Diff of the two buildlogs: -- --- b1/build.log 2024-11-18 20:57:11.778846619 +0000 +++ b2/build.log 2024-11-18 21:02:37.460102980 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Nov 18 08:54:01 -12 2024 -I: pbuilder-time-stamp: 1731963241 +I: Current time: Mon Dec 22 17:21:30 +14 2025 +I: pbuilder-time-stamp: 1766373690 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -45,52 +45,84 @@ dpkg-source: info: applying extending_Function_in_jung.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2301081/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/15447/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Dec 22 03:21 /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/15447/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/15447/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='3975f4abb4694ecf830280171a2587f3' - 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='2301081' - PS1='# ' - PS2='> ' + INVOCATION_ID=68cbf41384844b4799b874262deff477 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=15447 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.tkQX82D9/pbuilderrc_MVo4 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.tkQX82D9/b1 --logfile b1/build.log trinityrnaseq_2.15.2+dfsg-1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.tkQX82D9/pbuilderrc_ImI3 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.tkQX82D9/b2 --logfile b2/build.log trinityrnaseq_2.15.2+dfsg-1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2301081/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/15447/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -454,7 +486,7 @@ Get: 308 http://deb.debian.org/debian trixie/main arm64 libhts-dev arm64 1.20+ds-2 [1626 kB] Get: 309 http://deb.debian.org/debian trixie/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 310 http://deb.debian.org/debian trixie/main arm64 libjung-free-java all 2.1.1-3 [1484 kB] -Fetched 264 MB in 1s (209 MB/s) +Fetched 264 MB in 1s (214 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libapparmor1:arm64. (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 ... 20087 files and directories currently installed.) @@ -1485,8 +1517,8 @@ Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Nov 18 20:54:45 UTC 2024. -Universal Time is now: Mon Nov 18 20:54:45 UTC 2024. +Local time is now: Mon Dec 22 03:22:30 UTC 2025. +Universal Time is now: Mon Dec 22 03:22:30 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:arm64 (1.17.0-2+b1) ... @@ -1939,7 +1971,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/trinityrnaseq-2.15.2+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_2.15.2+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/15447/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/15447/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/trinityrnaseq-2.15.2+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_2.15.2+dfsg-1_source.changes dpkg-buildpackage: info: source package trinityrnaseq dpkg-buildpackage: info: source version 2.15.2+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -2007,12 +2043,12 @@ make[3]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/trinity-plugins' make[1]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg' jh_clean -Duplicate specification "u=s" for option "u" +Duplicate specification "unlink|u" for option "u" dh_clean debian/rules binary dh binary --with javahelper @@ -2049,7 +2085,7 @@ -- Detecting CXX compile features -- Detecting CXX compile features - done -- system: Linux --- Configuring done (1.0s) +-- Configuring done (1.7s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -2087,7 +2123,7 @@ -- Detecting CXX compile features -- Detecting CXX compile features - done -- system: Linux --- Configuring done (0.9s) +-- Configuring done (1.4s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -2116,51 +2152,51 @@ make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build' make -f CMakeFiles/inchworm.dir/build.make CMakeFiles/inchworm.dir/depend -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-2.15.2+dfsg/Inchworm_build' cd /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build/CMakeFiles/inchworm.dir/DependInfo.cmake "--color=" +make -f CMakeFiles/FastaToDeBruijn.dir/build.make CMakeFiles/FastaToDeBruijn.dir/depend make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build' cd /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build/CMakeFiles/FastaToDeBruijn.dir/DependInfo.cmake "--color=" +make -f CMakeFiles/fastaToKmerCoverageStats.dir/build.make CMakeFiles/fastaToKmerCoverageStats.dir/depend make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build' cd /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build/CMakeFiles/fastaToKmerCoverageStats.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build' -make -f CMakeFiles/FastaToDeBruijn.dir/build.make CMakeFiles/FastaToDeBruijn.dir/build -make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build' -make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build' make -f CMakeFiles/inchworm.dir/build.make CMakeFiles/inchworm.dir/build -make -f CMakeFiles/fastaToKmerCoverageStats.dir/build.make CMakeFiles/fastaToKmerCoverageStats.dir/build make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build' +make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build' +make -f CMakeFiles/FastaToDeBruijn.dir/build.make CMakeFiles/FastaToDeBruijn.dir/build +make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build' make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build' +make -f CMakeFiles/fastaToKmerCoverageStats.dir/build.make CMakeFiles/fastaToKmerCoverageStats.dir/build +[ 3%] Building CXX object CMakeFiles/inchworm.dir/src/Fasta_entry.cpp.o make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build' -[ 3%] Building CXX object CMakeFiles/inchworm.dir/src/IRKE_run.cpp.o -[ 7%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/FastaToDeBruijn.cpp.o -[ 10%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/argProcessor.cpp.o -[ 14%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/fastaToKmerCoverageStats.cpp.o -[ 21%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/Fasta_entry.cpp.o -[ 21%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/Fasta_entry.cpp +[ 7%] Building CXX object CMakeFiles/inchworm.dir/src/IRKE_run.cpp.o +[ 10%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/FastaToDeBruijn.cpp.o +[ 14%] Building CXX object CMakeFiles/inchworm.dir/src/sequenceUtil.cpp.o +[ 17%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/argProcessor.cpp.o +[ 21%] Building CXX object CMakeFiles/inchworm.dir/src/IRKE.cpp.o [ 25%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/argProcessor.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/FastaToDeBruijn.cpp /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/IRKE_run.cpp -[ 28%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/Fasta_reader.cpp.o -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp +[ 32%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_reader.cpp.o +[ 28%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/fastaToKmerCoverageStats.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/argProcessor.cpp -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/argProcessor.cpp -[ 32%] Building CXX object CMakeFiles/inchworm.dir/src/Fasta_entry.cpp.o -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/FastaToDeBruijn.cpp -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/Fasta_entry.cpp +[ 35%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/Fasta_reader.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/sequenceUtil.cpp +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/Fasta_reader.cpp -[ 35%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/string_util.cpp.o -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/Fasta_entry.cpp -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/sequenceUtil.cpp -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/string_util.cpp -[ 39%] Building CXX object CMakeFiles/inchworm.dir/src/sequenceUtil.cpp.o -[ 42%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_reader.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/argProcessor.cpp +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/IRKE.cpp /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/Fasta_reader.cpp -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/sequenceUtil.cpp +[ 39%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_entry.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/Fasta_entry.cpp +[ 42%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/Fasta_entry.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/Fasta_entry.cpp In file included from /usr/include/c++/14/ext/hash_map:60, from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/KmerCounter.hpp:53, from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/IRKE.hpp:7, - from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/IRKE_run.cpp:11: + from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/IRKE.cpp:21: /usr/include/c++/14/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 \ | ^~~~~~~ @@ -2171,80 +2207,80 @@ /usr/include/c++/14/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/FastaToDeBruijn.dir/src/stacktrace.cpp.o -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/stacktrace.cpp -[ 50%] Building CXX object CMakeFiles/inchworm.dir/src/IRKE.cpp.o -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/IRKE.cpp -[ 53%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/DeBruijnGraph.cpp.o -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/DeBruijnGraph.cpp In file included from /usr/include/c++/14/ext/hash_map:60, from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/KmerCounter.hpp:53, from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/IRKE.hpp:7, - from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/IRKE.cpp:21: + from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/IRKE_run.cpp:11: /usr/include/c++/14/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/FastaToDeBruijn.cpp: In function 'void createGraphPerRecord(std::vector >, int, bool, ArgProcessor)': -/build/reproducible-path/trinityrnaseq-2.15.2+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) - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +[ 46%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/sequenceUtil.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/sequenceUtil.cpp +[ 50%] Building CXX object CMakeFiles/inchworm.dir/src/KmerCounter.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/KmerCounter.cpp /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp: In function 'void populate_kmer_counter_from_reads(KmerCounter&, std::string&)': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp:231:18: warning: unused variable 'kmer_length' [-Wunused-variable] 231 | unsigned int kmer_length = kcounter.get_kmer_length(); | ^~~~~~~~~~~ -[ 57%] Building CXX object CMakeFiles/inchworm.dir/src/KmerCounter.cpp.o -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/KmerCounter.cpp -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/DeBruijnGraph.cpp: In member function 'std::string DeBruijnKmer::get_annotations_string()': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/DeBruijnGraph.cpp:66:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 66 | for (int i=0; i < _annotations.size(); i++) { - | ~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/DeBruijnGraph.cpp: In member function 'std::string DeBruijnGraph::toDOT(bool)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/DeBruijnGraph.cpp:445:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 445 | for (int i=0; i < prev_kmers.size(); i++) { - | ~~^~~~~~~~~~~~~~~~~~~ -[ 60%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_entry.cpp.o -/build/reproducible-path/trinityrnaseq-2.15.2+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++) { - | ~~^~~~~~~~~~~~~~~~~~~ -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/Fasta_entry.cpp -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/DeBruijnGraph.cpp: In member function 'std::string DeBruijnGraph::toChrysalisFormat(int, bool)': -/build/reproducible-path/trinityrnaseq-2.15.2+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++) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~ +[ 53%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/sequenceUtil.cpp In file included from /usr/include/c++/14/ext/hash_map:60, from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/KmerCounter.hpp:53, from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/KmerCounter.cpp:1: /usr/include/c++/14/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 \ | ^~~~~~~ -[ 64%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/sequenceUtil.cpp.o -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/sequenceUtil.cpp -[ 67%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/string_util.cpp.o -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/string_util.cpp -[ 71%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/stacktrace.cpp.o -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/stacktrace.cpp +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/FastaToDeBruijn.cpp: In function 'void createGraphPerRecord(std::vector >, int, bool, ArgProcessor)': +/build/reproducible-path/trinityrnaseq-2.15.2+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) + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +[ 57%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/string_util.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/string_util.cpp /build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp:235:26: note: 'end' was declared here 235 | unsigned long start, end; | ^~~ -[ 75%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/KmerCounter.cpp.o +[ 60%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/string_util.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/string_util.cpp +[ 64%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/stacktrace.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/stacktrace.cpp +[ 67%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/stacktrace.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/stacktrace.cpp +[ 71%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/KmerCounter.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/KmerCounter.cpp +[ 75%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/DeBruijnGraph.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/DeBruijnGraph.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-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/string_util.cpp In file included from /usr/include/c++/14/ext/hash_map:60, from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/KmerCounter.hpp:53, from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/KmerCounter.cpp:1: /usr/include/c++/14/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 \ | ^~~~~~~ +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/string_util.cpp [ 82%] Building CXX object CMakeFiles/inchworm.dir/src/Fasta_reader.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+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-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+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-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Inchworm/src/argProcessor.cpp +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/DeBruijnGraph.cpp: In member function 'std::string DeBruijnKmer::get_annotations_string()': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/DeBruijnGraph.cpp:66:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 66 | for (int i=0; i < _annotations.size(); i++) { + | ~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/DeBruijnGraph.cpp: In member function 'std::string DeBruijnGraph::toDOT(bool)': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/DeBruijnGraph.cpp:445:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 445 | for (int i=0; i < prev_kmers.size(); i++) { + | ~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Inchworm/src/DeBruijnGraph.cpp: In member function 'std::string DeBruijnGraph::toChrysalisFormat(int, bool)': +/build/reproducible-path/trinityrnaseq-2.15.2+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++) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~ [ 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-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 @@ -2270,78 +2306,65 @@ make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' make -f CMakeFiles/Chrysalis.dir/build.make CMakeFiles/Chrysalis.dir/depend +make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' make -f CMakeFiles/GraphFromFasta.dir/build.make CMakeFiles/GraphFromFasta.dir/depend +cd /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build/CMakeFiles/Chrysalis.dir/DependInfo.cmake "--color=" make -f CMakeFiles/QuantifyGraph.dir/build.make CMakeFiles/QuantifyGraph.dir/depend -make -f CMakeFiles/ReadsToTranscripts.dir/build.make CMakeFiles/ReadsToTranscripts.dir/depend -make -f CMakeFiles/BubbleUpClustering.dir/build.make CMakeFiles/BubbleUpClustering.dir/depend make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' cd /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build/CMakeFiles/GraphFromFasta.dir/DependInfo.cmake "--color=" -make -f CMakeFiles/CreateIwormFastaBundle.dir/build.make CMakeFiles/CreateIwormFastaBundle.dir/depend make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' +make -f CMakeFiles/ReadsToTranscripts.dir/build.make CMakeFiles/ReadsToTranscripts.dir/depend cd /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build/CMakeFiles/QuantifyGraph.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' -cd /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build/CMakeFiles/Chrysalis.dir/DependInfo.cmake "--color=" +make -f CMakeFiles/BubbleUpClustering.dir/build.make CMakeFiles/BubbleUpClustering.dir/depend +cd /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build/CMakeFiles/ReadsToTranscripts.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' +make -f CMakeFiles/CreateIwormFastaBundle.dir/build.make CMakeFiles/CreateIwormFastaBundle.dir/depend cd /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build/CMakeFiles/BubbleUpClustering.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' -cd /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis 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'/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' make -f CMakeFiles/Chrysalis.dir/build.make CMakeFiles/Chrysalis.dir/build make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' +cd /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build/CMakeFiles/CreateIwormFastaBundle.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' -make -f CMakeFiles/QuantifyGraph.dir/build.make 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-I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/Chrysalis.cc +[ 15%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/analysis/AACodons.cc.o [ 15%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/AACodons.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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CMakeFiles/CreateIwormFastaBundle.dir/analysis/AACodons.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/AACodons.cc -In file included from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc:9: -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberExact::BasesToNumber(const DNAVector&, int) const': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:52:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 52 | if (v == -1 || v == 4) - | ~~^~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberProtein::BasesToNumber(const DNAVector&, int) const': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:93:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 93 | if (v == -1) - | ~~^~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberDoubleComb::BasesToNumber(const DNAVector&, int) const': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:126:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 126 | if (v == -1 || v == 4) - | ~~^~~~~ +[ 17%] Building CXX object CMakeFiles/BubbleUpClustering.dir/aligns/KmerAlignCore.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/AACodons.cc +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/DNAVector.cc +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc In file included from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:6: /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberExact::BasesToNumber(const DNAVector&, int) const': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:52:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] @@ -2355,10 +2378,6 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:126:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] 126 | if (v == -1 || v == 4) | ~~^~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/AACodons.cc: In static member function 'static const std::string& AACodons::GetBases(char, int)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/AACodons.cc:152:16: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 152 | if (aa < 0) { - | ~~~^~~ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function 'void KmerAlignCore::AddData(const vecDNAVector&, const vecNumVector&, int)': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:79:49: warning: unused variable 't' [-Wunused-variable] 79 | KmerAlignCoreRecordStoreTable & t = m_table; // not used? @@ -2366,6 +2385,10 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:49:9: warning: unused variable 'i' [-Wunused-variable] 49 | int i, j, k; | ^ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/AACodons.cc: In static member function 'static const std::string& AACodons::GetBases(char, int)': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/AACodons.cc:152:16: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 152 | if (aa < 0) { + | ~~~^~~ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function 'void KmerAlignCore::AddData(const DNAVector&, int, int, bool)': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:128:9: warning: unused variable 'i' [-Wunused-variable] 128 | int i, j, k; @@ -2387,29 +2410,10 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:159:12: warning: unused variable 'j' [-Wunused-variable] 159 | int i, j; | ^ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/AACodons.cc: In static member function 'static const std::string& AACodons::GetBases(char, int)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/AACodons.cc:152:16: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 152 | if (aa < 0) { - | ~~~^~~ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function 'void KmerAlignCore::MergeSortFilter(svec&, const svec&, const svec&)': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:291:9: warning: unused variable 'i' [-Wunused-variable] 291 | int i; | ^ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc: In member function 'void KmerSequence::Setup()': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc:177:19: warning: unused variable 'i' [-Wunused-variable] - 177 | long long i; - | ^ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc: In member function 'void KmerSearch::Extend(long long int, DNAVector&, const svec&, DNAVector&)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc:547:16: warning: unused variable 'plusminus' [-Wunused-variable] - 547 | static int plusminus = 0; - | ^~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc: In function 'int TranscriptomeGraph(vecDNAVector&, FILE*, int, bool)': -/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc:647:10: warning: unused variable 'bAppend' [-Wunused-variable] - 647 | bool bAppend = true; - | ^~~~~~~ In file included from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:6: /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberExact::BasesToNumber(const DNAVector&, int) const': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:52:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] @@ -2455,31 +2459,10 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:291:9: warning: unused variable 'i' [-Wunused-variable] 291 | int i; | ^ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/Chrysalis.cc: In function 'int main(int, char**)': -/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/Chrysalis.cc:570:16: warning: unused variable 'pOut' [-Wunused-variable] - 570 | FILE * pOut = NULL; - | ^~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/Chrysalis.cc:342:10: warning: unused variable 'bSkip' [-Wunused-variable] - 342 | bool bSkip = P.GetBoolValueFor(skipCmmd); - | ^~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/Chrysalis.cc:347:9: warning: unused variable 'pairDist' [-Wunused-variable] - 347 | int pairDist = P.GetIntValueFor(distCmmd); - | ^~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/Chrysalis.cc:359:10: warning: unused variable 'bButt' [-Wunused-variable] - 359 | bool bButt = P.GetBoolValueFor(buttCmmd); - | ^~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/Chrysalis.cc:372:10: warning: unused variable 'DEBUG' [-Wunused-variable] - 372 | bool DEBUG = P.GetBoolValueFor(debugCmmd); - | ^~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/AACodons.cc: In static member function 'static const std::string& AACodons::GetBases(char, int)': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/AACodons.cc:152:16: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 152 | if (aa < 0) { + | ~~~^~~ In file included from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:6: /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberExact::BasesToNumber(const DNAVector&, int) const': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:52:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] @@ -2493,6 +2476,10 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:126:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] 126 | if (v == -1 || v == 4) | ~~^~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/AACodons.cc: In static member function 'static const std::string& AACodons::GetBases(char, int)': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/AACodons.cc:152:16: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 152 | if (aa < 0) { + | ~~~^~~ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function 'void KmerAlignCore::AddData(const vecDNAVector&, const vecNumVector&, int)': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:79:49: warning: unused variable 't' [-Wunused-variable] 79 | KmerAlignCoreRecordStoreTable & t = m_table; // not used? @@ -2521,21 +2508,35 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:159:12: warning: unused variable 'j' [-Wunused-variable] 159 | int i, j; | ^ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/AACodons.cc: In static member function 'static const std::string& AACodons::GetBases(char, int)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/AACodons.cc:152:16: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 152 | if (aa < 0) { - | ~~~^~~ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function 'void KmerAlignCore::MergeSortFilter(svec&, const svec&, const svec&)': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:291:9: warning: unused variable 'i' [-Wunused-variable] 291 | int i; | ^ -/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/AACodons.cc: In static member function 'static const std::string& AACodons::GetBases(char, int)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/AACodons.cc:152:16: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 152 | if (aa < 0) { - | ~~~^~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/Chrysalis.cc: In function 'int main(int, char**)': +/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/Chrysalis.cc:570:16: warning: unused variable 'pOut' [-Wunused-variable] + 570 | FILE * pOut = NULL; + | ^~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/Chrysalis.cc:342:10: warning: unused variable 'bSkip' [-Wunused-variable] + 342 | bool bSkip = P.GetBoolValueFor(skipCmmd); + | ^~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/Chrysalis.cc:347:9: warning: unused variable 'pairDist' [-Wunused-variable] + 347 | int pairDist = P.GetIntValueFor(distCmmd); + | ^~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/Chrysalis.cc:359:10: warning: unused variable 'bButt' [-Wunused-variable] + 359 | bool bButt = P.GetBoolValueFor(buttCmmd); + | ^~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/Chrysalis.cc:372:10: warning: unused variable 'DEBUG' [-Wunused-variable] + 372 | bool DEBUG = P.GetBoolValueFor(debugCmmd); + | ^~~~~ In file included from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:6: /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberExact::BasesToNumber(const DNAVector&, int) const': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:52:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] @@ -2577,28 +2578,57 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:159:12: warning: unused variable 'j' [-Wunused-variable] 159 | int i, j; | ^ +In file included from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc:9: +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberExact::BasesToNumber(const DNAVector&, int) const': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:52:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 52 | if (v == -1 || v == 4) + | ~~^~~~~ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function 'void KmerAlignCore::MergeSortFilter(svec&, const svec&, const svec&)': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:291:9: warning: unused variable 'i' [-Wunused-variable] 291 | int i; | ^ -[ 18%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/AACodons.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/AACodons.cc -[ 20%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/AACodons.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/AACodons.cc +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberProtein::BasesToNumber(const DNAVector&, int) const': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:93:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 93 | if (v == -1) + | ~~^~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberDoubleComb::BasesToNumber(const DNAVector&, int) const': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:126:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 126 | if (v == -1 || v == 4) + | ~~^~~~~ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/AACodons.cc: In static member function 'static const std::string& AACodons::GetBases(char, int)': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/AACodons.cc:152:16: warning: comparison is always false due to limited range of data type [-Wtype-limits] 152 | if (aa < 0) { | ~~~^~~ -[ 21%] Building CXX object CMakeFiles/Chrysalis.dir/base/ErrorHandling.cc.o /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/AACodons.cc: In static member function 'static const std::string& AACodons::GetBases(char, int)': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/AACodons.cc:152:16: warning: comparison is always false due to limited range of data type [-Wtype-limits] 152 | if (aa < 0) { | ~~~^~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc: In member function 'void KmerSequence::Setup()': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc:177:19: warning: unused variable 'i' [-Wunused-variable] + 177 | long long i; + | ^ +/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc: In member function 'void KmerSearch::Extend(long long int, DNAVector&, const svec&, DNAVector&)': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc:547:16: warning: unused variable 'plusminus' [-Wunused-variable] + 547 | static int plusminus = 0; + | ^~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc: In function 'int TranscriptomeGraph(vecDNAVector&, FILE*, int, bool)': +/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc:647:10: warning: unused variable 'bAppend' [-Wunused-variable] + 647 | bool bAppend = true; + | ^~~~~~~ +[ 18%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/DNAVector.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/DNAVector.cc +[ 20%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/AACodons.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/AACodons.cc +[ 21%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/DNAVector.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/DNAVector.cc +[ 22%] Building CXX object CMakeFiles/Chrysalis.dir/base/ErrorHandling.cc.o /usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc -[ 22%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/KmerTable.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/KmerTable.cc -[ 24%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/NonRedKmerTable.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc: In function 'void print_trace(FILE*, const char*, int)': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc:7:24: warning: unused parameter 'out' [-Wunused-parameter] 7 | void print_trace(FILE *out, const char *file, int line) @@ -2609,51 +2639,46 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc:7:51: warning: unused parameter 'line' [-Wunused-parameter] 7 | void print_trace(FILE *out, const char *file, int line) | ~~~~^~~~ -[ 25%] Building CXX object CMakeFiles/Chrysalis.dir/base/FileParser.cc.o +[ 24%] Building CXX object CMakeFiles/Chrysalis.dir/base/FileParser.cc.o /usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/FileParser.cc -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::SetUp(const vecDNAVector&, bool)': -/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+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-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::AddData(const vecDNAVector&)': -/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::AddData(vecDNAVectorStream&)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:125:9: warning: unused variable 'i' [-Wunused-variable] - 125 | int i, j; - | ^ -[ 27%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/analysis/CreateIwormFastaBundle.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc -In file included from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/KmerTable.cc:1: -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberExact::BasesToNumber(const DNAVector&, int) const': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:52:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 52 | if (v == -1 || v == 4) - | ~~^~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberProtein::BasesToNumber(const DNAVector&, int) const': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:93:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 93 | if (v == -1) - | ~~^~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberDoubleComb::BasesToNumber(const DNAVector&, int) const': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:126:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 126 | if (v == -1 || v == 4) - | ~~^~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/KmerTable.cc: In member function 'long long int KmerSequence::BasesToNumber(const DNAVector&, int)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/KmerTable.cc:27:13: warning: unused variable 'i' [-Wunused-variable] - 27 | long long i; - | ^ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/AACodons.cc: In static member function 'static const std::string& AACodons::GetBases(char, int)': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/AACodons.cc:152:16: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 152 | if (aa < 0) { + | ~~~^~~ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/FileParser.cc: In member function 'bool StringParser::IsString(int)': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter 'index' [-Wunused-parameter] 50 | bool StringParser::IsString(int index) | ~~~~^~~~~ -[ 28%] Building CXX object CMakeFiles/Chrysalis.dir/base/StringUtil.cc.o +[ 25%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/analysis/CreateIwormFastaBundle.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc +[ 27%] Building CXX object CMakeFiles/Chrysalis.dir/base/StringUtil.cc.o /usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/StringUtil.cc +[ 28%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/DeBruijnGraph.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/DeBruijnGraph.cc +[ 30%] Building CXX object CMakeFiles/Chrysalis.dir/util/mutil.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/util/mutil.cc +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'void DeBruijnKmer::add_next_kmer(kmer_int_type_t, unsigned int)': +/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'std::vector DeBruijnGraph::deconvolute_DS_mirror_graph()': +/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'std::vector > DeBruijnGraph::get_candidate_weldmers(kmer_int_type_t, int)': +/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+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-2.15.2+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-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/DeBruijnGraph.cc:527:41: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 527 | if (kmer_extension_chars.size() == flank_extension_length) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc: In function 'int main(int, char**)': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc:181:17: warning: unused variable 'num_iworm_contigs' [-Wunused-variable] 181 | int num_iworm_contigs = parser.AsInt(2); @@ -2664,14 +2689,6 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc:166:12: warning: unused variable 'pOut' [-Wunused-variable] 166 | FILE * pOut = NULL; | ^~~~ -[ 30%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/DNAVector.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/DNAVector.cc -[ 31%] Building CXX object CMakeFiles/Chrysalis.dir/util/mutil.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/util/mutil.cc -[ 32%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/NonRedKmerTable.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc -[ 34%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/QuantifyGraph.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/QuantifyGraph.cc /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': /build/reproducible-path/trinityrnaseq-2.15.2+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) { @@ -2716,10 +2733,6 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:1688:16: warning: unused variable 'p' [-Wunused-variable] 1688 | const char * p = (const char*)string; | ^ -[ 35%] Building CXX object CMakeFiles/QuantifyGraph.dir/base/ErrorHandling.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc -[ 37%] Building CXX object CMakeFiles/QuantifyGraph.dir/base/FileParser.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/FileParser.cc /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': /build/reproducible-path/trinityrnaseq-2.15.2+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) { @@ -2735,6 +2748,31 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:311:8: note: 'szText' declared here 311 | char szText[2048 * 10]; | ^~~~~~ +[ 31%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/KmerTable.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/KmerTable.cc +[ 32%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/DNAVector.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/DNAVector.cc +[ 34%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/NonRedKmerTable.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc +[ 35%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/ReadsToTranscripts.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/ReadsToTranscripts.cc +In file included from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/KmerTable.cc:1: +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberExact::BasesToNumber(const DNAVector&, int) const': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:52:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 52 | if (v == -1 || v == 4) + | ~~^~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberProtein::BasesToNumber(const DNAVector&, int) const': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:93:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 93 | if (v == -1) + | ~~^~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberDoubleComb::BasesToNumber(const DNAVector&, int) const': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:126:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 126 | if (v == -1 || v == 4) + | ~~^~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/KmerTable.cc: In member function 'long long int KmerSequence::BasesToNumber(const DNAVector&, int)': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/KmerTable.cc:27:13: warning: unused variable 'i' [-Wunused-variable] + 27 | long long i; + | ^ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::SetUp(const vecDNAVector&, bool)': /build/reproducible-path/trinityrnaseq-2.15.2+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++) { @@ -2753,54 +2791,10 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:125:9: warning: unused variable 'i' [-Wunused-variable] 125 | int i, j; | ^ -/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/QuantifyGraph.cc: In function 'int main(int, char**)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/QuantifyGraph.cc:372:29: warning: unused variable 'prevNode' [-Wunused-variable] - 372 | int prevNode = parser.AsInt(1); - | ^~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc: In function 'void print_trace(FILE*, const char*, int)': -/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/QuantifyGraph.cc:409:13: warning: unused variable 'node' [-Wunused-variable] - 409 | int node = parser.AsInt(0); - | ^~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/QuantifyGraph.cc:412:30: warning: unused variable 'p2' [-Wunused-variable] - 412 | const char * p2 = s.c_str(); - | ^~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/QuantifyGraph.cc:337:16: warning: unused variable 'j' [-Wunused-variable] - 337 | int i, j; - | ^ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/QuantifyGraph.cc:350:16: warning: unused variable 'm' [-Wunused-variable] - 350 | size_t m = kmers.size(); - | ^ -/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc:7:51: warning: unused parameter 'line' [-Wunused-parameter] - 7 | void print_trace(FILE *out, const char *file, int line) - | ~~~~^~~~ -[ 38%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/DNAVector.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/DNAVector.cc -[ 40%] Building CXX object CMakeFiles/QuantifyGraph.dir/base/StringUtil.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/StringUtil.cc -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/FileParser.cc: In member function 'bool StringParser::IsString(int)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter 'index' [-Wunused-parameter] - 50 | bool StringParser::IsString(int index) - | ~~~~^~~~~ -[ 41%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/sequenceUtil.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.cc -[ 42%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/BubbleUpClustering.cc.o +[ 37%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/sequenceUtil.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.cc +[ 38%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/BubbleUpClustering.cc.o /usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/BubbleUpClustering.cc -[ 44%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/DNAVector.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/DNAVector.cc -[ 45%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/stacktrace.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/stacktrace.cc -[ 47%] Building CXX object CMakeFiles/QuantifyGraph.dir/util/mutil.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/util/mutil.cc /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'bool contains_non_gatc(std::string)': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.cc:33:26: warning: array subscript has type 'char' [-Wchar-subscripts] 33 | if (_base_to_int[c] > 3) @@ -2809,12 +2803,71 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.cc:264:32: warning: array subscript has type 'char' [-Wchar-subscripts] 264 | int val = _base_to_int[c]; | ^ -[ 48%] Linking CXX executable Chrysalis +[ 40%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/GraphFromFasta.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc +[ 41%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/stacktrace.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/stacktrace.cc +[ 42%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/NonRedKmerTable.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc +In file included from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/BubbleUpClustering.cc:10: +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberExact::BasesToNumber(const DNAVector&, int) const': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:52:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 52 | if (v == -1 || v == 4) + | ~~^~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberProtein::BasesToNumber(const DNAVector&, int) const': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:93:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 93 | if (v == -1) + | ~~^~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberDoubleComb::BasesToNumber(const DNAVector&, int) const': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:126:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 126 | if (v == -1 || v == 4) + | ~~^~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/BubbleUpClustering.cc: In function 'svec grow_prioritized_clusters(std::string&, std::map&)': +/build/reproducible-path/trinityrnaseq-2.15.2+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) { + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/BubbleUpClustering.cc: In function 'svec sl_cluster_pools(std::map&, std::map&)': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/BubbleUpClustering.cc:326:40: warning: implicitly-declared 'Pool& Pool::operator=(const Pool&)' is deprecated [-Wdeprecated-copy] + 326 | pool_vec[oldpool_id] = tmp; + | ^~~ +In file included from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/BubbleUpClustering.cc:19: +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/Pool.h:24:5: note: because 'Pool' has user-provided 'Pool::Pool(const Pool&)' + 24 | Pool(const Pool& p) { + | ^~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/BubbleUpClustering.cc: In function 'void populate_weld_reinforced_iworm_clusters(std::string&, std::map&)': +/build/reproducible-path/trinityrnaseq-2.15.2+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; + | ^ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/Pool.h:24:5: note: because 'Pool' has user-provided 'Pool::Pool(const Pool&)' + 24 | Pool(const Pool& p) { + | ^~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/BubbleUpClustering.cc: In function 'int main(int, char**)': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/BubbleUpClustering.cc:628:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 628 | for (size_t j = 0; j < p.size(); j++) { + | ~~^~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+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++) { + | ~~^~~~~~~~~~ +[ 44%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/analysis/DNAVector.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/DNAVector.cc +[ 45%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/base/ErrorHandling.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc +[ 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-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -[ 50%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/DeBruijnGraph.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/DeBruijnGraph.cc -In file included from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/BubbleUpClustering.cc:10: +[ 48%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/base/ErrorHandling.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc: In function 'void print_trace(FILE*, const char*, int)': +/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+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-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc:7:51: warning: unused parameter 'line' [-Wunused-parameter] + 7 | void print_trace(FILE *out, const char *file, int line) + | ~~~~^~~~ +In file included from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:10: /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberExact::BasesToNumber(const DNAVector&, int) const': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:52:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] 52 | if (v == -1 || v == 4) @@ -2827,6 +2880,115 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:126:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] 126 | if (v == -1 || v == 4) | ~~^~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::SetUp(const vecDNAVector&, bool)': +/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+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-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::AddData(const vecDNAVector&)': +/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::AddData(vecDNAVectorStream&)': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:125:9: warning: unused variable 'i' [-Wunused-variable] + 125 | int i, j; + | ^ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'bool SimpleHalves(const DNAVector&)': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:272:15: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 271 | ( (! DISABLE_REPEAT_CHECK) + | ~~~~~~~~~~~~~~~~~~~~~~~~ + 272 | && + | ^~ + 273 | is_simple_repeat(left) || is_simple_repeat(right) ) + | ~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'float align_get_per_id(const DNAVector&, const DNAVector&, int, int, int)': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:351:94: warning: unused parameter 'k' [-Wunused-parameter] + 351 | float align_get_per_id(const DNAVector & a, const DNAVector & b, int startA, int startB, int k) + | ~~~~^ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In member function 'bool Welder::Weldable(const DNAVector&, int, const DNAVector&, int, int, std::string&, unsigned int&)': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:523:13: warning: unused variable 'i' [-Wunused-variable] + 523 | int i; + | ^ +[ 50%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/base/FileParser.cc.o +make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/FileParser.cc +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'void report_iworm_graph(std::map&, std::map&, std::map&)': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:713:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 713 | for (int j = 0; j < adjacent_nodes.size(); j++) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +[ 50%] Built target Chrysalis +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'svec sl_cluster_pools(std::map&, std::map&)': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:847:40: warning: implicitly-declared 'Pool& Pool::operator=(const Pool&)' is deprecated [-Wdeprecated-copy] + 847 | pool_vec[oldpool_id] = tmp; + | ^~~ +In file included from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:19: +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/Pool.h:24:5: note: because 'Pool' has user-provided 'Pool::Pool(const Pool&)' + 24 | Pool(const Pool& p) { + | ^~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'void add_scaffolds_to_clusters(std::map&, std::string, vecDNAVector&, int, float)': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:961:33: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 961 | if (pair_link_count >= minCov) { + | ~~~~~~~~~~~~~~~~^~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'void add_iworm_link(std::map&, int, int)': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:1006:55: warning: implicitly-declared 'Pool& Pool::operator=(const Pool&)' is deprecated [-Wdeprecated-copy] + 1006 | weld_reinforced_iworm_clusters[iworm_index] = p; + | ^ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/Pool.h:24:5: note: because 'Pool' has user-provided 'Pool::Pool(const Pool&)' + 24 | Pool(const Pool& p) { + | ^~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'int main(int, char**)': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:1310:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 1310 | for (i=0; i grow_prioritized_clusters(std::string&, std::map&)': -/build/reproducible-path/trinityrnaseq-2.15.2+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) { - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/BubbleUpClustering.cc: In function 'svec sl_cluster_pools(std::map&, std::map&)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/BubbleUpClustering.cc:326:40: warning: implicitly-declared 'Pool& Pool::operator=(const Pool&)' is deprecated [-Wdeprecated-copy] - 326 | pool_vec[oldpool_id] = tmp; - | ^~~ -In file included from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/BubbleUpClustering.cc:19: -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/Pool.h:24:5: note: because 'Pool' has user-provided 'Pool::Pool(const Pool&)' - 24 | Pool(const Pool& p) { - | ^~~~ -[ 51%] Built target Chrysalis -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/BubbleUpClustering.cc: In function 'void populate_weld_reinforced_iworm_clusters(std::string&, std::map&)': -/build/reproducible-path/trinityrnaseq-2.15.2+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; - | ^ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/Pool.h:24:5: note: because 'Pool' has user-provided 'Pool::Pool(const Pool&)' - 24 | Pool(const Pool& p) { - | ^~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/BubbleUpClustering.cc: In function 'int main(int, char**)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/BubbleUpClustering.cc:628:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 628 | for (size_t j = 0; j < p.size(); j++) { - | ~~^~~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+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++) { - | ~~^~~~~~~~~~ -[ 52%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/stacktrace.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/stacktrace.cc -[ 54%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/sequenceUtil.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.cc -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'void DeBruijnKmer::add_next_kmer(kmer_int_type_t, unsigned int)': -/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'std::vector DeBruijnGraph::deconvolute_DS_mirror_graph()': -/build/reproducible-path/trinityrnaseq-2.15.2+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; - | ^~~ -[ 55%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/base/ErrorHandling.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'std::vector > DeBruijnGraph::get_candidate_weldmers(kmer_int_type_t, int)': -/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+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-2.15.2+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-2.15.2+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-2.15.2+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) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +[ 64%] Building CXX object CMakeFiles/QuantifyGraph.dir/base/FileParser.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/FileParser.cc +In file included from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/KmerTable.cc:1: +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberExact::BasesToNumber(const DNAVector&, int) const': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:52:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 52 | if (v == -1 || v == 4) + | ~~^~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberProtein::BasesToNumber(const DNAVector&, int) const': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:93:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 93 | if (v == -1) + | ~~^~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberDoubleComb::BasesToNumber(const DNAVector&, int) const': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:126:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 126 | if (v == -1 || v == 4) + | ~~^~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/KmerTable.cc: In member function 'long long int KmerSequence::BasesToNumber(const DNAVector&, int)': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/KmerTable.cc:27:13: warning: unused variable 'i' [-Wunused-variable] + 27 | long long i; + | ^ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': /build/reproducible-path/trinityrnaseq-2.15.2+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) { @@ -2944,8 +3071,6 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:311:8: note: 'szText' declared here 311 | char szText[2048 * 10]; | ^~~~~~ -[ 57%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/base/FileParser.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/FileParser.cc /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc: In function 'void print_trace(FILE*, const char*, int)': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc:7:24: warning: unused parameter 'out' [-Wunused-parameter] 7 | void print_trace(FILE *out, const char *file, int line) @@ -2956,28 +3081,6 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc:7:51: warning: unused parameter 'line' [-Wunused-parameter] 7 | void print_trace(FILE *out, const char *file, int line) | ~~~~^~~~ -[ 58%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/base/StringUtil.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/StringUtil.cc -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/FileParser.cc: In member function 'bool StringParser::IsString(int)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter 'index' [-Wunused-parameter] - 50 | bool StringParser::IsString(int index) - | ~~~~^~~~~ -[ 60%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/analysis/DNAVector.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/DNAVector.cc -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'bool contains_non_gatc(std::string)': -/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'kmer_int_type_t kmer_to_intval(std::string)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.cc:264:32: warning: array subscript has type 'char' [-Wchar-subscripts] - 264 | int val = _base_to_int[c]; - | ^ -[ 61%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/util/mutil.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/util/mutil.cc -[ 62%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/GraphFromFasta.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc -[ 64%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/KmerTable.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/KmerTable.cc /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': /build/reproducible-path/trinityrnaseq-2.15.2+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) { @@ -3022,8 +3125,8 @@ /build/reproducible-path/trinityrnaseq-2.15.2+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/analysis/NonRedKmerTable.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc +[ 65%] Building CXX object CMakeFiles/QuantifyGraph.dir/base/StringUtil.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/StringUtil.cc /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': /build/reproducible-path/trinityrnaseq-2.15.2+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) { @@ -3039,93 +3142,10 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:311:8: note: 'szText' declared here 311 | char szText[2048 * 10]; | ^~~~~~ -[ 67%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/sequenceUtil.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.cc -In file included from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:10: -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberExact::BasesToNumber(const DNAVector&, int) const': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:52:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 52 | if (v == -1 || v == 4) - | ~~^~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberProtein::BasesToNumber(const DNAVector&, int) const': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:93:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 93 | if (v == -1) - | ~~^~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberDoubleComb::BasesToNumber(const DNAVector&, int) const': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:126:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 126 | if (v == -1 || v == 4) - | ~~^~~~~ -In file included from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/KmerTable.cc:1: -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberExact::BasesToNumber(const DNAVector&, int) const': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:52:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 52 | if (v == -1 || v == 4) - | ~~^~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberProtein::BasesToNumber(const DNAVector&, int) const': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:93:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 93 | if (v == -1) - | ~~^~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberDoubleComb::BasesToNumber(const DNAVector&, int) const': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:126:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 126 | if (v == -1 || v == 4) - | ~~^~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'bool SimpleHalves(const DNAVector&)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:272:15: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 271 | ( (! DISABLE_REPEAT_CHECK) - | ~~~~~~~~~~~~~~~~~~~~~~~~ - 272 | && - | ^~ - 273 | is_simple_repeat(left) || is_simple_repeat(right) ) - | ~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'float align_get_per_id(const DNAVector&, const DNAVector&, int, int, int)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:351:94: warning: unused parameter 'k' [-Wunused-parameter] - 351 | float align_get_per_id(const DNAVector & a, const DNAVector & b, int startA, int startB, int k) - | ~~~~^ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In member function 'bool Welder::Weldable(const DNAVector&, int, const DNAVector&, int, int, std::string&, unsigned int&)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:523:13: warning: unused variable 'i' [-Wunused-variable] - 523 | int i; - | ^ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/KmerTable.cc: In member function 'long long int KmerSequence::BasesToNumber(const DNAVector&, int)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/KmerTable.cc:27:13: warning: unused variable 'i' [-Wunused-variable] - 27 | long long i; - | ^ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'void report_iworm_graph(std::map&, std::map&, std::map&)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:713:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 713 | for (int j = 0; j < adjacent_nodes.size(); j++) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'svec sl_cluster_pools(std::map&, std::map&)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:847:40: warning: implicitly-declared 'Pool& Pool::operator=(const Pool&)' is deprecated [-Wdeprecated-copy] - 847 | pool_vec[oldpool_id] = tmp; - | ^~~ -In file included from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:19: -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/Pool.h:24:5: note: because 'Pool' has user-provided 'Pool::Pool(const Pool&)' - 24 | Pool(const Pool& p) { - | ^~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'void add_scaffolds_to_clusters(std::map&, std::string, vecDNAVector&, int, float)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:961:33: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 961 | if (pair_link_count >= minCov) { - | ~~~~~~~~~~~~~~~~^~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'void add_iworm_link(std::map&, int, int)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:1006:55: warning: implicitly-declared 'Pool& Pool::operator=(const Pool&)' is deprecated [-Wdeprecated-copy] - 1006 | weld_reinforced_iworm_clusters[iworm_index] = p; - | ^ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/Pool.h:24:5: note: because 'Pool' has user-provided 'Pool::Pool(const Pool&)' - 24 | Pool(const Pool& p) { - | ^~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'int main(int, char**)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:1310:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 1310 | for (i=0; i >&, svec&, long long int&, const DNAVector&, int, const vecDNAVector&, int)': +/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/QuantifyGraph.cc: In function 'int main(int, char**)': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/QuantifyGraph.cc:372:29: warning: unused variable 'prevNode' [-Wunused-variable] + 372 | int prevNode = parser.AsInt(1); + | ^~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/QuantifyGraph.cc:409:13: warning: unused variable 'node' [-Wunused-variable] + 409 | int node = parser.AsInt(0); + | ^~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/QuantifyGraph.cc:412:30: warning: unused variable 'p2' [-Wunused-variable] + 412 | const char * p2 = s.c_str(); + | ^~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/QuantifyGraph.cc:337:16: warning: unused variable 'j' [-Wunused-variable] + 337 | int i, j; + | ^ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/QuantifyGraph.cc:350:16: warning: unused variable 'm' [-Wunused-variable] + 350 | size_t m = kmers.size(); + | ^ +[ 67%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/sequenceUtil.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.cc +[ 68%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/stacktrace.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/stacktrace.cc +[ 70%] Building CXX object CMakeFiles/QuantifyGraph.dir/util/mutil.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/util/mutil.cc +[ 71%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/sequenceUtil.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.cc +[ 72%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/stacktrace.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/stacktrace.cc +[ 74%] Building CXX object CMakeFiles/GraphFromFasta.dir/base/ErrorHandling.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc +[ 75%] Building CXX object CMakeFiles/GraphFromFasta.dir/base/FileParser.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/FileParser.cc /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'bool contains_non_gatc(std::string)': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.cc:33:26: warning: array subscript has type 'char' [-Wchar-subscripts] 33 | if (_base_to_int[c] > 3) @@ -3152,44 +3206,6 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.cc:264:32: warning: array subscript has type 'char' [-Wchar-subscripts] 264 | int val = _base_to_int[c]; | ^ -[ 68%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/stacktrace.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/stacktrace.cc -[ 70%] Building CXX object CMakeFiles/GraphFromFasta.dir/base/ErrorHandling.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc -[ 71%] Building CXX object CMakeFiles/GraphFromFasta.dir/base/FileParser.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/FileParser.cc -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc: In function 'void print_trace(FILE*, const char*, int)': -/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+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-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc:7:51: warning: unused parameter 'line' [-Wunused-parameter] - 7 | void print_trace(FILE *out, const char *file, int line) - | ~~~~^~~~ -[ 72%] Building CXX object CMakeFiles/GraphFromFasta.dir/base/StringUtil.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/StringUtil.cc -[ 74%] Building CXX object CMakeFiles/GraphFromFasta.dir/util/mutil.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/util/mutil.cc -[ 75%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/base/ErrorHandling.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc -[ 77%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/base/FileParser.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/FileParser.cc -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/FileParser.cc: In member function 'bool StringParser::IsString(int)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter 'index' [-Wunused-parameter] - 50 | bool StringParser::IsString(int index) - | ~~~~^~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc: In function 'void print_trace(FILE*, const char*, int)': -/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+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-2.15.2+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-2.15.2+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': /build/reproducible-path/trinityrnaseq-2.15.2+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) { @@ -3234,15 +3250,18 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:1688:16: warning: unused variable 'p' [-Wunused-variable] 1688 | const char * p = (const char*)string; | ^ -[ 78%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/base/StringUtil.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/StringUtil.cc -[ 80%] 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-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/FileParser.cc: In member function 'bool StringParser::IsString(int)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter 'index' [-Wunused-parameter] - 50 | bool StringParser::IsString(int index) - | ~~~~^~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc: In function 'void print_trace(FILE*, const char*, int)': +/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+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-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc:7:51: warning: unused parameter 'line' [-Wunused-parameter] + 7 | void print_trace(FILE *out, const char *file, int line) + | ~~~~^~~~ +[ 77%] Building CXX object CMakeFiles/GraphFromFasta.dir/base/StringUtil.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/StringUtil.cc /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': /build/reproducible-path/trinityrnaseq-2.15.2+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) { @@ -3258,22 +3277,33 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:311:8: note: 'szText' declared here 311 | char szText[2048 * 10]; | ^~~~~~ -make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' -[ 80%] Built target QuantifyGraph -[ 81%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/util/mutil.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/util/mutil.cc -[ 82%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/DeBruijnGraph.cc.o +[ 78%] Building CXX object CMakeFiles/GraphFromFasta.dir/util/mutil.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/util/mutil.cc +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'bool contains_non_gatc(std::string)': +/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'kmer_int_type_t kmer_to_intval(std::string)': +/build/reproducible-path/trinityrnaseq-2.15.2+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/analysis/DNAVector.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/DNAVector.cc +[ 81%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/DeBruijnGraph.cc.o /usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/DeBruijnGraph.cc -[ 84%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/KmerTable.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/KmerTable.cc -[ 85%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/NonRedKmerTable.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc -[ 87%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/sequenceUtil.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.cc +[ 82%] 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-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/ReadsToTranscripts.dir/analysis/AACodons.cc.o CMakeFiles/ReadsToTranscripts.dir/analysis/DNAVector.cc.o CMakeFiles/ReadsToTranscripts.dir/analysis/NonRedKmerTable.cc.o CMakeFiles/ReadsToTranscripts.dir/analysis/ReadsToTranscripts.cc.o CMakeFiles/ReadsToTranscripts.dir/analysis/sequenceUtil.cc.o CMakeFiles/ReadsToTranscripts.dir/analysis/stacktrace.cc.o CMakeFiles/ReadsToTranscripts.dir/base/ErrorHandling.cc.o CMakeFiles/ReadsToTranscripts.dir/base/FileParser.cc.o CMakeFiles/ReadsToTranscripts.dir/base/StringUtil.cc.o CMakeFiles/ReadsToTranscripts.dir/util/mutil.cc.o -o ReadsToTranscripts +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/FileParser.cc: In member function 'bool StringParser::IsString(int)': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter 'index' [-Wunused-parameter] + 50 | bool StringParser::IsString(int index) + | ~~~~^~~~~ +make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': /build/reproducible-path/trinityrnaseq-2.15.2+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) { | ^~~~~~~ ~~~~~~~ +[ 82%] Built target ReadsToTranscripts /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:303:51: warning: unused parameter 'pData' [-Wunused-parameter] 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) | ~~~~~~~^~~~~ @@ -3314,9 +3344,14 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:1688:16: warning: unused variable 'p' [-Wunused-variable] 1688 | const char * p = (const char*)string; | ^ -[ 88%] 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-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +[ 84%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/KmerTable.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/KmerTable.cc +[ 85%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/NonRedKmerTable.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc +[ 87%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/sequenceUtil.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.cc +[ 88%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/stacktrace.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/stacktrace.cc /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': /build/reproducible-path/trinityrnaseq-2.15.2+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) { @@ -3332,10 +3367,33 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:311:8: note: 'szText' declared here 311 | char szText[2048 * 10]; | ^~~~~~ -[ 90%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/stacktrace.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/analysis/stacktrace.cc -[ 91%] Building CXX object CMakeFiles/BubbleUpClustering.dir/base/ErrorHandling.cc.o +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'void DeBruijnKmer::add_next_kmer(kmer_int_type_t, unsigned int)': +/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'std::vector DeBruijnGraph::deconvolute_DS_mirror_graph()': +/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'std::vector > DeBruijnGraph::get_candidate_weldmers(kmer_int_type_t, int)': +/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+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-2.15.2+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-2.15.2+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-2.15.2+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) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +[ 90%] Building CXX object CMakeFiles/BubbleUpClustering.dir/base/ErrorHandling.cc.o /usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc +[ 91%] 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-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 In file included from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/KmerTable.cc:1: /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberExact::BasesToNumber(const DNAVector&, int) const': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:52:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] @@ -3349,10 +3407,6 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.h:126:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] 126 | if (v == -1 || v == 4) | ~~^~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'void DeBruijnKmer::add_next_kmer(kmer_int_type_t, unsigned int)': -/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/KmerTable.cc: In member function 'long long int KmerSequence::BasesToNumber(const DNAVector&, int)': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/KmerTable.cc:27:13: warning: unused variable 'i' [-Wunused-variable] 27 | long long i; @@ -3376,37 +3430,10 @@ 125 | int i, j; | ^ make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'std::vector DeBruijnGraph::deconvolute_DS_mirror_graph()': -/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'std::vector > DeBruijnGraph::get_candidate_weldmers(kmer_int_type_t, int)': -/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+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-2.15.2+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-2.15.2+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-2.15.2+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) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 91%] Built target ReadsToTranscripts -[ 92%] Building CXX object CMakeFiles/BubbleUpClustering.dir/base/FileParser.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/FileParser.cc -[ 94%] Building CXX object CMakeFiles/BubbleUpClustering.dir/base/StringUtil.cc.o -/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/StringUtil.cc /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'bool contains_non_gatc(std::string)': /build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'kmer_int_type_t kmer_to_intval(std::string)': -/build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc: In function 'void print_trace(FILE*, const char*, int)': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc:7:24: warning: unused parameter 'out' [-Wunused-parameter] 7 | void print_trace(FILE *out, const char *file, int line) @@ -3417,12 +3444,17 @@ /build/reproducible-path/trinityrnaseq-2.15.2+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-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'kmer_int_type_t kmer_to_intval(std::string)': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.cc:264:32: warning: array subscript has type 'char' [-Wchar-subscripts] + 264 | int val = _base_to_int[c]; + | ^ +[ 91%] Built target CreateIwormFastaBundle +[ 92%] Building CXX object CMakeFiles/BubbleUpClustering.dir/base/FileParser.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/FileParser.cc +[ 94%] Building CXX object CMakeFiles/BubbleUpClustering.dir/base/StringUtil.cc.o +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/StringUtil.cc [ 95%] Building CXX object CMakeFiles/BubbleUpClustering.dir/util/mutil.cc.o /usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/util/mutil.cc -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/FileParser.cc: In member function 'bool StringParser::IsString(int)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter 'index' [-Wunused-parameter] - 50 | bool StringParser::IsString(int index) - | ~~~~^~~~~ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': /build/reproducible-path/trinityrnaseq-2.15.2+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) { @@ -3482,21 +3514,25 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:311:8: note: 'szText' declared here 311 | char szText[2048 * 10]; | ^~~~~~ -[ 97%] 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-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis/base/FileParser.cc: In member function 'bool StringParser::IsString(int)': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter 'index' [-Wunused-parameter] + 50 | bool StringParser::IsString(int index) + | ~~~~^~~~~ +[ 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-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' +[ 97%] Built target GraphFromFasta +[ 98%] 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-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis_build' -[ 97%] Built target CreateIwormFastaBundle -[ 98%] Linking CXX executable BubbleUpClustering +[ 98%] Built target QuantifyGraph +[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-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2.15.2+dfsg/Chrysalis_build' -[ 98%] Built target BubbleUpClustering -[100%] 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-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' -[100%] Built target GraphFromFasta +[100%] Built target BubbleUpClustering make[3]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' @@ -12493,13 +12529,13 @@ -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 -Nov 18, 2024 8:55:51 AM jaligner.NeedlemanWunschGotoh construct +Dec 22, 2025 5:23:55 PM jaligner.NeedlemanWunschGotoh construct INFO: Started... -Nov 18, 2024 8:55:51 AM jaligner.NeedlemanWunschGotoh construct +Dec 22, 2025 5:23:55 PM jaligner.NeedlemanWunschGotoh construct INFO: Finished. -Nov 18, 2024 8:55:51 AM jaligner.NeedlemanWunschGotoh traceback +Dec 22, 2025 5:23:55 PM jaligner.NeedlemanWunschGotoh traceback INFO: Started... -Nov 18, 2024 8:55:51 AM jaligner.NeedlemanWunschGotoh traceback +Dec 22, 2025 5:23:55 PM jaligner.NeedlemanWunschGotoh traceback INFO: Finished. A 1 GGCCACACGATGGCTTATCACGTCCACATTTCTACTGGCTACAAACAGAC 50 .|..||||||..|.| @@ -13327,8 +13363,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'trinityrnaseq' in '../trinityrnaseq_2.15.2+dfsg-1_arm64.deb'. dpkg-deb: building package 'trinityrnaseq-dbgsym' in '../trinityrnaseq-dbgsym_2.15.2+dfsg-1_arm64.deb'. +dpkg-deb: building package 'trinityrnaseq' in '../trinityrnaseq_2.15.2+dfsg-1_arm64.deb'. dpkg-deb: building package 'trinityrnaseq-examples' in '../trinityrnaseq-examples_2.15.2+dfsg-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../trinityrnaseq_2.15.2+dfsg-1_arm64.buildinfo dpkg-genchanges --build=binary -O../trinityrnaseq_2.15.2+dfsg-1_arm64.changes @@ -13337,12 +13373,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/15447/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/15447/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/2301081 and its subdirectories -I: Current time: Mon Nov 18 08:57:10 -12 2024 -I: pbuilder-time-stamp: 1731963430 +I: removing directory /srv/workspace/pbuilder/15447 and its subdirectories +I: Current time: Mon Dec 22 17:25:33 +14 2025 +I: pbuilder-time-stamp: 1766373933