Diff of the two buildlogs: -- --- b1/build.log 2024-12-20 06:48:28.106236823 +0000 +++ b2/build.log 2024-12-20 07:17:42.850207547 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jan 22 01:07:31 -12 2026 -I: pbuilder-time-stamp: 1769087251 +I: Current time: Fri Dec 20 20:48:49 +14 2024 +I: pbuilder-time-stamp: 1734677329 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/1564733/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1591290/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Dec 20 06:50 /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/1591290/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1591290/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='f664347a04584b04bac62e9e97080fc1' - 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='1564733' - PS1='# ' - PS2='> ' + INVOCATION_ID=b091328ee30241ed9c7fd8609e3bc1c4 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1591290 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.TWcziTds/pbuilderrc_2fN0 --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.TWcziTds/b1 --logfile b1/build.log trinityrnaseq_2.15.2+dfsg-1.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.TWcziTds/pbuilderrc_8HDw --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.TWcziTds/b2 --logfile b2/build.log trinityrnaseq_2.15.2+dfsg-1.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1564733/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1591290/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -456,7 +488,7 @@ Get: 310 http://deb.debian.org/debian trixie/main amd64 libhts-dev amd64 1.20+ds-2 [1701 kB] Get: 311 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 312 http://deb.debian.org/debian trixie/main amd64 libjung-free-java all 2.1.1-3 [1484 kB] -Fetched 276 MB in 7s (38.6 MB/s) +Fetched 276 MB in 22s (12.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libapparmor1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19959 files and directories currently installed.) @@ -1494,8 +1526,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Jan 22 13:08:38 UTC 2026. -Universal Time is now: Thu Jan 22 13:08:38 UTC 2026. +Local time is now: Fri Dec 20 06:55:55 UTC 2024. +Universal Time is now: Fri Dec 20 06:55:55 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.17.0-2+b1) ... @@ -1949,7 +1981,11 @@ 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/1591290/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1591290/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 @@ -1964,7 +2000,7 @@ --sourcedirectory=${target} --builddirectory=${target}_build; done for target in trinity-plugins/slclust trinity-plugins/scaffold_iworm_contigs trinity-plugins/bamsifter; do dh_auto_clean \ --sourcedirectory=${target}; done - cd trinity-plugins/slclust && make -j42 clean + cd trinity-plugins/slclust && make -j20 clean make[2]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/trinity-plugins/slclust' X=`pwd`; \ for i in src; \ @@ -1975,7 +2011,7 @@ ../bin/slclust make[3]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/trinity-plugins/slclust/src' make[2]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/trinity-plugins/slclust' - cd trinity-plugins/scaffold_iworm_contigs && make -j42 clean + cd trinity-plugins/scaffold_iworm_contigs && make -j20 clean make[2]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/trinity-plugins/scaffold_iworm_contigs' rm -f scaffold_iworm_contigs make[2]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/trinity-plugins/scaffold_iworm_contigs' @@ -2017,12 +2053,12 @@ 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 "unlink|u" for option "u" +Duplicate specification "u=s" for option "u" dh_clean debian/rules binary dh binary --with javahelper @@ -2059,8 +2095,8 @@ -- Detecting CXX compile features -- Detecting CXX compile features - done -- system: Linux --- Configuring done (0.4s) --- Generating done (0.0s) +-- Configuring done (5.4s) +-- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: @@ -2097,8 +2133,8 @@ -- Detecting CXX compile features -- Detecting CXX compile features - done -- system: Linux --- Configuring done (0.4s) --- Generating done (0.0s) +-- Configuring done (3.7s) +-- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: @@ -2119,7 +2155,7 @@ make[1]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg' for target in Inchworm Chrysalis; do dh_auto_build \ --sourcedirectory=${target} --builddirectory=${target}_build; done - cd Inchworm_build && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd Inchworm_build && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build' /usr/bin/cmake -S/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm -B/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build/CMakeFiles /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build//CMakeFiles/progress.marks @@ -2127,72 +2163,62 @@ 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/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/FastaToDeBruijn.dir/DependInfo.cmake "--color=" 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/inchworm.dir/build.make CMakeFiles/inchworm.dir/build -make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build' make -f CMakeFiles/fastaToKmerCoverageStats.dir/build.make CMakeFiles/fastaToKmerCoverageStats.dir/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]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build' +make -f CMakeFiles/inchworm.dir/build.make CMakeFiles/inchworm.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]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build' -[ 3%] Building CXX object CMakeFiles/inchworm.dir/src/Fasta_entry.cpp.o -[ 17%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/fastaToKmerCoverageStats.cpp.o -[ 17%] Building CXX object CMakeFiles/inchworm.dir/src/KmerCounter.cpp.o -[ 21%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/argProcessor.cpp.o -[ 17%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/argProcessor.cpp.o -[ 21%] Building CXX object CMakeFiles/inchworm.dir/src/string_util.cpp.o -[ 25%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/FastaToDeBruijn.cpp.o -[ 32%] Building CXX object CMakeFiles/inchworm.dir/src/Fasta_reader.cpp.o -[ 32%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/Fasta_reader.cpp.o -[ 39%] Building CXX object CMakeFiles/inchworm.dir/src/stacktrace.cpp.o -[ 39%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/inchworm.dir/src/Fasta_entry.cpp.o -MF CMakeFiles/inchworm.dir/src/Fasta_entry.cpp.o.d -o CMakeFiles/inchworm.dir/src/Fasta_entry.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.2+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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/fastaToKmerCoverageStats.dir/src/argProcessor.cpp.o -MF CMakeFiles/fastaToKmerCoverageStats.dir/src/argProcessor.cpp.o.d -o CMakeFiles/fastaToKmerCoverageStats.dir/src/argProcessor.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.2+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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/inchworm.dir/src/KmerCounter.cpp.o -MF CMakeFiles/inchworm.dir/src/KmerCounter.cpp.o.d -o CMakeFiles/inchworm.dir/src/KmerCounter.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/KmerCounter.cpp -[ 42%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/stacktrace.cpp.o -[ 46%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/Fasta_entry.cpp.o +[ 7%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_reader.cpp.o +[ 3%] Building CXX object CMakeFiles/inchworm.dir/src/IRKE_run.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_reader.cpp.o -MF CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_reader.cpp.o.d -o CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_reader.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/Fasta_reader.cpp +[ 10%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/fastaToKmerCoverageStats.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/inchworm.dir/src/IRKE_run.cpp.o -MF CMakeFiles/inchworm.dir/src/IRKE_run.cpp.o.d -o CMakeFiles/inchworm.dir/src/IRKE_run.cpp.o -c 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-o CMakeFiles/FastaToDeBruijn.dir/src/string_util.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/string_util.cpp -[ 89%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/DeBruijnGraph.cpp.o -/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o -MF CMakeFiles/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o.d -o CMakeFiles/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.2+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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp 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-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 +/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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/FastaToDeBruijn.dir/src/Fasta_reader.cpp.o -MF CMakeFiles/FastaToDeBruijn.dir/src/Fasta_reader.cpp.o.d -o CMakeFiles/FastaToDeBruijn.dir/src/Fasta_reader.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/Fasta_reader.cpp +[ 71%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/FastaToDeBruijn.dir/src/Fasta_entry.cpp.o -MF CMakeFiles/FastaToDeBruijn.dir/src/Fasta_entry.cpp.o.d -o CMakeFiles/FastaToDeBruijn.dir/src/Fasta_entry.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.2+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/KmerCounter.cpp:1: @@ -2201,21 +2227,21 @@ | ^~~~~~~ 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/fastaToKmerCoverageStats.cpp:20: + 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 \ | ^~~~~~~ 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/fastaToKmerCoverageStats.cpp:20: /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 \ | ^~~~~~~ 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: + 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: /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 \ | ^~~~~~~ @@ -2226,6 +2252,16 @@ /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 \ | ^~~~~~~ +[ 75%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o -MF CMakeFiles/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o.d -o CMakeFiles/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/sequenceUtil.cpp +[ 78%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/inchworm.dir/src/argProcessor.cpp.o -MF CMakeFiles/inchworm.dir/src/argProcessor.cpp.o.d -o CMakeFiles/inchworm.dir/src/argProcessor.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/argProcessor.cpp +[ 82%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/string_util.cpp.o +/usr/bin/g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/FastaToDeBruijn.dir/src/string_util.cpp.o -MF CMakeFiles/FastaToDeBruijn.dir/src/string_util.cpp.o.d -o CMakeFiles/FastaToDeBruijn.dir/src/string_util.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/string_util.cpp +[ 85%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/FastaToDeBruijn.dir/src/DeBruijnGraph.cpp.o -MF CMakeFiles/FastaToDeBruijn.dir/src/DeBruijnGraph.cpp.o.d -o CMakeFiles/FastaToDeBruijn.dir/src/DeBruijnGraph.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm/src/DeBruijnGraph.cpp +[ 89%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/FastaToDeBruijn.dir/src/stacktrace.cpp.o -MF CMakeFiles/FastaToDeBruijn.dir/src/stacktrace.cpp.o.d -o CMakeFiles/FastaToDeBruijn.dir/src/stacktrace.cpp.o -c /build/reproducible-path/trinityrnaseq-2.15.2+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) @@ -2273,184 +2309,96 @@ make[3]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build' - cd Chrysalis_build && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd Chrysalis_build && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' /usr/bin/cmake -S/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -B/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build/CMakeFiles /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build//CMakeFiles/progress.marks 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 -f CMakeFiles/GraphFromFasta.dir/build.make CMakeFiles/GraphFromFasta.dir/depend -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' +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/CreateIwormFastaBundle.dir/build.make CMakeFiles/CreateIwormFastaBundle.dir/depend +make -f CMakeFiles/QuantifyGraph.dir/build.make CMakeFiles/QuantifyGraph.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[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' +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 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'/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/GraphFromFasta.dir/build.make CMakeFiles/GraphFromFasta.dir/build make[4]: Leaving directory '/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[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' -make -f CMakeFiles/GraphFromFasta.dir/build.make CMakeFiles/GraphFromFasta.dir/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' make -f CMakeFiles/QuantifyGraph.dir/build.make CMakeFiles/QuantifyGraph.dir/build -make -f CMakeFiles/ReadsToTranscripts.dir/build.make CMakeFiles/ReadsToTranscripts.dir/build -make[4]: Leaving directory '/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[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' -make -f CMakeFiles/CreateIwormFastaBundle.dir/build.make CMakeFiles/CreateIwormFastaBundle.dir/build make[4]: Entering directory '/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/BubbleUpClustering.dir/build.make CMakeFiles/BubbleUpClustering.dir/build make[4]: Entering directory '/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/CreateIwormFastaBundle.dir/build.make CMakeFiles/CreateIwormFastaBundle.dir/build make[4]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' +[ 1%] Building CXX object CMakeFiles/GraphFromFasta.dir/aligns/KmerAlignCore.cc.o +make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' +make -f CMakeFiles/ReadsToTranscripts.dir/build.make CMakeFiles/ReadsToTranscripts.dir/build +[ 2%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/AACodons.cc.o +/usr/bin/g++ 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CMakeFiles/CreateIwormFastaBundle.dir/base/FileParser.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/FileParser.cc -[ 60%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/CreateIwormFastaBundle.dir/base/StringUtil.cc.o -MF CMakeFiles/CreateIwormFastaBundle.dir/base/StringUtil.cc.o.d -o CMakeFiles/CreateIwormFastaBundle.dir/base/StringUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/StringUtil.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=. 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-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 -/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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/base/FileParser.cc.o -MF CMakeFiles/QuantifyGraph.dir/base/FileParser.cc.o.d -o CMakeFiles/QuantifyGraph.dir/base/FileParser.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/FileParser.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/base/StringUtil.cc.o -MF CMakeFiles/QuantifyGraph.dir/base/StringUtil.cc.o.d -o CMakeFiles/QuantifyGraph.dir/base/StringUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/StringUtil.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/analysis/ReadsToTranscripts.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/analysis/ReadsToTranscripts.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/analysis/ReadsToTranscripts.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/ReadsToTranscripts.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/analysis/sequenceUtil.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/analysis/sequenceUtil.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/analysis/sequenceUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.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) - | ~~~~^~~~ -/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/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) - | ~~~~^~~~ -[ 61%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/analysis/sequenceUtil.cc.o -MF CMakeFiles/QuantifyGraph.dir/analysis/sequenceUtil.cc.o.d -o CMakeFiles/QuantifyGraph.dir/analysis/sequenceUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.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) - | ~~~~^~~~ -[ 62%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/base/FileParser.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/base/FileParser.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/base/FileParser.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/FileParser.cc -[ 64%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/analysis/stacktrace.cc.o -MF CMakeFiles/QuantifyGraph.dir/analysis/stacktrace.cc.o.d -o CMakeFiles/QuantifyGraph.dir/analysis/stacktrace.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/stacktrace.cc +[ 22%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/Chrysalis.dir/analysis/Chrysalis.cc.o -MF CMakeFiles/Chrysalis.dir/analysis/Chrysalis.cc.o.d -o CMakeFiles/Chrysalis.dir/analysis/Chrysalis.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/Chrysalis.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/analysis/DNAVector.cc.o -MF CMakeFiles/QuantifyGraph.dir/analysis/DNAVector.cc.o.d -o CMakeFiles/QuantifyGraph.dir/analysis/DNAVector.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/DNAVector.cc +[ 24%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/Chrysalis.dir/analysis/AACodons.cc.o -MF CMakeFiles/Chrysalis.dir/analysis/AACodons.cc.o.d -o CMakeFiles/Chrysalis.dir/analysis/AACodons.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/AACodons.cc +[ 21%] Building CXX object CMakeFiles/Chrysalis.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/analysis/BubbleUpClustering.cc.o -MF CMakeFiles/BubbleUpClustering.dir/analysis/BubbleUpClustering.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/analysis/BubbleUpClustering.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/BubbleUpClustering.cc +[ 27%] Building CXX object CMakeFiles/CreateIwormFastaBundle.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/analysis/KmerTable.cc.o -MF CMakeFiles/QuantifyGraph.dir/analysis/KmerTable.cc.o.d -o CMakeFiles/QuantifyGraph.dir/analysis/KmerTable.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/KmerTable.cc +[ 28%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/CreateIwormFastaBundle.dir/analysis/AACodons.cc.o -MF CMakeFiles/CreateIwormFastaBundle.dir/analysis/AACodons.cc.o.d -o CMakeFiles/CreateIwormFastaBundle.dir/analysis/AACodons.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/Chrysalis.dir/analysis/DNAVector.cc.o -MF CMakeFiles/Chrysalis.dir/analysis/DNAVector.cc.o.d -o CMakeFiles/Chrysalis.dir/analysis/DNAVector.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/DNAVector.cc +[ 28%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/analysis/NonRedKmerTable.cc.o -MF CMakeFiles/GraphFromFasta.dir/analysis/NonRedKmerTable.cc.o.d -o CMakeFiles/GraphFromFasta.dir/analysis/NonRedKmerTable.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/NonRedKmerTable.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/analysis/AACodons.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/analysis/AACodons.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/analysis/AACodons.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/AACodons.cc +/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/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) { | ~~~~~~~~~~~~~^~~~~~~~~~~ -[ 65%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/base/StringUtil.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/base/StringUtil.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/base/StringUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/StringUtil.cc /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; @@ -2469,10 +2417,6 @@ /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/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/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? @@ -2501,14 +2445,36 @@ /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/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? - | ^ /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/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++) { + | ~^~~~~~~~~~~~~~ +/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/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? + | ^ /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; | ^ @@ -2537,32 +2503,6 @@ /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/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/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/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? @@ -2602,7 +2542,6 @@ /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; | ^ -[ 67%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/util/mutil.cc.o /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; @@ -2624,61 +2563,22 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:159:12: warning: unused variable 'j' [-Wunused-variable] 159 | int i, j; | ^ -/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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/util/mutil.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/util/mutil.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/util/mutil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc /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/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/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/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/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/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/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/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(); - | ^ +/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/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); @@ -2686,6 +2586,10 @@ /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/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/Chrysalis.cc:342:10: warning: unused variable 'bSkip' [-Wunused-variable] 342 | bool bSkip = P.GetBoolValueFor(skipCmmd); | ^~~~~ @@ -2704,108 +2608,6 @@ /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/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; - | ^~~~~~~ -/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/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/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); - | ^~~~~~~~~~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc:143:10: warning: unused variable 'DEBUG' [-Wunused-variable] - 143 | bool DEBUG = P.GetBoolValueFor(debugCmmd); - | ^~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc:166:12: warning: unused variable 'pOut' [-Wunused-variable] - 166 | FILE * pOut = NULL; - | ^~~~ -/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/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/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/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/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/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++) { - | ~~^~~~~~~~~~ -[ 68%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/Chrysalis.dir/util/mutil.cc.o -MF CMakeFiles/Chrysalis.dir/util/mutil.cc.o.d -o CMakeFiles/Chrysalis.dir/util/mutil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.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++) { @@ -2822,10 +2624,6 @@ /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/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/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; @@ -2843,10 +2641,158 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:1442:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1442 | 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) { + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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++) { + | ~~^~~~~~~~~~ +/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()); + | ~~~~~~^~~~~~~~~~~~~~~~~ +[ 30%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/analysis/sequenceUtil.cc.o -MF CMakeFiles/GraphFromFasta.dir/analysis/sequenceUtil.cc.o.d -o CMakeFiles/GraphFromFasta.dir/analysis/sequenceUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.cc +[ 31%] Building CXX object CMakeFiles/Chrysalis.dir/analysis/TranscriptomeGraph.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/Chrysalis.dir/analysis/TranscriptomeGraph.cc.o -MF CMakeFiles/Chrysalis.dir/analysis/TranscriptomeGraph.cc.o.d -o CMakeFiles/Chrysalis.dir/analysis/TranscriptomeGraph.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc +[ 32%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/analysis/NonRedKmerTable.cc.o -MF CMakeFiles/QuantifyGraph.dir/analysis/NonRedKmerTable.cc.o.d -o CMakeFiles/QuantifyGraph.dir/analysis/NonRedKmerTable.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/analysis/QuantifyGraph.cc.o -MF CMakeFiles/QuantifyGraph.dir/analysis/QuantifyGraph.cc.o.d -o CMakeFiles/QuantifyGraph.dir/analysis/QuantifyGraph.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/QuantifyGraph.cc +[ 35%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/analysis/DNAVector.cc.o -MF CMakeFiles/BubbleUpClustering.dir/analysis/DNAVector.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/analysis/DNAVector.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/DNAVector.cc +[ 37%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/analysis/stacktrace.cc.o -MF CMakeFiles/GraphFromFasta.dir/analysis/stacktrace.cc.o.d -o CMakeFiles/GraphFromFasta.dir/analysis/stacktrace.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/stacktrace.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]; + | ^ +[ 38%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/base/ErrorHandling.cc.o -MF CMakeFiles/GraphFromFasta.dir/base/ErrorHandling.cc.o.d -o CMakeFiles/GraphFromFasta.dir/base/ErrorHandling.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc +[ 40%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/base/FileParser.cc.o -MF CMakeFiles/GraphFromFasta.dir/base/FileParser.cc.o.d -o CMakeFiles/GraphFromFasta.dir/base/FileParser.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+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; + | ^ +/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]; + | ^~~~~~~ +[ 41%] Building CXX object CMakeFiles/GraphFromFasta.dir/base/StringUtil.cc.o +/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); + | ^~~~~~~~ +/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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/base/StringUtil.cc.o -MF CMakeFiles/GraphFromFasta.dir/base/StringUtil.cc.o.d -o CMakeFiles/GraphFromFasta.dir/base/StringUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/StringUtil.cc +/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/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; + | ^~~~~~~ +/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) + | ~~~~^~~~ +[ 42%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/util/mutil.cc.o -MF CMakeFiles/GraphFromFasta.dir/util/mutil.cc.o.d -o CMakeFiles/GraphFromFasta.dir/util/mutil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc +[ 44%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/Chrysalis.dir/base/ErrorHandling.cc.o -MF CMakeFiles/Chrysalis.dir/base/ErrorHandling.cc.o.d -o CMakeFiles/Chrysalis.dir/base/ErrorHandling.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/ErrorHandling.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) + | ~~~~^~~~~ +[ 45%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/analysis/DeBruijnGraph.cc.o -MF CMakeFiles/BubbleUpClustering.dir/analysis/DeBruijnGraph.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/analysis/DeBruijnGraph.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/DeBruijnGraph.cc +[ 47%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/analysis/DNAVector.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/analysis/DNAVector.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/analysis/DNAVector.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/DNAVector.cc +[ 48%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/base/ErrorHandling.cc.o -MF CMakeFiles/QuantifyGraph.dir/base/ErrorHandling.cc.o.d -o CMakeFiles/QuantifyGraph.dir/base/ErrorHandling.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+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) + | ~~~~^~~~ +[ 50%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/CreateIwormFastaBundle.dir/analysis/CreateIwormFastaBundle.cc.o -MF CMakeFiles/CreateIwormFastaBundle.dir/analysis/CreateIwormFastaBundle.cc.o.d -o CMakeFiles/CreateIwormFastaBundle.dir/analysis/CreateIwormFastaBundle.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc +[ 51%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/Chrysalis.dir/base/FileParser.cc.o -MF CMakeFiles/Chrysalis.dir/base/FileParser.cc.o.d -o CMakeFiles/Chrysalis.dir/base/FileParser.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+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:313:14: warning: passing argument 1 to 'restrict'-qualified parameter aliases with argument 4 [-Wrestrict] 313 | if (fscanf(m_pFile, szText, sizeof(szText), m_pFile) == EOF) { @@ -2857,10 +2803,6 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:303:63: warning: unused parameter 'lenInBytes' [-Wunused-parameter] 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) | ~~~~~^~~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+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/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadString(CMString&)': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:436:14: warning: passing argument 1 to 'restrict'-qualified parameter aliases with argument 4 [-Wrestrict] 436 | if (fscanf(m_pFile, pData, len, m_pFile) == EOF) { @@ -2879,22 +2821,14 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:738:53: warning: unused parameter 'bLineFeed' [-Wunused-parameter] 738 | MDLLEXPORT void MLog(const MCL_TCHAR * szText, bool bLineFeed) | ~~~~~^~~~~~~~~ -[ 70%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/DeBruijnGraph.cc.o -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:1454:13: warning: unused variable 'cutoff' [-Wunused-variable] - 1454 | int cutoff = 0; - | ^~~~~~ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc: In function 'void MLog(const MCL_TCHAR*, long int, bool)': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:761:63: warning: unused parameter 'bLineFeed' [-Wunused-parameter] 761 | MDLLEXPORT void MLog(const MCL_TCHAR * szText, long val, bool bLineFeed) | ~~~~~^~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:1268:9: warning: unused variable 'total_iworm_contigs' [-Wunused-variable] - 1268 | int total_iworm_contigs = dna.size(); - | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc: In function 'void MLog(const MCL_TCHAR*, const MCL_TCHAR*, bool)': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:787:80: warning: unused parameter 'bLineFeed' [-Wunused-parameter] 787 | MDLLEXPORT void MLog(const MCL_TCHAR * szText, const MCL_TCHAR * szText2, bool bLineFeed) | ~~~~~^~~~~~~~~ -/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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/analysis/DeBruijnGraph.cc.o -MF CMakeFiles/BubbleUpClustering.dir/analysis/DeBruijnGraph.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/analysis/DeBruijnGraph.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/DeBruijnGraph.cc /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc: In function 'void MCLSetUTF8Encode(bool)': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:1288:39: warning: unused parameter 'b' [-Wunused-parameter] 1288 | MDLLEXPORT void MCLSetUTF8Encode(bool b) @@ -2903,16 +2837,20 @@ /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; | ^ -[ 71%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/CreateIwormFastaBundle.dir/util/mutil.cc.o -MF CMakeFiles/CreateIwormFastaBundle.dir/util/mutil.cc.o.d -o CMakeFiles/CreateIwormFastaBundle.dir/util/mutil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc -[ 72%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/util/mutil.cc.o -MF CMakeFiles/QuantifyGraph.dir/util/mutil.cc.o.d -o CMakeFiles/QuantifyGraph.dir/util/mutil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc -[ 74%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/analysis/stacktrace.cc.o -MF CMakeFiles/GraphFromFasta.dir/analysis/stacktrace.cc.o.d -o CMakeFiles/GraphFromFasta.dir/analysis/stacktrace.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/stacktrace.cc -[ 75%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/analysis/KmerTable.cc.o -MF CMakeFiles/BubbleUpClustering.dir/analysis/KmerTable.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/analysis/KmerTable.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/KmerTable.cc -[ 77%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/base/ErrorHandling.cc.o -MF CMakeFiles/GraphFromFasta.dir/base/ErrorHandling.cc.o.d -o CMakeFiles/GraphFromFasta.dir/base/ErrorHandling.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc +[ 52%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/Chrysalis.dir/base/StringUtil.cc.o -MF CMakeFiles/Chrysalis.dir/base/StringUtil.cc.o.d -o CMakeFiles/Chrysalis.dir/base/StringUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/StringUtil.cc +[ 54%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/Chrysalis.dir/util/mutil.cc.o -MF CMakeFiles/Chrysalis.dir/util/mutil.cc.o.d -o CMakeFiles/Chrysalis.dir/util/mutil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.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) + | ~~~~^~~~ /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) { @@ -2928,6 +2866,20 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:311:8: note: 'szText' declared here 311 | char szText[2048 * 10]; | ^~~~~~ +[ 55%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/CreateIwormFastaBundle.dir/analysis/DNAVector.cc.o -MF CMakeFiles/CreateIwormFastaBundle.dir/analysis/DNAVector.cc.o.d -o CMakeFiles/CreateIwormFastaBundle.dir/analysis/DNAVector.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/DNAVector.cc +[ 57%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/base/FileParser.cc.o -MF CMakeFiles/QuantifyGraph.dir/base/FileParser.cc.o.d -o CMakeFiles/QuantifyGraph.dir/base/FileParser.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/FileParser.cc +[ 58%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/base/StringUtil.cc.o -MF CMakeFiles/QuantifyGraph.dir/base/StringUtil.cc.o.d -o CMakeFiles/QuantifyGraph.dir/base/StringUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/StringUtil.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/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) { @@ -2946,6 +2898,10 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:526:53: warning: unused parameter 'pData' [-Wunused-parameter] 526 | bool CMAsciiWriteFileStream::WriteBlob(const void * pData, long lenInElements, long elSize) | ~~~~~~~~~~~~~^~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+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/util/mutil.cc:526:65: warning: unused parameter 'lenInElements' [-Wunused-parameter] 526 | bool CMAsciiWriteFileStream::WriteBlob(const void * pData, long lenInElements, long elSize) | ~~~~~^~~~~~~~~~~~~ @@ -2964,14 +2920,114 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:787:80: warning: unused parameter 'bLineFeed' [-Wunused-parameter] 787 | MDLLEXPORT void MLog(const MCL_TCHAR * szText, const MCL_TCHAR * szText2, bool bLineFeed) | ~~~~~^~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+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/util/mutil.cc: In function 'void MCLSetUTF8Encode(bool)': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:1288:39: warning: unused parameter 'b' [-Wunused-parameter] 1288 | MDLLEXPORT void MCLSetUTF8Encode(bool b) | ~~~~~^ +/build/reproducible-path/trinityrnaseq-2.15.2+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/util/mutil.cc: In function 'bool AddUTF8Sig(CMString&)': /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; | ^ +/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); + | ^~~~~~~~~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc:143:10: warning: unused variable 'DEBUG' [-Wunused-variable] + 143 | bool DEBUG = P.GetBoolValueFor(debugCmmd); + | ^~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc:166:12: warning: unused variable 'pOut' [-Wunused-variable] + 166 | FILE * pOut = NULL; + | ^~~~ +[ 60%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/analysis/sequenceUtil.cc.o -MF CMakeFiles/QuantifyGraph.dir/analysis/sequenceUtil.cc.o.d -o CMakeFiles/QuantifyGraph.dir/analysis/sequenceUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.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) { + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/features.h:510, + from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, + from /usr/include/string.h:26, + from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.h:19, + from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:9: +/usr/include/stdio.h:442:12: note: by argument 2 of type 'const char*' to 'int fscanf(FILE*, const char*, ...)' declared here + 442 | extern int __REDIRECT (fscanf, (FILE *__restrict __stream, + | ^~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:311:8: note: 'szText' declared here + 311 | char szText[2048 * 10]; + | ^~~~~~ +[ 61%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/analysis/NonRedKmerTable.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/analysis/NonRedKmerTable.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/analysis/NonRedKmerTable.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/NonRedKmerTable.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) + | ~~~~^~~~~ +[ 62%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/analysis/stacktrace.cc.o -MF CMakeFiles/QuantifyGraph.dir/analysis/stacktrace.cc.o.d -o CMakeFiles/QuantifyGraph.dir/analysis/stacktrace.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/stacktrace.cc +[ 64%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/analysis/ReadsToTranscripts.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/analysis/ReadsToTranscripts.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/analysis/ReadsToTranscripts.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/ReadsToTranscripts.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; + | ^ +/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]; + | ^ +[ 65%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/analysis/sequenceUtil.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/analysis/sequenceUtil.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/analysis/sequenceUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.cc +[ 67%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/QuantifyGraph.dir/util/mutil.cc.o -MF CMakeFiles/QuantifyGraph.dir/util/mutil.cc.o.d -o CMakeFiles/QuantifyGraph.dir/util/mutil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc +[ 68%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/base/ErrorHandling.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/base/ErrorHandling.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/base/ErrorHandling.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc +[ 70%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/analysis/stacktrace.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/analysis/stacktrace.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/analysis/stacktrace.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/stacktrace.cc +[ 71%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/analysis/KmerTable.cc.o -MF CMakeFiles/BubbleUpClustering.dir/analysis/KmerTable.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/analysis/KmerTable.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/KmerTable.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/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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/base/FileParser.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/base/FileParser.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/base/FileParser.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/FileParser.cc +[ 74%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/base/StringUtil.cc.o /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) { @@ -2982,6 +3038,7 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:303:63: warning: unused parameter 'lenInBytes' [-Wunused-parameter] 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) | ~~~~~^~~~~~~~~~ +/usr/bin/g++ -I/build/reproducible-path/trinityrnaseq-2.15.2+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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/base/StringUtil.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/base/StringUtil.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/base/StringUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/StringUtil.cc /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadString(CMString&)': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:436:14: warning: passing argument 1 to 'restrict'-qualified parameter aliases with argument 4 [-Wrestrict] 436 | if (fscanf(m_pFile, pData, len, m_pFile) == EOF) { @@ -3008,8 +3065,6 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:787:80: warning: unused parameter 'bLineFeed' [-Wunused-parameter] 787 | MDLLEXPORT void MLog(const MCL_TCHAR * szText, const MCL_TCHAR * szText2, bool bLineFeed) | ~~~~~^~~~~~~~~ -[ 78%] Building CXX object CMakeFiles/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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/analysis/NonRedKmerTable.cc.o -MF CMakeFiles/BubbleUpClustering.dir/analysis/NonRedKmerTable.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/analysis/NonRedKmerTable.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc: In function 'void MCLSetUTF8Encode(bool)': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:1288:39: warning: unused parameter 'b' [-Wunused-parameter] 1288 | MDLLEXPORT void MCLSetUTF8Encode(bool b) @@ -3018,48 +3073,12 @@ /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; | ^ -[ 80%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/analysis/sequenceUtil.cc.o -MF CMakeFiles/BubbleUpClustering.dir/analysis/sequenceUtil.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/analysis/sequenceUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.cc -[ 81%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/base/FileParser.cc.o -MF CMakeFiles/GraphFromFasta.dir/base/FileParser.cc.o.d -o CMakeFiles/GraphFromFasta.dir/base/FileParser.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/FileParser.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) { - | ~~~~~~~~~~~~~^~~~~~~~~~~ -[ 82%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/base/StringUtil.cc.o -MF CMakeFiles/GraphFromFasta.dir/base/StringUtil.cc.o.d -o CMakeFiles/GraphFromFasta.dir/base/StringUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/StringUtil.cc -/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; - | ^~~ -[ 84%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/base/ErrorHandling.cc.o -MF CMakeFiles/BubbleUpClustering.dir/base/ErrorHandling.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/base/ErrorHandling.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc -[ 85%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/analysis/stacktrace.cc.o -MF CMakeFiles/BubbleUpClustering.dir/analysis/stacktrace.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/analysis/stacktrace.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/stacktrace.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) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/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) - | ~~~~^~~~ +[ 75%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/analysis/NonRedKmerTable.cc.o -MF CMakeFiles/BubbleUpClustering.dir/analysis/NonRedKmerTable.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/analysis/NonRedKmerTable.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/NonRedKmerTable.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:313:13: warning: 'szText' may be used uninitialized [-Wmaybe-uninitialized] 313 | if (fscanf(m_pFile, szText, sizeof(szText), m_pFile) == EOF) { @@ -3075,6 +3094,31 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:311:8: note: 'szText' declared here 311 | char szText[2048 * 10]; | ^~~~~~ +[ 77%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/analysis/sequenceUtil.cc.o -MF CMakeFiles/BubbleUpClustering.dir/analysis/sequenceUtil.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/analysis/sequenceUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/sequenceUtil.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]; + | ^ +[ 78%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/ReadsToTranscripts.dir/util/mutil.cc.o -MF CMakeFiles/ReadsToTranscripts.dir/util/mutil.cc.o.d -o CMakeFiles/ReadsToTranscripts.dir/util/mutil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc +[ 80%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/analysis/stacktrace.cc.o -MF CMakeFiles/BubbleUpClustering.dir/analysis/stacktrace.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/analysis/stacktrace.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/analysis/stacktrace.cc +/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; + | ^ +[ 81%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/base/ErrorHandling.cc.o -MF CMakeFiles/BubbleUpClustering.dir/base/ErrorHandling.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/base/ErrorHandling.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/ErrorHandling.cc +[ 82%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/Chrysalis.dir/aligns/KmerAlignCore.cc.o CMakeFiles/Chrysalis.dir/analysis/AACodons.cc.o CMakeFiles/Chrysalis.dir/analysis/Chrysalis.cc.o CMakeFiles/Chrysalis.dir/analysis/DNAVector.cc.o CMakeFiles/Chrysalis.dir/analysis/TranscriptomeGraph.cc.o CMakeFiles/Chrysalis.dir/base/ErrorHandling.cc.o CMakeFiles/Chrysalis.dir/base/FileParser.cc.o CMakeFiles/Chrysalis.dir/base/StringUtil.cc.o CMakeFiles/Chrysalis.dir/util/mutil.cc.o -o Chrysalis +[ 84%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/base/FileParser.cc.o -MF CMakeFiles/BubbleUpClustering.dir/base/FileParser.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/base/FileParser.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+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:313:14: warning: passing argument 1 to 'restrict'-qualified parameter aliases with argument 4 [-Wrestrict] 313 | if (fscanf(m_pFile, szText, sizeof(szText), m_pFile) == EOF) { @@ -3115,52 +3159,18 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:1288:39: warning: unused parameter 'b' [-Wunused-parameter] 1288 | MDLLEXPORT void MCLSetUTF8Encode(bool b) | ~~~~~^ -[ 87%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/base/FileParser.cc.o -MF CMakeFiles/BubbleUpClustering.dir/base/FileParser.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/base/FileParser.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/FileParser.cc /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc: In function 'bool AddUTF8Sig(CMString&)': /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%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/base/StringUtil.cc.o -MF CMakeFiles/BubbleUpClustering.dir/base/StringUtil.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/base/StringUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/StringUtil.cc -[ 90%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/util/mutil.cc.o -MF CMakeFiles/GraphFromFasta.dir/util/mutil.cc.o.d -o CMakeFiles/GraphFromFasta.dir/util/mutil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.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) { - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/features.h:510, - from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, - from /usr/include/string.h:26, - from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.h:19, - from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:9: -/usr/include/stdio.h:442:12: note: by argument 2 of type 'const char*' to 'int fscanf(FILE*, const char*, ...)' declared here - 442 | extern int __REDIRECT (fscanf, (FILE *__restrict __stream, - | ^~~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:311:8: note: 'szText' declared here - 311 | char szText[2048 * 10]; - | ^~~~~~ -[ 91%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/util/mutil.cc.o -MF CMakeFiles/BubbleUpClustering.dir/util/mutil.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/util/mutil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc -/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) { - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/features.h:510, - from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, - from /usr/include/string.h:26, - from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.h:19, - from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:9: -/usr/include/stdio.h:442:12: note: by argument 2 of type 'const char*' to 'int fscanf(FILE*, const char*, ...)' declared here - 442 | extern int __REDIRECT (fscanf, (FILE *__restrict __stream, - | ^~~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:311:8: note: 'szText' declared here - 311 | char szText[2048 * 10]; - | ^~~~~~ +/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) @@ -3171,6 +3181,8 @@ /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) | ~~~~^~~~ +[ 85%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/base/StringUtil.cc.o -MF CMakeFiles/BubbleUpClustering.dir/base/StringUtil.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/base/StringUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/StringUtil.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++) { @@ -3181,10 +3193,6 @@ /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/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/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++) { @@ -3193,14 +3201,47 @@ /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/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]; - | ^ +make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' +[ 87%] Built target Chrysalis +[ 87%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/util/mutil.cc.o -MF CMakeFiles/BubbleUpClustering.dir/util/mutil.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/util/mutil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc +[ 88%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/base/FileParser.cc.o +[ 90%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/CreateIwormFastaBundle.dir/base/ErrorHandling.cc.o -MF CMakeFiles/CreateIwormFastaBundle.dir/base/ErrorHandling.cc.o.d -o CMakeFiles/CreateIwormFastaBundle.dir/base/ErrorHandling.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/ErrorHandling.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/CreateIwormFastaBundle.dir/base/FileParser.cc.o -MF CMakeFiles/CreateIwormFastaBundle.dir/base/FileParser.cc.o.d -o CMakeFiles/CreateIwormFastaBundle.dir/base/FileParser.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/FileParser.cc +[ 91%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/CreateIwormFastaBundle.dir/base/StringUtil.cc.o -MF CMakeFiles/CreateIwormFastaBundle.dir/base/StringUtil.cc.o.d -o CMakeFiles/CreateIwormFastaBundle.dir/base/StringUtil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/base/StringUtil.cc +[ 92%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/CreateIwormFastaBundle.dir/util/mutil.cc.o -MF CMakeFiles/CreateIwormFastaBundle.dir/util/mutil.cc.o.d -o CMakeFiles/CreateIwormFastaBundle.dir/util/mutil.cc.o -c /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.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) { + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/features.h:510, + from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, + from /usr/include/string.h:26, + from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.h:19, + from /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:9: +/usr/include/stdio.h:442:12: note: by argument 2 of type 'const char*' to 'int fscanf(FILE*, const char*, ...)' declared here + 442 | extern int __REDIRECT (fscanf, (FILE *__restrict __stream, + | ^~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:311:8: note: 'szText' declared here + 311 | char szText[2048 * 10]; + | ^~~~~~ +/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) { @@ -3233,18 +3274,6 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:761:63: warning: unused parameter 'bLineFeed' [-Wunused-parameter] 761 | MDLLEXPORT void MLog(const MCL_TCHAR * szText, long val, bool bLineFeed) | ~~~~~^~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc: In function 'void MLog(const MCL_TCHAR*, const MCL_TCHAR*, bool)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:787:80: warning: unused parameter 'bLineFeed' [-Wunused-parameter] - 787 | MDLLEXPORT void MLog(const MCL_TCHAR * szText, const MCL_TCHAR * szText2, bool bLineFeed) - | ~~~~~^~~~~~~~~ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc: In function 'void MCLSetUTF8Encode(bool)': -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:1288:39: warning: unused parameter 'b' [-Wunused-parameter] - 1288 | MDLLEXPORT void MCLSetUTF8Encode(bool b) - | ~~~~~^ -/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc: In function 'bool AddUTF8Sig(CMString&)': -/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; - | ^ /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) { @@ -3255,6 +3284,10 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:303:63: warning: unused parameter 'lenInBytes' [-Wunused-parameter] 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) | ~~~~~^~~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc: In function 'void MLog(const MCL_TCHAR*, const MCL_TCHAR*, bool)': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:787:80: warning: unused parameter 'bLineFeed' [-Wunused-parameter] + 787 | MDLLEXPORT void MLog(const MCL_TCHAR * szText, const MCL_TCHAR * szText2, bool bLineFeed) + | ~~~~~^~~~~~~~~ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadString(CMString&)': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:436:14: warning: passing argument 1 to 'restrict'-qualified parameter aliases with argument 4 [-Wrestrict] 436 | if (fscanf(m_pFile, pData, len, m_pFile) == EOF) { @@ -3269,6 +3302,10 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:526:85: warning: unused parameter 'elSize' [-Wunused-parameter] 526 | bool CMAsciiWriteFileStream::WriteBlob(const void * pData, long lenInElements, long elSize) | ~~~~~^~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc: In function 'void MCLSetUTF8Encode(bool)': +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:1288:39: warning: unused parameter 'b' [-Wunused-parameter] + 1288 | MDLLEXPORT void MCLSetUTF8Encode(bool b) + | ~~~~~^ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc: In function 'void MLog(const MCL_TCHAR*, bool)': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:738:53: warning: unused parameter 'bLineFeed' [-Wunused-parameter] 738 | MDLLEXPORT void MLog(const MCL_TCHAR * szText, bool bLineFeed) @@ -3281,6 +3318,10 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:787:80: warning: unused parameter 'bLineFeed' [-Wunused-parameter] 787 | MDLLEXPORT void MLog(const MCL_TCHAR * szText, const MCL_TCHAR * szText2, bool bLineFeed) | ~~~~~^~~~~~~~~ +/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc: In function 'bool AddUTF8Sig(CMString&)': +/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; + | ^ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc: In function 'void MCLSetUTF8Encode(bool)': /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:1288:39: warning: unused parameter 'b' [-Wunused-parameter] 1288 | MDLLEXPORT void MCLSetUTF8Encode(bool b) @@ -3289,10 +3330,12 @@ /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; | ^ -/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) - | ~~~~^~~~~ +[ 94%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/QuantifyGraph.dir/aligns/KmerAlignCore.cc.o CMakeFiles/QuantifyGraph.dir/analysis/AACodons.cc.o CMakeFiles/QuantifyGraph.dir/analysis/DNAVector.cc.o CMakeFiles/QuantifyGraph.dir/analysis/KmerTable.cc.o CMakeFiles/QuantifyGraph.dir/analysis/NonRedKmerTable.cc.o CMakeFiles/QuantifyGraph.dir/analysis/QuantifyGraph.cc.o CMakeFiles/QuantifyGraph.dir/base/ErrorHandling.cc.o CMakeFiles/QuantifyGraph.dir/base/FileParser.cc.o CMakeFiles/QuantifyGraph.dir/base/StringUtil.cc.o CMakeFiles/QuantifyGraph.dir/analysis/sequenceUtil.cc.o CMakeFiles/QuantifyGraph.dir/analysis/stacktrace.cc.o CMakeFiles/QuantifyGraph.dir/util/mutil.cc.o -o QuantifyGraph +[ 95%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/GraphFromFasta.dir/aligns/KmerAlignCore.cc.o CMakeFiles/GraphFromFasta.dir/analysis/AACodons.cc.o CMakeFiles/GraphFromFasta.dir/analysis/DNAVector.cc.o CMakeFiles/GraphFromFasta.dir/analysis/DeBruijnGraph.cc.o CMakeFiles/GraphFromFasta.dir/analysis/GraphFromFasta.cc.o CMakeFiles/GraphFromFasta.dir/analysis/KmerTable.cc.o CMakeFiles/GraphFromFasta.dir/analysis/NonRedKmerTable.cc.o CMakeFiles/GraphFromFasta.dir/analysis/sequenceUtil.cc.o CMakeFiles/GraphFromFasta.dir/analysis/stacktrace.cc.o CMakeFiles/GraphFromFasta.dir/base/ErrorHandling.cc.o CMakeFiles/GraphFromFasta.dir/base/FileParser.cc.o CMakeFiles/GraphFromFasta.dir/base/StringUtil.cc.o CMakeFiles/GraphFromFasta.dir/util/mutil.cc.o -o GraphFromFasta /build/reproducible-path/trinityrnaseq-2.15.2+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) { @@ -3308,6 +3351,13 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:311:8: note: 'szText' declared here 311 | char szText[2048 * 10]; | ^~~~~~ +/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' +make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' +[ 95%] Built target QuantifyGraph /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) { @@ -3323,42 +3373,28 @@ /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis/util/mutil.cc:311:8: note: 'szText' declared here 311 | char szText[2048 * 10]; | ^~~~~~ -[ 92%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/QuantifyGraph.dir/aligns/KmerAlignCore.cc.o CMakeFiles/QuantifyGraph.dir/analysis/AACodons.cc.o CMakeFiles/QuantifyGraph.dir/analysis/DNAVector.cc.o CMakeFiles/QuantifyGraph.dir/analysis/KmerTable.cc.o CMakeFiles/QuantifyGraph.dir/analysis/NonRedKmerTable.cc.o CMakeFiles/QuantifyGraph.dir/analysis/QuantifyGraph.cc.o CMakeFiles/QuantifyGraph.dir/base/ErrorHandling.cc.o CMakeFiles/QuantifyGraph.dir/base/FileParser.cc.o CMakeFiles/QuantifyGraph.dir/base/StringUtil.cc.o CMakeFiles/QuantifyGraph.dir/analysis/sequenceUtil.cc.o CMakeFiles/QuantifyGraph.dir/analysis/stacktrace.cc.o CMakeFiles/QuantifyGraph.dir/util/mutil.cc.o -o QuantifyGraph -[ 94%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/ReadsToTranscripts.dir/analysis/AACodons.cc.o CMakeFiles/ReadsToTranscripts.dir/analysis/DNAVector.cc.o CMakeFiles/ReadsToTranscripts.dir/analysis/NonRedKmerTable.cc.o CMakeFiles/ReadsToTranscripts.dir/analysis/ReadsToTranscripts.cc.o CMakeFiles/ReadsToTranscripts.dir/analysis/sequenceUtil.cc.o CMakeFiles/ReadsToTranscripts.dir/analysis/stacktrace.cc.o CMakeFiles/ReadsToTranscripts.dir/base/ErrorHandling.cc.o CMakeFiles/ReadsToTranscripts.dir/base/FileParser.cc.o CMakeFiles/ReadsToTranscripts.dir/base/StringUtil.cc.o CMakeFiles/ReadsToTranscripts.dir/util/mutil.cc.o -o ReadsToTranscripts -make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' -[ 94%] Built target QuantifyGraph +[ 95%] Built target GraphFromFasta +[ 97%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/BubbleUpClustering.dir/aligns/KmerAlignCore.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/AACodons.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/BubbleUpClustering.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/DNAVector.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/DeBruijnGraph.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/KmerTable.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/NonRedKmerTable.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/sequenceUtil.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/stacktrace.cc.o CMakeFiles/BubbleUpClustering.dir/base/ErrorHandling.cc.o CMakeFiles/BubbleUpClustering.dir/base/FileParser.cc.o CMakeFiles/BubbleUpClustering.dir/base/StringUtil.cc.o CMakeFiles/BubbleUpClustering.dir/util/mutil.cc.o -o BubbleUpClustering make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' -[ 94%] Built target ReadsToTranscripts -[ 95%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/Chrysalis.dir/aligns/KmerAlignCore.cc.o CMakeFiles/Chrysalis.dir/analysis/AACodons.cc.o CMakeFiles/Chrysalis.dir/analysis/Chrysalis.cc.o CMakeFiles/Chrysalis.dir/analysis/DNAVector.cc.o CMakeFiles/Chrysalis.dir/analysis/TranscriptomeGraph.cc.o CMakeFiles/Chrysalis.dir/base/ErrorHandling.cc.o CMakeFiles/Chrysalis.dir/base/FileParser.cc.o CMakeFiles/Chrysalis.dir/base/StringUtil.cc.o CMakeFiles/Chrysalis.dir/util/mutil.cc.o -o Chrysalis -[ 97%] Linking CXX executable CreateIwormFastaBundle +[ 97%] Built target BubbleUpClustering +[ 98%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/CreateIwormFastaBundle.dir/analysis/AACodons.cc.o CMakeFiles/CreateIwormFastaBundle.dir/analysis/CreateIwormFastaBundle.cc.o CMakeFiles/CreateIwormFastaBundle.dir/analysis/DNAVector.cc.o CMakeFiles/CreateIwormFastaBundle.dir/base/ErrorHandling.cc.o CMakeFiles/CreateIwormFastaBundle.dir/base/FileParser.cc.o CMakeFiles/CreateIwormFastaBundle.dir/base/StringUtil.cc.o CMakeFiles/CreateIwormFastaBundle.dir/util/mutil.cc.o -o CreateIwormFastaBundle make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' -[ 97%] Built target Chrysalis -make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' -[ 98%] Linking CXX executable BubbleUpClustering -/usr/bin/cmake -E cmake_link_script CMakeFiles/BubbleUpClustering.dir/link.txt --verbose=1 [ 98%] Built target CreateIwormFastaBundle -/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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/BubbleUpClustering.dir/aligns/KmerAlignCore.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/AACodons.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/BubbleUpClustering.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/DNAVector.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/DeBruijnGraph.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/KmerTable.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/NonRedKmerTable.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/sequenceUtil.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/stacktrace.cc.o CMakeFiles/BubbleUpClustering.dir/base/ErrorHandling.cc.o CMakeFiles/BubbleUpClustering.dir/base/FileParser.cc.o CMakeFiles/BubbleUpClustering.dir/base/StringUtil.cc.o CMakeFiles/BubbleUpClustering.dir/util/mutil.cc.o -o BubbleUpClustering -make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/GraphFromFasta.dir/aligns/KmerAlignCore.cc.o CMakeFiles/GraphFromFasta.dir/analysis/AACodons.cc.o CMakeFiles/GraphFromFasta.dir/analysis/DNAVector.cc.o CMakeFiles/GraphFromFasta.dir/analysis/DeBruijnGraph.cc.o CMakeFiles/GraphFromFasta.dir/analysis/GraphFromFasta.cc.o CMakeFiles/GraphFromFasta.dir/analysis/KmerTable.cc.o CMakeFiles/GraphFromFasta.dir/analysis/NonRedKmerTable.cc.o CMakeFiles/GraphFromFasta.dir/analysis/sequenceUtil.cc.o CMakeFiles/GraphFromFasta.dir/analysis/stacktrace.cc.o CMakeFiles/GraphFromFasta.dir/base/ErrorHandling.cc.o CMakeFiles/GraphFromFasta.dir/base/FileParser.cc.o CMakeFiles/GraphFromFasta.dir/base/StringUtil.cc.o CMakeFiles/GraphFromFasta.dir/util/mutil.cc.o -o GraphFromFasta +[100%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/ReadsToTranscripts.dir/analysis/AACodons.cc.o CMakeFiles/ReadsToTranscripts.dir/analysis/DNAVector.cc.o CMakeFiles/ReadsToTranscripts.dir/analysis/NonRedKmerTable.cc.o CMakeFiles/ReadsToTranscripts.dir/analysis/ReadsToTranscripts.cc.o CMakeFiles/ReadsToTranscripts.dir/analysis/sequenceUtil.cc.o CMakeFiles/ReadsToTranscripts.dir/analysis/stacktrace.cc.o CMakeFiles/ReadsToTranscripts.dir/base/ErrorHandling.cc.o CMakeFiles/ReadsToTranscripts.dir/base/FileParser.cc.o CMakeFiles/ReadsToTranscripts.dir/base/StringUtil.cc.o CMakeFiles/ReadsToTranscripts.dir/util/mutil.cc.o -o ReadsToTranscripts make[4]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' -[100%] Built target GraphFromFasta +[100%] Built target ReadsToTranscripts 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' for target in trinity-plugins/slclust trinity-plugins/scaffold_iworm_contigs trinity-plugins/bamsifter trinity-plugins/seqtk-trinity; do dh_auto_build \ --sourcedirectory=${target}; done - cd trinity-plugins/slclust && make -j42 "INSTALL=install --strip-program=true" + cd trinity-plugins/slclust && make -j20 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/trinity-plugins/slclust' X=`pwd`; \ for i in src; \ @@ -3373,16 +3409,16 @@ chmod 755 slclust make[3]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/trinity-plugins/slclust/src' make[2]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/trinity-plugins/slclust' - cd trinity-plugins/scaffold_iworm_contigs && make -j42 "INSTALL=install --strip-program=true" + cd trinity-plugins/scaffold_iworm_contigs && make -j20 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/trinity-plugins/scaffold_iworm_contigs' g++ -Wl,-z,relro -Wl,-z,now -I../htslib -L../htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection ScaffoldIwormContigs.cpp error_checker.cpp -lhts -o scaffold_iworm_contigs make[2]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/trinity-plugins/scaffold_iworm_contigs' - cd trinity-plugins/bamsifter && make -j42 "INSTALL=install --strip-program=true" + cd trinity-plugins/bamsifter && make -j20 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/trinity-plugins/bamsifter' g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++11 -o bamsifter sift_bam_max_cov.cpp -Wall -O2 -L./htslib/build/lib/ -I./htslib/build/include -lhts cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ make[2]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/trinity-plugins/bamsifter' - cd trinity-plugins/seqtk-trinity && make -j42 "INSTALL=install --strip-program=true" + cd trinity-plugins/seqtk-trinity && make -j20 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/trinity-plugins/seqtk-trinity' cc -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/trinityrnaseq-2.15.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wno-unused-function -Wdate-time -D_FORTIFY_SOURCE=2 seqtk.c -o seqtk-trinity -lz -lm make[2]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/trinity-plugins/seqtk-trinity' @@ -3393,39 +3429,6 @@ warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. -./Butterfly/Butterfly/src/src/AlignmentStats.java:54: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal - alignedBaseCounter.put(nameA, new Integer(0)); - ^ -./Butterfly/Butterfly/src/src/AlignmentStats.java:55: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal - alignedBaseCounter.put(nameB, new Integer(0)); - ^ -./Butterfly/Butterfly/src/src/AlignmentStats.java:126: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal - alignedBaseCounter.put(nameA, new Integer(alignedBaseCounter.get(nameA) + 1)); - ^ -./Butterfly/Butterfly/src/src/AlignmentStats.java:130: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal - alignedBaseCounter.put(nameB, new Integer (alignedBaseCounter.get(nameB) + 1)); - ^ -./Butterfly/Butterfly/src/src/ZipperAlignment.java:39: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal - as.alignedBaseCounter.put(nameA, new Integer(shorter_len)); - ^ -./Butterfly/Butterfly/src/src/ZipperAlignment.java:40: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal - as.alignedBaseCounter.put(nameB, new Integer(shorter_len)); - ^ -./Butterfly/Butterfly/src/src/ZipperAlignment.java:71: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal - as.alignedBaseCounter.put(nameA, new Integer(shorter_len)); - ^ -./Butterfly/Butterfly/src/src/ZipperAlignment.java:72: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal - as.alignedBaseCounter.put(nameB, new Integer(shorter_len)); - ^ -./Butterfly/Butterfly/src/src/IsoformExpressionLearning.java:396: warning: [removal] Double(double) in Double has been deprecated and marked for removal - Double len = new Double(0); - ^ -./Butterfly/Butterfly/src/src/IsoformExpressionLearning.java:515: warning: [removal] Double(double) in Double has been deprecated and marked for removal - Double sum = new Double(0); - ^ -./Butterfly/Butterfly/src/src/IsoformExpressionLearning.java:576: warning: [removal] Double(double) in Double has been deprecated and marked for removal - vec.set(i, new Double(0)); - ^ ./Butterfly/Butterfly/src/src/TransAssembly_allProbPaths.java:4043: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal transcripts.put(path, new Pair(new Integer(1), new Integer(1))); ^ @@ -3459,6 +3462,39 @@ ./Butterfly/Butterfly/src/src/TransAssembly_allProbPaths.java:15118: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal path_index.put(node, new Boolean(true)); ^ +./Butterfly/Butterfly/src/src/AlignmentStats.java:54: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal + alignedBaseCounter.put(nameA, new Integer(0)); + ^ +./Butterfly/Butterfly/src/src/AlignmentStats.java:55: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal + alignedBaseCounter.put(nameB, new Integer(0)); + ^ +./Butterfly/Butterfly/src/src/AlignmentStats.java:126: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal + alignedBaseCounter.put(nameA, new Integer(alignedBaseCounter.get(nameA) + 1)); + ^ +./Butterfly/Butterfly/src/src/AlignmentStats.java:130: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal + alignedBaseCounter.put(nameB, new Integer (alignedBaseCounter.get(nameB) + 1)); + ^ +./Butterfly/Butterfly/src/src/ZipperAlignment.java:39: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal + as.alignedBaseCounter.put(nameA, new Integer(shorter_len)); + ^ +./Butterfly/Butterfly/src/src/ZipperAlignment.java:40: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal + as.alignedBaseCounter.put(nameB, new Integer(shorter_len)); + ^ +./Butterfly/Butterfly/src/src/ZipperAlignment.java:71: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal + as.alignedBaseCounter.put(nameA, new Integer(shorter_len)); + ^ +./Butterfly/Butterfly/src/src/ZipperAlignment.java:72: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal + as.alignedBaseCounter.put(nameB, new Integer(shorter_len)); + ^ +./Butterfly/Butterfly/src/src/IsoformExpressionLearning.java:396: warning: [removal] Double(double) in Double has been deprecated and marked for removal + Double len = new Double(0); + ^ +./Butterfly/Butterfly/src/src/IsoformExpressionLearning.java:515: warning: [removal] Double(double) in Double has been deprecated and marked for removal + Double sum = new Double(0); + ^ +./Butterfly/Butterfly/src/src/IsoformExpressionLearning.java:576: warning: [removal] Double(double) in Double has been deprecated and marked for removal + vec.set(i, new Double(0)); + ^ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 26 warnings @@ -12349,13 +12385,13 @@ -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 -Jan 22, 2026 1:09:29 AM jaligner.NeedlemanWunschGotoh construct +Dec 20, 2024 9:05:13 PM jaligner.NeedlemanWunschGotoh construct INFO: Started... -Jan 22, 2026 1:09:29 AM jaligner.NeedlemanWunschGotoh construct +Dec 20, 2024 9:05:14 PM jaligner.NeedlemanWunschGotoh construct INFO: Finished. -Jan 22, 2026 1:09:29 AM jaligner.NeedlemanWunschGotoh traceback +Dec 20, 2024 9:05:14 PM jaligner.NeedlemanWunschGotoh traceback INFO: Started... -Jan 22, 2026 1:09:29 AM jaligner.NeedlemanWunschGotoh traceback +Dec 20, 2024 9:05:14 PM jaligner.NeedlemanWunschGotoh traceback INFO: Finished. A 1 GGCCACACGATGGCTTATCACGTCCACATTTCTACTGGCTACAAACAGAC 50 .|..||||||..|.| @@ -13090,7 +13126,7 @@ make[1]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg' for target in Inchworm Chrysalis; do dh_auto_install \ --sourcedirectory=${target} --builddirectory=${target}_build; done - cd Inchworm_build && make -j42 install DESTDIR=/build/reproducible-path/trinityrnaseq-2.15.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd Inchworm_build && make -j20 install DESTDIR=/build/reproducible-path/trinityrnaseq-2.15.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build' /usr/bin/cmake -S/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm -B/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -13104,7 +13140,7 @@ -- Installing: /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/debian/tmp/usr/bin/FastaToDeBruijn -- Installing: /build/reproducible-path/trinityrnaseq-2.15.2+dfsg/debian/tmp/usr/bin/fastaToKmerCoverageStats make[2]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Inchworm_build' - cd Chrysalis_build && make -j42 install DESTDIR=/build/reproducible-path/trinityrnaseq-2.15.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd Chrysalis_build && make -j20 install DESTDIR=/build/reproducible-path/trinityrnaseq-2.15.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' /usr/bin/cmake -S/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis -B/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -13123,7 +13159,7 @@ make[2]: Leaving directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/Chrysalis_build' for target in trinity-plugins/slclust trinity-plugins/scaffold_iworm_contigs trinity-plugins/bamsifter trinity-plugins/seqtk-trinity; do dh_auto_install \ --sourcedirectory=${target}; done - cd trinity-plugins/slclust && make -j42 install DESTDIR=/build/reproducible-path/trinityrnaseq-2.15.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd trinity-plugins/slclust && make -j20 install DESTDIR=/build/reproducible-path/trinityrnaseq-2.15.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/trinityrnaseq-2.15.2+dfsg/trinity-plugins/slclust' X=`pwd`; \ for i in src; \ @@ -13179,9 +13215,9 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'trinityrnaseq-examples' in '../trinityrnaseq-examples_2.15.2+dfsg-1_amd64.deb'. dpkg-deb: building package 'trinityrnaseq-dbgsym' in '../trinityrnaseq-dbgsym_2.15.2+dfsg-1_amd64.deb'. dpkg-deb: building package 'trinityrnaseq' in '../trinityrnaseq_2.15.2+dfsg-1_amd64.deb'. +dpkg-deb: building package 'trinityrnaseq-examples' in '../trinityrnaseq-examples_2.15.2+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../trinityrnaseq_2.15.2+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../trinityrnaseq_2.15.2+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -13189,12 +13225,14 @@ 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/1591290/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1591290/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/1564733 and its subdirectories -I: Current time: Thu Jan 22 01:11:27 -12 2026 -I: pbuilder-time-stamp: 1769087487 +I: removing directory /srv/workspace/pbuilder/1591290 and its subdirectories +I: Current time: Fri Dec 20 21:17:42 +14 2024 +I: pbuilder-time-stamp: 1734679062