@ -816,46 +842,8 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, Metadata**, CompressionType*, ArchiveVersion**, uint64_t*, Boolean*, Boolean)': -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 2221 | strncpy(recTokBuf, token, strlen(token) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here - 2221 | strncpy(recTokBuf, token, strlen(token) + 1); - | ~~~~~~^~~~~~~ -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)': -../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here - 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); - | ~~~~~~^~~~~~~~ -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(Metadata**, const FILE*, CompressionType, const char*, const char*)': -../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here - 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - | ~~~~~~^~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, Metadata**, CompressionType, const char*, const char*, Boolean, Boolean, Bed::LineCountType)': -../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here - 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - | ~~~~~~^~~~~~~~~~~~ -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers -../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, Metadata**, CompressionType*, ArchiveVersion**, uint64_t*, Boolean*, Boolean)': -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 2221 | strncpy(recTokBuf, token, strlen(token) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here - 2221 | strncpy(recTokBuf, token, strlen(token) + 1); - | ~~~~~~^~~~~~~ -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); @@ -875,7 +863,28 @@ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)': +../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here + 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); + | ~~~~~~^~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)': +../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here + 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); + | ~~~~~~^~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)': +../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here + 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); + | ~~~~~~^~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); @@ -895,19 +904,41 @@ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, Metadata**, CompressionType, const char*, const char*, Boolean, Boolean, Bed::LineCountType)': -../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(Metadata**, const FILE*, CompressionType, const char*, const char*)': +../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here - 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); +../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here + 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(Metadata**, const FILE*, CompressionType, const char*, const char*)': +../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here + 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + | ~~~~~~^~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(Metadata**, const FILE*, CompressionType, const char*, const char*)': +../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here + 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + | ~~~~~~^~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, Metadata**, CompressionType*, ArchiveVersion**, uint64_t*, Boolean*, Boolean)': +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 2221 | strncpy(recTokBuf, token, strlen(token) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here + 2221 | strncpy(recTokBuf, token, strlen(token) + 1); + | ~~~~~~^~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, Metadata**, CompressionType*, ArchiveVersion**, uint64_t*, Boolean*, Boolean)': +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 2221 | strncpy(recTokBuf, token, strlen(token) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here + 2221 | strncpy(recTokBuf, token, strlen(token) + 1); + | ~~~~~~^~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)': ../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); @@ -928,17 +959,6 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(Metadata**, const FILE*, CompressionType, const char*, const char*)': -../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here - 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - | ~~~~~~^~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, Boolean)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] - 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, Boolean)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); @@ -952,6 +972,34 @@ ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(Metadata**, const FILE*, CompressionType, const char*, const char*)': +../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here + 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + | ~~~~~~^~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, Boolean, Boolean, char*, Bed::LineLengthType)': +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 311 | strncpy(iter->filename, fn, strlen(fn) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here + 311 | strncpy(iter->filename, fn, strlen(fn) + 1); + | ~~~~~~^~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 330 | strncpy(iter->signature, signature, strlen(signature) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here + 330 | strncpy(iter->signature, signature, strlen(signature) + 1); + | ~~~~~~^~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, Boolean)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] + 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, Metadata**, CompressionType, const char*, const char*, Boolean, Boolean, Bed::LineCountType)': +../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -961,33 +1009,10 @@ ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here - 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here - 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here - 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)': -../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here - 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); - | ~~~~~~^~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here + 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + | ~~~~~~^~~~~~~~~~~~ +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, Metadata**, CompressionType, const char*, const char*, Boolean, Boolean, Bed::LineCountType)': ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); @@ -995,14 +1020,10 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(Metadata**, const FILE*, CompressionType, const char*, const char*)': -../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, Metadata**, CompressionType, const char*, const char*, Boolean, Boolean, Bed::LineCountType)': +../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here - 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - | ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, Metadata**, CompressionType*, ArchiveVersion**, uint64_t*, Boolean*, Boolean)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] 2221 | strncpy(recTokBuf, token, strlen(token) + 1); @@ -1010,52 +1031,9 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, Boolean)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] - 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here - 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] - 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here - 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers -../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, Boolean, Boolean, char*, Bed::LineLengthType)': -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 311 | strncpy(iter->filename, fn, strlen(fn) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here - 311 | strncpy(iter->filename, fn, strlen(fn) + 1); - | ~~~~~~^~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 330 | strncpy(iter->signature, signature, strlen(signature) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here - 330 | strncpy(iter->signature, signature, strlen(signature) + 1); - | ~~~~~~^~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, CompressionType)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] - 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here - 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -make -C applications/bed/sort-bed/src -f Makefile build -mkdir -p ../bin && g++ -o ../bin/bedextract-typical -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -ljansson -lz -lbz2 ExtractRows.cpp -make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/sort-bed/src' -mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects-typical/starchConstants.o -iquote../../../../interfaces/general-headers -make -C applications/bed/starch/src -f Makefile build -make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/starch/src' -mkdir -p objects -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchConstants.c -o objects/starchConstants.o -iquote../../../../interfaces/general-headers -iquote../../../.. -mkdir -p objects -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects/unstarchHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. -mkdir -p objects +../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here + 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + | ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, Metadata**, CompressionType, const char*, const char*, Boolean, Boolean, Bed::LineCountType)': ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); @@ -1063,8 +1041,6 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchHelpers.c -o objects/starchHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. -mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects-typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, Metadata**, CompressionType*, ArchiveVersion**, uint64_t*, Boolean*, Boolean)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] 2221 | strncpy(recTokBuf, token, strlen(token) + 1); @@ -1072,6 +1048,16 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, CompressionType)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] + 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here + 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); @@ -1098,30 +1084,36 @@ ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'void starch::UNSTARCH_printMetadataSignature(const unsigned char*)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:2276:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 2276 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, CompressionType)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] - 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here - 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:2278:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 2278 | static_cast( mdSha1BufferLength )); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, CompressionType)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:2640:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 2640 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:2642:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 2642 | static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers +make -C applications/bed/sort-bed/src -f Makefile build +make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/sort-bed/src' +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers +mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects-typical/starchConstants.o -iquote../../../../interfaces/general-headers +mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects-typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, Boolean)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] + 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here + 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] + 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here + 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +make -C applications/bed/starch/src -f Makefile build +make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/starch/src' +mkdir -p objects +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchConstants.c -o objects/starchConstants.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects-typical/starchHelpers.o -iquote../../../../interfaces/general-headers +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers +mkdir -p objects +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects/unstarchHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects-typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers -mkdir -p ../bin && g++ -o ../bin/bedmap-typical -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -ljansson -lz -lbz2 Bedmap.cpp ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); @@ -1141,18 +1133,6 @@ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects-typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers -../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_JSONMetadataExists(FILE**, const char*)': -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1089:20: warning: comparison is always true due to limited range of data type [-Wtype-limits] - 1089 | } while (currC != EOF); - | ^ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1090:63: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 1090 | if ((nReadBytes == STARCH_LEGACY_METADATA_SIZE) || (currC == EOF)) { - | ^ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, Metadata**, CompressionType*, ArchiveVersion**, char**, char**, uint64_t*, Boolean*, Boolean, Boolean)': -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1306:24: warning: comparison is always true due to limited range of data type [-Wtype-limits] - 1306 | } while (currC != EOF); - | ^ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'void starch::UNSTARCH_printMetadataSignature(const unsigned char*)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:2276:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2276 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), @@ -1167,6 +1147,22 @@ ../../../../interfaces/src/data/starch/unstarchHelpers.c:2642:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 2642 | static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mkdir -p ../bin && g++ -o ../bin/bedextract-typical -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -ljansson -lz -lbz2 ExtractRows.cpp +mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects-typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers +../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_JSONMetadataExists(FILE**, const char*)': +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1089:20: warning: comparison is always true due to limited range of data type [-Wtype-limits] + 1089 | } while (currC != EOF); + | ^ +mkdir -p objects +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1090:63: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 1090 | if ((nReadBytes == STARCH_LEGACY_METADATA_SIZE) || (currC == EOF)) { + | ^ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, Metadata**, CompressionType*, ArchiveVersion**, char**, char**, uint64_t*, Boolean*, Boolean, Boolean)': +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1306:24: warning: comparison is always true due to limited range of data type [-Wtype-limits] + 1306 | } while (currC != EOF); + | ^ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchHelpers.c -o objects/starchHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. +mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects-typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, Boolean)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); @@ -1180,13 +1176,20 @@ ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)': -../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here - 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); - | ~~~~~~^~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'void starch::UNSTARCH_printMetadataSignature(const unsigned char*)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:2276:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 2276 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:2278:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 2278 | static_cast( mdSha1BufferLength )); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, CompressionType)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:2640:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 2640 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:2642:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 2642 | static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); @@ -1206,7 +1209,14 @@ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects-typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers +mkdir -p ../bin && g++ -o ../bin/bedmap-typical -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -ljansson -lz -lbz2 Bedmap.cpp +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)': +../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here + 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); + | ~~~~~~^~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, Boolean, Boolean, char*, Bed::LineLengthType)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] 311 | strncpy(iter->filename, fn, strlen(fn) + 1); @@ -1220,6 +1230,48 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, CompressionType)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] + 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here + 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(Metadata**, const FILE*, CompressionType, const char*, const char*)': +../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here + 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + | ~~~~~~^~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here + 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here + 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here + 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects-typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers +mkdir -p ../bin && g++ -o ../bin/bedops-typical -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -ljansson -lz -lbz2 Bedops.cpp +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)': +../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here + 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); + | ~~~~~~^~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, Boolean)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); @@ -1228,12 +1280,34 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here - 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - | ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here + 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + | ~~~~~~^~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, CompressionType)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] + 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here + 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -Wextra -pedantic -ansi -O3 -std=c++11 SortDetails.cpp -o objects-typical/SortDetails.o -iquote../../../../interfaces/general-headers +../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, Metadata**, CompressionType*, ArchiveVersion**, uint64_t*, Boolean*, Boolean)': +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 2221 | strncpy(recTokBuf, token, strlen(token) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here + 2221 | strncpy(recTokBuf, token, strlen(token) + 1); + | ~~~~~~^~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, Metadata**, CompressionType, const char*, const char*, Boolean, Boolean, Bed::LineCountType)': +../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here + 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + | ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, Boolean)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); @@ -1247,14 +1321,8 @@ ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)': -../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here - 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); - | ~~~~~~^~~~~~~~ -mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects-typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers +mkdir -p ../bin && g++ -o ../bin/closest-features-typical -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -ljansson -lz -lbz2 ClosestFeature.cpp +mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -Wextra -pedantic -ansi -O3 -std=c++11 Sort.cpp -o objects-typical/Sort.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, Metadata**, CompressionType, const char*, const char*, Boolean, Boolean, Bed::LineCountType)': ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); @@ -1262,28 +1330,6 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, Metadata**, CompressionType*, ArchiveVersion**, uint64_t*, Boolean*, Boolean)': -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 2221 | strncpy(recTokBuf, token, strlen(token) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here - 2221 | strncpy(recTokBuf, token, strlen(token) + 1); - | ~~~~~~^~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(Metadata**, const FILE*, CompressionType, const char*, const char*)': -../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here - 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - | ~~~~~~^~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, CompressionType)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] - 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here - 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -Wextra -pedantic -ansi -O3 -std=c++11 SortDetails.cpp -o objects-typical/SortDetails.o -iquote../../../../interfaces/general-headers In file included from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ExtractRows.cpp:40: ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:38:20: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -1371,16 +1417,6 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -Wextra -pedantic -ansi -O3 -std=c++11 Sort.cpp -o objects-typical/Sort.o -iquote../../../../interfaces/general-headers -mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -Wextra -pedantic -ansi -O3 -std=c++11 CheckSort.cpp -o objects-typical/CheckSort.o -iquote../../../../interfaces/general-headers -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, CompressionType)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] - 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here - 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mkdir -p ../bin && g++ -o ../bin/closest-features-typical -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -ljansson -lz -lbz2 ClosestFeature.cpp ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, CompressionType)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); @@ -1388,9 +1424,7 @@ ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mkdir -p ../bin && g++ -o ../bin/bedops-typical -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -ljansson -lz -lbz2 Bedops.cpp -mkdir -p ../bin && cp update-sort-bed-slurm.py ../bin/update-sort-bed-slurm-typical -mkdir -p ../bin && cp update-sort-bed-starch-slurm.py ../bin/update-sort-bed-starch-slurm-typical +mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -Wextra -pedantic -ansi -O3 -std=c++11 CheckSort.cpp -o objects-typical/CheckSort.o -iquote../../../../interfaces/general-headers In file included from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:36, from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27, @@ -1483,80 +1517,39 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -mkdir -p ../bin && cp update-sort-bed-migrate-candidates.py ../bin/update-sort-bed-migrate-candidates-typical +mkdir -p ../bin && cp update-sort-bed-slurm.py ../bin/update-sort-bed-slurm-typical +mkdir -p ../bin && cp update-sort-bed-starch-slurm.py ../bin/update-sort-bed-starch-slurm-typical mkdir -p objects g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, Metadata**, CompressionType, const char*, const char*, Boolean, Boolean, Bed::LineCountType)': -../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here - 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - | ~~~~~~^~~~~~~~~~~~ +mkdir -p ../bin && cp update-sort-bed-migrate-candidates.py ../bin/update-sort-bed-migrate-candidates-typical mkdir -p objects g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects/starchFileHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, CompressionType)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] + 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here + 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_JSONMetadataExists(FILE**, const char*)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1089:20: warning: comparison is always true due to limited range of data type [-Wtype-limits] 1089 | } while (currC != EOF); | ^ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1090:63: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 1090 | if ((nReadBytes == STARCH_LEGACY_METADATA_SIZE) || (currC == EOF)) { - | ^ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, Metadata**, CompressionType*, ArchiveVersion**, char**, char**, uint64_t*, Boolean*, Boolean, Boolean)': -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1306:24: warning: comparison is always true due to limited range of data type [-Wtype-limits] - 1306 | } while (currC != EOF); - | ^ -In file included from ../../../../interfaces/general-headers/algorithm/visitors/NumericalVisitors.hpp:32, - from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:34: -../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:43:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 43 | struct abs_diff : std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -mkdir -p objects -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects/starchSha1Digest.o -iquote../../../../interfaces/general-headers -iquote../../../.. -../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, Boolean, Boolean, char*, Bed::LineLengthType)': -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 311 | strncpy(iter->filename, fn, strlen(fn) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here - 311 | strncpy(iter->filename, fn, strlen(fn) + 1); - | ~~~~~~^~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 330 | strncpy(iter->signature, signature, strlen(signature) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here - 330 | strncpy(iter->signature, signature, strlen(signature) + 1); - | ~~~~~~^~~~~~~~~~~ -mkdir -p objects -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects/starchBase64Coding.o -iquote../../../../interfaces/general-headers -iquote../../../.. -mkdir -p ../bin -cp starchcluster_gnuParallel.tcsh ../bin/starchcluster_gnuParallel-typical -mkdir -p ../bin -cp starchcluster_sge.tcsh ../bin/starchcluster_sge-typical -mkdir -p ../bin -cp starchcluster_slurm.tcsh ../bin/starchcluster_slurm-typical -mkdir -p ../bin -cp starch-diff.py ../bin/starch-diff-typical -../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, Metadata**, CompressionType*, ArchiveVersion**, uint64_t*, Boolean*, Boolean)': -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 2221 | strncpy(recTokBuf, token, strlen(token) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here - 2221 | strncpy(recTokBuf, token, strlen(token) + 1); - | ~~~~~~^~~~~~~ -In file included from ../../../../interfaces/general-headers/algorithm/visitors/helpers/ProcessBedVisitorRow.hpp:33, - from Bedops.cpp:40: +In file included from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, + from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:39, + from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:38:20: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 38 | : public std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/deque:67, - from Bedops.cpp:27: + from ClosestFeature.cpp:27: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1090:63: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 1090 | if ((nReadBytes == STARCH_LEGACY_METADATA_SIZE) || (currC == EOF)) { + | ^ ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:52:20: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 52 | : public std::binary_function { | ^~~~~~~~~~~~~~~ @@ -1569,6 +1562,10 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, Metadata**, CompressionType*, ArchiveVersion**, char**, char**, uint64_t*, Boolean*, Boolean, Boolean)': +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1306:24: warning: comparison is always true due to limited range of data type [-Wtype-limits] + 1306 | } while (currC != EOF); + | ^ ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:88:20: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 88 | : public std::binary_function { | ^~~~~~~~~~~~~~~ @@ -1629,15 +1626,23 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, - from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:39, - from ClosestFeature.cpp:38: +In file included from ../../../../interfaces/general-headers/algorithm/visitors/NumericalVisitors.hpp:32, + from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:34: +../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:43:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 43 | struct abs_diff : std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +mkdir -p objects +In file included from ../../../../interfaces/general-headers/algorithm/visitors/helpers/ProcessBedVisitorRow.hpp:33, + from Bedops.cpp:40: ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:38:20: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 38 | : public std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/deque:67, - from ClosestFeature.cpp:27: + from Bedops.cpp:27: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1671,6 +1676,7 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects/starchSha1Digest.o -iquote../../../../interfaces/general-headers -iquote../../../.. ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:242:20: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 242 | : public std::binary_function { | ^~~~~~~~~~~~~~~ @@ -1689,12 +1695,6 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, - from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, - from CheckSort.cpp:28: -../../../../interfaces/general-headers/data/bed/BedCompare.hpp:38:20: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 38 | : public std::binary_function { - | ^~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:274:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 274 | : public std::binary_function { | ^~~~~~~~~~~~~~~ @@ -1719,6 +1719,65 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +mkdir -p objects +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects/starchBase64Coding.o -iquote../../../../interfaces/general-headers -iquote../../../.. +../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, Boolean, Boolean, char*, Bed::LineLengthType)': +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 311 | strncpy(iter->filename, fn, strlen(fn) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here + 311 | strncpy(iter->filename, fn, strlen(fn) + 1); + | ~~~~~~^~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 330 | strncpy(iter->signature, signature, strlen(signature) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here + 330 | strncpy(iter->signature, signature, strlen(signature) + 1); + | ~~~~~~^~~~~~~~~~~ +mkdir -p ../bin +cp starchcluster_gnuParallel.tcsh ../bin/starchcluster_gnuParallel-typical +mkdir -p ../bin +cp starchcluster_sge.tcsh ../bin/starchcluster_sge-typical +SortDetails.cpp: In function 'ChromBedData* initializeChromBedData(char*, double*)': +SortDetails.cpp:250:12: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] + 250 | strncpy(chrom->chromName, chromBuf, chromBufLen); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +SortDetails.cpp:249:25: note: length computed here + 249 | chromBufLen = strlen(chromBuf); // we know >= 1 + | ~~~~~~^~~~~~~~~~ +mkdir -p ../bin +cp starchcluster_slurm.tcsh ../bin/starchcluster_slurm-typical +mkdir -p ../bin +cp starch-diff.py ../bin/starch-diff-typical +convert2bed.c: In function 'c2b_line_convert_sam_to_bed_unsorted_with_split_operation': +convert2bed.c:5017:25: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] + 5017 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +convert2bed.c:5043:21: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] + 5043 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +convert2bed.c:5061:21: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] + 5061 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, Metadata**, CompressionType*, ArchiveVersion**, uint64_t*, Boolean*, Boolean)': +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 2221 | strncpy(recTokBuf, token, strlen(token) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +convert2bed.c:4950:25: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] + 4950 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +convert2bed.c:4974:21: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] + 4974 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here + 2221 | strncpy(recTokBuf, token, strlen(token) + 1); + | ~~~~~~^~~~~~~ +In file included from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, + from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, + from CheckSort.cpp:28: +../../../../interfaces/general-headers/data/bed/BedCompare.hpp:38:20: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 38 | : public std::binary_function { + | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, @@ -1806,6 +1865,13 @@ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1226:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 1226 | static_cast( getArchiveType() ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +SortDetails.cpp: In function 'void lexSortBedData(BedData*)': +SortDetails.cpp:1343:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 1343 | strncpy(chromBuf, beds->chroms[i]->chromName, chromBufLen); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +SortDetails.cpp:1342:33: note: length computed here + 1342 | chromBufLen = strlen(beds->chroms[i]->chromName); // we know >= 1 + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1230:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 1230 | static_cast( getArchiveHeaderFlag() ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1835,8 +1901,9 @@ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:308:10: note: because 'Bed::bed_check_iterator*, 16>' has user-provided 'bool Bed::bed_check_iterator::operator=(const Bed::bed_check_iterator&) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]' 308 | bool operator=(const bed_check_iterator& b); | ^~~~~~~~ -SortDetails.cpp: In function 'ChromBedData* initializeChromBedData(char*, double*)': -SortDetails.cpp:250:12: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] +In function 'ChromBedData* initializeChromBedData(char*, double*)', + inlined from 'int processData(const char**, unsigned int, double, char*, bool, bool)' at SortDetails.cpp:909:59: +SortDetails.cpp:250:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] 250 | strncpy(chrom->chromName, chromBuf, chromBufLen); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SortDetails.cpp:249:25: note: length computed here @@ -1847,8 +1914,8 @@ mkdir -p ../bin g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c starch.c -o objects/starch.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p ../bin -mkdir -p ../bin g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c unstarch.c -o objects/unstarch.o -iquote../../../../interfaces/general-headers -iquote../../../.. +mkdir -p ../bin g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c starchcat.c -o objects/starchcat.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p ../bin g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c starchstrip.c -o objects/starchstrip.o -iquote../../../../interfaces/general-headers -iquote../../../.. @@ -1927,6 +1994,7 @@ unstarch.c:1336:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 1336 | static_cast( sha1BufferLength )); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/starch.o -o ../bin/starch-typical ../lib/libstarch.a -ljansson -lz -lbz2 starchstrip.c: In function 'void starch::STARCHSTRIP_write_updated_metadata(FILE*)': starchstrip.c:124:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 124 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), @@ -2012,7 +2080,6 @@ starchcat.c:3152:54: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 3152 | if (STARCHCAT2_setupBzip2InputStream(static_cast( inRecIdx ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/starch.o -o ../bin/starch-typical ../lib/libstarch.a -ljansson -lz -lbz2 starchcat.c:3316:69: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 3316 | static_cast( summary->numRecords ), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2081,30 +2148,6 @@ starchcat.h:107:30: note: 'starch::transformState::r_chromosome' declared here 107 | char r_chromosome[TOKEN_CHR_MAX_LENGTH]; | ^~~~~~~~~~~~ -SortDetails.cpp: In function 'void lexSortBedData(BedData*)': -SortDetails.cpp:1343:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 1343 | strncpy(chromBuf, beds->chroms[i]->chromName, chromBufLen); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -SortDetails.cpp:1342:33: note: length computed here - 1342 | chromBufLen = strlen(beds->chroms[i]->chromName); // we know >= 1 - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -convert2bed.c: In function 'c2b_line_convert_sam_to_bed_unsorted_with_split_operation': -convert2bed.c:5017:25: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] - 5017 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -convert2bed.c:5043:21: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] - 5043 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -convert2bed.c:5061:21: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] - 5061 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -convert2bed.c:4950:25: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] - 4950 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -convert2bed.c:4974:21: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] - 4974 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/starchstrip.o -o ../bin/starchstrip-typical ../lib/libstarch.a -ljansson -lz -lbz2 In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)': @@ -2114,15 +2157,17 @@ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ -In function 'ChromBedData* initializeChromBedData(char*, double*)', - inlined from 'int processData(const char**, unsigned int, double, char*, bool, bool)' at SortDetails.cpp:909:59: -SortDetails.cpp:250:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 250 | strncpy(chrom->chromName, chromBuf, chromBufLen); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/starchstrip.o -o ../bin/starchstrip-typical ../lib/libstarch.a -ljansson -lz -lbz2 +rm -rf objects +make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/conversion/src' +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::zReadLine()': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here + 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/unstarch.o -o ../bin/unstarch-typical ../lib/libstarch.a -ljansson -lz -lbz2 -SortDetails.cpp:249:25: note: length computed here - 249 | chromBufLen = strlen(chromBuf); // we know >= 1 - | ~~~~~~^~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::zReadLine()': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); @@ -2145,15 +2190,6 @@ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::zReadLine()': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here - 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -rm -rf objects -make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/conversion/src' starchcat.c: In function 'int starch::STARCHCAT2_mergeInputRecordsToOutput(const char*, Metadata**, const char*, CompressionType, const ChromosomeSummary*, size_t*)': starchcat.c:3123:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] 3123 | strncpy(transformStates[inRecIdx]->t_currentChromosome, inChr, strlen(inChr) + 1); @@ -2550,234 +2586,234 @@ dh_perl dh_link dh_strip_nondeterminism -debian/bedops-doc/usr/share/doc/bedops/html/_images/bedops_macosx_installer_icon.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/source_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/set_operations_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/statistics_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/file_management_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/performance_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_elementof_ba@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/bedops_macosx_installer_icon.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/toc_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/support_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/starch_specification.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/starch_specification_magicbytes.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_images/bedops_macosx_installer_screen_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/starch_specification_chromosomestreams.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/starch_specification_metadata.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/linux.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/file-management/compression/starch_specification.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_notelementof_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_symmetricdifference_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_notelementof_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/starch_specification_metadataoffset.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_images/bedops_cygwin_installer_screen.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_merge_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/toc_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_symmetricdifference_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_merge_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/bedops_cygwin_installer_gcc_screen.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_stagger_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/starch_specification_metadatachecksum.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_partition_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_partition_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/bedops_cygwin_installer_git_screen.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_bedextract_nested_elements.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/index/reference_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/performance_bedops_complement_sorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_notelementof_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/file_management_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/support_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/starch_specification_padding.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_notelementof_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/file_management.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/support.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/downloads_v3.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_bedextract_mechanism.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_complement_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_images/bedops_cygwin_installer_gcc_screen.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_bedextract_nested_elements.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/BEDOPS_Presentation_bedmap_ops.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_notelementof_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_inputs@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_merge_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/BEDOPS_Presentation_grok_tests.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/overview/BEDOPS_Presentation_grok_tests.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_everything@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/overview/BEDOPS_Presentation_bedmap_ops.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/BEDOPS_Presentation_starch_efficiency.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_difference_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_images/bedops_cygwin_installer_git_screen.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_merge_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. 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+debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_intersect_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_merge_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_images/BEDOPS_Presentation_grok_tests.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/note.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_partition_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. 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/usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_chop_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_images/BEDOPS_Presentation_starch_efficiency.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/starchcluster_mechanism.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/BEDOPS_Presentation_grok_tests.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_stagger_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/source.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/set_operations_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/logo_with_label_v3.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/BEDOPS_Presentation_bedmap_ops.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/index/performance.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. 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line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/index/macosx_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/starch_specification_metadataoffset.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_inputs.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/starch_specification_metadatachecksum.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/starch_specification_metadata.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. 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-debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_bedmap_mapref_ref1.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_bedmap_mapref_ref3_padded.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/bedops_macosx_installer_screen.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_images/performance_bedops_intersect_sorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_bedmap_mapref_ref2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. 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IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/performance/performance_bedops_intersect_sorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_complement_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_static/index/linux.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/linux_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/index/file_management_v2.png: 1 bytes of garbage after IEND chunk at 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IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_elementof_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/installation/bedops_cygwin_installer_screen.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/file-management/compression/starch_specification_metadataoffset.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/statistics/reference_bedmap_mapref_ref2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. 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bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/bioinformatics.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/SNP_DHS_matrix.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_static/index/support_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/linux_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/SNP_DHS_matrix_diseaseSorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_static/index/support.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/performance_unstarch_extractiontime.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_static/index/statistics_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_static/index/statistics.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_notelementof_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_merge_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_merge_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_intersect_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_intersect_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_inputs@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_inputs.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_everything@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_everything.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_elementof_ba@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_elementof_ba.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_elementof_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/starchcluster_mechanism.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_static/index/source_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/performance_starch_efficiency.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_static/index/source.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_static/index/set_operations_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_static/index/set_operations.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_elementof_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_difference_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_difference_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_complement_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_complement_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_chop_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_chop_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/performance_independent_grok.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/performance_bedops_merge_unsorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/performance_bedops_merge_sorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/performance_bedops_intersect_sorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. dh_compress dh_fixperms dh_missing @@ -2800,9 +2836,9 @@ dpkg-gencontrol: warning: package bedops-doc: substitution variable ${sphinxdoc:Depends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'bedops-doc' in '../bedops-doc_2.4.41+dfsg-3_all.deb'. -dpkg-deb: building package 'bedops-dbgsym' in '../bedops-dbgsym_2.4.41+dfsg-3_arm64.deb'. dpkg-deb: building package 'bedops' in '../bedops_2.4.41+dfsg-3_arm64.deb'. +dpkg-deb: building package 'bedops-dbgsym' in '../bedops-dbgsym_2.4.41+dfsg-3_arm64.deb'. +dpkg-deb: building package 'bedops-doc' in '../bedops-doc_2.4.41+dfsg-3_all.deb'. dpkg-genbuildinfo --build=binary -O../bedops_2.4.41+dfsg-3_arm64.buildinfo dpkg-genchanges --build=binary -O../bedops_2.4.41+dfsg-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2810,12 +2846,14 @@ 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/763732/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/763732/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/2443124 and its subdirectories -I: Current time: Mon Jan 19 18:43:11 -12 2026 -I: pbuilder-time-stamp: 1768891391 +I: removing directory /srv/workspace/pbuilder/763732 and its subdirectories +I: Current time: Wed Dec 18 14:32:16 +14 2024 +I: pbuilder-time-stamp: 1734481936