Diff of the two buildlogs: -- --- b1/build.log 2024-12-19 16:53:46.185643492 +0000 +++ b2/build.log 2024-12-19 17:06:56.110003711 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jan 21 11:10:15 -12 2026 -I: pbuilder-time-stamp: 1769037015 +I: Current time: Fri Dec 20 06:53:48 +14 2024 +I: pbuilder-time-stamp: 1734627228 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -34,53 +34,86 @@ dpkg-source: info: applying intersphinx I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/10591/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/42342/tmp/hooks/D01_modify_environment starting +debug: Running on ionos2-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Dec 19 16:54 /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/42342/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/42342/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=6 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='04920558a9854d04b7a6a6c3bbf7507b' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='10591' - PS1='# ' - PS2='> ' + INVOCATION_ID=ae4ccabab20448bea318809fc34e5b81 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=42342 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.gos5HWLf/pbuilderrc_hu96 --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.gos5HWLf/b1 --logfile b1/build.log bedops_2.4.41+dfsg-3.dsc' - SUDO_GID='111' - 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.gos5HWLf/pbuilderrc_Ev7D --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.gos5HWLf/b2 --logfile b2/build.log bedops_2.4.41+dfsg-3.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux infom08-i386 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/10591/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/42342/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -230,7 +263,7 @@ Get: 94 http://deb.debian.org/debian unstable/main i386 python3-sphinx all 8.1.3-2 [468 kB] Get: 95 http://deb.debian.org/debian unstable/main i386 tcsh i386 6.24.13-2 [469 kB] Get: 96 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB] -Fetched 48.6 MB in 1s (32.5 MB/s) +Fetched 48.6 MB in 1s (73.7 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 ... 19953 files and directories currently installed.) @@ -555,8 +588,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Jan 21 23:10:37 UTC 2026. -Universal Time is now: Wed Jan 21 23:10:37 UTC 2026. +Local time is now: Thu Dec 19 16:54:22 UTC 2024. +Universal Time is now: Thu Dec 19 16:54:22 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -655,7 +688,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/bedops-2.4.41+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../bedops_2.4.41+dfsg-3_source.changes +I: user script /srv/workspace/pbuilder/42342/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/42342/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/bedops-2.4.41+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../bedops_2.4.41+dfsg-3_source.changes dpkg-buildpackage: info: source package bedops dpkg-buildpackage: info: source version 2.4.41+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -667,7 +704,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg' dh_auto_clean - make -j6 clean + make -j10 clean make[2]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg' make clean -f system.mk/Makefile.linux make[3]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg' @@ -676,42 +713,42 @@ rm -rf bin make -C applications/bed/bedextract/src -f Makefile clean make -C applications/bed/bedmap/src -f Makefile clean -make -C applications/bed/bedops/src -f Makefile clean rm -rf modules +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[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/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/closestfeats/src' -rm -rf objects_typical -make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/conversion/src' +make -C applications/bed/starch/src -f Makefile clean rm -rf ../bin +make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedops/src' +rm -rf objects_typical +make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/sort-bed/src' rm -rf ../bin +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/conversion/src' rm -rf ../bin rm -rf ../bin -make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedops/src' +make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/starch/src' +make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/closestfeats/src' +rm -rf objects_typical +rm -rf ../lib rm -rf objects +make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedmap/src' +make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedops/src' rm -rf ../bin -make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedextract/src' -make -C applications/bed/starch/src -f Makefile clean rm -rf objects-typical -make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedmap/src' -make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/closestfeats/src' rm -rf *.so *~ -rm -rf ../bin -make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/sort-bed/src' -make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/starch/src' -rm -rf ../lib -make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/conversion/src' rm -f ../lib/libstarch_debug.a rm -f ../lib/libstarch_gprof.a +make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/closestfeats/src' +rm -rf ../bin rm -rf objects +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 make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/starch/src' rm -rf third-party/bzip2-1.0.6 @@ -732,15 +769,15 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j6 "INSTALL=install --strip-program=true" + make -j10 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg' make -f system.mk/Makefile.linux make[2]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg' #bzcat | tar -x -C third-party +#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/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 make build -f /build/reproducible-path/bedops-2.4.41+dfsg/system.mk/Makefile.linux make[3]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg' @@ -750,32 +787,87 @@ make -C applications/bed/closestfeats/src -f Makefile build make -C applications/bed/conversion/src -f Makefile build make -C applications/bed/sort-bed/src -f Makefile build +make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedextract/src' +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 -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers -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 -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers -make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/sort-bed/src' +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedops/src' mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.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 -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers +make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/sort-bed/src' +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchConstants.c -o objects/starchConstants.o -iquote../../../../interfaces/general-headers -iquote../../../.. +mkdir -p objects +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.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 -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -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 -Wformat -Werror=format-security -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../../../.. convert2bed.c: In function 'c2b_process_intermediate_bytes_by_lines': +../../../../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 )); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ convert2bed.c:6716:103: warning: format '%zu' expects argument of type 'size_t', but argument 3 has type 'long unsigned int' [-Wformat=] 6716 | fprintf(stderr, "Error: Could not find newline in intermediate buffer; check input [%zu | %zu | %zu]\n", (unsigned long) src_bytes_read, (unsigned long) remainder_length, (unsigned long) src_buffer_capacity); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int long unsigned int | %lu +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, CompressionType)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:2640:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 2640 | static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:2642:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] + 2642 | static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/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:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow] + 2171 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +../../../../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:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow] + 2171 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow] + 2908 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow] + 2908 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ convert2bed.c:6716:109: warning: format '%zu' expects argument of type 'size_t', but argument 4 has type 'long unsigned int' [-Wformat=] 6716 | fprintf(stderr, "Error: Could not find newline in intermediate buffer; check input [%zu | %zu | %zu]\n", (unsigned long) src_bytes_read, (unsigned long) remainder_length, (unsigned long) src_buffer_capacity); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int long unsigned int | %lu +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, Metadata**, CompressionType, const char*, const char*, Boolean, Boolean, Bed::LineCountType)': +../../../../interfaces/src/data/starch/starchHelpers.c:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow] + 3434 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, Metadata**, CompressionType, const char*, const char*, Boolean, Boolean, Bed::LineCountType)': +../../../../interfaces/src/data/starch/starchHelpers.c:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow] + 3434 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow] + 4202 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow] + 4202 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers convert2bed.c:6716:115: warning: format '%zu' expects argument of type 'size_t', but argument 5 has type 'long unsigned int' [-Wformat=] 6716 | fprintf(stderr, "Error: Could not find newline in intermediate buffer; check input [%zu | %zu | %zu]\n", (unsigned long) src_bytes_read, (unsigned long) remainder_length, (unsigned long) src_buffer_capacity); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -787,6 +879,25 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow] 2171 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here + 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here + 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here + 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow] 2908 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ @@ -797,17 +908,32 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow] 4202 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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/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 -Wformat -Werror=format-security -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] @@ -816,24 +942,28 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); | ~~~~~~^~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(Metadata**, const FILE*, CompressionType, const char*, const char*)': +../../../../interfaces/src/data/starch/starchHelpers.c:964:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here + 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + | ~~~~~~^~~~~~~~~~~~ +../../../../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:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow] 2171 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -../../../../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:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow] - 2171 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow] - 2908 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow] 2908 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, Metadata**, CompressionType, const char*, const char*, Boolean, Boolean, Bed::LineCountType)': -../../../../interfaces/src/data/starch/starchHelpers.c:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow] - 3434 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, Metadata**, CompressionType, const char*, const char*, Boolean, Boolean, Bed::LineCountType)': ../../../../interfaces/src/data/starch/starchHelpers.c:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow] 3434 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; @@ -841,13 +971,21 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow] 4202 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow] - 4202 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -../../../../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:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow] - 2171 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/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/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:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow] 2171 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; @@ -855,17 +993,46 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow] 2908 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow] - 2908 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here + 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here + 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here + 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, Metadata**, CompressionType, const char*, const char*, Boolean, Boolean, Bed::LineCountType)': ../../../../interfaces/src/data/starch/starchHelpers.c:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow] 3434 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow] + 4202 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +../../../../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:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow] + 2171 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow] + 2908 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, Metadata**, CompressionType, const char*, const char*, Boolean, Boolean, Bed::LineCountType)': ../../../../interfaces/src/data/starch/starchHelpers.c:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow] 3434 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow] + 4202 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ ../../../../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); @@ -873,26 +1040,27 @@ ../../../../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:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow] - 4202 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow] - 4202 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)': -../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here - 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); - | ~~~~~~^~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)': -../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here - 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); - | ~~~~~~^~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, Metadata**, CompressionType*, ArchiveVersion**, uint64_t*, Boolean*, Boolean)': +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 2221 | strncpy(recTokBuf, token, strlen(token) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here + 2221 | strncpy(recTokBuf, token, strlen(token) + 1); + | ~~~~~~^~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, Metadata**, CompressionType, const char*, const char*, Boolean, Boolean, Bed::LineCountType)': +../../../../interfaces/src/data/starch/starchHelpers.c:2464:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here + 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); + | ~~~~~~^~~~~~~~~~~~ +../../../../interfaces/src/data/starch/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_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); @@ -907,17 +1075,19 @@ ../../../../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/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 ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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); @@ -925,9 +1095,13 @@ ../../../../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:964:98: note: length computed here - 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); - | ~~~~~~^~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, CompressionType)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] + 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here + 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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); @@ -935,6 +1109,20 @@ ../../../../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/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); @@ -942,17 +1130,13 @@ ../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here 964 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ +mkdir -p objects +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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:2464:98: note: length computed here 2464 | strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); | ~~~~~~^~~~~~~~~~~~ @@ -963,6 +1147,13 @@ ../../../../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 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, CompressionType)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] + 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here + 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::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); @@ -970,7 +1161,6 @@ ../../../../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 -Wformat -Werror=format-security -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/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); @@ -984,10 +1174,7 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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_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); @@ -995,6 +1182,25 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here 2221 | strncpy(recTokBuf, token, strlen(token) + 1); | ~~~~~~^~~~~~~ +mkdir -p objects +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers +mkdir -p ../bin && g++ -o ../bin/bedmap-typical -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects-typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_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); @@ -1008,74 +1214,6 @@ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here 330 | strncpy(iter->signature, signature, strlen(signature) + 1); | ~~~~~~^~~~~~~~~~~ -../../../../interfaces/src/data/starch/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_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_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); - | ~~~~~~^~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, Metadata**, CompressionType*, ArchiveVersion**, uint64_t*, Boolean*, Boolean)': -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 2221 | strncpy(recTokBuf, token, strlen(token) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here - 2221 | strncpy(recTokBuf, token, strlen(token) + 1); - | ~~~~~~^~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, Metadata**, CompressionType*, ArchiveVersion**, uint64_t*, Boolean*, Boolean)': -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 2221 | strncpy(recTokBuf, token, strlen(token) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here - 2221 | strncpy(recTokBuf, token, strlen(token) + 1); - | ~~~~~~^~~~~~~ -../../../../interfaces/src/data/starch/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 -Wformat -Werror=format-security -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/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 ), @@ -1090,45 +1228,6 @@ ../../../../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 -Wformat -Werror=format-security -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 '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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers -convert2bed.c: In function 'c2b_line_convert_sam_to_bed_unsorted_with_split_operation': -convert2bed.c:5017:25: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] - 5017 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -convert2bed.c:5043:21: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] - 5043 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -convert2bed.c:5061:21: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] - 5061 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -convert2bed.c:4950:25: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] - 4950 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -convert2bed.c:4974:21: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] - 4974 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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); @@ -1167,6 +1266,67 @@ ../../../../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 -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers +../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, Boolean, Boolean, char*, Bed::LineLengthType)': +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 311 | strncpy(iter->filename, fn, strlen(fn) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here + 311 | strncpy(iter->filename, fn, strlen(fn) + 1); + | ~~~~~~^~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 330 | strncpy(iter->signature, signature, strlen(signature) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here + 330 | strncpy(iter->signature, signature, strlen(signature) + 1); + | ~~~~~~^~~~~~~~~~~ +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers +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 +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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../../../.. +../../../../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); + | ~~~~~~^~~~~~~ +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/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, Boolean)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); @@ -1180,6 +1340,228 @@ ../../../../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); + | ~~~~~~^~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 +../../../../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); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../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); + | ~~~~~~^~~~~~~~~~~ +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: +../../../../interfaces/general-headers/data/bed/BedCompare.hpp:38:20: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 38 | : public std::binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/string:49, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/istream:40, + from /usr/include/c++/14/fstream:40, + from Bedmap.cpp:29: +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/bed/BedCompare.hpp:52:20: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 52 | : public std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/bed/BedCompare.hpp:77:20: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 77 | : public std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/bed/BedCompare.hpp:88:20: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 88 | : public std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/bed/BedCompare.hpp:101:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 101 | : public std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/bed/BedCompare.hpp:165:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 165 | : public std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/bed/BedCompare.hpp:242:20: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 242 | : public std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/bed/BedCompare.hpp:254:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 254 | : public std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/bed/BedCompare.hpp:264:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 264 | : public std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/bed/BedCompare.hpp:274:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 274 | : public std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/bed/BedCompare.hpp:284:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 284 | : public std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/bed/BedCompare.hpp:294:20: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 294 | : public std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/bed/BedCompare.hpp:302:20: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 302 | : public std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +../../../../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 ../bin +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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../../../.. +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 )); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 )); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, Metadata**, CompressionType*, ArchiveVersion**, uint64_t*, Boolean*, Boolean)': +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 2221 | strncpy(recTokBuf, token, strlen(token) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2221:57: note: length computed here + 2221 | strncpy(recTokBuf, token, strlen(token) + 1); + | ~~~~~~^~~~~~~ +In file included from ../../../../interfaces/general-headers/algorithm/visitors/NumericalVisitors.hpp:32, + from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:34: +../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:43:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 43 | struct abs_diff : std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +../../../../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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 '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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects-typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, CompressionType)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] + 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here + 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: 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); @@ -1199,6 +1581,101 @@ ../../../../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 ../bin && g++ -o ../bin/bedops-typical -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -ljansson -lz -lbz2 Bedops.cpp +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects-typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 +mkdir -p ../bin +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c starchcat.c -o objects/starchcat.o -iquote../../../../interfaces/general-headers -iquote../../../.. +mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers +In file included from /usr/include/c++/14/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 ) ) ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:2131:78: warning: left shift count >= width of type [-Wshift-count-overflow] + 2131 | bzOutBytesWritten = static_cast( bzOutBytesWrittenHi32 ) << 32 | bzOutBytesWrittenLo32; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +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 ), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../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); @@ -1209,54 +1686,92 @@ ../../../../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: 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:1678:75: note: length computed here 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here + 200 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/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 ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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 ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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 ))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 )); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 Sort.cpp -o objects-typical/Sort.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 ))); @@ -1270,116 +1785,31 @@ ../../../../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: 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 -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects-typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, CompressionType)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] - 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here - 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c: 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: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, CompressionType)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] - 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here - 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here - 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function '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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers -rm -rf objects -make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/conversion/src' -mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -make -C applications/bed/starch/src -f Makefile build -make[4]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/starch/src' -mkdir -p objects -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 ../bin && g++ -o ../bin/bedextract-typical -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -ljansson -lz -lbz2 ExtractRows.cpp -mkdir -p ../bin && g++ -o ../bin/bedmap-typical -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -mkdir -p objects -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 ../bin && g++ -o ../bin/closest-features-typical -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -ljansson -lz -lbz2 ClosestFeature.cpp -../../../../interfaces/src/data/starch/unstarchHelpers.c: In function '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 ../bin && g++ -o ../bin/bedops-typical -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': -../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here - 1651 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here - 1678 | strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here - 1667 | strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/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 ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, - from ExtractRows.cpp:40: +mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 CheckSort.cpp -o objects-typical/CheckSort.o -iquote../../../../interfaces/general-headers +convert2bed.c: In function 'c2b_line_convert_sam_to_bed_unsorted_with_split_operation': +convert2bed.c:5017:25: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] + 5017 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +convert2bed.c:5043:21: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] + 5043 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +convert2bed.c:5061:21: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] + 5061 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +convert2bed.c:4950:25: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] + 4950 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +convert2bed.c:4974:21: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] + 4974 | sprintf(c2b_globals.sam->element->modified_cigar, "%s%d%c", c2b_globals.sam->element->modified_cigar, bases, current_op); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../../../interfaces/general-headers/algorithm/visitors/helpers/ProcessBedVisitorRow.hpp:33, + from Bedops.cpp:40: ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:38:20: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 38 | : public std::binary_function { | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/string:49, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/istream:40, - from /usr/include/c++/14/fstream:40, - from ExtractRows.cpp:29: +In file included from /usr/include/c++/14/bits/refwrap.h:39, + from /usr/include/c++/14/deque:67, + from Bedops.cpp:27: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1455,13 +1885,37 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +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 +mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../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++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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../../../.. +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 )); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -ljansson -lz -lbz2 ClosestFeature.cpp +../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, CompressionType)': +../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] + 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here + 2559 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/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 { | ^~~~~~~~~~~~~~~ @@ -1471,7 +1925,7 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, - from Bedmap.cpp:29: + from CheckSort.cpp:25: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1547,6 +2001,49 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 ../bin && g++ -o ../bin/bedextract-typical -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 +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 + | ~~~~~~^~~~~~~~~~ +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 ) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp: In instantiation of 'Bed::bed_check_iterator Bed::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; unsigned int SZ = 16]': +CheckSort.cpp:51:28: required from here + 51 | pool.release(*start++); + | ^~ +../../../../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; 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; 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.hpp:39, from ClosestFeature.cpp:38: @@ -1631,14 +2128,18 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from ../../../../interfaces/general-headers/algorithm/visitors/helpers/ProcessBedVisitorRow.hpp:33, - from Bedops.cpp:40: +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] 38 | : public std::binary_function { | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/bits/refwrap.h:39, - from /usr/include/c++/14/deque:67, - from Bedops.cpp:27: +In file included from /usr/include/c++/14/string:49, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/istream:40, + from /usr/include/c++/14/fstream:40, + from ExtractRows.cpp:29: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1714,44 +2215,6 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from ../../../../interfaces/general-headers/algorithm/visitors/NumericalVisitors.hpp:32, - from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:34: -../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:43:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 43 | struct abs_diff : std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -../../../../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 ))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -SortDetails.cpp: In function 'ChromBedData* initializeChromBedData(char*, double*)': -SortDetails.cpp:250:12: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] - 250 | strncpy(chrom->chromName, chromBuf, chromBufLen); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -SortDetails.cpp:249:25: note: length computed here - 249 | chromBufLen = strlen(chromBuf); // we know >= 1 - | ~~~~~~^~~~~~~~~~ -mkdir -p objects -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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::STARCH2_transformHeaderedBEDInput(const FILE*, Metadata**, CompressionType, const char*, const char*, Boolean, Boolean, Bed::LineCountType)': -../../../../interfaces/src/data/starch/starchHelpers.c:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow] - 2171 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow] - 2908 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, Metadata**, CompressionType, const char*, const char*, Boolean, Boolean, Bed::LineCountType)': -../../../../interfaces/src/data/starch/starchHelpers.c:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow] - 3434 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow] - 4202 | bzBytesWritten = static_cast( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 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); @@ -1759,20 +2222,8 @@ SortDetails.cpp:1342:33: note: length computed here 1342 | chromBufLen = strlen(beds->chroms[i]->chromName); // we know >= 1 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)': -../../../../interfaces/src/data/starch/starchHelpers.c:560:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here - 560 | strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); - | ~~~~~~^~~~~~~~ -../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_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); - | ~~~~~~^~~~~~~~~~~~ +rm -rf objects +make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/conversion/src' 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] @@ -1781,24 +2232,13 @@ SortDetails.cpp:249:25: note: length computed here 249 | chromBufLen = strlen(chromBuf); // we know >= 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 -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 Sort.cpp -o objects-typical/Sort.o -iquote../../../../interfaces/general-headers -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); - | ~~~~~~^~~~~~~~ -mkdir -p objects-typical && g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -pedantic -ansi -O3 -std=c++11 CheckSort.cpp -o objects-typical/CheckSort.o -iquote../../../../interfaces/general-headers +starchcat.c: In function 'int starch::STARCHCAT2_mergeInputRecordsToOutput(const char*, Metadata**, const char*, CompressionType, const ChromosomeSummary*, size_t*)': +starchcat.c:3123:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 3123 | strncpy(transformStates[inRecIdx]->t_currentChromosome, inChr, strlen(inChr) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +starchcat.c:3123:78: note: length computed here + 3123 | strncpy(transformStates[inRecIdx]->t_currentChromosome, inChr, strlen(inChr) + 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); @@ -1806,8 +2246,9 @@ ../../../../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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mkdir -p objects -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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../../../.. +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/starchcat.o -o ../bin/starchcat-typical ../lib/libstarch.a -ljansson -lz -lbz2 +rm -rf objects +make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/starch/src' In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42: ../../../../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] @@ -1816,125 +2257,15 @@ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here 541 | std::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); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../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); - | ~~~~~~^~~~~~~~~~~ -In file included from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32, - from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41, - from CheckSort.cpp:28: -../../../../interfaces/general-headers/data/bed/BedCompare.hpp:38:20: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 38 | : public std::binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/string:49, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/istream:40, - from /usr/include/c++/14/fstream:40, - from CheckSort.cpp:25: -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/bed/BedCompare.hpp:52:20: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 52 | : public std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/bed/BedCompare.hpp:77:20: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 77 | : public std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/bed/BedCompare.hpp:88:20: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 88 | : public std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/bed/BedCompare.hpp:101:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 101 | : public std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/bed/BedCompare.hpp:165:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 165 | : public std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/bed/BedCompare.hpp:242:20: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 242 | : public std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/bed/BedCompare.hpp:254:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 254 | : public std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/bed/BedCompare.hpp:264:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 264 | : public std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/bed/BedCompare.hpp:274:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 274 | : public std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/bed/BedCompare.hpp:284:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 284 | : public std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/bed/BedCompare.hpp:294:20: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 294 | : public std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/bed/BedCompare.hpp:302:20: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 302 | : public std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/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 ) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ~~~~~~^~~~~~~~ ../../../../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); @@ -1942,82 +2273,6 @@ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp: In instantiation of 'Bed::bed_check_iterator Bed::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; unsigned int SZ = 16]': -CheckSort.cpp:51:28: required from here - 51 | pool.release(*start++); - | ^~ -../../../../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; 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; unsigned int SZ = 16]' - 308 | bool operator=(const bed_check_iterator& b); - | ^~~~~~~~ -../../../../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 -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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 -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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../../../.. -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) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 ../../../../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); @@ -2025,49 +2280,16 @@ ../../../../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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mkdir -p ../bin -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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../../../.. -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 )); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)', + inlined from 'static bool starch::Starch::hasStarchRevision1LegacyHeader(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:634:52, + inlined from 'static bool starch::Starch::isStarch(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:698:56, + inlined from 'Bed::bed_check_iterator::bed_check_iterator(std::istream&, const std::string&, Ext::PooledMemory&, const std::string&, bool) [with BedType = Bed::BasicCoords; unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:92:90: +../../../../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 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, @@ -2078,170 +2300,6 @@ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -mkdir -p ../bin -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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../../../.. -In file included from /usr/include/c++/14/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 ) ) ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:2131:78: warning: left shift count >= width of type [-Wshift-count-overflow] - 2131 | bzOutBytesWritten = static_cast( bzOutBytesWrittenHi32 ) << 32 | bzOutBytesWrittenLo32; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -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 ), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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, - inlined from 'Bed::bed_check_iterator Bed::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:292:36, - inlined from 'Bed::bed_check_iterator Bed::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:267:24, - inlined from 'std::pair Bed::find_bed_range(FILE*, TargetIter, TargetIter, Op) [with TargetIter = bed_check_iterator*, 16>; Op = Visitors::BedHelpers::Println]' at ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:102:64: -../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here - 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); - | ~~~~~~^~~~~ -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 )); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]; - | ^~~~~~~~~~~~ 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*)': @@ -2258,16 +2316,6 @@ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here 1913 | strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)', - inlined from 'static bool starch::Starch::hasStarchRevision1LegacyHeader(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:634:52, - inlined from 'static bool starch::Starch::isStarch(std::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:698:56, - inlined from 'Bed::bed_check_iterator::bed_check_iterator(std::istream&, const std::string&, Ext::PooledMemory&, const std::string&, bool) [with BedType = Bed::BasicCoords; unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:92:90: -../../../../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 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, @@ -2278,28 +2326,6 @@ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ -rm -rf objects_typical -make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedextract/src' -mkdir -p ../bin -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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../../../.. -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 )); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -starchcat.c: In function 'int starch::STARCHCAT2_mergeInputRecordsToOutput(const char*, Metadata**, const char*, CompressionType, const ChromosomeSummary*, size_t*)': -starchcat.c:3123:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] - 3123 | strncpy(transformStates[inRecIdx]->t_currentChromosome, inChr, strlen(inChr) + 1); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -starchcat.c:3123:78: note: length computed here - 3123 | strncpy(transformStates[inRecIdx]->t_currentChromosome, inChr, strlen(inChr) + 1); - | ~~~~~~^~~~~~~ -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 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, @@ -2312,13 +2338,24 @@ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); | ~~~~~~^~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bedops-2.4.41+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/starchcat.o -o ../bin/starchcat-typical ../lib/libstarch.a -ljansson -lz -lbz2 -rm -rf objects -make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/starch/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, + inlined from 'Bed::bed_check_iterator Bed::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:292:36, + inlined from 'Bed::bed_check_iterator Bed::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:267:24, + inlined from 'std::pair Bed::find_bed_range(FILE*, TargetIter, TargetIter, Op) [with TargetIter = bed_check_iterator*, 16>; Op = Visitors::BedHelpers::Println]' at ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:102:64: +../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-truncation] + 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here + 887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1); + | ~~~~~~^~~~~ 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 -Wformat -Werror=format-security -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' rm -rf objects_typical +make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedextract/src' +rm -rf objects_typical make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/closestfeats/src' rm -rf objects_typical make[4]: Leaving directory '/build/reproducible-path/bedops-2.4.41+dfsg/applications/bed/bedops/src' @@ -2346,7 +2383,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - make -j6 install DESTDIR=/build/reproducible-path/bedops-2.4.41\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + make -j10 install DESTDIR=/build/reproducible-path/bedops-2.4.41\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/bedops-2.4.41+dfsg' mkdir -p bin cp applications/bed/conversion/src/wrappers/bam2bed applications/bed/conversion/src/wrappers/bam2bed_gnuParallel applications/bed/conversion/src/wrappers/bam2bed_sge applications/bed/conversion/src/wrappers/bam2bed_slurm applications/bed/conversion/src/wrappers/bam2starch applications/bed/conversion/src/wrappers/bam2starch_gnuParallel applications/bed/conversion/src/wrappers/bam2starch_sge applications/bed/conversion/src/wrappers/bam2starch_slurm applications/bed/conversion/src/wrappers/gff2bed applications/bed/conversion/src/wrappers/gff2starch applications/bed/conversion/src/wrappers/gtf2bed applications/bed/conversion/src/wrappers/gtf2starch applications/bed/conversion/src/wrappers/gvf2bed applications/bed/conversion/src/wrappers/gvf2starch applications/bed/conversion/src/wrappers/psl2bed applications/bed/conversion/src/wrappers/psl2starch applications/bed/conversion/src/wrappers/rmsk2bed applications/bed/conversion/src/wrappers/rmsk2starch applications/bed/conversion/src/wrappers/sam2bed applications/bed/conversion/src/wrappers/sam2starch applications/bed/conversion/src/wrappers/vcf2bed applications/bed/conversion/src/wrappers/vcf2starch applications/bed/conversion/src/wrappers/wig2bed applications/bed/conversion/src/wrappers/wig2starch bin @@ -2467,10 +2504,10 @@ copying static files... Writing evaluated template result to /build/reproducible-path/bedops-2.4.41+dfsg/docs/_build/html/_static/documentation_options.js -Writing evaluated template result to /build/reproducible-path/bedops-2.4.41+dfsg/docs/_build/html/_static/language_data.js Writing evaluated template result to /build/reproducible-path/bedops-2.4.41+dfsg/docs/_build/html/_static/basic.css -Writing evaluated template result to /build/reproducible-path/bedops-2.4.41+dfsg/docs/_build/html/_static/sidebar.js +Writing evaluated template result to /build/reproducible-path/bedops-2.4.41+dfsg/docs/_build/html/_static/language_data.js Writing evaluated template result to /build/reproducible-path/bedops-2.4.41+dfsg/docs/_build/html/_static/classic.css +Writing evaluated template result to /build/reproducible-path/bedops-2.4.41+dfsg/docs/_build/html/_static/sidebar.js copying static files: done copying extra files... copying extra files: done @@ -2617,234 +2654,234 @@ dh_perl dh_link dh_strip_nondeterminism -debian/bedops-doc/usr/share/doc/bedops/html/_images/bedops_macosx_installer_screen_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_images/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/performance_bedops_intersect_sorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_bedmap_mapref_ref2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_images/SNP_DHS_matrix.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/bedops_macosx_installer_screen.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_images/BEDOPS_Presentation_bedmap_ops.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_images/BEDOPS_Presentation_starch_efficiency.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_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/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/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_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/bedops_cygwin_installer_gcc_screen.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_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/starch_specification_chromosomestreams.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/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/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_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/overview/BEDOPS_Presentation_bedmap_ops.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_partition_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/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/BEDOPS_Presentation_bedmap_ops.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_images/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/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/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/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/_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/_images/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/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/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/_images/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/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_symmetricdifference_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_partition_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_images/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/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_setops_bedops_symmetricdifference_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_partition_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_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/_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/_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/set-operations/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/_images/SNP_DHS_matrix_diseaseSorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/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/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/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/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/_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/_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/performance_bedops_complement_sorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_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/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/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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/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/_images/starch_specification_padding.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/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_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/_images/performance_bedops_intersect_sorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_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/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/reference/set-operations/reference_setops_bedops_complement_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/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_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/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/reference_setops_bedops_difference_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/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/_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/_images/starch_specification_chromosomestreams.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_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/_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/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_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/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/_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/reference/set-operations/reference_setops_bedops_symmetricdifference_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/set_operations.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_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/_images/statistics_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_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/_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/_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/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/reference/set-operations/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/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/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/_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/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/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_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/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_setops_bedops_merge_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_everything.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/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/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/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/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/performance_bedops_complement_sorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_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/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/_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/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_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/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/overview.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/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/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/reference/set-operations/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/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/bedops_cygwin_installer_screen.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. 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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/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/_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/_static/reference_setops_bedops_inputs.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/performance_bedops_merge_unsorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. 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-debian/bedops-doc/usr/share/doc/bedops/html/_static/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/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/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/index/other.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/set_operations_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_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/_static/file_management.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_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_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/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/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/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. -debian/bedops-doc/usr/share/doc/bedops/html/_static/linux_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/index/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/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/reference/set-operations/reference_setops_bedops_merge_ab@2x.png: 1 bytes of garbage after IEND chunk at 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-debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_merge_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_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/reference_setops_bedops_complement_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_partition_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_notelementof_ab.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/_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_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/_images/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/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/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/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/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/_images/bedops_cygwin_installer_screen.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_partition_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_bedmap_mapref_all.png: 1 bytes of garbage after IEND chunk at 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172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/index/set_operations_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/installation/bedops_cygwin_installer_screen.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_elementof_ba@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_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/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/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. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_difference_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_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/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/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/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/other.png: 1 bytes 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_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/_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/set-operations/reference_setops_bedops_symmetricdifference_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_complement_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/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/_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/_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/_static/index/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/_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/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/starch_specification.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/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/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/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/set-operations/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/_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_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/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/_images/bedops_macosx_installer_screen_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_intersect_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_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/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_elementof_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/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/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/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/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/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/_images/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/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/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/reference_setops_bedops_difference_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_images/BEDOPS_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/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/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/bedops_macosx_installer_screen_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/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/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_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/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_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/index/source_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_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/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_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_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/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/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/_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/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_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/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/_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_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/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/index/statistics_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/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/set-operations/reference_setops_bedops_merge_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_bedextract_mechanism.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_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/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/_static/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_setops_bedops_elementof_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_intersect_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_images/bedops_cygwin_installer_screen.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/file-management/compression/starch_specification.png: 1 bytes 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/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/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/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/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/index/reference_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/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/other.png: 1 bytes 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/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/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/_images/statistics_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_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/reference_setops_bedops_merge_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_static/index/statistics.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_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@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_setops_bedops_inputs@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/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/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/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/_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_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/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/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/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/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/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/_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/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/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/_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/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/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/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/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/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/_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/_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/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/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/_images/set_operations_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_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/_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/_images/bedops_cygwin_installer_gcc_screen.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. debian/bedops-doc/usr/share/doc/bedops/html/_static/reference_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/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/_images/reference_setops_bedops_difference_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_static/support.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/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_setops_bedops_inputs@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/set-operations/reference_setops_bedops_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/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/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/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/overview/BEDOPS_Presentation_starch_efficiency.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. -debian/bedops-doc/usr/share/doc/bedops/html/_images/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_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_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/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/reference/set-operations/reference_setops_bedops_partition_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/performance.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. 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line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_images/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/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/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/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/performance/performance_bedops_merge_unsorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. 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+debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/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/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/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/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/reference/set-operations/reference_setops_bedops_notelementof_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/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/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_setops_bedops_chop_ab.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/performance/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_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/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/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/reference/file-management/compression/starch_specification.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 172. +debian/bedops-doc/usr/share/doc/bedops/html/_static/reference/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/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/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/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/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/index/set_operations_v2.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 @@ -2863,9 +2900,9 @@ dpkg-gencontrol: warning: package bedops-doc: substitution variable ${sphinxdoc:Depends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'bedops-dbgsym' in '../bedops-dbgsym_2.4.41+dfsg-3_i386.deb'. dpkg-deb: building package 'bedops' in '../bedops_2.4.41+dfsg-3_i386.deb'. dpkg-deb: building package 'bedops-doc' in '../bedops-doc_2.4.41+dfsg-3_all.deb'. +dpkg-deb: building package 'bedops-dbgsym' in '../bedops-dbgsym_2.4.41+dfsg-3_i386.deb'. dpkg-genbuildinfo --build=binary -O../bedops_2.4.41+dfsg-3_i386.buildinfo dpkg-genchanges --build=binary -O../bedops_2.4.41+dfsg-3_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2873,12 +2910,14 @@ 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/42342/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/42342/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/10591 and its subdirectories -I: Current time: Wed Jan 21 11:16:44 -12 2026 -I: pbuilder-time-stamp: 1769037404 +I: removing directory /srv/workspace/pbuilder/42342 and its subdirectories +I: Current time: Fri Dec 20 07:06:54 +14 2024 +I: pbuilder-time-stamp: 1734628014