Diff of the two buildlogs: -- --- b1/build.log 2024-06-01 23:35:59.313507958 +0000 +++ b2/build.log 2024-06-01 23:42:30.892893829 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Jul 4 17:52:06 -12 2025 -I: pbuilder-time-stamp: 1751694726 +I: Current time: Sun Jun 2 13:36:02 +14 2024 +I: pbuilder-time-stamp: 1717284962 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -32,51 +32,83 @@ dpkg-source: info: applying adapt_to_new_sphinx.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2508151/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/436381/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 1 23:36 /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/436381/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/436381/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='f12e2e31f7804a1887998f2757eb89ac' - 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='2508151' - PS1='# ' - PS2='> ' + INVOCATION_ID=b8ada48cd4dc4dbfb7eea999a90f18bd + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=436381 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.qIqZq4Ne/pbuilderrc_owaY --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.qIqZq4Ne/b1 --logfile b1/build.log bedops_2.4.41+dfsg-2.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' + 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.qIqZq4Ne/pbuilderrc_2V5J --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.qIqZq4Ne/b2 --logfile b2/build.log bedops_2.4.41+dfsg-2.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' I: uname -a - Linux infom02-amd64 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 30 14:05 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2508151/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 28 07:42 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/436381/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -205,7 +237,7 @@ Get: 77 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 7.2.6-8 [702 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 7.2.6-8 [552 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] -Fetched 45.6 MB in 0s (116 MB/s) +Fetched 45.6 MB in 0s (119 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 ... 19719 files and directories currently installed.) @@ -473,8 +505,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Jul 5 05:53:05 UTC 2025. -Universal Time is now: Sat Jul 5 05:53:05 UTC 2025. +Local time is now: Sat Jun 1 23:36:45 UTC 2024. +Universal Time is now: Sat Jun 1 23:36:45 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -558,7 +590,11 @@ 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-2_source.changes +I: user script /srv/workspace/pbuilder/436381/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/436381/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-2_source.changes dpkg-buildpackage: info: source package bedops dpkg-buildpackage: info: source version 2.4.41+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -583,38 +619,38 @@ make -C applications/bed/bedops/src -f Makefile clean make -C applications/bed/closestfeats/src -f Makefile clean make -C applications/bed/conversion/src -f Makefile clean +make -C applications/bed/sort-bed/src -f Makefile clean +make -C applications/bed/starch/src -f Makefile clean make[4]: Entering 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/bedmap/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 -make -C applications/bed/sort-bed/src -f Makefile clean +make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedmap/src' +rm -rf objects_typical +make[4]: Entering 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/conversion/src' rm -rf ../bin rm -rf ../bin -make -C applications/bed/starch/src -f Makefile clean make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/closestfeats/src' rm -rf objects_typical rm -rf ../bin +make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/starch/src' +rm -rf ../lib rm -rf ../bin -rm -rf objects make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedextract/src' -make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/sort-bed/src' +rm -rf objects 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/starch/src' -rm -rf ../lib make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedops/src' -rm -rf *.so *~ -make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/closestfeats/src' -rm -rf objects-typical rm -f ../lib/libstarch_debug.a -rm -rf ../bin +make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedmap/src' +rm -rf objects-typical +make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/closestfeats/src' +rm -rf *.so *~ rm -f ../lib/libstarch_gprof.a -make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/conversion/src' -make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/sort-bed/src' +rm -rf ../bin rm -rf objects +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 ../bin make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/starch/src' rm -rf third-party/bzip2-1.0.6 @@ -640,8 +676,8 @@ make -f system.mk/Makefile.linux make[2]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg' #bzcat | tar -x -C third-party -#cd third-party/jansson-2.6 && ./configure --prefix=/build/reproducible-path/bedops-2.4.41+dfsg/third-party/jansson-2.6 && make && make install && cd /build/reproducible-path/bedops-2.4.41+dfsg && rm -f jansson && ln -sf jansson-2.6 third-party/jansson #bzcat | tar -x -C third-party +#cd third-party/jansson-2.6 && ./configure --prefix=/build/reproducible-path/bedops-2.4.41+dfsg/third-party/jansson-2.6 && make && make install && cd /build/reproducible-path/bedops-2.4.41+dfsg && rm -f jansson && ln -sf jansson-2.6 third-party/jansson #cd third-party/bzip2-1.0.6 && make libbz2.a && cd /build/reproducible-path/bedops-2.4.41+dfsg && rm -f bzip2 && ln -sf bzip2-1.0.6 third-party/bzip2 #bzcat | tar -x -C third-party #cd third-party/zlib-1.2.7 && ./configure --static && make && cd /build/reproducible-path/bedops-2.4.41+dfsg && rm -f zlib && ln -sf zlib-1.2.7 third-party/zlib @@ -651,34 +687,34 @@ make -C applications/bed/bedmap/src -f Makefile build make -C applications/bed/bedops/src -f Makefile build make -C applications/bed/closestfeats/src -f Makefile build +make -C applications/bed/conversion/src -f Makefile build make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedextract/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 -fcf-protection -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers -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 -fcf-protection -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers make -C applications/bed/sort-bed/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 -fcf-protection -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.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/bedmap/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 -fcf-protection -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 -fcf-protection -Wall -pedantic -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/bedops/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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers +make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/closestfeats/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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 make[4]: Entering 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/closestfeats/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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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/starch/src' mkdir -p objects 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 -fcf-protection -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects-typical/starchConstants.o -iquote../../../../interfaces/general-headers g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -Wall -Wextra -pedantic -ansi -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.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); @@ -686,7 +722,7 @@ | | | | 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 -fcf-protection -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 -fcf-protection -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 '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 ), @@ -701,11 +737,22 @@ ../../../../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 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 -fcf-protection -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 -fcf-protection -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers -mkdir -p objects -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 -fcf-protection -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../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_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); @@ -725,63 +772,7 @@ ../../../../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 -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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../../../.. -mkdir -p objects -../../../../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); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/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 -fcf-protection -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::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 -fcf-protection -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 -fcf-protection -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: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 -fcf-protection -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::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); - | ~~~~~~^~~~~~~~~~~ -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 -fcf-protection -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_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 ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 -fcf-protection -Wall -Wextra -pedantic -ansi -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::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); @@ -789,19 +780,8 @@ ../../../../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); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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_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 -fcf-protection -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 -fcf-protection -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/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); @@ -821,13 +801,7 @@ ../../../../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::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 -fcf-protection -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/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); @@ -835,13 +809,15 @@ ../../../../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 -fcf-protection -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 -fcf-protection -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_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/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); @@ -856,20 +832,7 @@ ../../../../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/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 -fcf-protection -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::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); @@ -877,6 +840,13 @@ ../../../../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_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 ))); @@ -897,6 +867,53 @@ ../../../../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/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::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/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 '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 ))); @@ -911,6 +928,21 @@ ../../../../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); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../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); + | ~~~~~~^~~~~~~ +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 -fcf-protection -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_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); @@ -918,15 +950,6 @@ ../../../../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 -fcf-protection -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 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 -fcf-protection -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/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); @@ -934,29 +957,16 @@ ../../../../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); +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 -fcf-protection -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.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 -fcf-protection -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../../../.. +../../../../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 -fcf-protection -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 '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 )); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 -fcf-protection -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/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 ))); @@ -964,6 +974,13 @@ ../../../../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_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_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); @@ -977,6 +994,8 @@ ../../../../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 -fcf-protection -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 -fcf-protection -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::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); @@ -984,7 +1003,29 @@ ../../../../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 -fcf-protection -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 -fcf-protection -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_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 ../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 -fcf-protection -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 +../../../../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/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); @@ -1004,29 +1045,36 @@ ../../../../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 -fcf-protection -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 -fcf-protection -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers -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 -fcf-protection -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 -../../../../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/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 -fcf-protection -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 -fcf-protection -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); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../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 -fcf-protection -Wall -Wextra -pedantic -ansi -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::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 ))); @@ -1040,21 +1088,7 @@ ../../../../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/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 -fcf-protection -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../../../.. +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 -fcf-protection -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/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); @@ -1074,21 +1108,22 @@ ../../../../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/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 -fcf-protection -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_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/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 -fcf-protection -Wall -Wextra -pedantic -ansi -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 -fcf-protection -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 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 -fcf-protection -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/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); @@ -1102,7 +1137,13 @@ ../../../../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 -fcf-protection -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/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 '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 ))); @@ -1116,15 +1157,13 @@ ../../../../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 -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_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/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 )); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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] @@ -1212,13 +1251,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -../../../../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 -fcf-protection -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects-typical/starchBase64Coding.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); @@ -1238,72 +1271,13 @@ ../../../../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 -fcf-protection -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 -fcf-protection -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 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -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 -mkdir -p ../lib -ar rcs ../lib/libstarch.a objects/starchConstants.o objects/unstarchHelpers.o objects/starchHelpers.o objects/starchMetadataHelpers.o objects/starchFileHelpers.o objects/starchSha1Digest.o objects/starchBase64Coding.o -mkdir -p ../bin -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 -fcf-protection -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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 -fcf-protection -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/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 ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starch.c: In function 'int main(int, char**)': -starch.c:106:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 106 | static_cast( type ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starch.c:121:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 121 | static_cast( type ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starch.c:123:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 123 | static_cast( kStarchFinalizeTransformTrue ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starch.c:146:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 146 | static_cast( type ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starch.c:161:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 161 | static_cast( type ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starch.c:163:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 163 | static_cast( kStarchFinalizeTransformTrue ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starch.c:191:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 191 | static_cast( type ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starch.c:194:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 194 | static_cast( bedGeneratePerChrSignatureFlag ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starch.c:195:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 195 | static_cast( bedHeaderFlag ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starch.c:196:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 196 | static_cast( bedReportProgressFlag ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starch.c:197:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 197 | static_cast( bedReportProgressN )) != STARCH_EXIT_SUCCESS) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../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/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 ))); @@ -1312,75 +1286,15 @@ 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 -fcf-protection -Wall -Wextra -pedantic -ansi -O3 -std=c++11 SortDetails.cpp -o objects-typical/SortDetails.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 -fcf-protection -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/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); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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 -fcf-protection -Wall -Wextra -pedantic -ansi -O3 -std=c++11 Sort.cpp -o objects-typical/Sort.o -iquote../../../../interfaces/general-headers -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 -fcf-protection -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../../../.. +../../../../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 -fcf-protection -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 -unstarch.c: In function 'int main(int, char**)': -unstarch.c:401:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 401 | static_cast( metadataOffset ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unstarch.c:402:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 402 | static_cast( headerFlag )) != 0) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unstarch.c:422:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 422 | static_cast( metadataOffset ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unstarch.c:423:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 423 | static_cast( headerFlag )) != 0) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unstarch.c:452:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 452 | static_cast( sizeof(starchRevision2HeaderBytes) ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unstarch.c:453:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 453 | static_cast( headerFlag )) != 0) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unstarch.c:473:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 473 | static_cast( sizeof(starchRevision2HeaderBytes) ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unstarch.c:474:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 474 | static_cast( headerFlag )) != 0) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unstarch.c:567:39: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 567 | UNSTARCH_printCompressionType(static_cast( type )); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mkdir -p ../bin -unstarch.c:798:78: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 798 | static_cast( sizeof(starchRevision2HeaderBytes) ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unstarch.c:809:82: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 809 | static_cast( sizeof(starchRevision2HeaderBytes) ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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../../../.. -unstarch.c: In function 'void starch::UNSTARCH_printMetadataSha1Signature(unsigned char*)': -unstarch.c:1334:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 1334 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -unstarch.c:1336:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 1336 | static_cast( sha1BufferLength )); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 -fcf-protection -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 '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 ))); @@ -1394,174 +1308,49 @@ ../../../../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 ../bin && cp update-sort-bed-slurm.py ../bin/update-sort-bed-slurm-typical -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 -fcf-protection -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../../../.. -In file included from /usr/include/c++/13/cassert:44, - from starchcat.c:33: -starchcat.c: In function 'int main(int, char**)': -starchcat.c:136:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 136 | assert( STARCHCAT_allocMetadataRecords ( &mdRecords, static_cast( numRecords ) ) ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:137:75: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 137 | assert( STARCHCAT_allocMetadataJSONObjects ( &metadataJSONs, static_cast( numRecords ) ) ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:138:87: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 138 | assert( STARCHCAT_buildMetadataRecords ( &metadataJSONs, &mdRecords, static_cast( firstArgc ), static_cast( argc ), const_cast( argv ) ) ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:138:133: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 138 | assert( STARCHCAT_buildMetadataRecords ( &metadataJSONs, &mdRecords, static_cast( firstArgc ), static_cast( argc ), const_cast( argv ) ) ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:139:75: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 139 | assert( STARCHCAT_checkMetadataJSONVersions ( &metadataJSONs, static_cast( numRecords ) ) ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:140:145: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 140 | assert( STARCHCAT_buildUniqueChromosomeList ( &chromosomes, &numChromosomes, reinterpret_cast( mdRecords ), static_cast( numRecords ) ) ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:141:69: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 141 | assert( STARCHCAT_allocChromosomeSummary ( &summary, static_cast( numChromosomes ) ) ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:142:124: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 142 | assert( STARCHCAT_buildChromosomeSummary ( &summary, reinterpret_cast( mdRecords ), static_cast( numRecords ), const_cast( chromosomes ), static_cast( numChromosomes ) ) ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:142:213: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 142 | assert( STARCHCAT_buildChromosomeSummary ( &summary, reinterpret_cast( mdRecords ), static_cast( numRecords ), const_cast( chromosomes ), static_cast( numChromosomes ) ) ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:143:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 143 | assert( STARCHCAT_allocChromosomeSummaries ( &summaries, static_cast( numChromosomes ) ) ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:144:127: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 144 | assert( STARCHCAT_buildChromosomeSummaries ( &summaries, reinterpret_cast( summary ), static_cast( numChromosomes ) ) ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:164:61: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 164 | static_cast( outputType ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:178:61: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 178 | static_cast( outputType ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:223:60: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 223 | assert( STARCHCAT_freeMetadataRecords( &mdRecords, static_cast( numRecords ) ) ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:233:68: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 233 | assert (STARCHCAT_freeMetadataJSONObjects( &metadataJSONs, static_cast( numRecords ) ) ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchstrip.c:126:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 126 | static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c: In function 'int starch::STARCHCAT2_rewriteInputRecordToOutput(Metadata**, const char*, CompressionType, const char*, const MetadataRecord*, size_t*, Boolean, Boolean, Bed::LineCountType)': -starchcat.c:1338:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 1338 | UNSTARCH_reverseTransformCoordinates( static_cast( t_lineIdx ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 -fcf-protection -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../../../.. +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 -fcf-protection -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 '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 ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:1806:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 1806 | UNSTARCH_reverseTransformCoordinates( static_cast( t_lineIdx ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c: In function 'int starch::STARCHCAT_rewriteInputRecordToOutput(Metadata**, const char*, CompressionType, const char*, const MetadataRecord*)': -starchcat.c:2450:25: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 2450 | static_cast( inRec->mdOffset ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:2451:25: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 2451 | static_cast( inRec->hFlag )) != 0 ) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:2471:28: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 2471 | static_cast( inRec->mdOffset ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:2472:28: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 2472 | static_cast( inRec->hFlag )) != 0 ) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:2509:23: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 2509 | static_cast( outType ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:2511:23: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 2511 | static_cast( kStarchFinalizeTransformFalse ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c: In function 'int starch::STARCHCAT2_mergeInputRecordsToOutput(const char*, Metadata**, const char*, CompressionType, const ChromosomeSummary*, size_t*)': -starchcat.c:3152:54: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 3152 | if (STARCHCAT2_setupBzip2InputStream(static_cast( inRecIdx ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:3316:69: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 3316 | static_cast( summary->numRecords ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:3455:77: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 3455 | static_cast( flushZStreamFlag ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c: In function 'int starch::STARCHCAT_mergeInputRecordsToOutput(Metadata**, const char*, CompressionType, const ChromosomeSummary*)': -starchcat.c:4265:43: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 4265 | static_cast( outType ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:4267:43: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 4267 | static_cast( kStarchFinalizeTransformFalse ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c: In function 'int starch::STARCHCAT_mergeChromosomeStreams(const ChromosomeSummaries*, CompressionType, const char*)': -starchcat.c:4402:60: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 4402 | static_cast( outputType ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:4420:63: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 4420 | static_cast( outputType ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:4447:57: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 4447 | static_cast( outputType ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:4479:39: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 4479 | static_cast( hFlag ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c: In function 'int starch::STARCHCAT_freeChromosomeSummaries(ChromosomeSummaries**)': -starchcat.c:4541:62: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 4541 | STARCHCAT_freeChromosomeSummary( &((*chrSums)->summary), static_cast( (*chrSums)->numChromosomes )); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 -fcf-protection -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 -fcf-protection -Wall -Wextra -pedantic -ansi -O3 -std=c++11 CheckSort.cpp -o objects-typical/CheckSort.o -iquote../../../../interfaces/general-headers +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 ../bin && cp update-sort-bed-migrate-candidates.py ../bin/update-sort-bed-migrate-candidates-typical -starchcat.c: In function 'int starch::STARCHCAT2_mergeChromosomeStreams(const ChromosomeSummaries*, CompressionType, const char*, size_t*, Boolean, Boolean, Bed::LineCountType)': -starchcat.c:5902:61: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 5902 | static_cast( outputType ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:5929:64: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 5929 | static_cast( outputType ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:5952:64: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 5952 | static_cast( outputType ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:5990:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 5990 | static_cast( outputType ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:6025:38: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 6025 | static_cast( hFlag ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:6053:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 6053 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:6055:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 6055 | static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c: In function 'int starch::STARCHCAT2_fillExtractionBufferFromBzip2Stream(Boolean*, char*, char*, size_t*, BZFILE**, size_t*, char*, size_t*, TransformState*)': -starchcat.c:6719:55: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 6719 | UNSTARCH_reverseTransformCoordinates( static_cast( *t_lineIdxPtr ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c: In function 'int starch::STARCHCAT2_fillExtractionBufferFromGzipStream(Boolean*, FILE**, char*, char*, size_t*, z_stream*, size_t*, char**, size_t*, TransformState*)': -starchcat.c:7060:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 7060 | UNSTARCH_reverseTransformCoordinates( static_cast( *t_lineIdxPtr ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c: In function 'int starch::STARCHCAT2_transformCompressionBuffer(const char*, char*, TransformState*)': -starchcat.c:7428:25: warning: the address of 'starch::transformState::r_chromosome' will never be NULL [-Waddress] - 7428 | if ((!retransState->r_chromosome) || (strlen(retransState->r_chromosome) == 0)) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from starchcat.c:50: -starchcat.h:107:30: note: 'starch::transformState::r_chromosome' declared here - 107 | char r_chromosome[TOKEN_CHR_MAX_LENGTH]; - | ^~~~~~~~~~~~ -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 -fcf-protection -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 -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +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 -fcf-protection -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../../../.. +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 -fcf-protection -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../../../.. +mkdir -p objects +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 -fcf-protection -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/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); + | ~~~~~~^~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/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 ))); @@ -1569,15 +1358,26 @@ ../../../../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_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/bed/FindBedRange.hpp:32, - from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:39, - from ClosestFeature.cpp:38: + 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++/13/bits/refwrap.h:39, - from /usr/include/c++/13/deque:67, - from ClosestFeature.cpp:27: +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from CheckSort.cpp:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1623,6 +1423,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +convert2bed.c: In function 'c2b_line_convert_sam_to_bed_unsorted_with_split_operation': ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:264:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 264 | : public std::binary_function { | ^~~~~~~~~~~~~~~ @@ -1653,7 +1454,6 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1669,10 +1469,13 @@ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 -fcf-protection -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 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: + from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:36, + from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27, + from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91, + from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, + from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, + from Bedmap.cpp:37: ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:38:20: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 38 | : public std::binary_function { | ^~~~~~~~~~~~~~~ @@ -1682,7 +1485,7 @@ from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, - from CheckSort.cpp:25: + from Bedmap.cpp:29: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1758,62 +1561,15 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44: -../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::listJSONMetadata(FILE*, FILE*)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:1226:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 1226 | static_cast( getArchiveType() ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/starch/starchApi.hpp:1230:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 1230 | static_cast( getArchiveHeaderFlag() ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/starch/starchApi.hpp:1231:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 1231 | static_cast( getArchiveShowNewlineFlag() )); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractAllData(const std::string&, FILE*)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:2003:51: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 2003 | static_cast( getArchiveHeaderFlag() )) != 0 ) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/starch/starchApi.hpp:2014:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] - 2014 | static_cast( getArchiveHeaderFlag() )) != 0 ) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 - | ~~~~~~^~~~~~~~~~ -../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp: In instantiation of 'Bed::bed_check_iterator Bed::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]': -CheckSort.cpp:51:28: required from here -../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:268:12: warning: implicitly-declared 'Bed::bed_check_iterator*, 16>::bed_check_iterator(const Bed::bed_check_iterator*, 16>&)' is deprecated [-Wdeprecated-copy] - 268 | auto __tmp = *this; - | ^~~~~ -../../../../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); - | ^~~~~~~~ -../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:295:14: warning: implicitly-declared 'Bed::bed_check_iterator*, 16>::bed_check_iterator(const Bed::bed_check_iterator*, 16>&)' is deprecated [-Wdeprecated-copy] - 295 | return __tmp; - | ^~~~~ -../../../../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); - | ^~~~~~~~ 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, - from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91, - from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, - from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, - from Bedmap.cpp:37: + 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++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from Bedmap.cpp:29: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/deque:67, + from ClosestFeature.cpp:27: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1889,37 +1645,34 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -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*)': -../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here - 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); - | ~~~~~~^~~~~~~~ -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: 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); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ +In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44: +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::listJSONMetadata(FILE*, FILE*)': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:1226:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 1226 | static_cast( getArchiveType() ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/starch/starchApi.hpp:1230:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 1230 | static_cast( getArchiveHeaderFlag() ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/starch/starchApi.hpp:1231:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 1231 | static_cast( getArchiveShowNewlineFlag() )); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mkdir -p ../lib +ar rcs ../lib/libstarch.a objects/starchConstants.o objects/unstarchHelpers.o objects/starchHelpers.o objects/starchMetadataHelpers.o objects/starchFileHelpers.o objects/starchSha1Digest.o objects/starchBase64Coding.o +../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractAllData(const std::string&, FILE*)': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:2003:51: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 2003 | static_cast( getArchiveHeaderFlag() )) != 0 ) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/starch/starchApi.hpp:2014:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 2014 | static_cast( getArchiveHeaderFlag() )) != 0 ) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mkdir -p ../bin +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 -fcf-protection -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 +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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../../../.. +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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../../../.. +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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../../../.. 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] @@ -2003,6 +1756,282 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +starch.c: In function 'int main(int, char**)': +starch.c:106:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 106 | static_cast( type ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starch.c:121:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 121 | static_cast( type ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starch.c:123:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 123 | static_cast( kStarchFinalizeTransformTrue ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starch.c:146:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 146 | static_cast( type ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starch.c:161:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 161 | static_cast( type ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starch.c:163:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 163 | static_cast( kStarchFinalizeTransformTrue ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starch.c:191:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 191 | static_cast( type ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starch.c:194:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 194 | static_cast( bedGeneratePerChrSignatureFlag ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starch.c:195:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 195 | static_cast( bedHeaderFlag ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starch.c:196:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 196 | static_cast( bedReportProgressFlag ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starch.c:197:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 197 | static_cast( bedReportProgressN )) != STARCH_EXIT_SUCCESS) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +unstarch.c: In function 'int main(int, char**)': +unstarch.c:401:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 401 | static_cast( metadataOffset ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchstrip.c:126:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 126 | static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +unstarch.c:402:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 402 | static_cast( headerFlag )) != 0) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +unstarch.c:422:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 422 | static_cast( metadataOffset ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +unstarch.c:423:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 423 | static_cast( headerFlag )) != 0) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +unstarch.c:452:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 452 | static_cast( sizeof(starchRevision2HeaderBytes) ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +unstarch.c:453:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 453 | static_cast( headerFlag )) != 0) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +unstarch.c:473:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 473 | static_cast( sizeof(starchRevision2HeaderBytes) ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +unstarch.c:474:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 474 | static_cast( headerFlag )) != 0) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +unstarch.c:567:39: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 567 | UNSTARCH_printCompressionType(static_cast( type )); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 + | ~~~~~~^~~~~~~~~~ +unstarch.c:798:78: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 798 | static_cast( sizeof(starchRevision2HeaderBytes) ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +unstarch.c:809:82: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 809 | static_cast( sizeof(starchRevision2HeaderBytes) ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +unstarch.c: In function 'void starch::UNSTARCH_printMetadataSha1Signature(unsigned char*)': +unstarch.c:1334:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 1334 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +unstarch.c:1336:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 1336 | static_cast( sha1BufferLength )); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/cassert:44, + from starchcat.c:33: +starchcat.c: In function 'int main(int, char**)': +starchcat.c:136:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 136 | assert( STARCHCAT_allocMetadataRecords ( &mdRecords, static_cast( numRecords ) ) ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:137:75: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 137 | assert( STARCHCAT_allocMetadataJSONObjects ( &metadataJSONs, static_cast( numRecords ) ) ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:138:87: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 138 | assert( STARCHCAT_buildMetadataRecords ( &metadataJSONs, &mdRecords, static_cast( firstArgc ), static_cast( argc ), const_cast( argv ) ) ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:138:133: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 138 | assert( STARCHCAT_buildMetadataRecords ( &metadataJSONs, &mdRecords, static_cast( firstArgc ), static_cast( argc ), const_cast( argv ) ) ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:139:75: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 139 | assert( STARCHCAT_checkMetadataJSONVersions ( &metadataJSONs, static_cast( numRecords ) ) ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:140:145: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 140 | assert( STARCHCAT_buildUniqueChromosomeList ( &chromosomes, &numChromosomes, reinterpret_cast( mdRecords ), static_cast( numRecords ) ) ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:141:69: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 141 | assert( STARCHCAT_allocChromosomeSummary ( &summary, static_cast( numChromosomes ) ) ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:142:124: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 142 | assert( STARCHCAT_buildChromosomeSummary ( &summary, reinterpret_cast( mdRecords ), static_cast( numRecords ), const_cast( chromosomes ), static_cast( numChromosomes ) ) ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:142:213: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 142 | assert( STARCHCAT_buildChromosomeSummary ( &summary, reinterpret_cast( mdRecords ), static_cast( numRecords ), const_cast( chromosomes ), static_cast( numChromosomes ) ) ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:143:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 143 | assert( STARCHCAT_allocChromosomeSummaries ( &summaries, static_cast( numChromosomes ) ) ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:144:127: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 144 | assert( STARCHCAT_buildChromosomeSummaries ( &summaries, reinterpret_cast( summary ), static_cast( numChromosomes ) ) ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:164:61: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 164 | static_cast( outputType ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:178:61: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 178 | static_cast( outputType ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:223:60: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 223 | assert( STARCHCAT_freeMetadataRecords( &mdRecords, static_cast( numRecords ) ) ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:233:68: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 233 | assert (STARCHCAT_freeMetadataJSONObjects( &metadataJSONs, static_cast( numRecords ) ) ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +starchcat.c: In function 'int starch::STARCHCAT2_rewriteInputRecordToOutput(Metadata**, const char*, CompressionType, const char*, const MetadataRecord*, size_t*, Boolean, Boolean, Bed::LineCountType)': +starchcat.c:1338:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 1338 | UNSTARCH_reverseTransformCoordinates( static_cast( t_lineIdx ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:1806:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 1806 | UNSTARCH_reverseTransformCoordinates( static_cast( t_lineIdx ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp: In instantiation of 'Bed::bed_check_iterator Bed::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]': +CheckSort.cpp:51:28: required from here +../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:268:12: warning: implicitly-declared 'Bed::bed_check_iterator*, 16>::bed_check_iterator(const Bed::bed_check_iterator*, 16>&)' is deprecated [-Wdeprecated-copy] + 268 | auto __tmp = *this; + | ^~~~~ +../../../../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); + | ^~~~~~~~ +../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:295:14: warning: implicitly-declared 'Bed::bed_check_iterator*, 16>::bed_check_iterator(const Bed::bed_check_iterator*, 16>&)' is deprecated [-Wdeprecated-copy] + 295 | return __tmp; + | ^~~~~ +../../../../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); + | ^~~~~~~~ +starchcat.c: In function 'int starch::STARCHCAT_rewriteInputRecordToOutput(Metadata**, const char*, CompressionType, const char*, const MetadataRecord*)': +starchcat.c:2450:25: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 2450 | static_cast( inRec->mdOffset ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:2451:25: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 2451 | static_cast( inRec->hFlag )) != 0 ) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:2471:28: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 2471 | static_cast( inRec->mdOffset ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:2472:28: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 2472 | static_cast( inRec->hFlag )) != 0 ) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:2509:23: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 2509 | static_cast( outType ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:2511:23: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 2511 | static_cast( kStarchFinalizeTransformFalse ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c: In function 'int starch::STARCHCAT2_mergeInputRecordsToOutput(const char*, Metadata**, const char*, CompressionType, const ChromosomeSummary*, size_t*)': +starchcat.c:3152:54: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 3152 | if (STARCHCAT2_setupBzip2InputStream(static_cast( inRecIdx ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:3316:69: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 3316 | static_cast( summary->numRecords ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:3455:77: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 3455 | static_cast( flushZStreamFlag ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c: In function 'int starch::STARCHCAT_mergeInputRecordsToOutput(Metadata**, const char*, CompressionType, const ChromosomeSummary*)': +starchcat.c:4265:43: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 4265 | static_cast( outType ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:4267:43: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 4267 | static_cast( kStarchFinalizeTransformFalse ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c: In function 'int starch::STARCHCAT_mergeChromosomeStreams(const ChromosomeSummaries*, CompressionType, const char*)': +starchcat.c:4402:60: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 4402 | static_cast( outputType ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:4420:63: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 4420 | static_cast( outputType ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:4447:57: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 4447 | static_cast( outputType ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:4479:39: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 4479 | static_cast( hFlag ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c: In function 'int starch::STARCHCAT_freeChromosomeSummaries(ChromosomeSummaries**)': +starchcat.c:4541:62: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 4541 | STARCHCAT_freeChromosomeSummary( &((*chrSums)->summary), static_cast( (*chrSums)->numChromosomes )); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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: In function 'int starch::STARCHCAT2_mergeChromosomeStreams(const ChromosomeSummaries*, CompressionType, const char*, size_t*, Boolean, Boolean, Bed::LineCountType)': +starchcat.c:5902:61: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 5902 | static_cast( outputType ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:5929:64: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 5929 | static_cast( outputType ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:5952:64: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 5952 | static_cast( outputType ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:5990:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 5990 | static_cast( outputType ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:6025:38: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 6025 | static_cast( hFlag ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:6053:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 6053 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:6055:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 6055 | static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c: In function 'int starch::STARCHCAT2_fillExtractionBufferFromBzip2Stream(Boolean*, char*, char*, size_t*, BZFILE**, size_t*, char*, size_t*, TransformState*)': +starchcat.c:6719:55: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 6719 | UNSTARCH_reverseTransformCoordinates( static_cast( *t_lineIdxPtr ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c: In function 'int starch::STARCHCAT2_fillExtractionBufferFromGzipStream(Boolean*, FILE**, char*, char*, size_t*, z_stream*, size_t*, char**, size_t*, TransformState*)': +starchcat.c:7060:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 7060 | UNSTARCH_reverseTransformCoordinates( static_cast( *t_lineIdxPtr ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c: In function 'int starch::STARCHCAT2_transformCompressionBuffer(const char*, char*, TransformState*)': +starchcat.c:7428:25: warning: the address of 'starch::transformState::r_chromosome' will never be NULL [-Waddress] + 7428 | if ((!retransState->r_chromosome) || (strlen(retransState->r_chromosome) == 0)) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from starchcat.c:50: +starchcat.h:107:30: note: 'starch::transformState::r_chromosome' declared here + 107 | char r_chromosome[TOKEN_CHR_MAX_LENGTH]; + | ^~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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: 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 + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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*)': +../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../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] @@ -2011,6 +2040,13 @@ 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); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../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*)': @@ -2087,7 +2123,6 @@ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ -rm -rf objects_typical In member function 'void starch::Starch::setCurrentChromosome(char*)', inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, @@ -2100,10 +2135,6 @@ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ -make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedextract/src' -mkdir -p ../bin && g++ -o ../bin/sort-bed-typical -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -s -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -iquote../../../../interfaces/general-headers 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 objects-typical/SortDetails.o objects-typical/Sort.o objects-typical/CheckSort.o -ljansson -lz -lbz2 -rm -rf objects-typical -make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/sort-bed/src' In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)': @@ -2114,7 +2145,8 @@ 541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1); | ~~~~~~^~~~~~~~ rm -rf objects_typical -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/bedextract/src' +mkdir -p ../bin && g++ -o ../bin/sort-bed-typical -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -s -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -iquote../../../../interfaces/general-headers 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 objects-typical/SortDetails.o objects-typical/Sort.o objects-typical/CheckSort.o -ljansson -lz -lbz2 ../../../../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); @@ -2122,6 +2154,10 @@ ../../../../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-typical +make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/sort-bed/src' +rm -rf objects_typical +make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/closestfeats/src' In member function 'void starch::Starch::setCurrentChromosome(char*)', inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, @@ -2212,7 +2248,7 @@ WARNING: The pre-Sphinx 1.0 'intersphinx_mapping' format is deprecated and will be removed in Sphinx 8. Update to the current format as described in the documentation. Hint: "intersphinx_mapping = {'': ('http://docs.python.org/', None)}".https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html#confval-intersphinx_mapping loading intersphinx inventory from http://docs.python.org/objects.inv... WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'http://docs.python.org/objects.inv' not fetchable due to : HTTPConnectionPool(host='docs.python.org', port=80): Max retries exceeded with url: /objects.inv (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -3] Temporary failure in name resolution')) +intersphinx inventory 'http://docs.python.org/objects.inv' not fetchable due to : HTTPConnectionPool(host='docs.python.org', port=80): Max retries exceeded with url: /objects.inv (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -3] Temporary failure in name resolution')) building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 47 source files that are out of date @@ -2271,234 +2307,234 @@ dh_perl dh_link dh_strip_nondeterminism -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/reference_bedmap_mapref_ref3.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/_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/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/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/_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/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_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/_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/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/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/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/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_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 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line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_images/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/_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/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/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/_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/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/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/_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/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_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/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/_images/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/_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/_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/_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/reference_setops_bedops_inputs.png: 1 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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/_static/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/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/_images/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/_images/reference_bedmap_mapref_ref3_padded.png: 1 bytes of garbage after IEND chunk at 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/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/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/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/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/reference/set-operations/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/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/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/_images/reference_bedmap_mapref_ref2.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/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/_static/reference/set-operations/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/documentation.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/statistics/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/performance.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/index/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_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/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_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/_images/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/_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/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_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/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/set-operations/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/index/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/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/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/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/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/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/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/reference/statistics/reference_bedmap_mapref_all.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/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/_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_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/set-operations/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/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/_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/quick_start.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_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/statistics/reference_bedmap_mapref_ref2.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/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/_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/_static/index/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/reference/set-operations/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/statistics/reference_bedmap_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/usage-examples/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/_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/_static/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_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/index/downloads_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_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_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/overview.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/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/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/index/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/_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/_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/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/performance/performance_starch_efficiency.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_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/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/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/_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/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/reference_bedmap_mapref_all.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_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/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/reference_bedmap_mapref_ref3.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_cygwin_installer_git_screen.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/_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/_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_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/_static/index/macosx.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_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/reference/statistics/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/reference/set-operations/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/index/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/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. 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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_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/file-management/compression/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/reference/statistics/reference_bedmap_mapref_ref3.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_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/_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/reference/file-management/compression/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/_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/_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/_static/support.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_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_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/_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_bedmap_mapref_ref3_padded.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. 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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_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_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/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/reference/set-operations/reference_setops_bedops_everything.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/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/file-management/compression/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/_static/reference/set-operations/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_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_bedmap_mapref_all.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_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/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/set-operations/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/performance/performance_independent_grok.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. 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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/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/reference/set-operations/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_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/reference/set-operations/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/_static/installation/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_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/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/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/performance/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/readme/documentation.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_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/statistics/reference_bedmap_mapref_ref2.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/readme/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/_static/readme/overview.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_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/_static/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/usage-examples/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/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/_static/usage-examples/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/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/_static/installation/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/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/installation/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/_static/performance/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/installation/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/_static/performance/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/installation/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/_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/installation/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/performance/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/performance/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/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/readme/overview.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/readme/documentation.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/installation/bedops_cygwin_installer_git_screen.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 @@ -2515,9 +2551,9 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'bedops' in '../bedops_2.4.41+dfsg-2_amd64.deb'. dpkg-deb: building package 'bedops-dbgsym' in '../bedops-dbgsym_2.4.41+dfsg-2_amd64.deb'. dpkg-deb: building package 'bedops-doc' in '../bedops-doc_2.4.41+dfsg-2_all.deb'. +dpkg-deb: building package 'bedops' in '../bedops_2.4.41+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../bedops_2.4.41+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../bedops_2.4.41+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2525,12 +2561,14 @@ 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/436381/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/436381/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/2508151 and its subdirectories -I: Current time: Fri Jul 4 17:58:58 -12 2025 -I: pbuilder-time-stamp: 1751695138 +I: removing directory /srv/workspace/pbuilder/436381 and its subdirectories +I: Current time: Sun Jun 2 13:42:29 +14 2024 +I: pbuilder-time-stamp: 1717285349