Diff of the two buildlogs: -- --- b1/build.log 2024-05-30 01:20:51.824799462 +0000 +++ b2/build.log 2024-05-30 01:24:42.814991530 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed May 29 13:15:43 -12 2024 -I: pbuilder-time-stamp: 1717031743 +I: Current time: Wed Jul 2 21:44:00 +14 2025 +I: pbuilder-time-stamp: 1751442240 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/4062624/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1114741/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-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 Jul 2 07:44 /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/1114741/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1114741/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='f819c151e46a4276b0b6236778f11701' - 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='4062624' - PS1='# ' - PS2='> ' + INVOCATION_ID=bc67e2f278db4168ac1649780c66b804 + 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=1114741 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.8QNvAgjV/pbuilderrc_Nhj3 --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.8QNvAgjV/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.8QNvAgjV/pbuilderrc_vAWz --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.8QNvAgjV/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 infom01-amd64 6.1.0-21-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 28 07:42 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4062624/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 30 14:05 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1114741/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -394,7 +426,7 @@ Get: 247 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.20+ds-1 [1684 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 libjung-free-java all 2.1.1-2 [1477 kB] -Fetched 237 MB in 2s (112 MB/s) +Fetched 237 MB in 2s (109 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 ... 19716 files and directories currently installed.) @@ -1213,8 +1245,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu May 30 01:17:09 UTC 2024. -Universal Time is now: Thu May 30 01:17:09 UTC 2024. +Local time is now: Wed Jul 2 07:45:25 UTC 2025. +Universal Time is now: Wed Jul 2 07:45:25 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libasound2-data (1.2.11-1) ... @@ -1611,7 +1643,11 @@ 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/1114741/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1114741/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 @@ -1679,8 +1715,8 @@ 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 @@ -1720,7 +1756,7 @@ -- Detecting CXX compile features -- Detecting CXX compile features - done -- system: Linux --- Configuring done (1.6s) +-- Configuring done (0.6s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -1758,7 +1794,7 @@ -- Detecting CXX compile features -- Detecting CXX compile features - done -- system: Linux --- Configuring done (0.5s) +-- Configuring done (0.6s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -1790,44 +1826,50 @@ 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' +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/fastaToKmerCoverageStats.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/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=" -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/fastaToKmerCoverageStats.dir/DependInfo.cmake "--color=" make[4]: Leaving 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/inchworm.dir/build.make CMakeFiles/inchworm.dir/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' -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 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/inchworm.dir/build.make CMakeFiles/inchworm.dir/build -[ 7%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/Fasta_entry.cpp.o -[ 7%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/Fasta_reader.cpp.o +make -f CMakeFiles/fastaToKmerCoverageStats.dir/build.make CMakeFiles/fastaToKmerCoverageStats.dir/build make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build' -[ 10%] 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/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 -/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 -[ 14%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/FastaToDeBruijn.cpp.o -[ 21%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o -[ 21%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_reader.cpp.o -[ 25%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/string_util.cpp.o -[ 28%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/fastaToKmerCoverageStats.cpp.o +[ 3%] 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/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/FastaToDeBruijn.dir/src/FastaToDeBruijn.cpp.o +[ 17%] Building CXX object CMakeFiles/inchworm.dir/src/Fasta_entry.cpp.o +[ 17%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o +[ 17%] Building CXX object CMakeFiles/inchworm.dir/src/string_util.cpp.o +[ 21%] Building CXX object CMakeFiles/inchworm.dir/src/KmerCounter.cpp.o +[ 28%] 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/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/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/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 +/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/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 [ 32%] 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/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 -/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 -/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 +[ 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/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 +[ 42%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/Fasta_reader.cpp.o +[ 42%] 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/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 /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 -[ 35%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/stacktrace.cpp.o -[ 39%] Building CXX object CMakeFiles/inchworm.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/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/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 -[ 42%] 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/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 -/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/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 +/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 +/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/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 +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 \ + | ^~~~~~~ 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, @@ -1835,38 +1877,60 @@ /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/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 -[ 50%] 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 -[ 53%] 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/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 -[ 57%] 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 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/IRKE.cpp:21: /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/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/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) - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -[ 64%] 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 -[ 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 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.cpp:21: + 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/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 +[ 50%] 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/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 +[ 53%] 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 +/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) + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +/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/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 +[ 60%] 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 +[ 64%] 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 +[ 67%] 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 +[ 71%] 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 +/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; + | ^~~ +[ 75%] 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 +[ 78%] 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 +[ 82%] 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 +[ 85%] 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 +[ 89%] 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/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++) { @@ -1878,44 +1942,16 @@ /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++) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~ -/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(); - | ^~~~~~~~~~~ -[ 71%] 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 -[ 75%] 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 -[ 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 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 \ | ^~~~~~~ -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 \ - | ^~~~~~~ -[ 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 -[ 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 -[ 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 -/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; - | ^~~ +/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++) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~ 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, @@ -1947,16 +1983,16 @@ /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; | ^~~~~~~~~~~~~~ -[ 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 -make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build' -[ 92%] Built target fastaToKmerCoverageStats -[ 96%] Linking CXX executable inchworm +[ 92%] 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 make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build' -[ 96%] Built target inchworm +[ 92%] Built target inchworm +[ 96%] 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 +make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Inchworm_build' +[ 96%] Built target fastaToKmerCoverageStats [100%] Linking CXX executable FastaToDeBruijn /usr/bin/cmake -E cmake_link_script CMakeFiles/FastaToDeBruijn.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/FastaToDeBruijn.dir/src/FastaToDeBruijn.cpp.o CMakeFiles/FastaToDeBruijn.dir/src/argProcessor.cpp.o CMakeFiles/FastaToDeBruijn.dir/src/Fasta_reader.cpp.o CMakeFiles/FastaToDeBruijn.dir/src/Fasta_entry.cpp.o CMakeFiles/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o CMakeFiles/FastaToDeBruijn.dir/src/string_util.cpp.o CMakeFiles/FastaToDeBruijn.dir/src/stacktrace.cpp.o CMakeFiles/FastaToDeBruijn.dir/src/DeBruijnGraph.cpp.o -o FastaToDeBruijn @@ -1978,71 +2014,59 @@ 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 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/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=" +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/ReadsToTranscripts.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=" -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]: Leaving 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/ReadsToTranscripts.dir/build.make CMakeFiles/ReadsToTranscripts.dir/build -make -f CMakeFiles/CreateIwormFastaBundle.dir/build.make CMakeFiles/CreateIwormFastaBundle.dir/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[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' +make -f CMakeFiles/QuantifyGraph.dir/build.make CMakeFiles/QuantifyGraph.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]: Entering 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/CreateIwormFastaBundle.dir/build.make CMakeFiles/CreateIwormFastaBundle.dir/build make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_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 -f CMakeFiles/QuantifyGraph.dir/build.make CMakeFiles/QuantifyGraph.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]: Leaving 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 -f CMakeFiles/ReadsToTranscripts.dir/build.make CMakeFiles/ReadsToTranscripts.dir/build make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' -[ 4%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/analysis/CreateIwormFastaBundle.cc.o -[ 4%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/base/ErrorHandling.cc.o -[ 4%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/DNAVector.cc.o -[ 5%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/base/FileParser.cc.o -[ 7%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/analysis/AACodons.cc.o -[ 8%] 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/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/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 -[ 10%] 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=. 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-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 -/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 -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis -g -O2 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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 +[ 1%] Building CXX object CMakeFiles/Chrysalis.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/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++ 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CMakeFiles/Chrysalis.dir/analysis/Chrysalis.cc.o +[ 7%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/AACodons.cc.o +[ 7%] Building CXX object CMakeFiles/QuantifyGraph.dir/aligns/KmerAlignCore.cc.o +[ 8%] Building CXX object CMakeFiles/Chrysalis.dir/analysis/TranscriptomeGraph.cc.o +[ 10%] 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/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/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 +[ 11%] Building CXX object CMakeFiles/Chrysalis.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/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 +[ 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/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 +[ 15%] Building CXX object CMakeFiles/Chrysalis.dir/analysis/AACodons.cc.o +[ 15%] 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/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 +[ 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/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 /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/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 -/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) - | ~~~~^~~~ -[ 18%] 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 +/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/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/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 /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? @@ -2139,38 +2163,34 @@ /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/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; - | ^ -/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/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/CreateIwormFastaBundle.cc:166:12: warning: unused variable 'pOut' [-Wunused-variable] - 166 | FILE * pOut = NULL; - | ^~~~ -/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/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/analysis/Chrysalis.cc:384:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 384 | system(command.c_str()); + | ~~~~~~^~~~~~~~~~~~~~~~~ /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? @@ -2203,93 +2223,41 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/aligns/KmerAlignCore.cc:291:9: warning: unused variable 'i' [-Wunused-variable] 291 | int i; | ^ -[ 20%] 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 -[ 21%] 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/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 -[ 22%] 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 -[ 24%] 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 -[ 25%] 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) { - | ^~~~~~~ ~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:303:51: warning: unused parameter 'pData' [-Wunused-parameter] - 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) - | ~~~~~~~^~~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:303:63: warning: unused parameter 'lenInBytes' [-Wunused-parameter] - 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) - | ~~~~~^~~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadString(CMString&)': -/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) { - | ^~~~~~~ ~~~~~~~ -/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) - | ~~~~~~~~~~~~~^~~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:526:65: warning: unused parameter 'lenInElements' [-Wunused-parameter] - 526 | bool CMAsciiWriteFileStream::WriteBlob(const void * pData, long lenInElements, long elSize) - | ~~~~~^~~~~~~~~~~~~ -/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) - | ~~~~~^~~~~~ -/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) - | ~~~~~^~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc: In function 'void MLog(const MCL_TCHAR*, long int, bool)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:761:63: warning: unused parameter 'bLineFeed' [-Wunused-parameter] - 761 | MDLLEXPORT void MLog(const MCL_TCHAR * szText, long val, bool bLineFeed) - | ~~~~~^~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc: In function 'void MLog(const MCL_TCHAR*, const MCL_TCHAR*, bool)': -/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) - | ~~~~~^~~~~~~~~ -/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) - | ~~~~~^ -/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; - | ^ -[ 27%] 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/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]; - | ^~~~~~ -[ 28%] 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 -[ 30%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/AACodons.cc.o -[ 31%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/BubbleUpClustering.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/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 +/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; + | ^ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc: In member function 'void KmerSearch::Extend(long long int, DNAVector&, const svec&, DNAVector&)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc:547:16: warning: unused variable 'plusminus' [-Wunused-variable] + 547 | static int plusminus = 0; + | ^~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc: In function 'int TranscriptomeGraph(vecDNAVector&, FILE*, int, bool)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc:668:20: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 668 | for (i=0; i<=d.isize()-k; i++) { + | ~^~~~~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc:647:10: warning: unused variable 'bAppend' [-Wunused-variable] + 647 | bool bAppend = true; + | ^~~~~~~ +[ 18%] Building CXX object CMakeFiles/BubbleUpClustering.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/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 -/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]; - | ^ -[ 32%] Building CXX object CMakeFiles/Chrysalis.dir/analysis/Chrysalis.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/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 +[ 20%] 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 +[ 21%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/BubbleUpClustering.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/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 +/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) + | ~~~~^~~~ +[ 22%] 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 +[ 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 /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/BubbleUpClustering.cc: In function 'svec 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) { @@ -2302,6 +2270,8 @@ /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) { | ^~~~ +[ 25%] 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/analysis/BubbleUpClustering.cc: In function 'void populate_weld_reinforced_iworm_clusters(std::string&, std::map&)': /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/BubbleUpClustering.cc:525:57: warning: implicitly-declared 'Pool& Pool::operator=(const Pool&)' is deprecated [-Wdeprecated-copy] 525 | weld_reinforced_iworm_clusters[ node_id ] = p; @@ -2316,86 +2286,62 @@ /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++) { | ~~^~~~~~~~~~ -[ 34%] Building CXX object CMakeFiles/Chrysalis.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/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 -[ 35%] 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 -[ 37%] 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 -[ 38%] 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 -[ 40%] 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 -/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); +[ 27%] 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/Chrysalis.cc:384:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 384 | system(command.c_str()); - | ~~~~~~^~~~~~~~~~~~~~~~~ -[ 41%] 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 -/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) - | ~~~~^~~~ -[ 42%] 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 -/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; - | ^ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc: In member function 'void KmerSearch::Extend(long long int, DNAVector&, const svec&, DNAVector&)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc:547:16: warning: unused variable 'plusminus' [-Wunused-variable] - 547 | static int plusminus = 0; - | ^~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc: In function 'int TranscriptomeGraph(vecDNAVector&, FILE*, int, bool)': -/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc:668:20: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 668 | for (i=0; i<=d.isize()-k; i++) { - | ~^~~~~~~~~~~~~ -/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/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/analysis/CreateIwormFastaBundle.cc:166:12: warning: unused variable 'pOut' [-Wunused-variable] + 166 | FILE * pOut = NULL; + | ^~~~ +[ 28%] 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 +[ 30%] 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/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; + | ^ +[ 31%] 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 /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) | ~~~~^~~~~ +[ 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/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 +[ 35%] 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/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; + | ^ +[ 37%] 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) { | ~~~~~~~~~~~~~^~~~~~~~~~~ -[ 45%] 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 /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; @@ -2414,11 +2360,13 @@ /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) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' -[ 45%] Built target CreateIwormFastaBundle -[ 47%] 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/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 -[ 48%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/GraphFromFasta.cc.o +[ 38%] 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 +[ 40%] 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 +[ 41%] 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 +[ 42%] 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 /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] @@ -2464,8 +2412,24 @@ /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; | ^ -[ 50%] Building CXX object CMakeFiles/GraphFromFasta.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/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 +/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; + | ^ /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) { @@ -2481,8 +2445,8 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:311:8: note: 'szText' declared here 311 | char szText[2048 * 10]; | ^~~~~~ -[ 51%] 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 +[ 44%] 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/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) @@ -2538,12 +2502,87 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/GraphFromFasta.cc:1268:9: warning: unused variable 'total_iworm_contigs' [-Wunused-variable] 1268 | int total_iworm_contigs = dna.size(); | ^~~~~~~~~~~~~~~~~~~ -[ 52%] 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 +[ 45%] 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/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) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +[ 47%] Linking CXX executable Chrysalis +/usr/bin/cmake -E cmake_link_script CMakeFiles/Chrysalis.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/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 +[ 48%] 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/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' +[ 48%] Built target Chrysalis +[ 50%] 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 +[ 51%] 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 /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; | ^ +[ 52%] 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 +[ 54%] 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 +/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/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/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(); + | ^ /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) @@ -2554,28 +2593,50 @@ /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) | ~~~~^~~~ -[ 54%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/NonRedKmerTable.cc.o +[ 55%] Building CXX object CMakeFiles/GraphFromFasta.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/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 +[ 57%] 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 +/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; + | ^ +/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; + | ^ +[ 58%] 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 +[ 60%] Building CXX object CMakeFiles/GraphFromFasta.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/GraphFromFasta.dir/analysis/NonRedKmerTable.cc.o -MF CMakeFiles/GraphFromFasta.dir/analysis/NonRedKmerTable.cc.o.d -o CMakeFiles/GraphFromFasta.dir/analysis/NonRedKmerTable.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc -[ 55%] 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 -[ 57%] 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 -[ 58%] 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 +[ 61%] 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/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]; - | ^ -[ 60%] 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 +[ 62%] 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 +/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/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/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++) { @@ -2594,12 +2655,34 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:125:9: warning: unused variable 'i' [-Wunused-variable] 125 | int i, j; | ^ -[ 61%] 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 -[ 62%] 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 -[ 64%] 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 +[ 65%] 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 +[ 67%] 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 +[ 68%] 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 +[ 70%] 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 +[ 71%] 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 +[ 72%] 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 +[ 74%] 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 +/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) + | ~~~~^~~~ +[ 75%] 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 +[ 77%] 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:313:14: warning: passing argument 1 to 'restrict'-qualified parameter aliases with argument 4 [-Wrestrict] 313 | if (fscanf(m_pFile, szText, sizeof(szText), m_pFile) == EOF) { @@ -2610,6 +2693,10 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:303:63: warning: unused parameter 'lenInBytes' [-Wunused-parameter] 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) | ~~~~~^~~~~~~~~~ +/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/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadString(CMString&)': /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) { @@ -2636,6 +2723,10 @@ /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) | ~~~~~^~~~~~~~~ +/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 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) @@ -2644,45 +2735,26 @@ /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; | ^ -[ 65%] 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 -/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/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:313:13: 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]; - | ^~~~~~ -[ 67%] 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 -[ 68%] 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 -[ 70%] 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 -[ 71%] 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 +/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]; + | ^ +[ 78%] 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/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]; + | ^ +[ 80%] 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 /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) { @@ -2727,19 +2799,6 @@ /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; | ^ -[ 72%] 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 -[ 74%] 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/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: 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/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) { @@ -2755,139 +2814,10 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:311:8: note: 'szText' declared here 311 | char szText[2048 * 10]; | ^~~~~~ -[ 75%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/QuantifyGraph.cc.o -make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' -/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 -[ 77%] 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 -/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) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 77%] Built target ReadsToTranscripts -[ 78%] 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 -[ 80%] 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/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/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; - | ^ -[ 81%] Linking CXX executable Chrysalis -/usr/bin/cmake -E cmake_link_script CMakeFiles/Chrysalis.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/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/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/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; - | ^ -[ 82%] 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 -[ 84%] 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 -make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' -[ 84%] Built target Chrysalis -[ 85%] 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 -/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) - | ~~~~^~~~ -[ 87%] 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/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/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(); - | ^ -[ 88%] 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 -[ 90%] 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 -/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/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) | ~~~~^~~~~ -[ 91%] 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/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) @@ -2899,6 +2829,36 @@ 7 | void print_trace(FILE *out, const char *file, int line) | ~~~~^~~~ /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, + | ^~~~~~~~~~ +[ 81%] Building CXX object CMakeFiles/BubbleUpClustering.dir/base/FileParser.cc.o +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:311:8: note: 'szText' declared here + 311 | char szText[2048 * 10]; + | ^~~~~~ +/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 +[ 82%] 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 +[ 84%] 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/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 +[ 85%] 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 +[ 87%] 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 +/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) + | ~~~~^~~~~ +[ 88%] Building CXX object CMakeFiles/BubbleUpClustering.dir/base/StringUtil.cc.o +/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) { | ^~~~~~~ ~~~~~~~ @@ -2908,6 +2868,7 @@ /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:303:63: warning: unused parameter 'lenInBytes' [-Wunused-parameter] 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) | ~~~~~^~~~~~~~~~ +/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 /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadString(CMString&)': /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) { @@ -2942,12 +2903,22 @@ /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; | ^ -[ 92%] 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 -[ 94%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/stacktrace.cc.o -[ 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/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 -/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/GraphFromFasta.dir/base/StringUtil.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/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 +[ 91%] 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 +[ 92%] 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/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) { @@ -2963,14 +2934,59 @@ /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/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/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) + | ~~~~^~~~~ +[ 94%] 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 +/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) { + | ^~~~~~~ ~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:303:51: warning: unused parameter 'pData' [-Wunused-parameter] + 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) + | ~~~~~~~^~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:303:63: warning: unused parameter 'lenInBytes' [-Wunused-parameter] + 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) + | ~~~~~^~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadString(CMString&)': +/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) { + | ^~~~~~~ ~~~~~~~ +/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) + | ~~~~~~~~~~~~~^~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:526:65: warning: unused parameter 'lenInElements' [-Wunused-parameter] + 526 | bool CMAsciiWriteFileStream::WriteBlob(const void * pData, long lenInElements, long elSize) + | ~~~~~^~~~~~~~~~~~~ +/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) + | ~~~~~^~~~~~ +/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) + | ~~~~~^~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc: In function 'void MLog(const MCL_TCHAR*, long int, bool)': +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc:761:63: warning: unused parameter 'bLineFeed' [-Wunused-parameter] + 761 | MDLLEXPORT void MLog(const MCL_TCHAR * szText, long val, bool bLineFeed) + | ~~~~~^~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis/util/mutil.cc: In function 'void MLog(const MCL_TCHAR*, const MCL_TCHAR*, bool)': +/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) + | ~~~~~^~~~~~~~~ +/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) + | ~~~~~^ +/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; + | ^ +make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' +[ 94%] Built target CreateIwormFastaBundle /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) { @@ -3015,9 +3031,6 @@ /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; | ^ -[ 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 /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) { @@ -3033,18 +3046,41 @@ /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/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]; + | ^~~~~~ +[ 95%] 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 make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' -[ 97%] Built target GraphFromFasta -[ 98%] Linking CXX executable BubbleUpClustering +[ 95%] Built target QuantifyGraph +[ 97%] 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' +[ 97%] Built target ReadsToTranscripts +[ 98%] Linking CXX executable GraphFromFasta +/usr/bin/cmake -E cmake_link_script CMakeFiles/GraphFromFasta.dir/link.txt --verbose=1 +[100%] 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/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 /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 make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' -[ 98%] Built target BubbleUpClustering -[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 +[100%] Built target GraphFromFasta make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' -[100%] Built target QuantifyGraph +[100%] Built target BubbleUpClustering make[3]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.1+dfsg/Chrysalis_build' @@ -3084,27 +3120,6 @@ 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/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)); - ^ -./Butterfly/Butterfly/src/src/ZipperAlignment.java:40: 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/ZipperAlignment.java:71: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal - as.alignedBaseCounter.put(nameA, new Integer(shorter_len)); - ^ -./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/AlignmentStats.java:54: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal alignedBaseCounter.put(nameA, new Integer(0)); ^ @@ -3117,6 +3132,27 @@ ./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/ZipperAlignment.java:39: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal + as.alignedBaseCounter.put(nameA, new Integer(shorter_len)); + ^ +./Butterfly/Butterfly/src/src/ZipperAlignment.java:40: 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/ZipperAlignment.java:71: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal + as.alignedBaseCounter.put(nameA, new Integer(shorter_len)); + ^ +./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/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))); ^ @@ -12044,13 +12080,13 @@ -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 -May 29, 2024 1:18:11 PM jaligner.NeedlemanWunschGotoh construct +Jul 02, 2025 9:46:28 PM jaligner.NeedlemanWunschGotoh construct INFO: Started... -May 29, 2024 1:18:11 PM jaligner.NeedlemanWunschGotoh construct +Jul 02, 2025 9:46:28 PM jaligner.NeedlemanWunschGotoh construct INFO: Finished. -May 29, 2024 1:18:11 PM jaligner.NeedlemanWunschGotoh traceback +Jul 02, 2025 9:46:28 PM jaligner.NeedlemanWunschGotoh traceback INFO: Started... -May 29, 2024 1:18:11 PM jaligner.NeedlemanWunschGotoh traceback +Jul 02, 2025 9:46:28 PM jaligner.NeedlemanWunschGotoh traceback INFO: Finished. A 1 GGCCACACGATGGCTTATCACGTCCACATTTCTACTGGCTACAAACAGAC 50 .|..||||||..|.| @@ -12874,9 +12910,9 @@ 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-examples' in '../trinityrnaseq-examples_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' 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) @@ -12884,12 +12920,14 @@ 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/1114741/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1114741/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/4062624 and its subdirectories -I: Current time: Wed May 29 13:20:50 -12 2024 -I: pbuilder-time-stamp: 1717032050 +I: removing directory /srv/workspace/pbuilder/1114741 and its subdirectories +I: Current time: Wed Jul 2 21:47:42 +14 2025 +I: pbuilder-time-stamp: 1751442462