Diff of the two buildlogs: -- --- b1/build.log 2024-05-09 18:17:48.798352830 +0000 +++ b2/build.log 2024-05-09 18:23:07.448789944 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jun 11 12:33:45 -12 2025 -I: pbuilder-time-stamp: 1749688425 +I: Current time: Fri May 10 08:17:57 +14 2024 +I: pbuilder-time-stamp: 1715278677 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -47,51 +47,83 @@ dpkg-source: info: applying R_4.2_fix I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2069237/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1261467/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 9 18:18 /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/1261467/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1261467/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='a303524a747d4d60b3c8528094ffc1ff' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='2069237' - PS1='# ' - PS2='> ' + INVOCATION_ID=88fcd980809743c88540798cff1c736e + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1261467 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.HpGxifsP/pbuilderrc_N81K --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.HpGxifsP/b1 --logfile b1/build.log trinityrnaseq_2.15.1+dfsg-5.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.HpGxifsP/pbuilderrc_op5U --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.HpGxifsP/b2 --logfile b2/build.log trinityrnaseq_2.15.1+dfsg-5.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom02-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 10 14:05 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2069237/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 8 07:42 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1261467/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -396,7 +428,7 @@ Get: 249 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.19+ds-1.1+b1 [1667 kB] Get: 250 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 251 http://deb.debian.org/debian unstable/main amd64 libjung-free-java all 2.1.1-2 [1477 kB] -Fetched 242 MB in 3s (72.3 MB/s) +Fetched 242 MB in 7s (32.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1:amd64. (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 ... 19699 files and directories currently installed.) @@ -1221,8 +1253,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Jun 12 00:37:54 UTC 2025. -Universal Time is now: Thu Jun 12 00:37:54 UTC 2025. +Local time is now: Thu May 9 18:20:00 UTC 2024. +Universal Time is now: Thu May 9 18:20:00 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libasound2-data (1.2.11-1) ... @@ -1621,7 +1653,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/trinityrnaseq-2.15.1+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 > ../trinityrnaseq_2.15.1+dfsg-5_source.changes +I: user script /srv/workspace/pbuilder/1261467/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1261467/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/trinityrnaseq-2.15.1+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 > ../trinityrnaseq_2.15.1+dfsg-5_source.changes dpkg-buildpackage: info: source package trinityrnaseq dpkg-buildpackage: info: source version 2.15.1+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -1689,8 +1725,8 @@ make[3]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/trinity-plugins/slclust' cd COLLECTL && rm -rf "collectl-4.1.0" && rm -f collectl cd htslib && /usr/bin/make clean -/bin/sh: 1: cd: can't cd to htslib -make[2]: *** [Makefile:54: clean] Error 2 +/bin/sh: line 1: cd: htslib: No such file or directory +make[2]: *** [Makefile:54: clean] Error 1 make[2]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/trinity-plugins' make[1]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg' jh_clean @@ -1730,7 +1766,7 @@ -- Detecting CXX compile features -- Detecting CXX compile features - done -- system: Linux --- Configuring done (0.6s) +-- Configuring done (0.9s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -1800,58 +1836,72 @@ make -f CMakeFiles/FastaToDeBruijn.dir/build.make CMakeFiles/FastaToDeBruijn.dir/depend make -f CMakeFiles/fastaToKmerCoverageStats.dir/build.make CMakeFiles/fastaToKmerCoverageStats.dir/depend make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build' +cd /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build/CMakeFiles/inchworm.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build' cd /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build/CMakeFiles/FastaToDeBruijn.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build/CMakeFiles/fastaToKmerCoverageStats.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build' -cd /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build/CMakeFiles/inchworm.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build' -make -f CMakeFiles/fastaToKmerCoverageStats.dir/build.make CMakeFiles/fastaToKmerCoverageStats.dir/build +cd /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build/CMakeFiles/fastaToKmerCoverageStats.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build' +make -f CMakeFiles/FastaToDeBruijn.dir/build.make CMakeFiles/FastaToDeBruijn.dir/build make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build' +[ 14%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/DeBruijnGraph.cpp.o +[ 21%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/string_util.cpp.o +[ 25%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/Fasta_entry.cpp.o +[ 28%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/FastaToDeBruijn.cpp.o +[ 28%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/stacktrace.cpp.o +[ 28%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/FastaToDeBruijn.dir/src/Fasta_entry.cpp.o -MF CMakeFiles/FastaToDeBruijn.dir/src/Fasta_entry.cpp.o.d -o CMakeFiles/FastaToDeBruijn.dir/src/Fasta_entry.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/Fasta_entry.cpp +make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build' +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/FastaToDeBruijn.dir/src/FastaToDeBruijn.cpp.o -MF CMakeFiles/FastaToDeBruijn.dir/src/FastaToDeBruijn.cpp.o.d -o CMakeFiles/FastaToDeBruijn.dir/src/FastaToDeBruijn.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/FastaToDeBruijn.cpp +[ 28%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/argProcessor.cpp.o +[ 28%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/Fasta_reader.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o -MF CMakeFiles/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o.d -o CMakeFiles/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/sequenceUtil.cpp make -f CMakeFiles/inchworm.dir/build.make CMakeFiles/inchworm.dir/build -make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build' make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build' -make -f CMakeFiles/FastaToDeBruijn.dir/build.make CMakeFiles/FastaToDeBruijn.dir/build +make -f CMakeFiles/fastaToKmerCoverageStats.dir/build.make CMakeFiles/fastaToKmerCoverageStats.dir/build +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/FastaToDeBruijn.dir/src/string_util.cpp.o -MF CMakeFiles/FastaToDeBruijn.dir/src/string_util.cpp.o.d -o CMakeFiles/FastaToDeBruijn.dir/src/string_util.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/string_util.cpp +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/FastaToDeBruijn.dir/src/stacktrace.cpp.o -MF CMakeFiles/FastaToDeBruijn.dir/src/stacktrace.cpp.o.d -o CMakeFiles/FastaToDeBruijn.dir/src/stacktrace.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/stacktrace.cpp make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build' -[ 10%] Building CXX object CMakeFiles/inchworm.dir/src/IRKE_run.cpp.o -[ 7%] Building CXX object CMakeFiles/inchworm.dir/src/Fasta_entry.cpp.o -[ 10%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/fastaToKmerCoverageStats.cpp.o -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/inchworm.dir/src/Fasta_entry.cpp.o -MF CMakeFiles/inchworm.dir/src/Fasta_entry.cpp.o.d -o CMakeFiles/inchworm.dir/src/Fasta_entry.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/Fasta_entry.cpp +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/FastaToDeBruijn.dir/src/argProcessor.cpp.o -MF CMakeFiles/FastaToDeBruijn.dir/src/argProcessor.cpp.o.d -o CMakeFiles/FastaToDeBruijn.dir/src/argProcessor.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/argProcessor.cpp +make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build' +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/FastaToDeBruijn.dir/src/Fasta_reader.cpp.o -MF CMakeFiles/FastaToDeBruijn.dir/src/Fasta_reader.cpp.o.d -o CMakeFiles/FastaToDeBruijn.dir/src/Fasta_reader.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/Fasta_reader.cpp +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/FastaToDeBruijn.dir/src/DeBruijnGraph.cpp.o -MF CMakeFiles/FastaToDeBruijn.dir/src/DeBruijnGraph.cpp.o.d -o CMakeFiles/FastaToDeBruijn.dir/src/DeBruijnGraph.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/DeBruijnGraph.cpp +[ 35%] Building CXX object CMakeFiles/inchworm.dir/src/Fasta_entry.cpp.o +[ 35%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/fastaToKmerCoverageStats.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/fastaToKmerCoverageStats.dir/src/fastaToKmerCoverageStats.cpp.o -MF CMakeFiles/fastaToKmerCoverageStats.dir/src/fastaToKmerCoverageStats.cpp.o.d -o CMakeFiles/fastaToKmerCoverageStats.dir/src/fastaToKmerCoverageStats.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp -[ 14%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/argProcessor.cpp.o -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/inchworm.dir/src/IRKE_run.cpp.o -MF CMakeFiles/inchworm.dir/src/IRKE_run.cpp.o.d -o CMakeFiles/inchworm.dir/src/IRKE_run.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/IRKE_run.cpp -[ 17%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/sequenceUtil.cpp.o +[ 39%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/argProcessor.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/inchworm.dir/src/Fasta_entry.cpp.o -MF CMakeFiles/inchworm.dir/src/Fasta_entry.cpp.o.d -o CMakeFiles/inchworm.dir/src/Fasta_entry.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/Fasta_entry.cpp +[ 42%] Building CXX object CMakeFiles/inchworm.dir/src/IRKE_run.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/fastaToKmerCoverageStats.dir/src/argProcessor.cpp.o -MF CMakeFiles/fastaToKmerCoverageStats.dir/src/argProcessor.cpp.o.d -o CMakeFiles/fastaToKmerCoverageStats.dir/src/argProcessor.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/argProcessor.cpp -[ 21%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/string_util.cpp.o -[ 28%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_reader.cpp.o -[ 28%] Building CXX object CMakeFiles/inchworm.dir/src/sequenceUtil.cpp.o -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/fastaToKmerCoverageStats.dir/src/sequenceUtil.cpp.o -MF CMakeFiles/fastaToKmerCoverageStats.dir/src/sequenceUtil.cpp.o.d -o CMakeFiles/fastaToKmerCoverageStats.dir/src/sequenceUtil.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/sequenceUtil.cpp -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/inchworm.dir/src/sequenceUtil.cpp.o -MF CMakeFiles/inchworm.dir/src/sequenceUtil.cpp.o.d -o CMakeFiles/inchworm.dir/src/sequenceUtil.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/sequenceUtil.cpp -[ 32%] Building CXX object CMakeFiles/inchworm.dir/src/IRKE.cpp.o -[ 35%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_entry.cpp.o -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_reader.cpp.o -MF CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_reader.cpp.o.d -o CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_reader.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/Fasta_reader.cpp -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/fastaToKmerCoverageStats.dir/src/string_util.cpp.o -MF CMakeFiles/fastaToKmerCoverageStats.dir/src/string_util.cpp.o.d -o CMakeFiles/fastaToKmerCoverageStats.dir/src/string_util.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/string_util.cpp -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/inchworm.dir/src/IRKE.cpp.o -MF CMakeFiles/inchworm.dir/src/IRKE.cpp.o.d -o CMakeFiles/inchworm.dir/src/IRKE.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/IRKE.cpp -[ 39%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/FastaToDeBruijn.cpp.o -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_entry.cpp.o -MF CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_entry.cpp.o.d -o CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_entry.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/Fasta_entry.cpp -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/FastaToDeBruijn.dir/src/FastaToDeBruijn.cpp.o -MF CMakeFiles/FastaToDeBruijn.dir/src/FastaToDeBruijn.cpp.o.d -o CMakeFiles/FastaToDeBruijn.dir/src/FastaToDeBruijn.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/FastaToDeBruijn.cpp -[ 42%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/stacktrace.cpp.o -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/fastaToKmerCoverageStats.dir/src/stacktrace.cpp.o -MF CMakeFiles/fastaToKmerCoverageStats.dir/src/stacktrace.cpp.o.d -o CMakeFiles/fastaToKmerCoverageStats.dir/src/stacktrace.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/stacktrace.cpp +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/inchworm.dir/src/IRKE_run.cpp.o -MF CMakeFiles/inchworm.dir/src/IRKE_run.cpp.o.d -o CMakeFiles/inchworm.dir/src/IRKE_run.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/IRKE_run.cpp In file included from /usr/include/c++/13/ext/hash_map:60, from /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/KmerCounter.hpp:53, from /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/IRKE.hpp:7, - from /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/IRKE_run.cpp:11: + from /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp:20: /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ In file included from /usr/include/c++/13/ext/hash_map:60, from /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/KmerCounter.hpp:53, from /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/IRKE.hpp:7, - from /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp:20: + from /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/IRKE_run.cpp:11: /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ +[ 46%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_reader.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_reader.cpp.o -MF CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_reader.cpp.o.d -o CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_reader.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/Fasta_reader.cpp +[ 50%] Building CXX object CMakeFiles/inchworm.dir/src/sequenceUtil.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/inchworm.dir/src/sequenceUtil.cpp.o -MF CMakeFiles/inchworm.dir/src/sequenceUtil.cpp.o.d -o CMakeFiles/inchworm.dir/src/sequenceUtil.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/sequenceUtil.cpp +[ 53%] Building CXX object CMakeFiles/inchworm.dir/src/IRKE.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/inchworm.dir/src/IRKE.cpp.o -MF CMakeFiles/inchworm.dir/src/IRKE.cpp.o.d -o CMakeFiles/inchworm.dir/src/IRKE.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/IRKE.cpp +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/DeBruijnGraph.cpp: In member function 'std::string DeBruijnKmer::get_annotations_string()': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/DeBruijnGraph.cpp:66:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 66 | for (int i=0; i < _annotations.size(); i++) { + | ~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/FastaToDeBruijn.cpp: In function 'void createGraphPerRecord(std::vector >, int, bool, ArgProcessor)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/FastaToDeBruijn.cpp:215:39: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 215 | if (seq_region.size() < kmer_length) { continue; } // can be encountered in jaccard-clip mode (rarely) + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ In file included from /usr/include/c++/13/ext/hash_map:60, from /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/KmerCounter.hpp:53, from /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/IRKE.hpp:7, @@ -1859,56 +1909,59 @@ /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ -[ 46%] Building CXX object CMakeFiles/inchworm.dir/src/KmerCounter.cpp.o +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/DeBruijnGraph.cpp: In member function 'std::string DeBruijnGraph::toDOT(bool)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/DeBruijnGraph.cpp:445:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 445 | for (int i=0; i < prev_kmers.size(); i++) { + | ~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/DeBruijnGraph.cpp:494:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 494 | for (int i=0; i < next_kmers.size(); i++) { + | ~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/DeBruijnGraph.cpp: In member function 'std::string DeBruijnGraph::toChrysalisFormat(int, bool)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/DeBruijnGraph.cpp:725:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 725 | for (int i = 0; i < collected_kmers.size(); i++) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~ +[ 57%] Building CXX object CMakeFiles/inchworm.dir/src/KmerCounter.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/inchworm.dir/src/KmerCounter.cpp.o -MF CMakeFiles/inchworm.dir/src/KmerCounter.cpp.o.d -o CMakeFiles/inchworm.dir/src/KmerCounter.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/KmerCounter.cpp -[ 50%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/KmerCounter.cpp.o -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/fastaToKmerCoverageStats.dir/src/KmerCounter.cpp.o -MF CMakeFiles/fastaToKmerCoverageStats.dir/src/KmerCounter.cpp.o.d -o CMakeFiles/fastaToKmerCoverageStats.dir/src/KmerCounter.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/KmerCounter.cpp +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp: In function 'void populate_kmer_counter_from_reads(KmerCounter&, std::string&)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp:231:18: warning: unused variable 'kmer_length' [-Wunused-variable] + 231 | unsigned int kmer_length = kcounter.get_kmer_length(); + | ^~~~~~~~~~~ In file included from /usr/include/c++/13/ext/hash_map:60, from /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/KmerCounter.hpp:53, from /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/KmerCounter.cpp:1: /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ +[ 60%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_entry.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_entry.cpp.o -MF CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_entry.cpp.o.d -o CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_entry.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/Fasta_entry.cpp +[ 64%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/sequenceUtil.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/fastaToKmerCoverageStats.dir/src/sequenceUtil.cpp.o -MF CMakeFiles/fastaToKmerCoverageStats.dir/src/sequenceUtil.cpp.o.d -o CMakeFiles/fastaToKmerCoverageStats.dir/src/sequenceUtil.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/sequenceUtil.cpp +[ 67%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/string_util.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/fastaToKmerCoverageStats.dir/src/string_util.cpp.o -MF CMakeFiles/fastaToKmerCoverageStats.dir/src/string_util.cpp.o.d -o CMakeFiles/fastaToKmerCoverageStats.dir/src/string_util.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/string_util.cpp +[ 71%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/stacktrace.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/fastaToKmerCoverageStats.dir/src/stacktrace.cpp.o -MF CMakeFiles/fastaToKmerCoverageStats.dir/src/stacktrace.cpp.o.d -o CMakeFiles/fastaToKmerCoverageStats.dir/src/stacktrace.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/stacktrace.cpp +[ 75%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/KmerCounter.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/fastaToKmerCoverageStats.dir/src/KmerCounter.cpp.o -MF CMakeFiles/fastaToKmerCoverageStats.dir/src/KmerCounter.cpp.o.d -o CMakeFiles/fastaToKmerCoverageStats.dir/src/KmerCounter.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/KmerCounter.cpp +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp:250:9: warning: 'end' may be used uninitialized [-Wmaybe-uninitialized] + 250 | #pragma omp parallel private (myTid) + | ^~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp:235:26: note: 'end' was declared here + 235 | unsigned long start, end; + | ^~~ In file included from /usr/include/c++/13/ext/hash_map:60, from /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/KmerCounter.hpp:53, from /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/KmerCounter.cpp:1: /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/FastaToDeBruijn.cpp: In function 'void createGraphPerRecord(std::vector >, int, bool, ArgProcessor)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/FastaToDeBruijn.cpp:215:39: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 215 | if (seq_region.size() < kmer_length) { continue; } // can be encountered in jaccard-clip mode (rarely) - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -[ 53%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/argProcessor.cpp.o -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/FastaToDeBruijn.dir/src/argProcessor.cpp.o -MF CMakeFiles/FastaToDeBruijn.dir/src/argProcessor.cpp.o.d -o CMakeFiles/FastaToDeBruijn.dir/src/argProcessor.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/argProcessor.cpp -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp: In function 'void populate_kmer_counter_from_reads(KmerCounter&, std::string&)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp:231:18: warning: unused variable 'kmer_length' [-Wunused-variable] - 231 | unsigned int kmer_length = kcounter.get_kmer_length(); - | ^~~~~~~~~~~ -[ 57%] Building CXX object CMakeFiles/inchworm.dir/src/string_util.cpp.o +[ 78%] Building CXX object CMakeFiles/inchworm.dir/src/string_util.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/inchworm.dir/src/string_util.cpp.o -MF CMakeFiles/inchworm.dir/src/string_util.cpp.o.d -o CMakeFiles/inchworm.dir/src/string_util.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/string_util.cpp -[ 60%] Building CXX object CMakeFiles/inchworm.dir/src/Fasta_reader.cpp.o +[ 82%] Building CXX object CMakeFiles/inchworm.dir/src/Fasta_reader.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/inchworm.dir/src/Fasta_reader.cpp.o -MF CMakeFiles/inchworm.dir/src/Fasta_reader.cpp.o.d -o CMakeFiles/inchworm.dir/src/Fasta_reader.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/Fasta_reader.cpp -[ 64%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/Fasta_reader.cpp.o -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/FastaToDeBruijn.dir/src/Fasta_reader.cpp.o -MF CMakeFiles/FastaToDeBruijn.dir/src/Fasta_reader.cpp.o.d -o CMakeFiles/FastaToDeBruijn.dir/src/Fasta_reader.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/Fasta_reader.cpp -[ 67%] Building CXX object CMakeFiles/inchworm.dir/src/stacktrace.cpp.o +[ 85%] Building CXX object CMakeFiles/inchworm.dir/src/stacktrace.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/inchworm.dir/src/stacktrace.cpp.o -MF CMakeFiles/inchworm.dir/src/stacktrace.cpp.o.d -o CMakeFiles/inchworm.dir/src/stacktrace.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/stacktrace.cpp -[ 71%] Building CXX object CMakeFiles/inchworm.dir/src/argProcessor.cpp.o +[ 89%] Building CXX object CMakeFiles/inchworm.dir/src/argProcessor.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/inchworm.dir/src/argProcessor.cpp.o -MF CMakeFiles/inchworm.dir/src/argProcessor.cpp.o.d -o CMakeFiles/inchworm.dir/src/argProcessor.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/argProcessor.cpp -[ 75%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/Fasta_entry.cpp.o -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/FastaToDeBruijn.dir/src/Fasta_entry.cpp.o -MF CMakeFiles/FastaToDeBruijn.dir/src/Fasta_entry.cpp.o.d -o CMakeFiles/FastaToDeBruijn.dir/src/Fasta_entry.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/Fasta_entry.cpp -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp:250:9: warning: 'end' may be used uninitialized [-Wmaybe-uninitialized] - 250 | #pragma omp parallel private (myTid) - | ^~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp:235:26: note: 'end' was declared here - 235 | unsigned long start, end; - | ^~~ -[ 78%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o -MF CMakeFiles/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o.d -o CMakeFiles/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/sequenceUtil.cpp -[ 82%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/string_util.cpp.o -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/FastaToDeBruijn.dir/src/string_util.cpp.o -MF CMakeFiles/FastaToDeBruijn.dir/src/string_util.cpp.o.d -o CMakeFiles/FastaToDeBruijn.dir/src/string_util.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/string_util.cpp -[ 85%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/stacktrace.cpp.o -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/FastaToDeBruijn.dir/src/stacktrace.cpp.o -MF CMakeFiles/FastaToDeBruijn.dir/src/stacktrace.cpp.o.d -o CMakeFiles/FastaToDeBruijn.dir/src/stacktrace.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/stacktrace.cpp In file included from /usr/include/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/bits/stl_tree.h:64, @@ -1940,28 +1993,11 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/IRKE.cpp:483:24: note: 'tmpfile_struct' declared here 483 | iworm_tmp_file tmpfile_struct; | ^~~~~~~~~~~~~~ -[ 89%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/DeBruijnGraph.cpp.o -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/FastaToDeBruijn.dir/src/DeBruijnGraph.cpp.o -MF CMakeFiles/FastaToDeBruijn.dir/src/DeBruijnGraph.cpp.o.d -o CMakeFiles/FastaToDeBruijn.dir/src/DeBruijnGraph.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/DeBruijnGraph.cpp [ 92%] Linking CXX executable fastaToKmerCoverageStats /usr/bin/cmake -E cmake_link_script CMakeFiles/fastaToKmerCoverageStats.dir/link.txt --verbose=1 /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/fastaToKmerCoverageStats.dir/src/fastaToKmerCoverageStats.cpp.o CMakeFiles/fastaToKmerCoverageStats.dir/src/argProcessor.cpp.o CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_reader.cpp.o CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_entry.cpp.o CMakeFiles/fastaToKmerCoverageStats.dir/src/sequenceUtil.cpp.o CMakeFiles/fastaToKmerCoverageStats.dir/src/string_util.cpp.o CMakeFiles/fastaToKmerCoverageStats.dir/src/stacktrace.cpp.o CMakeFiles/fastaToKmerCoverageStats.dir/src/KmerCounter.cpp.o -o fastaToKmerCoverageStats -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/DeBruijnGraph.cpp: In member function 'std::string DeBruijnKmer::get_annotations_string()': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/DeBruijnGraph.cpp:66:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 66 | for (int i=0; i < _annotations.size(); i++) { - | ~~^~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build' -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/DeBruijnGraph.cpp: In member function 'std::string DeBruijnGraph::toDOT(bool)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/DeBruijnGraph.cpp:445:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 445 | for (int i=0; i < prev_kmers.size(); i++) { - | ~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/DeBruijnGraph.cpp:494:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 494 | for (int i=0; i < next_kmers.size(); i++) { - | ~~^~~~~~~~~~~~~~~~~~~ [ 92%] Built target fastaToKmerCoverageStats -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/DeBruijnGraph.cpp: In member function 'std::string DeBruijnGraph::toChrysalisFormat(int, bool)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm/src/DeBruijnGraph.cpp:725:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 725 | for (int i = 0; i < collected_kmers.size(); i++) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~ [ 96%] Linking CXX executable inchworm /usr/bin/cmake -E cmake_link_script CMakeFiles/inchworm.dir/link.txt --verbose=1 /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/inchworm.dir/src/Fasta_entry.cpp.o CMakeFiles/inchworm.dir/src/IRKE_run.cpp.o CMakeFiles/inchworm.dir/src/sequenceUtil.cpp.o CMakeFiles/inchworm.dir/src/IRKE.cpp.o CMakeFiles/inchworm.dir/src/KmerCounter.cpp.o CMakeFiles/inchworm.dir/src/string_util.cpp.o CMakeFiles/inchworm.dir/src/Fasta_reader.cpp.o CMakeFiles/inchworm.dir/src/stacktrace.cpp.o CMakeFiles/inchworm.dir/src/argProcessor.cpp.o -o inchworm @@ -1987,8 +2023,8 @@ make -f CMakeFiles/ReadsToTranscripts.dir/build.make CMakeFiles/ReadsToTranscripts.dir/depend make -f CMakeFiles/BubbleUpClustering.dir/build.make CMakeFiles/BubbleUpClustering.dir/depend make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' -cd /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build/CMakeFiles/Chrysalis.dir/DependInfo.cmake "--color=" make -f CMakeFiles/CreateIwormFastaBundle.dir/build.make CMakeFiles/CreateIwormFastaBundle.dir/depend +cd /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build/CMakeFiles/Chrysalis.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' cd /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build/CMakeFiles/QuantifyGraph.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' @@ -1996,51 +2032,51 @@ make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' cd /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build/CMakeFiles/ReadsToTranscripts.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' -make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' cd /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build/CMakeFiles/BubbleUpClustering.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' cd /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build/CMakeFiles/CreateIwormFastaBundle.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' +make -f CMakeFiles/Chrysalis.dir/build.make CMakeFiles/Chrysalis.dir/build make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' -make -f CMakeFiles/GraphFromFasta.dir/build.make CMakeFiles/GraphFromFasta.dir/build -make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' +make -f CMakeFiles/BubbleUpClustering.dir/build.make CMakeFiles/BubbleUpClustering.dir/build make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' -make -f CMakeFiles/Chrysalis.dir/build.make CMakeFiles/Chrysalis.dir/build +make -f CMakeFiles/GraphFromFasta.dir/build.make CMakeFiles/GraphFromFasta.dir/build +make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' make -f CMakeFiles/QuantifyGraph.dir/build.make CMakeFiles/QuantifyGraph.dir/build make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' -make -f CMakeFiles/ReadsToTranscripts.dir/build.make CMakeFiles/ReadsToTranscripts.dir/build -make -f CMakeFiles/BubbleUpClustering.dir/build.make CMakeFiles/BubbleUpClustering.dir/build -make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' make -f CMakeFiles/CreateIwormFastaBundle.dir/build.make CMakeFiles/CreateIwormFastaBundle.dir/build +make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' +make -f CMakeFiles/ReadsToTranscripts.dir/build.make CMakeFiles/ReadsToTranscripts.dir/build make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' -[ 1%] Building CXX object CMakeFiles/GraphFromFasta.dir/aligns/KmerAlignCore.cc.o -[ 5%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/DNAVector.cc.o -[ 5%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/DeBruijnGraph.cc.o -[ 7%] Building CXX object CMakeFiles/Chrysalis.dir/aligns/KmerAlignCore.cc.o -[ 8%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/GraphFromFasta.cc.o +[ 2%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/AACodons.cc.o +[ 2%] Building CXX object CMakeFiles/Chrysalis.dir/analysis/DNAVector.cc.o +[ 4%] Building CXX object CMakeFiles/Chrysalis.dir/aligns/KmerAlignCore.cc.o +[ 5%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/BubbleUpClustering.cc.o +[ 7%] Building CXX object CMakeFiles/BubbleUpClustering.dir/aligns/KmerAlignCore.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/analysis/AACodons.cc.o -MF CMakeFiles/BubbleUpClustering.dir/analysis/AACodons.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/analysis/AACodons.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/AACodons.cc +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/Chrysalis.dir/aligns/KmerAlignCore.cc.o -MF CMakeFiles/Chrysalis.dir/aligns/KmerAlignCore.cc.o.d -o CMakeFiles/Chrysalis.dir/aligns/KmerAlignCore.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/aligns/KmerAlignCore.cc +[ 10%] Building CXX object CMakeFiles/Chrysalis.dir/analysis/AACodons.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/Chrysalis.dir/analysis/DNAVector.cc.o -MF CMakeFiles/Chrysalis.dir/analysis/DNAVector.cc.o.d -o CMakeFiles/Chrysalis.dir/analysis/DNAVector.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DNAVector.cc +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/analysis/BubbleUpClustering.cc.o -MF CMakeFiles/BubbleUpClustering.dir/analysis/BubbleUpClustering.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/analysis/BubbleUpClustering.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/BubbleUpClustering.cc +[ 11%] Building CXX object CMakeFiles/Chrysalis.dir/analysis/Chrysalis.cc.o [ 10%] Building CXX object CMakeFiles/QuantifyGraph.dir/aligns/KmerAlignCore.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/analysis/DNAVector.cc.o -MF CMakeFiles/GraphFromFasta.dir/analysis/DNAVector.cc.o.d -o CMakeFiles/GraphFromFasta.dir/analysis/DNAVector.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DNAVector.cc -[ 11%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/KmerTable.cc.o +[ 12%] Building CXX object CMakeFiles/GraphFromFasta.dir/aligns/KmerAlignCore.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/aligns/KmerAlignCore.cc.o -MF CMakeFiles/BubbleUpClustering.dir/aligns/KmerAlignCore.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/aligns/KmerAlignCore.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/aligns/KmerAlignCore.cc +[ 14%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/analysis/AACodons.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/Chrysalis.dir/analysis/AACodons.cc.o -MF CMakeFiles/Chrysalis.dir/analysis/AACodons.cc.o.d -o CMakeFiles/Chrysalis.dir/analysis/AACodons.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/AACodons.cc +[ 15%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/DNAVector.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/aligns/KmerAlignCore.cc.o -MF CMakeFiles/QuantifyGraph.dir/aligns/KmerAlignCore.cc.o.d -o CMakeFiles/QuantifyGraph.dir/aligns/KmerAlignCore.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/aligns/KmerAlignCore.cc /usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/aligns/KmerAlignCore.cc.o -MF CMakeFiles/GraphFromFasta.dir/aligns/KmerAlignCore.cc.o.d -o CMakeFiles/GraphFromFasta.dir/aligns/KmerAlignCore.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/aligns/KmerAlignCore.cc -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/Chrysalis.dir/aligns/KmerAlignCore.cc.o -MF CMakeFiles/Chrysalis.dir/aligns/KmerAlignCore.cc.o.d -o CMakeFiles/Chrysalis.dir/aligns/KmerAlignCore.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/aligns/KmerAlignCore.cc -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/analysis/DeBruijnGraph.cc.o -MF CMakeFiles/GraphFromFasta.dir/analysis/DeBruijnGraph.cc.o.d -o CMakeFiles/GraphFromFasta.dir/analysis/DeBruijnGraph.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DeBruijnGraph.cc -[ 5%] Building CXX object CMakeFiles/Chrysalis.dir/analysis/AACodons.cc.o -[ 15%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/analysis/AACodons.cc.o -[ 14%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/AACodons.cc.o -[ 12%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/AACodons.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/analysis/GraphFromFasta.cc.o -MF CMakeFiles/GraphFromFasta.dir/analysis/GraphFromFasta.cc.o.d -o CMakeFiles/GraphFromFasta.dir/analysis/GraphFromFasta.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/analysis/KmerTable.cc.o -MF CMakeFiles/GraphFromFasta.dir/analysis/KmerTable.cc.o.d -o CMakeFiles/GraphFromFasta.dir/analysis/KmerTable.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/KmerTable.cc /usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/CreateIwormFastaBundle.dir/analysis/AACodons.cc.o -MF CMakeFiles/CreateIwormFastaBundle.dir/analysis/AACodons.cc.o.d -o CMakeFiles/CreateIwormFastaBundle.dir/analysis/AACodons.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/AACodons.cc -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/aligns/KmerAlignCore.cc.o -MF CMakeFiles/QuantifyGraph.dir/aligns/KmerAlignCore.cc.o.d -o CMakeFiles/QuantifyGraph.dir/aligns/KmerAlignCore.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/aligns/KmerAlignCore.cc -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/analysis/AACodons.cc.o -MF CMakeFiles/GraphFromFasta.dir/analysis/AACodons.cc.o.d -o CMakeFiles/GraphFromFasta.dir/analysis/AACodons.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/AACodons.cc -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/Chrysalis.dir/analysis/AACodons.cc.o -MF CMakeFiles/Chrysalis.dir/analysis/AACodons.cc.o.d -o CMakeFiles/Chrysalis.dir/analysis/AACodons.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/AACodons.cc +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/Chrysalis.dir/analysis/Chrysalis.cc.o -MF CMakeFiles/Chrysalis.dir/analysis/Chrysalis.cc.o.d -o CMakeFiles/Chrysalis.dir/analysis/Chrysalis.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/Chrysalis.cc +[ 17%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/AACodons.cc.o /usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/analysis/AACodons.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/analysis/AACodons.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/analysis/AACodons.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/AACodons.cc -[ 17%] Building CXX object CMakeFiles/BubbleUpClustering.dir/aligns/KmerAlignCore.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/aligns/KmerAlignCore.cc.o -MF CMakeFiles/BubbleUpClustering.dir/aligns/KmerAlignCore.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/aligns/KmerAlignCore.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/aligns/KmerAlignCore.cc +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/analysis/DNAVector.cc.o -MF CMakeFiles/BubbleUpClustering.dir/analysis/DNAVector.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/analysis/DNAVector.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DNAVector.cc /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function 'void KmerAlignCore::AddData(const vecDNAVector&, const vecNumVector&, int)': /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/aligns/KmerAlignCore.cc:79:49: warning: unused variable 't' [-Wunused-variable] 79 | KmerAlignCoreRecordStoreTable & t = m_table; // not used? @@ -2069,14 +2105,14 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/aligns/KmerAlignCore.cc:159:12: warning: unused variable 'j' [-Wunused-variable] 159 | int i, j; | ^ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function 'void KmerAlignCore::MergeSortFilter(svec&, const svec&, const svec&)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/aligns/KmerAlignCore.cc:291:9: warning: unused variable 'i' [-Wunused-variable] - 291 | int i; - | ^ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function 'void KmerAlignCore::AddData(const vecDNAVector&, const vecNumVector&, int)': /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/aligns/KmerAlignCore.cc:79:49: warning: unused variable 't' [-Wunused-variable] 79 | KmerAlignCoreRecordStoreTable & t = m_table; // not used? | ^ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function 'void KmerAlignCore::MergeSortFilter(svec&, const svec&, const svec&)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/aligns/KmerAlignCore.cc:291:9: warning: unused variable 'i' [-Wunused-variable] + 291 | int i; + | ^ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/aligns/KmerAlignCore.cc:49:9: warning: unused variable 'i' [-Wunused-variable] 49 | int i, j, k; | ^ @@ -2105,32 +2141,6 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/aligns/KmerAlignCore.cc:291:9: warning: unused variable 'i' [-Wunused-variable] 291 | int i; | ^ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'void DeBruijnKmer::add_next_kmer(kmer_int_type_t, unsigned int)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DeBruijnGraph.cc:154:66: warning: unused parameter 'kmer_length' [-Wunused-parameter] - 154 | void DeBruijnKmer::add_next_kmer(kmer_int_type_t k, unsigned int kmer_length) { - | ~~~~~~~~~~~~~^~~~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'std::vector DeBruijnGraph::deconvolute_DS_mirror_graph()': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DeBruijnGraph.cc:355:22: warning: variable 'rdk' set but not used [-Wunused-but-set-variable] - 355 | DeBruijnKmer rdk = _kmer_map.find(rk)->second; - | ^~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'std::vector > DeBruijnGraph::get_candidate_weldmers(kmer_int_type_t, int)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DeBruijnGraph.cc:473:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 473 | for (int i = 0; i < left_extensions.size(); i++) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/KmerTable.cc: In member function 'long long int KmerSequence::BasesToNumber(const DNAVector&, int)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/KmerTable.cc:27:13: warning: unused variable 'i' [-Wunused-variable] - 27 | long long i; - | ^ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DeBruijnGraph.cc:476:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 476 | for (int j = 0; j < right_extensions.size(); j++) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'void DeBruijnGraph::recursively_construct_kmer_extensions(kmer_int_type_t, std::vector&, std::vector >&, char, std::map&, int)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DeBruijnGraph.cc:513:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 513 | for (int i = 0; i < adjacent_kmers.size(); i++) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DeBruijnGraph.cc:527:41: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 527 | if (kmer_extension_chars.size() == flank_extension_length) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function 'void KmerAlignCore::AddData(const vecDNAVector&, const vecNumVector&, int)': /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/aligns/KmerAlignCore.cc:79:49: warning: unused variable 't' [-Wunused-variable] 79 | KmerAlignCoreRecordStoreTable & t = m_table; // not used? @@ -2163,6 +2173,31 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/aligns/KmerAlignCore.cc:291:9: warning: unused variable 'i' [-Wunused-variable] 291 | int i; | ^ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/Chrysalis.cc: In function 'int main(int, char**)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/Chrysalis.cc:582:21: warning: unused variable 'num_iworm_contigs' [-Wunused-variable] + 582 | int num_iworm_contigs = parser.AsInt(2); + | ^~~~~~~~~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/Chrysalis.cc:570:16: warning: unused variable 'pOut' [-Wunused-variable] + 570 | FILE * pOut = NULL; + | ^~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/Chrysalis.cc:342:10: warning: unused variable 'bSkip' [-Wunused-variable] + 342 | bool bSkip = P.GetBoolValueFor(skipCmmd); + | ^~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/Chrysalis.cc:347:9: warning: unused variable 'pairDist' [-Wunused-variable] + 347 | int pairDist = P.GetIntValueFor(distCmmd); + | ^~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/Chrysalis.cc:354:10: warning: variable 'bBreak' set but not used [-Wunused-but-set-variable] + 354 | bool bBreak = true; + | ^~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/Chrysalis.cc:359:10: warning: unused variable 'bButt' [-Wunused-variable] + 359 | bool bButt = P.GetBoolValueFor(buttCmmd); + | ^~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/Chrysalis.cc:361:10: warning: unused variable 'max_reads' [-Wunused-variable] + 361 | long max_reads = P.GetLongValueFor(maxReadsCmd); + | ^~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/Chrysalis.cc:372:10: warning: unused variable 'DEBUG' [-Wunused-variable] + 372 | bool DEBUG = P.GetBoolValueFor(debugCmmd); + | ^~~~~ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function 'void KmerAlignCore::AddData(const vecDNAVector&, const vecNumVector&, int)': /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/aligns/KmerAlignCore.cc:79:49: warning: unused variable 't' [-Wunused-variable] 79 | KmerAlignCoreRecordStoreTable & t = m_table; // not used? @@ -2195,125 +2230,9 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/aligns/KmerAlignCore.cc:291:9: warning: unused variable 'i' [-Wunused-variable] 291 | int i; | ^ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'bool SimpleHalves(const DNAVector&)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc:272:15: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 271 | ( (! DISABLE_REPEAT_CHECK) - | ~~~~~~~~~~~~~~~~~~~~~~~~ - 272 | && - | ^~ - 273 | is_simple_repeat(left) || is_simple_repeat(right) ) - | ~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'float align_get_per_id(const DNAVector&, const DNAVector&, int, int, int)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc:351:94: warning: unused parameter 'k' [-Wunused-parameter] - 351 | float align_get_per_id(const DNAVector & a, const DNAVector & b, int startA, int startB, int k) - | ~~~~^ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In member function 'bool Welder::Weldable(const DNAVector&, int, const DNAVector&, int, int, std::string&, unsigned int&)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc:523:13: warning: unused variable 'i' [-Wunused-variable] - 523 | int i; - | ^ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'void report_iworm_graph(std::map&, std::map&, std::map&)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc:713:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 713 | for (int j = 0; j < adjacent_nodes.size(); j++) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'svec sl_cluster_pools(std::map&, std::map&)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc:847:40: warning: implicitly-declared 'Pool& Pool::operator=(const Pool&)' is deprecated [-Wdeprecated-copy] - 847 | pool_vec[oldpool_id] = tmp; - | ^~~ -In file included from /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc:19: -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/Pool.h:24:5: note: because 'Pool' has user-provided 'Pool::Pool(const Pool&)' - 24 | Pool(const Pool& p) { - | ^~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'void add_scaffolds_to_clusters(std::map&, std::string, vecDNAVector&, int, float)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc:961:33: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 961 | if (pair_link_count >= minCov) { - | ~~~~~~~~~~~~~~~~^~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'void add_iworm_link(std::map&, int, int)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc:1006:55: warning: implicitly-declared 'Pool& Pool::operator=(const Pool&)' is deprecated [-Wdeprecated-copy] - 1006 | weld_reinforced_iworm_clusters[iworm_index] = p; - | ^ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/Pool.h:24:5: note: because 'Pool' has user-provided 'Pool::Pool(const Pool&)' - 24 | Pool(const Pool& p) { - | ^~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'int main(int, char**)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc:1310:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 1310 | for (i=0; i grow_prioritized_clusters(std::string&, std::map&)': /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/BubbleUpClustering.cc:111:78: warning: unused parameter 'weld_reinforced_iworm_clusters' [-Wunused-parameter] 111 | svec grow_prioritized_clusters(string& weld_graph_file, map& weld_reinforced_iworm_clusters) { @@ -2340,64 +2259,14 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/BubbleUpClustering.cc:641:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 641 | for (size_t j = 0; j < p.size(); j++) { | ~~^~~~~~~~~~ -[ 31%] Building CXX object CMakeFiles/Chrysalis.dir/analysis/DNAVector.cc.o -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc: In function 'int main(int, char**)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc:181:17: warning: unused variable 'num_iworm_contigs' [-Wunused-variable] - 181 | int num_iworm_contigs = parser.AsInt(2); - | ^~~~~~~~~~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc:143:10: warning: unused variable 'DEBUG' [-Wunused-variable] - 143 | bool DEBUG = P.GetBoolValueFor(debugCmmd); - | ^~~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc:166:12: warning: unused variable 'pOut' [-Wunused-variable] - 166 | FILE * pOut = NULL; - | ^~~~ -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/Chrysalis.dir/analysis/DNAVector.cc.o -MF CMakeFiles/Chrysalis.dir/analysis/DNAVector.cc.o.d -o CMakeFiles/Chrysalis.dir/analysis/DNAVector.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DNAVector.cc -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::SetUp(const vecDNAVector&, bool)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:46:20: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 46 | for (j=0; j<=d.size()-m_k; j++) { - | ~^~~~~~~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:56:20: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 56 | for (j=0; j<=d.size()-m_k; j++) { - | ~^~~~~~~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:79:18: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 79 | for (j=0; j<=d.size()-m_k; j++) { - | ~^~~~~~~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::AddData(const vecDNAVector&)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:109:16: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 109 | for (j=0; j<= d.isize()-m_k; j++) { - | ~^~~~~~~~~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::AddData(vecDNAVectorStream&)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:125:9: warning: unused variable 'i' [-Wunused-variable] - 125 | int i, j; - | ^ -[ 32%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/DNAVector.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/analysis/DNAVector.cc.o -MF CMakeFiles/BubbleUpClustering.dir/analysis/DNAVector.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/analysis/DNAVector.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DNAVector.cc -[ 34%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/KmerTable.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/analysis/KmerTable.cc.o -MF CMakeFiles/QuantifyGraph.dir/analysis/KmerTable.cc.o.d -o CMakeFiles/QuantifyGraph.dir/analysis/KmerTable.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/KmerTable.cc -[ 35%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/analysis/DNAVector.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/CreateIwormFastaBundle.dir/analysis/DNAVector.cc.o -MF CMakeFiles/CreateIwormFastaBundle.dir/analysis/DNAVector.cc.o.d -o CMakeFiles/CreateIwormFastaBundle.dir/analysis/DNAVector.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DNAVector.cc -[ 37%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/ReadsToTranscripts.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/analysis/ReadsToTranscripts.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/analysis/ReadsToTranscripts.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/analysis/ReadsToTranscripts.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/ReadsToTranscripts.cc -[ 38%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/base/ErrorHandling.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/CreateIwormFastaBundle.dir/base/ErrorHandling.cc.o -MF CMakeFiles/CreateIwormFastaBundle.dir/base/ErrorHandling.cc.o.d -o CMakeFiles/CreateIwormFastaBundle.dir/base/ErrorHandling.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/KmerTable.cc: In member function 'long long int KmerSequence::BasesToNumber(const DNAVector&, int)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/KmerTable.cc:27:13: warning: unused variable 'i' [-Wunused-variable] - 27 | long long i; - | ^ -[ 40%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/DeBruijnGraph.cc.o +[ 18%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/AACodons.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/analysis/AACodons.cc.o -MF CMakeFiles/QuantifyGraph.dir/analysis/AACodons.cc.o.d -o CMakeFiles/QuantifyGraph.dir/analysis/AACodons.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/AACodons.cc +[ 20%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/DeBruijnGraph.cc.o /usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/analysis/DeBruijnGraph.cc.o -MF CMakeFiles/BubbleUpClustering.dir/analysis/DeBruijnGraph.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/analysis/DeBruijnGraph.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DeBruijnGraph.cc -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc: In function 'void print_trace(FILE*, const char*, int)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc:7:24: warning: unused parameter 'out' [-Wunused-parameter] - 7 | void print_trace(FILE *out, const char *file, int line) - | ~~~~~~^~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc:7:41: warning: unused parameter 'file' [-Wunused-parameter] - 7 | void print_trace(FILE *out, const char *file, int line) - | ~~~~~~~~~~~~^~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc:7:51: warning: unused parameter 'line' [-Wunused-parameter] - 7 | void print_trace(FILE *out, const char *file, int line) - | ~~~~^~~~ -[ 41%] Building CXX object CMakeFiles/Chrysalis.dir/analysis/TranscriptomeGraph.cc.o +[ 21%] Building CXX object CMakeFiles/Chrysalis.dir/analysis/TranscriptomeGraph.cc.o /usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/Chrysalis.dir/analysis/TranscriptomeGraph.cc.o -MF CMakeFiles/Chrysalis.dir/analysis/TranscriptomeGraph.cc.o.d -o CMakeFiles/Chrysalis.dir/analysis/TranscriptomeGraph.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc +[ 22%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/AACodons.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/analysis/AACodons.cc.o -MF CMakeFiles/GraphFromFasta.dir/analysis/AACodons.cc.o.d -o CMakeFiles/GraphFromFasta.dir/analysis/AACodons.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/AACodons.cc /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'void DeBruijnKmer::add_next_kmer(kmer_int_type_t, unsigned int)': /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DeBruijnGraph.cc:154:66: warning: unused parameter 'kmer_length' [-Wunused-parameter] 154 | void DeBruijnKmer::add_next_kmer(kmer_int_type_t k, unsigned int kmer_length) { @@ -2420,8 +2289,14 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DeBruijnGraph.cc:527:41: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 527 | if (kmer_extension_chars.size() == flank_extension_length) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 42%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/sequenceUtil.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/analysis/sequenceUtil.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/analysis/sequenceUtil.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/analysis/sequenceUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc +[ 24%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/DNAVector.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/analysis/DNAVector.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/analysis/DNAVector.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/analysis/DNAVector.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DNAVector.cc +[ 25%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/analysis/CreateIwormFastaBundle.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/CreateIwormFastaBundle.dir/analysis/CreateIwormFastaBundle.cc.o -MF CMakeFiles/CreateIwormFastaBundle.dir/analysis/CreateIwormFastaBundle.cc.o.d -o CMakeFiles/CreateIwormFastaBundle.dir/analysis/CreateIwormFastaBundle.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc +[ 27%] Building CXX object CMakeFiles/Chrysalis.dir/base/ErrorHandling.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/Chrysalis.dir/base/ErrorHandling.cc.o -MF CMakeFiles/Chrysalis.dir/base/ErrorHandling.cc.o.d -o CMakeFiles/Chrysalis.dir/base/ErrorHandling.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc +[ 28%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/KmerTable.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/analysis/KmerTable.cc.o -MF CMakeFiles/BubbleUpClustering.dir/analysis/KmerTable.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/analysis/KmerTable.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/KmerTable.cc /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc: In member function 'void KmerSequence::Setup()': /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc:177:19: warning: unused variable 'i' [-Wunused-variable] 177 | long long i; @@ -2437,18 +2312,6 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc:647:10: warning: unused variable 'bAppend' [-Wunused-variable] 647 | bool bAppend = true; | ^~~~~~~ -[ 44%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/sequenceUtil.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/analysis/sequenceUtil.cc.o -MF CMakeFiles/GraphFromFasta.dir/analysis/sequenceUtil.cc.o.d -o CMakeFiles/GraphFromFasta.dir/analysis/sequenceUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'bool contains_non_gatc(std::string)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc:33:26: warning: array subscript has type 'char' [-Wchar-subscripts] - 33 | if (_base_to_int[c] > 3) - | ^ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'kmer_int_type_t kmer_to_intval(std::string)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc:264:32: warning: array subscript has type 'char' [-Wchar-subscripts] - 264 | int val = _base_to_int[c]; - | ^ -[ 45%] Building CXX object CMakeFiles/Chrysalis.dir/base/ErrorHandling.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/Chrysalis.dir/base/ErrorHandling.cc.o -MF CMakeFiles/Chrysalis.dir/base/ErrorHandling.cc.o.d -o CMakeFiles/Chrysalis.dir/base/ErrorHandling.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc: In function 'void print_trace(FILE*, const char*, int)': /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc:7:24: warning: unused parameter 'out' [-Wunused-parameter] 7 | void print_trace(FILE *out, const char *file, int line) @@ -2459,10 +2322,36 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc:7:51: warning: unused parameter 'line' [-Wunused-parameter] 7 | void print_trace(FILE *out, const char *file, int line) | ~~~~^~~~ -[ 47%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/base/FileParser.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/CreateIwormFastaBundle.dir/base/FileParser.cc.o -MF CMakeFiles/CreateIwormFastaBundle.dir/base/FileParser.cc.o.d -o CMakeFiles/CreateIwormFastaBundle.dir/base/FileParser.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/FileParser.cc -[ 48%] Building CXX object CMakeFiles/Chrysalis.dir/base/FileParser.cc.o +[ 30%] Building CXX object CMakeFiles/Chrysalis.dir/base/FileParser.cc.o /usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/Chrysalis.dir/base/FileParser.cc.o -MF CMakeFiles/Chrysalis.dir/base/FileParser.cc.o.d -o CMakeFiles/Chrysalis.dir/base/FileParser.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/FileParser.cc +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc: In function 'int main(int, char**)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc:181:17: warning: unused variable 'num_iworm_contigs' [-Wunused-variable] + 181 | int num_iworm_contigs = parser.AsInt(2); + | ^~~~~~~~~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc:143:10: warning: unused variable 'DEBUG' [-Wunused-variable] + 143 | bool DEBUG = P.GetBoolValueFor(debugCmmd); + | ^~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc:166:12: warning: unused variable 'pOut' [-Wunused-variable] + 166 | FILE * pOut = NULL; + | ^~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/KmerTable.cc: In member function 'long long int KmerSequence::BasesToNumber(const DNAVector&, int)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/KmerTable.cc:27:13: warning: unused variable 'i' [-Wunused-variable] + 27 | long long i; + | ^ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/FileParser.cc: In member function 'bool StringParser::IsString(int)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter 'index' [-Wunused-parameter] + 50 | bool StringParser::IsString(int index) + | ~~~~^~~~~ +[ 31%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/NonRedKmerTable.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/analysis/NonRedKmerTable.cc.o -MF CMakeFiles/BubbleUpClustering.dir/analysis/NonRedKmerTable.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/analysis/NonRedKmerTable.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc +[ 32%] Building CXX object CMakeFiles/Chrysalis.dir/base/StringUtil.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/Chrysalis.dir/base/StringUtil.cc.o -MF CMakeFiles/Chrysalis.dir/base/StringUtil.cc.o.d -o CMakeFiles/Chrysalis.dir/base/StringUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/StringUtil.cc +[ 34%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/sequenceUtil.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/analysis/sequenceUtil.cc.o -MF CMakeFiles/BubbleUpClustering.dir/analysis/sequenceUtil.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/analysis/sequenceUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc +[ 35%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/DNAVector.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/analysis/DNAVector.cc.o -MF CMakeFiles/QuantifyGraph.dir/analysis/DNAVector.cc.o.d -o CMakeFiles/QuantifyGraph.dir/analysis/DNAVector.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DNAVector.cc +[ 37%] Building CXX object CMakeFiles/Chrysalis.dir/util/mutil.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/Chrysalis.dir/util/mutil.cc.o -MF CMakeFiles/Chrysalis.dir/util/mutil.cc.o.d -o CMakeFiles/Chrysalis.dir/util/mutil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'bool contains_non_gatc(std::string)': /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc:33:26: warning: array subscript has type 'char' [-Wchar-subscripts] 33 | if (_base_to_int[c] > 3) @@ -2471,12 +2360,6 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc:264:32: warning: array subscript has type 'char' [-Wchar-subscripts] 264 | int val = _base_to_int[c]; | ^ -[ 50%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/NonRedKmerTable.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/analysis/NonRedKmerTable.cc.o -MF CMakeFiles/QuantifyGraph.dir/analysis/NonRedKmerTable.cc.o.d -o CMakeFiles/QuantifyGraph.dir/analysis/NonRedKmerTable.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc -[ 51%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/stacktrace.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/analysis/stacktrace.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/analysis/stacktrace.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/analysis/stacktrace.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/stacktrace.cc -[ 52%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/stacktrace.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/analysis/stacktrace.cc.o -MF CMakeFiles/GraphFromFasta.dir/analysis/stacktrace.cc.o.d -o CMakeFiles/GraphFromFasta.dir/analysis/stacktrace.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/stacktrace.cc /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::SetUp(const vecDNAVector&, bool)': /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:46:20: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 46 | for (j=0; j<=d.size()-m_k; j++) { @@ -2495,38 +2378,8 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:125:9: warning: unused variable 'i' [-Wunused-variable] 125 | int i, j; | ^ -[ 54%] Building CXX object CMakeFiles/GraphFromFasta.dir/base/ErrorHandling.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/base/ErrorHandling.cc.o -MF CMakeFiles/GraphFromFasta.dir/base/ErrorHandling.cc.o.d -o CMakeFiles/GraphFromFasta.dir/base/ErrorHandling.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc -[ 55%] Building CXX object CMakeFiles/Chrysalis.dir/base/StringUtil.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/Chrysalis.dir/base/StringUtil.cc.o -MF CMakeFiles/Chrysalis.dir/base/StringUtil.cc.o.d -o CMakeFiles/Chrysalis.dir/base/StringUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/StringUtil.cc -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/FileParser.cc: In member function 'bool StringParser::IsString(int)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter 'index' [-Wunused-parameter] - 50 | bool StringParser::IsString(int index) - | ~~~~^~~~~ -[ 57%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/base/StringUtil.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/CreateIwormFastaBundle.dir/base/StringUtil.cc.o -MF CMakeFiles/CreateIwormFastaBundle.dir/base/StringUtil.cc.o.d -o CMakeFiles/CreateIwormFastaBundle.dir/base/StringUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/StringUtil.cc -[ 58%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/util/mutil.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/CreateIwormFastaBundle.dir/util/mutil.cc.o -MF CMakeFiles/CreateIwormFastaBundle.dir/util/mutil.cc.o.d -o CMakeFiles/CreateIwormFastaBundle.dir/util/mutil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/FileParser.cc: In member function 'bool StringParser::IsString(int)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter 'index' [-Wunused-parameter] - 50 | bool StringParser::IsString(int index) - | ~~~~^~~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc: In function 'void print_trace(FILE*, const char*, int)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc:7:24: warning: unused parameter 'out' [-Wunused-parameter] - 7 | void print_trace(FILE *out, const char *file, int line) - | ~~~~~~^~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc:7:41: warning: unused parameter 'file' [-Wunused-parameter] - 7 | void print_trace(FILE *out, const char *file, int line) - | ~~~~~~~~~~~~^~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc:7:51: warning: unused parameter 'line' [-Wunused-parameter] - 7 | void print_trace(FILE *out, const char *file, int line) - | ~~~~^~~~ -[ 60%] Building CXX object CMakeFiles/Chrysalis.dir/util/mutil.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/Chrysalis.dir/util/mutil.cc.o -MF CMakeFiles/Chrysalis.dir/util/mutil.cc.o.d -o CMakeFiles/Chrysalis.dir/util/mutil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc -[ 61%] Building CXX object CMakeFiles/GraphFromFasta.dir/base/FileParser.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/base/FileParser.cc.o -MF CMakeFiles/GraphFromFasta.dir/base/FileParser.cc.o.d -o CMakeFiles/GraphFromFasta.dir/base/FileParser.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/FileParser.cc -[ 62%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/base/ErrorHandling.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/base/ErrorHandling.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/base/ErrorHandling.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/base/ErrorHandling.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc +[ 38%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/DNAVector.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/analysis/DNAVector.cc.o -MF CMakeFiles/GraphFromFasta.dir/analysis/DNAVector.cc.o.d -o CMakeFiles/GraphFromFasta.dir/analysis/DNAVector.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DNAVector.cc /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:313:14: warning: passing argument 1 to 'restrict'-qualified parameter aliases with argument 4 [-Wrestrict] 313 | if (fscanf(m_pFile, szText, sizeof(szText), m_pFile) == EOF) { @@ -2571,8 +2424,140 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:1688:16: warning: unused variable 'p' [-Wunused-variable] 1688 | const char * p = (const char*)string; | ^ -[ 64%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/KmerTable.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/analysis/KmerTable.cc.o -MF CMakeFiles/BubbleUpClustering.dir/analysis/KmerTable.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/analysis/KmerTable.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/KmerTable.cc +[ 40%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/DeBruijnGraph.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/analysis/DeBruijnGraph.cc.o -MF CMakeFiles/GraphFromFasta.dir/analysis/DeBruijnGraph.cc.o.d -o CMakeFiles/GraphFromFasta.dir/analysis/DeBruijnGraph.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DeBruijnGraph.cc +[ 41%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/GraphFromFasta.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/analysis/GraphFromFasta.cc.o -MF CMakeFiles/GraphFromFasta.dir/analysis/GraphFromFasta.cc.o.d -o CMakeFiles/GraphFromFasta.dir/analysis/GraphFromFasta.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc +[ 42%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/stacktrace.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/analysis/stacktrace.cc.o -MF CMakeFiles/BubbleUpClustering.dir/analysis/stacktrace.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/analysis/stacktrace.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/stacktrace.cc +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:313:13: warning: 'szText' may be used uninitialized [-Wmaybe-uninitialized] + 313 | if (fscanf(m_pFile, szText, sizeof(szText), m_pFile) == EOF) { + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/features.h:502, + from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, + from /usr/include/string.h:26, + from /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.h:19, + from /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:9: +/usr/include/stdio.h:440:12: note: by argument 2 of type 'const char*' to 'int fscanf(FILE*, const char*, ...)' declared here + 440 | extern int __REDIRECT (fscanf, (FILE *__restrict __stream, + | ^~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:311:8: note: 'szText' declared here + 311 | char szText[2048 * 10]; + | ^~~~~~ +[ 44%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/analysis/DNAVector.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/CreateIwormFastaBundle.dir/analysis/DNAVector.cc.o -MF CMakeFiles/CreateIwormFastaBundle.dir/analysis/DNAVector.cc.o.d -o CMakeFiles/CreateIwormFastaBundle.dir/analysis/DNAVector.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DNAVector.cc +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'void DeBruijnKmer::add_next_kmer(kmer_int_type_t, unsigned int)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DeBruijnGraph.cc:154:66: warning: unused parameter 'kmer_length' [-Wunused-parameter] + 154 | void DeBruijnKmer::add_next_kmer(kmer_int_type_t k, unsigned int kmer_length) { + | ~~~~~~~~~~~~~^~~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'std::vector DeBruijnGraph::deconvolute_DS_mirror_graph()': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DeBruijnGraph.cc:355:22: warning: variable 'rdk' set but not used [-Wunused-but-set-variable] + 355 | DeBruijnKmer rdk = _kmer_map.find(rk)->second; + | ^~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'std::vector > DeBruijnGraph::get_candidate_weldmers(kmer_int_type_t, int)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DeBruijnGraph.cc:473:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 473 | for (int i = 0; i < left_extensions.size(); i++) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DeBruijnGraph.cc:476:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 476 | for (int j = 0; j < right_extensions.size(); j++) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'void DeBruijnGraph::recursively_construct_kmer_extensions(kmer_int_type_t, std::vector&, std::vector >&, char, std::map&, int)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DeBruijnGraph.cc:513:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 513 | for (int i = 0; i < adjacent_kmers.size(); i++) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/DeBruijnGraph.cc:527:41: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 527 | if (kmer_extension_chars.size() == flank_extension_length) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +[ 45%] Building CXX object CMakeFiles/BubbleUpClustering.dir/base/ErrorHandling.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/base/ErrorHandling.cc.o -MF CMakeFiles/BubbleUpClustering.dir/base/ErrorHandling.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/base/ErrorHandling.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc +[ 47%] Building CXX object CMakeFiles/BubbleUpClustering.dir/base/FileParser.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/base/FileParser.cc.o -MF CMakeFiles/BubbleUpClustering.dir/base/FileParser.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/base/FileParser.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/FileParser.cc +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'bool SimpleHalves(const DNAVector&)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc:272:15: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 271 | ( (! DISABLE_REPEAT_CHECK) + | ~~~~~~~~~~~~~~~~~~~~~~~~ + 272 | && + | ^~ + 273 | is_simple_repeat(left) || is_simple_repeat(right) ) + | ~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'float align_get_per_id(const DNAVector&, const DNAVector&, int, int, int)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc:351:94: warning: unused parameter 'k' [-Wunused-parameter] + 351 | float align_get_per_id(const DNAVector & a, const DNAVector & b, int startA, int startB, int k) + | ~~~~^ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In member function 'bool Welder::Weldable(const DNAVector&, int, const DNAVector&, int, int, std::string&, unsigned int&)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc:523:13: warning: unused variable 'i' [-Wunused-variable] + 523 | int i; + | ^ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'void report_iworm_graph(std::map&, std::map&, std::map&)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc:713:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 713 | for (int j = 0; j < adjacent_nodes.size(); j++) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'svec sl_cluster_pools(std::map&, std::map&)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc:847:40: warning: implicitly-declared 'Pool& Pool::operator=(const Pool&)' is deprecated [-Wdeprecated-copy] + 847 | pool_vec[oldpool_id] = tmp; + | ^~~ +In file included from /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc:19: +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/Pool.h:24:5: note: because 'Pool' has user-provided 'Pool::Pool(const Pool&)' + 24 | Pool(const Pool& p) { + | ^~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'void add_scaffolds_to_clusters(std::map&, std::string, vecDNAVector&, int, float)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc:961:33: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 961 | if (pair_link_count >= minCov) { + | ~~~~~~~~~~~~~~~~^~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'void add_iworm_link(std::map&, int, int)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc:1006:55: warning: implicitly-declared 'Pool& Pool::operator=(const Pool&)' is deprecated [-Wdeprecated-copy] + 1006 | weld_reinforced_iworm_clusters[iworm_index] = p; + | ^ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/Pool.h:24:5: note: because 'Pool' has user-provided 'Pool::Pool(const Pool&)' + 24 | Pool(const Pool& p) { + | ^~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'int main(int, char**)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc:1310:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 1310 | for (i=0; i >&, svec&, long long int&, const DNAVector&, int, const vecDNAVector&, int)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/QuantifyGraph.cc:250:10: warning: ISO C++ forbids variable length array 'kmerseq' [-Wvla] - 250 | char kmerseq [kmer_length + 1]; - | ^~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/QuantifyGraph.cc: In function 'int main(int, char**)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/QuantifyGraph.cc:372:29: warning: unused variable 'prevNode' [-Wunused-variable] - 372 | int prevNode = parser.AsInt(1); - | ^~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/QuantifyGraph.cc:409:13: warning: unused variable 'node' [-Wunused-variable] - 409 | int node = parser.AsInt(0); - | ^~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/QuantifyGraph.cc:412:30: warning: unused variable 'p2' [-Wunused-variable] - 412 | const char * p2 = s.c_str(); - | ^~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/QuantifyGraph.cc:337:16: warning: unused variable 'j' [-Wunused-variable] - 337 | int i, j; - | ^ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/QuantifyGraph.cc:350:16: warning: unused variable 'm' [-Wunused-variable] - 350 | size_t m = kmers.size(); - | ^ -[ 77%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/sequenceUtil.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/analysis/sequenceUtil.cc.o -MF CMakeFiles/BubbleUpClustering.dir/analysis/sequenceUtil.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/analysis/sequenceUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:313:14: warning: passing argument 1 to 'restrict'-qualified parameter aliases with argument 4 [-Wrestrict] 313 | if (fscanf(m_pFile, szText, sizeof(szText), m_pFile) == EOF) { @@ -2749,8 +2672,6 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:787:80: warning: unused parameter 'bLineFeed' [-Wunused-parameter] 787 | MDLLEXPORT void MLog(const MCL_TCHAR * szText, const MCL_TCHAR * szText2, bool bLineFeed) | ~~~~~^~~~~~~~~ -[ 78%] Building CXX object CMakeFiles/QuantifyGraph.dir/base/FileParser.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/base/FileParser.cc.o -MF CMakeFiles/QuantifyGraph.dir/base/FileParser.cc.o.d -o CMakeFiles/QuantifyGraph.dir/base/FileParser.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/FileParser.cc /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc: In function 'void MCLSetUTF8Encode(bool)': /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:1288:39: warning: unused parameter 'b' [-Wunused-parameter] 1288 | MDLLEXPORT void MCLSetUTF8Encode(bool b) @@ -2759,6 +2680,10 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:1688:16: warning: unused variable 'p' [-Wunused-variable] 1688 | const char * p = (const char*)string; | ^ +[ 61%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/sequenceUtil.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/analysis/sequenceUtil.cc.o -MF CMakeFiles/GraphFromFasta.dir/analysis/sequenceUtil.cc.o.d -o CMakeFiles/GraphFromFasta.dir/analysis/sequenceUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc +[ 62%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/stacktrace.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/analysis/stacktrace.cc.o -MF CMakeFiles/GraphFromFasta.dir/analysis/stacktrace.cc.o.d -o CMakeFiles/GraphFromFasta.dir/analysis/stacktrace.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/stacktrace.cc /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::SetUp(const vecDNAVector&, bool)': /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:46:20: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 46 | for (j=0; j<=d.size()-m_k; j++) { @@ -2777,12 +2702,8 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:125:9: warning: unused variable 'i' [-Wunused-variable] 125 | int i, j; | ^ -[ 80%] Building CXX object CMakeFiles/QuantifyGraph.dir/base/StringUtil.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/base/StringUtil.cc.o -MF CMakeFiles/QuantifyGraph.dir/base/StringUtil.cc.o.d -o CMakeFiles/QuantifyGraph.dir/base/StringUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/StringUtil.cc -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/FileParser.cc: In member function 'bool StringParser::IsString(int)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter 'index' [-Wunused-parameter] - 50 | bool StringParser::IsString(int index) - | ~~~~^~~~~ +[ 64%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/NonRedKmerTable.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/analysis/NonRedKmerTable.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/analysis/NonRedKmerTable.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/analysis/NonRedKmerTable.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:313:13: warning: 'szText' may be used uninitialized [-Wmaybe-uninitialized] 313 | if (fscanf(m_pFile, szText, sizeof(szText), m_pFile) == EOF) { @@ -2798,11 +2719,65 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:311:8: note: 'szText' declared here 311 | char szText[2048 * 10]; | ^~~~~~ -[ 81%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/sequenceUtil.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/analysis/sequenceUtil.cc.o -MF CMakeFiles/QuantifyGraph.dir/analysis/sequenceUtil.cc.o.d -o CMakeFiles/QuantifyGraph.dir/analysis/sequenceUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc -[ 82%] Linking CXX executable CreateIwormFastaBundle -/usr/bin/cmake -E cmake_link_script CMakeFiles/CreateIwormFastaBundle.dir/link.txt --verbose=1 -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/CreateIwormFastaBundle.dir/analysis/AACodons.cc.o CMakeFiles/CreateIwormFastaBundle.dir/analysis/CreateIwormFastaBundle.cc.o CMakeFiles/CreateIwormFastaBundle.dir/analysis/DNAVector.cc.o CMakeFiles/CreateIwormFastaBundle.dir/base/ErrorHandling.cc.o CMakeFiles/CreateIwormFastaBundle.dir/base/FileParser.cc.o CMakeFiles/CreateIwormFastaBundle.dir/base/StringUtil.cc.o CMakeFiles/CreateIwormFastaBundle.dir/util/mutil.cc.o -o CreateIwormFastaBundle +[ 65%] Building CXX object CMakeFiles/GraphFromFasta.dir/base/ErrorHandling.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/base/ErrorHandling.cc.o -MF CMakeFiles/GraphFromFasta.dir/base/ErrorHandling.cc.o.d -o CMakeFiles/GraphFromFasta.dir/base/ErrorHandling.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/KmerTable.cc: In member function 'long long int KmerSequence::BasesToNumber(const DNAVector&, int)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/KmerTable.cc:27:13: warning: unused variable 'i' [-Wunused-variable] + 27 | long long i; + | ^ +[ 67%] Linking CXX executable BubbleUpClustering +/usr/bin/cmake -E cmake_link_script CMakeFiles/BubbleUpClustering.dir/link.txt --verbose=1 +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/BubbleUpClustering.dir/aligns/KmerAlignCore.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/AACodons.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/BubbleUpClustering.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/DNAVector.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/DeBruijnGraph.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/KmerTable.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/NonRedKmerTable.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/sequenceUtil.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/stacktrace.cc.o CMakeFiles/BubbleUpClustering.dir/base/ErrorHandling.cc.o CMakeFiles/BubbleUpClustering.dir/base/FileParser.cc.o CMakeFiles/BubbleUpClustering.dir/base/StringUtil.cc.o CMakeFiles/BubbleUpClustering.dir/util/mutil.cc.o -o BubbleUpClustering +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'bool contains_non_gatc(std::string)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc:33:26: warning: array subscript has type 'char' [-Wchar-subscripts] + 33 | if (_base_to_int[c] > 3) + | ^ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'kmer_int_type_t kmer_to_intval(std::string)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc:264:32: warning: array subscript has type 'char' [-Wchar-subscripts] + 264 | int val = _base_to_int[c]; + | ^ +[ 68%] Building CXX object CMakeFiles/GraphFromFasta.dir/base/FileParser.cc.o +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc: In function 'void print_trace(FILE*, const char*, int)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc:7:24: warning: unused parameter 'out' [-Wunused-parameter] + 7 | void print_trace(FILE *out, const char *file, int line) + | ~~~~~~^~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc:7:41: warning: unused parameter 'file' [-Wunused-parameter] + 7 | void print_trace(FILE *out, const char *file, int line) + | ~~~~~~~~~~~~^~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc:7:51: warning: unused parameter 'line' [-Wunused-parameter] + 7 | void print_trace(FILE *out, const char *file, int line) + | ~~~~^~~~ +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/base/FileParser.cc.o -MF CMakeFiles/GraphFromFasta.dir/base/FileParser.cc.o.d -o CMakeFiles/GraphFromFasta.dir/base/FileParser.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/FileParser.cc +make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' +[ 68%] Built target BubbleUpClustering +[ 70%] Building CXX object CMakeFiles/GraphFromFasta.dir/base/StringUtil.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/base/StringUtil.cc.o -MF CMakeFiles/GraphFromFasta.dir/base/StringUtil.cc.o.d -o CMakeFiles/GraphFromFasta.dir/base/StringUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/StringUtil.cc +[ 71%] Building CXX object CMakeFiles/GraphFromFasta.dir/util/mutil.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/util/mutil.cc.o -MF CMakeFiles/GraphFromFasta.dir/util/mutil.cc.o.d -o CMakeFiles/GraphFromFasta.dir/util/mutil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::SetUp(const vecDNAVector&, bool)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:46:20: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 46 | for (j=0; j<=d.size()-m_k; j++) { + | ~^~~~~~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:56:20: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 56 | for (j=0; j<=d.size()-m_k; j++) { + | ~^~~~~~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:79:18: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 79 | for (j=0; j<=d.size()-m_k; j++) { + | ~^~~~~~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::AddData(const vecDNAVector&)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:109:16: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 109 | for (j=0; j<= d.isize()-m_k; j++) { + | ~^~~~~~~~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::AddData(vecDNAVectorStream&)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:125:9: warning: unused variable 'i' [-Wunused-variable] + 125 | int i, j; + | ^ +[ 72%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/ReadsToTranscripts.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/analysis/ReadsToTranscripts.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/analysis/ReadsToTranscripts.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/analysis/ReadsToTranscripts.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/ReadsToTranscripts.cc +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/FileParser.cc: In member function 'bool StringParser::IsString(int)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter 'index' [-Wunused-parameter] + 50 | bool StringParser::IsString(int index) + | ~~~~^~~~~ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:313:14: warning: passing argument 1 to 'restrict'-qualified parameter aliases with argument 4 [-Wrestrict] 313 | if (fscanf(m_pFile, szText, sizeof(szText), m_pFile) == EOF) { @@ -2847,27 +2822,12 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:1688:16: warning: unused variable 'p' [-Wunused-variable] 1688 | const char * p = (const char*)string; | ^ -[ 84%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/stacktrace.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/analysis/stacktrace.cc.o -MF CMakeFiles/QuantifyGraph.dir/analysis/stacktrace.cc.o.d -o CMakeFiles/QuantifyGraph.dir/analysis/stacktrace.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/stacktrace.cc -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'bool contains_non_gatc(std::string)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc:33:26: warning: array subscript has type 'char' [-Wchar-subscripts] - 33 | if (_base_to_int[c] > 3) - | ^ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'kmer_int_type_t kmer_to_intval(std::string)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc:264:32: warning: array subscript has type 'char' [-Wchar-subscripts] - 264 | int val = _base_to_int[c]; - | ^ -make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' -[ 85%] Linking CXX executable Chrysalis -/usr/bin/cmake -E cmake_link_script CMakeFiles/Chrysalis.dir/link.txt --verbose=1 -[ 85%] Built target CreateIwormFastaBundle -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/Chrysalis.dir/aligns/KmerAlignCore.cc.o CMakeFiles/Chrysalis.dir/analysis/AACodons.cc.o CMakeFiles/Chrysalis.dir/analysis/Chrysalis.cc.o CMakeFiles/Chrysalis.dir/analysis/DNAVector.cc.o CMakeFiles/Chrysalis.dir/analysis/TranscriptomeGraph.cc.o CMakeFiles/Chrysalis.dir/base/ErrorHandling.cc.o CMakeFiles/Chrysalis.dir/base/FileParser.cc.o CMakeFiles/Chrysalis.dir/base/StringUtil.cc.o CMakeFiles/Chrysalis.dir/util/mutil.cc.o -o Chrysalis -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/FileParser.cc: In member function 'bool StringParser::IsString(int)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter 'index' [-Wunused-parameter] - 50 | bool StringParser::IsString(int index) - | ~~~~^~~~~ -[ 87%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/stacktrace.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/analysis/stacktrace.cc.o -MF CMakeFiles/BubbleUpClustering.dir/analysis/stacktrace.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/analysis/stacktrace.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/stacktrace.cc +[ 74%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/sequenceUtil.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/analysis/sequenceUtil.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/analysis/sequenceUtil.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/analysis/sequenceUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc +[ 75%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/KmerTable.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/analysis/KmerTable.cc.o -MF CMakeFiles/QuantifyGraph.dir/analysis/KmerTable.cc.o.d -o CMakeFiles/QuantifyGraph.dir/analysis/KmerTable.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/KmerTable.cc +[ 77%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/NonRedKmerTable.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/analysis/NonRedKmerTable.cc.o -MF CMakeFiles/QuantifyGraph.dir/analysis/NonRedKmerTable.cc.o.d -o CMakeFiles/QuantifyGraph.dir/analysis/NonRedKmerTable.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:313:13: warning: 'szText' may be used uninitialized [-Wmaybe-uninitialized] 313 | if (fscanf(m_pFile, szText, sizeof(szText), m_pFile) == EOF) { @@ -2883,6 +2843,32 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:311:8: note: 'szText' declared here 311 | char szText[2048 * 10]; | ^~~~~~ +[ 78%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/QuantifyGraph.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/analysis/QuantifyGraph.cc.o -MF CMakeFiles/QuantifyGraph.dir/analysis/QuantifyGraph.cc.o.d -o CMakeFiles/QuantifyGraph.dir/analysis/QuantifyGraph.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/QuantifyGraph.cc +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::SetUp(const vecDNAVector&, bool)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:46:20: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 46 | for (j=0; j<=d.size()-m_k; j++) { + | ~^~~~~~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:56:20: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 56 | for (j=0; j<=d.size()-m_k; j++) { + | ~^~~~~~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:79:18: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 79 | for (j=0; j<=d.size()-m_k; j++) { + | ~^~~~~~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::AddData(const vecDNAVector&)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:109:16: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 109 | for (j=0; j<= d.isize()-m_k; j++) { + | ~^~~~~~~~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::AddData(vecDNAVectorStream&)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:125:9: warning: unused variable 'i' [-Wunused-variable] + 125 | int i, j; + | ^ +[ 80%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/stacktrace.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/analysis/stacktrace.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/analysis/stacktrace.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/analysis/stacktrace.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/stacktrace.cc +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/KmerTable.cc: In member function 'long long int KmerSequence::BasesToNumber(const DNAVector&, int)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/KmerTable.cc:27:13: warning: unused variable 'i' [-Wunused-variable] + 27 | long long i; + | ^ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'bool contains_non_gatc(std::string)': /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc:33:26: warning: array subscript has type 'char' [-Wchar-subscripts] 33 | if (_base_to_int[c] > 3) @@ -2891,18 +2877,66 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc:264:32: warning: array subscript has type 'char' [-Wchar-subscripts] 264 | int val = _base_to_int[c]; | ^ -make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' -[ 87%] Built target Chrysalis -[ 88%] Building CXX object CMakeFiles/QuantifyGraph.dir/util/mutil.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/util/mutil.cc.o -MF CMakeFiles/QuantifyGraph.dir/util/mutil.cc.o.d -o CMakeFiles/QuantifyGraph.dir/util/mutil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc -[ 90%] Building CXX object CMakeFiles/BubbleUpClustering.dir/base/ErrorHandling.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/base/ErrorHandling.cc.o -MF CMakeFiles/BubbleUpClustering.dir/base/ErrorHandling.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/base/ErrorHandling.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc -[ 91%] Building CXX object CMakeFiles/BubbleUpClustering.dir/base/FileParser.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/base/FileParser.cc.o -MF CMakeFiles/BubbleUpClustering.dir/base/FileParser.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/base/FileParser.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/FileParser.cc -[ 92%] Building CXX object CMakeFiles/BubbleUpClustering.dir/base/StringUtil.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/base/StringUtil.cc.o -MF CMakeFiles/BubbleUpClustering.dir/base/StringUtil.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/base/StringUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/StringUtil.cc -[ 94%] Building CXX object CMakeFiles/BubbleUpClustering.dir/util/mutil.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/util/mutil.cc.o -MF CMakeFiles/BubbleUpClustering.dir/util/mutil.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/util/mutil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc +[ 81%] Building CXX object CMakeFiles/QuantifyGraph.dir/base/ErrorHandling.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/base/ErrorHandling.cc.o -MF CMakeFiles/QuantifyGraph.dir/base/ErrorHandling.cc.o.d -o CMakeFiles/QuantifyGraph.dir/base/ErrorHandling.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc +[ 82%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/base/ErrorHandling.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/base/ErrorHandling.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/base/ErrorHandling.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/base/ErrorHandling.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc +[ 84%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/base/FileParser.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/base/FileParser.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/base/FileParser.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/base/FileParser.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/FileParser.cc +[ 85%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/base/StringUtil.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/base/StringUtil.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/base/StringUtil.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/base/StringUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/StringUtil.cc +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc: In function 'void print_trace(FILE*, const char*, int)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc:7:24: warning: unused parameter 'out' [-Wunused-parameter] + 7 | void print_trace(FILE *out, const char *file, int line) + | ~~~~~~^~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc:7:41: warning: unused parameter 'file' [-Wunused-parameter] + 7 | void print_trace(FILE *out, const char *file, int line) + | ~~~~~~~~~~~~^~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc:7:51: warning: unused parameter 'line' [-Wunused-parameter] + 7 | void print_trace(FILE *out, const char *file, int line) + | ~~~~^~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/QuantifyGraph.cc: In function 'long long int BasesToNumberCountPlus(const std::vector >&, svec&, long long int&, const DNAVector&, int, const vecDNAVector&, int)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/QuantifyGraph.cc:250:10: warning: ISO C++ forbids variable length array 'kmerseq' [-Wvla] + 250 | char kmerseq [kmer_length + 1]; + | ^~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc: In function 'void print_trace(FILE*, const char*, int)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc:7:24: warning: unused parameter 'out' [-Wunused-parameter] + 7 | void print_trace(FILE *out, const char *file, int line) + | ~~~~~~^~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc:7:41: warning: unused parameter 'file' [-Wunused-parameter] + 7 | void print_trace(FILE *out, const char *file, int line) + | ~~~~~~~~~~~~^~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc:7:51: warning: unused parameter 'line' [-Wunused-parameter] + 7 | void print_trace(FILE *out, const char *file, int line) + | ~~~~^~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/QuantifyGraph.cc: In function 'int main(int, char**)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/QuantifyGraph.cc:372:29: warning: unused variable 'prevNode' [-Wunused-variable] + 372 | int prevNode = parser.AsInt(1); + | ^~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/QuantifyGraph.cc:409:13: warning: unused variable 'node' [-Wunused-variable] + 409 | int node = parser.AsInt(0); + | ^~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/QuantifyGraph.cc:412:30: warning: unused variable 'p2' [-Wunused-variable] + 412 | const char * p2 = s.c_str(); + | ^~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/QuantifyGraph.cc:337:16: warning: unused variable 'j' [-Wunused-variable] + 337 | int i, j; + | ^ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/QuantifyGraph.cc:350:16: warning: unused variable 'm' [-Wunused-variable] + 350 | size_t m = kmers.size(); + | ^ +[ 87%] Building CXX object CMakeFiles/QuantifyGraph.dir/base/FileParser.cc.o +[ 88%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/util/mutil.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/base/FileParser.cc.o -MF CMakeFiles/QuantifyGraph.dir/base/FileParser.cc.o.d -o CMakeFiles/QuantifyGraph.dir/base/FileParser.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/FileParser.cc +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/util/mutil.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/util/mutil.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/util/mutil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc +[ 90%] Building CXX object CMakeFiles/QuantifyGraph.dir/base/StringUtil.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/base/StringUtil.cc.o -MF CMakeFiles/QuantifyGraph.dir/base/StringUtil.cc.o.d -o CMakeFiles/QuantifyGraph.dir/base/StringUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/StringUtil.cc +[ 91%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/sequenceUtil.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/analysis/sequenceUtil.cc.o -MF CMakeFiles/QuantifyGraph.dir/analysis/sequenceUtil.cc.o.d -o CMakeFiles/QuantifyGraph.dir/analysis/sequenceUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/FileParser.cc: In member function 'bool StringParser::IsString(int)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter 'index' [-Wunused-parameter] + 50 | bool StringParser::IsString(int index) + | ~~~~^~~~~ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:313:14: warning: passing argument 1 to 'restrict'-qualified parameter aliases with argument 4 [-Wrestrict] 313 | if (fscanf(m_pFile, szText, sizeof(szText), m_pFile) == EOF) { @@ -2927,6 +2961,8 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:526:85: warning: unused parameter 'elSize' [-Wunused-parameter] 526 | bool CMAsciiWriteFileStream::WriteBlob(const void * pData, long lenInElements, long elSize) | ~~~~~^~~~~~ +[ 92%] Linking CXX executable CreateIwormFastaBundle +/usr/bin/cmake -E cmake_link_script CMakeFiles/CreateIwormFastaBundle.dir/link.txt --verbose=1 /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc: In function 'void MLog(const MCL_TCHAR*, bool)': /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:738:53: warning: unused parameter 'bLineFeed' [-Wunused-parameter] 738 | MDLLEXPORT void MLog(const MCL_TCHAR * szText, bool bLineFeed) @@ -2939,29 +2975,27 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:787:80: warning: unused parameter 'bLineFeed' [-Wunused-parameter] 787 | MDLLEXPORT void MLog(const MCL_TCHAR * szText, const MCL_TCHAR * szText2, bool bLineFeed) | ~~~~~^~~~~~~~~ -[ 95%] Linking CXX executable ReadsToTranscripts -/usr/bin/cmake -E cmake_link_script CMakeFiles/ReadsToTranscripts.dir/link.txt --verbose=1 /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc: In function 'void MCLSetUTF8Encode(bool)': /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:1288:39: warning: unused parameter 'b' [-Wunused-parameter] 1288 | MDLLEXPORT void MCLSetUTF8Encode(bool b) | ~~~~~^ +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/CreateIwormFastaBundle.dir/analysis/AACodons.cc.o CMakeFiles/CreateIwormFastaBundle.dir/analysis/CreateIwormFastaBundle.cc.o CMakeFiles/CreateIwormFastaBundle.dir/analysis/DNAVector.cc.o CMakeFiles/CreateIwormFastaBundle.dir/base/ErrorHandling.cc.o CMakeFiles/CreateIwormFastaBundle.dir/base/FileParser.cc.o CMakeFiles/CreateIwormFastaBundle.dir/base/StringUtil.cc.o CMakeFiles/CreateIwormFastaBundle.dir/util/mutil.cc.o -o CreateIwormFastaBundle /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc: In function 'bool AddUTF8Sig(CMString&)': /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:1688:16: warning: unused variable 'p' [-Wunused-variable] 1688 | const char * p = (const char*)string; | ^ -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/ReadsToTranscripts.dir/analysis/AACodons.cc.o CMakeFiles/ReadsToTranscripts.dir/analysis/DNAVector.cc.o CMakeFiles/ReadsToTranscripts.dir/analysis/NonRedKmerTable.cc.o CMakeFiles/ReadsToTranscripts.dir/analysis/ReadsToTranscripts.cc.o CMakeFiles/ReadsToTranscripts.dir/analysis/sequenceUtil.cc.o CMakeFiles/ReadsToTranscripts.dir/analysis/stacktrace.cc.o CMakeFiles/ReadsToTranscripts.dir/base/ErrorHandling.cc.o CMakeFiles/ReadsToTranscripts.dir/base/FileParser.cc.o CMakeFiles/ReadsToTranscripts.dir/base/StringUtil.cc.o CMakeFiles/ReadsToTranscripts.dir/util/mutil.cc.o -o ReadsToTranscripts -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc: In function 'void print_trace(FILE*, const char*, int)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc:7:24: warning: unused parameter 'out' [-Wunused-parameter] - 7 | void print_trace(FILE *out, const char *file, int line) - | ~~~~~~^~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc:7:41: warning: unused parameter 'file' [-Wunused-parameter] - 7 | void print_trace(FILE *out, const char *file, int line) - | ~~~~~~~~~~~~^~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/ErrorHandling.cc:7:51: warning: unused parameter 'line' [-Wunused-parameter] - 7 | void print_trace(FILE *out, const char *file, int line) - | ~~~~^~~~ -make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' -[ 95%] Built target ReadsToTranscripts +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/FileParser.cc: In member function 'bool StringParser::IsString(int)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter 'index' [-Wunused-parameter] + 50 | bool StringParser::IsString(int index) + | ~~~~^~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'bool contains_non_gatc(std::string)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc:33:26: warning: array subscript has type 'char' [-Wchar-subscripts] + 33 | if (_base_to_int[c] > 3) + | ^ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'kmer_int_type_t kmer_to_intval(std::string)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/sequenceUtil.cc:264:32: warning: array subscript has type 'char' [-Wchar-subscripts] + 264 | int val = _base_to_int[c]; + | ^ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:313:13: warning: 'szText' may be used uninitialized [-Wmaybe-uninitialized] 313 | if (fscanf(m_pFile, szText, sizeof(szText), m_pFile) == EOF) { @@ -2977,10 +3011,12 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:311:8: note: 'szText' declared here 311 | char szText[2048 * 10]; | ^~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/FileParser.cc: In member function 'bool StringParser::IsString(int)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter 'index' [-Wunused-parameter] - 50 | bool StringParser::IsString(int index) - | ~~~~^~~~~ +make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' +[ 94%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/stacktrace.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/analysis/stacktrace.cc.o -MF CMakeFiles/QuantifyGraph.dir/analysis/stacktrace.cc.o.d -o CMakeFiles/QuantifyGraph.dir/analysis/stacktrace.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/stacktrace.cc +[ 94%] Built target CreateIwormFastaBundle +[ 95%] Building CXX object CMakeFiles/QuantifyGraph.dir/util/mutil.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/util/mutil.cc.o -MF CMakeFiles/QuantifyGraph.dir/util/mutil.cc.o.d -o CMakeFiles/QuantifyGraph.dir/util/mutil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc [ 97%] Linking CXX executable GraphFromFasta /usr/bin/cmake -E cmake_link_script CMakeFiles/GraphFromFasta.dir/link.txt --verbose=1 /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/GraphFromFasta.dir/aligns/KmerAlignCore.cc.o CMakeFiles/GraphFromFasta.dir/analysis/AACodons.cc.o CMakeFiles/GraphFromFasta.dir/analysis/DNAVector.cc.o CMakeFiles/GraphFromFasta.dir/analysis/DeBruijnGraph.cc.o CMakeFiles/GraphFromFasta.dir/analysis/GraphFromFasta.cc.o CMakeFiles/GraphFromFasta.dir/analysis/KmerTable.cc.o CMakeFiles/GraphFromFasta.dir/analysis/NonRedKmerTable.cc.o CMakeFiles/GraphFromFasta.dir/analysis/sequenceUtil.cc.o CMakeFiles/GraphFromFasta.dir/analysis/stacktrace.cc.o CMakeFiles/GraphFromFasta.dir/base/ErrorHandling.cc.o CMakeFiles/GraphFromFasta.dir/base/FileParser.cc.o CMakeFiles/GraphFromFasta.dir/base/StringUtil.cc.o CMakeFiles/GraphFromFasta.dir/util/mutil.cc.o -o GraphFromFasta @@ -2998,6 +3034,7 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:436:14: warning: passing argument 1 to 'restrict'-qualified parameter aliases with argument 4 [-Wrestrict] 436 | if (fscanf(m_pFile, pData, len, m_pFile) == EOF) { | ^~~~~~~ ~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiWriteFileStream::WriteBlob(const void*, long int, long int)': /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:526:53: warning: unused parameter 'pData' [-Wunused-parameter] 526 | bool CMAsciiWriteFileStream::WriteBlob(const void * pData, long lenInElements, long elSize) @@ -3028,7 +3065,6 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:1688:16: warning: unused variable 'p' [-Wunused-variable] 1688 | const char * p = (const char*)string; | ^ -make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' [ 97%] Built target GraphFromFasta /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:313:13: warning: 'szText' may be used uninitialized [-Wmaybe-uninitialized] @@ -3045,11 +3081,11 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:311:8: note: 'szText' declared here 311 | char szText[2048 * 10]; | ^~~~~~ -[ 98%] Linking CXX executable BubbleUpClustering -/usr/bin/cmake -E cmake_link_script CMakeFiles/BubbleUpClustering.dir/link.txt --verbose=1 -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/BubbleUpClustering.dir/aligns/KmerAlignCore.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/AACodons.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/BubbleUpClustering.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/DNAVector.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/DeBruijnGraph.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/KmerTable.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/NonRedKmerTable.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/sequenceUtil.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/stacktrace.cc.o CMakeFiles/BubbleUpClustering.dir/base/ErrorHandling.cc.o CMakeFiles/BubbleUpClustering.dir/base/FileParser.cc.o CMakeFiles/BubbleUpClustering.dir/base/StringUtil.cc.o CMakeFiles/BubbleUpClustering.dir/util/mutil.cc.o -o BubbleUpClustering +[ 98%] Linking CXX executable ReadsToTranscripts +/usr/bin/cmake -E cmake_link_script CMakeFiles/ReadsToTranscripts.dir/link.txt --verbose=1 +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/ReadsToTranscripts.dir/analysis/AACodons.cc.o CMakeFiles/ReadsToTranscripts.dir/analysis/DNAVector.cc.o CMakeFiles/ReadsToTranscripts.dir/analysis/NonRedKmerTable.cc.o CMakeFiles/ReadsToTranscripts.dir/analysis/ReadsToTranscripts.cc.o CMakeFiles/ReadsToTranscripts.dir/analysis/sequenceUtil.cc.o CMakeFiles/ReadsToTranscripts.dir/analysis/stacktrace.cc.o CMakeFiles/ReadsToTranscripts.dir/base/ErrorHandling.cc.o CMakeFiles/ReadsToTranscripts.dir/base/FileParser.cc.o CMakeFiles/ReadsToTranscripts.dir/base/StringUtil.cc.o CMakeFiles/ReadsToTranscripts.dir/util/mutil.cc.o -o ReadsToTranscripts make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' -[ 98%] Built target BubbleUpClustering +[ 98%] Built target ReadsToTranscripts [100%] Linking CXX executable QuantifyGraph /usr/bin/cmake -E cmake_link_script CMakeFiles/QuantifyGraph.dir/link.txt --verbose=1 /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/QuantifyGraph.dir/aligns/KmerAlignCore.cc.o CMakeFiles/QuantifyGraph.dir/analysis/AACodons.cc.o CMakeFiles/QuantifyGraph.dir/analysis/DNAVector.cc.o CMakeFiles/QuantifyGraph.dir/analysis/KmerTable.cc.o CMakeFiles/QuantifyGraph.dir/analysis/NonRedKmerTable.cc.o CMakeFiles/QuantifyGraph.dir/analysis/QuantifyGraph.cc.o CMakeFiles/QuantifyGraph.dir/base/ErrorHandling.cc.o CMakeFiles/QuantifyGraph.dir/base/FileParser.cc.o CMakeFiles/QuantifyGraph.dir/base/StringUtil.cc.o CMakeFiles/QuantifyGraph.dir/analysis/sequenceUtil.cc.o CMakeFiles/QuantifyGraph.dir/analysis/stacktrace.cc.o CMakeFiles/QuantifyGraph.dir/util/mutil.cc.o -o QuantifyGraph @@ -3094,18 +3130,15 @@ warning: [options] source value 7 is obsolete and will be removed in a future release warning: [options] target value 7 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. -./Butterfly/Butterfly/src/src/AlignmentStats.java:54: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal - alignedBaseCounter.put(nameA, new Integer(0)); - ^ -./Butterfly/Butterfly/src/src/AlignmentStats.java:55: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal - alignedBaseCounter.put(nameB, new Integer(0)); - ^ -./Butterfly/Butterfly/src/src/AlignmentStats.java:126: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal - alignedBaseCounter.put(nameA, new Integer(alignedBaseCounter.get(nameA) + 1)); - ^ -./Butterfly/Butterfly/src/src/AlignmentStats.java:130: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal - alignedBaseCounter.put(nameB, new Integer (alignedBaseCounter.get(nameB) + 1)); - ^ +./Butterfly/Butterfly/src/src/IsoformExpressionLearning.java:396: warning: [removal] Double(double) in Double has been deprecated and marked for removal + Double len = new Double(0); + ^ +./Butterfly/Butterfly/src/src/IsoformExpressionLearning.java:515: warning: [removal] Double(double) in Double has been deprecated and marked for removal + Double sum = new Double(0); + ^ +./Butterfly/Butterfly/src/src/IsoformExpressionLearning.java:576: warning: [removal] Double(double) in Double has been deprecated and marked for removal + vec.set(i, new Double(0)); + ^ ./Butterfly/Butterfly/src/src/ZipperAlignment.java:39: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal as.alignedBaseCounter.put(nameA, new Integer(shorter_len)); ^ @@ -3118,15 +3151,18 @@ ./Butterfly/Butterfly/src/src/ZipperAlignment.java:72: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal as.alignedBaseCounter.put(nameB, new Integer(shorter_len)); ^ -./Butterfly/Butterfly/src/src/IsoformExpressionLearning.java:396: warning: [removal] Double(double) in Double has been deprecated and marked for removal - Double len = new Double(0); - ^ -./Butterfly/Butterfly/src/src/IsoformExpressionLearning.java:515: warning: [removal] Double(double) in Double has been deprecated and marked for removal - Double sum = new Double(0); - ^ -./Butterfly/Butterfly/src/src/IsoformExpressionLearning.java:576: warning: [removal] Double(double) in Double has been deprecated and marked for removal - vec.set(i, new Double(0)); - ^ +./Butterfly/Butterfly/src/src/AlignmentStats.java:54: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal + alignedBaseCounter.put(nameA, new Integer(0)); + ^ +./Butterfly/Butterfly/src/src/AlignmentStats.java:55: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal + alignedBaseCounter.put(nameB, new Integer(0)); + ^ +./Butterfly/Butterfly/src/src/AlignmentStats.java:126: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal + alignedBaseCounter.put(nameA, new Integer(alignedBaseCounter.get(nameA) + 1)); + ^ +./Butterfly/Butterfly/src/src/AlignmentStats.java:130: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal + alignedBaseCounter.put(nameB, new Integer (alignedBaseCounter.get(nameB) + 1)); + ^ ./Butterfly/Butterfly/src/src/TransAssembly_allProbPaths.java:4043: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal transcripts.put(path, new Pair(new Integer(1), new Integer(1))); ^ @@ -12054,13 +12090,13 @@ -no shared node, alignment not cached, computing: [-1, 380, 982, 440] to [-1, 945] -path1s length: 94, path2s length: 59 -running Needleman-Wunsch alignment of path sequences -Jun 11, 2025 12:39:31 PM jaligner.NeedlemanWunschGotoh construct +May 10, 2024 8:21:38 AM jaligner.NeedlemanWunschGotoh construct INFO: Started... -Jun 11, 2025 12:39:31 PM jaligner.NeedlemanWunschGotoh construct +May 10, 2024 8:21:38 AM jaligner.NeedlemanWunschGotoh construct INFO: Finished. -Jun 11, 2025 12:39:31 PM jaligner.NeedlemanWunschGotoh traceback +May 10, 2024 8:21:38 AM jaligner.NeedlemanWunschGotoh traceback INFO: Started... -Jun 11, 2025 12:39:31 PM jaligner.NeedlemanWunschGotoh traceback +May 10, 2024 8:21:38 AM jaligner.NeedlemanWunschGotoh traceback INFO: Finished. A 1 GGCCACACGATGGCTTATCACGTCCACATTTCTACTGGCTACAAACAGAC 50 .|..||||||..|.| @@ -12884,9 +12920,9 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'trinityrnaseq' in '../trinityrnaseq_2.15.1+dfsg-5_amd64.deb'. dpkg-deb: building package 'trinityrnaseq-dbgsym' in '../trinityrnaseq-dbgsym_2.15.1+dfsg-5_amd64.deb'. dpkg-deb: building package 'trinityrnaseq-examples' in '../trinityrnaseq-examples_2.15.1+dfsg-5_amd64.deb'. +dpkg-deb: building package 'trinityrnaseq' in '../trinityrnaseq_2.15.1+dfsg-5_amd64.deb'. dpkg-genbuildinfo --build=binary -O../trinityrnaseq_2.15.1+dfsg-5_amd64.buildinfo dpkg-genchanges --build=binary -O../trinityrnaseq_2.15.1+dfsg-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -12894,12 +12930,14 @@ 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/1261467/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1261467/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/2069237 and its subdirectories -I: Current time: Wed Jun 11 12:40:47 -12 2025 -I: pbuilder-time-stamp: 1749688847 +I: removing directory /srv/workspace/pbuilder/1261467 and its subdirectories +I: Current time: Fri May 10 08:23:06 +14 2024 +I: pbuilder-time-stamp: 1715278986