Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/t/trinityrnaseq/trinityrnaseq_2.13.2+dfsg-3_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/trinityrnaseq-2.13.2+dfsg-3iw5i1yot/trinityrnaseq_2.13.2+dfsg-3_amd64.buildinfo Get source package info: trinityrnaseq=2.13.2+dfsg-3 Source URL: http://snapshot.notset.fr/mr/package/trinityrnaseq/2.13.2+dfsg-3/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.118 ant=1.10.11-1 ant-optional=1.10.11-1 autoconf=2.71-2 automake=1:1.16.5-1 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.52 bash=5.1-3.1 binutils=2.37-8 binutils-common=2.37-8 binutils-x86-64-linux-gnu=2.37-8 bowtie2=2.4.4-1 bsdextrautils=2.37.2-4 bsdutils=1:2.37.2-4 build-essential=12.9 bzip2=1.0.8-4 ca-certificates=20211016 ca-certificates-java=20190909 cmake=3.21.4-1 cmake-data=3.21.4-1 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-10 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r-bioc-rhtslib=1.24.0+dfsg-1 r-bioc-rots=1.20.0-1 r-bioc-rsamtools=2.8.0-1 r-bioc-rtracklayer=1.52.1-1 r-bioc-s4vectors=0.30.2-1 r-bioc-summarizedexperiment=1.22.0+dfsg-1 r-bioc-tximport=1.20.0+dfsg-1 r-bioc-xvector=0.32.0-1 r-bioc-zlibbioc=1.38.0+dfsg-1 r-cran-amap=0.8-18-2+b1 r-cran-ape=5.5-1 r-cran-argparse=2.1.2-1 r-cran-askpass=1.1-2 r-cran-assertthat=0.2.1-2 r-cran-bh=1.74.0-2 r-cran-biasedurn=1.07-4 r-cran-bit=4.0.4+dfsg-1 r-cran-bit64=4.0.5-1 r-cran-bitops=1.0-7-1 r-cran-blob=1.2.2-1 r-cran-cachem=1.0.6-1 r-cran-catools=1.18.2-1 r-cran-cli=3.1.0-1 r-cran-clipr=0.7.1-1 r-cran-colorspace=2.0-2+dfsg-1 r-cran-cpp11=0.4.1-1 r-cran-crayon=1.4.2-1 r-cran-curl=4.3.2+dfsg-1 r-cran-dbi=1.1.1-1 r-cran-dbplyr=2.1.1-1 r-cran-digest=0.6.28-1 r-cran-dplyr=1.0.7-2 r-cran-ellipsis=0.3.2-2 r-cran-fansi=0.5.0-1 r-cran-farver=2.1.0-1 r-cran-fastcluster=1.2.3-1 r-cran-fastmap=1.1.0-1 r-cran-filelock=1.0.2-2 r-cran-findpython=1.0.7-1 r-cran-formatr=1.11-1 r-cran-futile.logger=1.4.3-4 r-cran-futile.options=1.0.1-3 r-cran-gdata=2.18.0-3 r-cran-generics=0.1.1-1 r-cran-ggplot2=3.3.5+dfsg-2 r-cran-glue=1.5.0-1 r-cran-gplots=3.1.1-1 r-cran-gtable=0.3.0+dfsg-2 r-cran-gtools=3.9.2-2 r-cran-hms=1.1.1-1 r-cran-httr=1.4.2-1 r-cran-hwriter=1.3.2-4 r-cran-isoband=0.2.5-1 r-cran-jsonlite=1.7.2+dfsg-1 r-cran-kernsmooth=2.23-20-1 r-cran-labeling=0.4.2-1 r-cran-lambda.r=1.2.4-2 r-cran-lattice=0.20-45-1 r-cran-lifecycle=1.0.1-1 r-cran-littler=0.3.14-1 r-cran-locfit=1.5-9.4-2+b1 r-cran-magrittr=2.0.1-1 r-cran-mass=7.3-54-2 r-cran-matrix=1.3-4-2 r-cran-matrixstats=0.61.0-1 r-cran-memoise=2.0.0-1 r-cran-mgcv=1.8-38-1 r-cran-mime=0.12-1 r-cran-munsell=0.5.0-2 r-cran-nlme=3.1.153-1 r-cran-openssl=1.4.5+dfsg-1 r-cran-pillar=1.6.4+dfsg-1 r-cran-pkgconfig=2.0.3-2 r-cran-pkgkitten=0.2.2-2 r-cran-plogr=0.2.0-3 r-cran-plyr=1.8.6-2 r-cran-png=0.1-7-4 r-cran-prettyunits=1.1.1-2 r-cran-progress=1.2.2-2 r-cran-purrr=0.3.4-1+b1 r-cran-r6=2.5.1-1 r-cran-rappdirs=0.3.3-1 r-cran-rcolorbrewer=1.1-2-3 r-cran-rcpp=1.0.7-2 r-cran-rcpparmadillo=0.10.7.3.0-1 r-cran-rcurl=1.98-1.5-1 r-cran-readr=2.1.0-1 r-cran-reshape2=1.4.4-2 r-cran-restfulr=0.0.13-2 r-cran-rjson=0.2.20-2 r-cran-rlang=0.4.12-2 r-cran-rsqlite=2.2.8-1 r-cran-scales=1.1.1-1 r-cran-snow=1:0.4.4-1 r-cran-statmod=1.4.36-1 r-cran-stringi=1.7.5-1 r-cran-stringr=1.4.0-2 r-cran-survival=3.2-13-1 r-cran-sys=3.4-1 r-cran-tibble=3.1.6+dfsg-1 r-cran-tidyselect=1.1.1+dfsg-1 r-cran-tzdb=0.2.0-1 r-cran-utf8=1.2.2-1 r-cran-vctrs=0.3.8-1 r-cran-viridislite=0.4.0-2 r-cran-vroom=1.5.6-1 r-cran-withr=2.4.2-1 r-cran-xml=3.99-0.8-1 r-cran-xml2=1.3.2-2 r-cran-xtable=1:1.8-4-2 r-cran-yaml=2.2.1-1+b1 readline-common=8.1-2 rna-star=2.7.9a+dfsg-3 rpcsvc-proto=1.4.2-4 salmon=1.5.2+ds1-1 sed=4.8-1 sensible-utils=0.0.17 subread=2.0.3+dfsg-1 sysvinit-utils=3.00-1 tabix=1.13+ds-2 tar=1.34+dfsg-1 tzdata=2021e-1 ucf=3.0043 unzip=6.0-26 util-linux=2.37.2-4 wdiff=1.2.2-2+b1 x11-common=1:7.7+23 xdg-utils=1.1.3-4.1 xz-utils=5.2.5-2 zip=3.0-12 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20211121T025700Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211121T025700Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211126T150138Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211115T152612Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d trinityrnaseq=2.13.2+dfsg-3 && mkdir -p /build/trinityrnaseq-GDdqzS && dpkg-source --no-check -x /*.dsc /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg && chown -R builduser:builduser /build/trinityrnaseq-GDdqzS" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1637009579" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/trinityrnaseq-GDdqzS /tmp/trinityrnaseq-2.13.2+dfsg-3iw5i1yot bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20211115T152612Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.t3ho_dzsWh as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.t3ho_dzsWh Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20211115T152612Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211115T152612Z unstable/main amd64 fakeroot amd64 1.26-1 [87.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1027 kB/s) Selecting previously unselected package libfakeroot: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 ... 4669 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.26-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.26-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.26-1_amd64.deb ... Unpacking fakeroot (1.26-1) ... Setting up libfakeroot:amd64 (1.26-1) ... Setting up fakeroot (1.26-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.32-4) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20211121T025700Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211121T025700Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211126T150138Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211115T152612Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.t3ho_dzsWh Get:1 http://snapshot.notset.fr/archive/debian/20211121T025700Z bookworm InRelease [129 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211126T150138Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20211115T152612Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20211121T025700Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211121T025700Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211121T025700Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211121T025700Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211121T025700Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211121T025700Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20211121T025700Z bookworm/main Sources [11.7 MB] Get:5 http://snapshot.notset.fr/archive/debian/20211121T025700Z bookworm/main amd64 Packages [11.2 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20211126T150138Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20211126T150138Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20211126T150138Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20211126T150138Z unstable/main amd64 Packages [12.0 MB] Fetched 35.2 MB in 29s (1215 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.t3ho_dzsWh I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d trinityrnaseq=2.13.2+dfsg-3 && mkdir -p /build/trinityrnaseq-GDdqzS && dpkg-source --no-check -x /*.dsc /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg && chown -R builduser:builduser /build/trinityrnaseq-GDdqzS"' exec /tmp/mmdebstrap.t3ho_dzsWh Reading package lists... NOTICE: 'trinityrnaseq' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/trinityrnaseq.git Please use: git clone https://salsa.debian.org/med-team/trinityrnaseq.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 279 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20211121T025700Z bookworm/main trinityrnaseq 2.13.2+dfsg-3 (dsc) [2663 B] Get:2 http://snapshot.notset.fr/archive/debian/20211121T025700Z bookworm/main trinityrnaseq 2.13.2+dfsg-3 (tar) [279 MB] Get:3 http://snapshot.notset.fr/archive/debian/20211121T025700Z bookworm/main trinityrnaseq 2.13.2+dfsg-3 (diff) [39.9 kB] Fetched 279 MB in 3min 38s (1281 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'trinityrnaseq_2.13.2+dfsg-3.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting trinityrnaseq in /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg dpkg-source: info: unpacking trinityrnaseq_2.13.2+dfsg.orig.tar.xz dpkg-source: info: unpacking trinityrnaseq_2.13.2+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying which_command_v dpkg-source: info: applying update-paths dpkg-source: info: applying collections15-to-4 dpkg-source: info: applying 0002-fix_istream_failure_call.patch dpkg-source: info: applying fix_system_paths dpkg-source: info: applying disable-version-check dpkg-source: info: applying adjust-trimmomatic-adapters-path dpkg-source: info: applying NeedlemanWunschGotohBanded.patch dpkg-source: info: applying python3 dpkg-source: info: applying unfix_num_of_cores dpkg-source: info: applying hardening dpkg-source: info: applying seqtk-trinity-hardening dpkg-source: info: applying skip_gatk_test dpkg-source: info: applying skip_tximportData_tests dpkg-source: info: applying submake dpkg-source: info: applying skip_blat dpkg-source: info: applying fix-gcc-10.patch dpkg-source: info: applying bamsifter_build dpkg-source: info: applying strip_m64 dpkg-source: info: applying extending_Function_in_jung.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1637009579" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.t3ho_dzsWh dpkg-buildpackage: info: source package trinityrnaseq dpkg-buildpackage: info: source version 2.13.2+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pierre Gruet dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with javahelper debian/rules override_dh_auto_clean make[1]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg' for target in Inchworm Chrysalis; do dh_auto_clean \ --sourcedirectory=${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 -j10 clean make[2]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/slclust' X=`pwd`; \ for i in src; \ do echo '<<<' $i '>>>'; cd $X/$i; make clean; done <<< src >>> make[3]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/slclust/src' rm -f slcluster.o graph.o graphnode.o cmd_line_opts.o core a.out *~ \#* slclust Makefile.bak \ ../bin/slclust make[3]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/slclust/src' make[2]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/slclust' cd trinity-plugins/scaffold_iworm_contigs && make -j10 clean make[2]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/scaffold_iworm_contigs' rm -f scaffold_iworm_contigs make[2]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/scaffold_iworm_contigs' rm --force Chrysalis/Makefile_auto rm --force trinity-plugins/slclust/bin/slclust cd trinity-plugins && /usr/bin/make clean || true make[2]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins' cd seqtk-trinity && /usr/bin/make clean make[3]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/seqtk-trinity' rm -fr gmon.out *.o ext/*.o a.out seqtk trimadap *~ *.a *.dSYM session* make[3]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/seqtk-trinity' cd scaffold_iworm_contigs && /usr/bin/make clean make[3]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/scaffold_iworm_contigs' rm -f scaffold_iworm_contigs make[3]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/scaffold_iworm_contigs' cd "ParaFly" && /usr/bin/make clean make[3]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/ParaFly' Making clean in src make[4]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/ParaFly/src' test -z "ParaFly" || rm -f ParaFly rm -f *.o make[4]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/ParaFly/src' Making clean in . make[4]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/ParaFly' make[4]: Nothing to be done for 'clean-am'. make[4]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/ParaFly' make[3]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/ParaFly' rm -f ./Trimmomatic # rm symlink cd slclust && /usr/bin/make clean make[3]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/slclust' X=`pwd`; \ for i in src; \ do echo '<<<' $i '>>>'; cd $X/$i; /usr/bin/make clean; done <<< src >>> make[4]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/slclust/src' rm -f slcluster.o graph.o graphnode.o cmd_line_opts.o core a.out *~ \#* slclust Makefile.bak \ ../bin/slclust make[4]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/slclust/src' make[3]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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 make[2]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins' make[1]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg' jh_clean dh_clean debian/rules binary-arch dh binary-arch --with javahelper dh_update_autotools_config -a debian/rules override_dh_autoreconf make[1]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg' echo No need to run autoreconf No need to run autoreconf make[1]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg' rm -f Chrysalis/Makefile for target in Inchworm Chrysalis; do dh_auto_configure \ --sourcedirectory=${target} --builddirectory=${target}_build; done cd Inchworm_build && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu ../Inchworm -- The C compiler identification is GNU 11.2.0 -- The CXX compiler identification is GNU 11.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- system: Linux -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_FIND_USE_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build cd Chrysalis_build && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu ../Chrysalis -- The C compiler identification is GNU 11.2.0 -- The CXX compiler identification is GNU 11.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- system: Linux -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_FIND_USE_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis_build make[1]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg' jh_linkjars -a debian/rules override_dh_auto_build make[1]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg' for target in Inchworm Chrysalis; do dh_auto_build \ --sourcedirectory=${target} --builddirectory=${target}_build; done cd Inchworm_build && make -j10 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build' /usr/bin/cmake -S/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm -B/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build/CMakeFiles /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build' make -f CMakeFiles/fastaToKmerCoverageStats.dir/build.make CMakeFiles/fastaToKmerCoverageStats.dir/depend make -f CMakeFiles/FastaToDeBruijn.dir/build.make CMakeFiles/FastaToDeBruijn.dir/depend make -f CMakeFiles/inchworm.dir/build.make CMakeFiles/inchworm.dir/depend make[4]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build' cd /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build/CMakeFiles/fastaToKmerCoverageStats.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build' cd /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build/CMakeFiles/inchworm.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build' cd /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build/CMakeFiles/FastaToDeBruijn.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build' make -f CMakeFiles/fastaToKmerCoverageStats.dir/build.make CMakeFiles/fastaToKmerCoverageStats.dir/build make[4]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build' make[4]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build' make -f CMakeFiles/FastaToDeBruijn.dir/build.make CMakeFiles/FastaToDeBruijn.dir/build make[4]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build' make -f CMakeFiles/inchworm.dir/build.make CMakeFiles/inchworm.dir/build make[4]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build' make[4]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build' [ 3%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_entry.cpp.o [ 7%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_reader.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/Fasta_reader.cpp [ 10%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/FastaToDeBruijn.cpp.o [ 14%] Building CXX object CMakeFiles/inchworm.dir/src/sequenceUtil.cpp.o [ 17%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/argProcessor.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/inchworm.dir/src/sequenceUtil.cpp.o -MF CMakeFiles/inchworm.dir/src/sequenceUtil.cpp.o.d -o CMakeFiles/inchworm.dir/src/sequenceUtil.cpp.o -c /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/sequenceUtil.cpp /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/argProcessor.cpp [ 21%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/string_util.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/FastaToDeBruijn.dir/src/FastaToDeBruijn.cpp.o -MF CMakeFiles/FastaToDeBruijn.dir/src/FastaToDeBruijn.cpp.o.d -o CMakeFiles/FastaToDeBruijn.dir/src/FastaToDeBruijn.cpp.o -c /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/FastaToDeBruijn.cpp [ 25%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/fastaToKmerCoverageStats.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/fastaToKmerCoverageStats.dir/src/string_util.cpp.o -MF CMakeFiles/fastaToKmerCoverageStats.dir/src/string_util.cpp.o.d -o CMakeFiles/fastaToKmerCoverageStats.dir/src/string_util.cpp.o -c /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/string_util.cpp [ 28%] Building CXX object CMakeFiles/inchworm.dir/src/Fasta_entry.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/Fasta_entry.cpp /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/fastaToKmerCoverageStats.dir/src/fastaToKmerCoverageStats.cpp.o -MF CMakeFiles/fastaToKmerCoverageStats.dir/src/fastaToKmerCoverageStats.cpp.o.d -o CMakeFiles/fastaToKmerCoverageStats.dir/src/fastaToKmerCoverageStats.cpp.o -c /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp [ 32%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/sequenceUtil.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_entry.cpp.o -MF CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_entry.cpp.o.d -o CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_entry.cpp.o -c /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/Fasta_entry.cpp /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/fastaToKmerCoverageStats.dir/src/sequenceUtil.cpp.o -MF CMakeFiles/fastaToKmerCoverageStats.dir/src/sequenceUtil.cpp.o.d -o CMakeFiles/fastaToKmerCoverageStats.dir/src/sequenceUtil.cpp.o -c /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/sequenceUtil.cpp [ 35%] Building CXX object CMakeFiles/inchworm.dir/src/IRKE_run.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/inchworm.dir/src/IRKE_run.cpp.o -MF CMakeFiles/inchworm.dir/src/IRKE_run.cpp.o.d -o CMakeFiles/inchworm.dir/src/IRKE_run.cpp.o -c /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/IRKE_run.cpp In file included from /usr/include/c++/11/ext/hash_map:60, from /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/KmerCounter.hpp:53, from /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/IRKE.hpp:7, from /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp:20: /usr/include/c++/11/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++/11/ext/hash_map:60, from /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/KmerCounter.hpp:53, from /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/IRKE.hpp:7, from /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/IRKE_run.cpp:11: /usr/include/c++/11/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 \ | ^~~~~~~ [ 39%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/stacktrace.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/fastaToKmerCoverageStats.dir/src/stacktrace.cpp.o -MF CMakeFiles/fastaToKmerCoverageStats.dir/src/stacktrace.cpp.o.d -o CMakeFiles/fastaToKmerCoverageStats.dir/src/stacktrace.cpp.o -c /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/stacktrace.cpp [ 42%] Building CXX object CMakeFiles/inchworm.dir/src/IRKE.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/inchworm.dir/src/IRKE.cpp.o -MF CMakeFiles/inchworm.dir/src/IRKE.cpp.o.d -o CMakeFiles/inchworm.dir/src/IRKE.cpp.o -c /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/IRKE.cpp [ 46%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/KmerCounter.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/fastaToKmerCoverageStats.dir/src/KmerCounter.cpp.o -MF CMakeFiles/fastaToKmerCoverageStats.dir/src/KmerCounter.cpp.o.d -o CMakeFiles/fastaToKmerCoverageStats.dir/src/KmerCounter.cpp.o -c /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/KmerCounter.cpp In file included from /usr/include/c++/11/ext/hash_map:60, from /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/KmerCounter.hpp:53, from /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/IRKE.hpp:7, from /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/IRKE.cpp:21: /usr/include/c++/11/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++/11/ext/hash_map:60, from /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/KmerCounter.hpp:53, from /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/KmerCounter.cpp:1: /usr/include/c++/11/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/FastaToDeBruijn.cpp: In function ‘void createGraphPerRecord(std::vector >, int, bool, ArgProcessor)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp: In function ‘void populate_kmer_counter_from_reads(KmerCounter&, std::string&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp:231:18: warning: unused variable ‘kmer_length’ [-Wunused-variable] 231 | unsigned int kmer_length = kcounter.get_kmer_length(); | ^~~~~~~~~~~ [ 50%] Building CXX object CMakeFiles/inchworm.dir/src/KmerCounter.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/KmerCounter.cpp In file included from /usr/include/c++/11/ext/hash_map:60, from /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/KmerCounter.hpp:53, from /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/KmerCounter.cpp:1: /usr/include/c++/11/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 \ | ^~~~~~~ [ 53%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/argProcessor.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/FastaToDeBruijn.dir/src/argProcessor.cpp.o -MF CMakeFiles/FastaToDeBruijn.dir/src/argProcessor.cpp.o.d -o CMakeFiles/FastaToDeBruijn.dir/src/argProcessor.cpp.o -c /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/argProcessor.cpp [ 57%] Building CXX object CMakeFiles/inchworm.dir/src/string_util.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/inchworm.dir/src/string_util.cpp.o -MF CMakeFiles/inchworm.dir/src/string_util.cpp.o.d -o CMakeFiles/inchworm.dir/src/string_util.cpp.o -c /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/string_util.cpp [ 60%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/Fasta_reader.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/Fasta_reader.cpp /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp:250:9: warning: ‘end’ may be used uninitialized [-Wmaybe-uninitialized] 250 | #pragma omp parallel private (myTid) | ^~~ [ 64%] Building CXX object CMakeFiles/inchworm.dir/src/Fasta_reader.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/inchworm.dir/src/Fasta_reader.cpp.o -MF CMakeFiles/inchworm.dir/src/Fasta_reader.cpp.o.d -o CMakeFiles/inchworm.dir/src/Fasta_reader.cpp.o -c /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/Fasta_reader.cpp [ 67%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/Fasta_entry.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/Fasta_entry.cpp [ 71%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/sequenceUtil.cpp [ 75%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/string_util.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/string_util.cpp [ 78%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/stacktrace.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/stacktrace.cpp [ 82%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/DeBruijnGraph.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/DeBruijnGraph.cpp [ 85%] Building CXX object CMakeFiles/inchworm.dir/src/stacktrace.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -MD -MT CMakeFiles/inchworm.dir/src/stacktrace.cpp.o -MF CMakeFiles/inchworm.dir/src/stacktrace.cpp.o.d -o CMakeFiles/inchworm.dir/src/stacktrace.cpp.o -c /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/stacktrace.cpp [ 89%] Building CXX object CMakeFiles/inchworm.dir/src/argProcessor.cpp.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/argProcessor.cpp /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/DeBruijnGraph.cpp: In member function ‘std::string DeBruijnKmer::get_annotations_string()’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/DeBruijnGraph.cpp:66:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 66 | for (int i=0; i < _annotations.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~ [ 92%] Linking CXX executable fastaToKmerCoverageStats /usr/bin/cmake -E cmake_link_script CMakeFiles/fastaToKmerCoverageStats.dir/link.txt --verbose=1 /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/fastaToKmerCoverageStats.dir/src/fastaToKmerCoverageStats.cpp.o CMakeFiles/fastaToKmerCoverageStats.dir/src/argProcessor.cpp.o CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_reader.cpp.o CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_entry.cpp.o CMakeFiles/fastaToKmerCoverageStats.dir/src/sequenceUtil.cpp.o CMakeFiles/fastaToKmerCoverageStats.dir/src/string_util.cpp.o CMakeFiles/fastaToKmerCoverageStats.dir/src/stacktrace.cpp.o CMakeFiles/fastaToKmerCoverageStats.dir/src/KmerCounter.cpp.o -o fastaToKmerCoverageStats /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/DeBruijnGraph.cpp: In member function ‘std::string DeBruijnGraph::toDOT(bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/DeBruijnGraph.cpp:445:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 445 | for (int i=0; i < prev_kmers.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/DeBruijnGraph.cpp:494:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 494 | for (int i=0; i < next_kmers.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/DeBruijnGraph.cpp: In member function ‘std::string DeBruijnGraph::toChrysalisFormat(int, bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm/src/DeBruijnGraph.cpp:725:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 725 | for (int i = 0; i < collected_kmers.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build' [ 96%] Linking CXX executable inchworm /usr/bin/cmake -E cmake_link_script CMakeFiles/inchworm.dir/link.txt --verbose=1 /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/inchworm.dir/src/Fasta_entry.cpp.o CMakeFiles/inchworm.dir/src/IRKE_run.cpp.o CMakeFiles/inchworm.dir/src/sequenceUtil.cpp.o CMakeFiles/inchworm.dir/src/IRKE.cpp.o CMakeFiles/inchworm.dir/src/KmerCounter.cpp.o CMakeFiles/inchworm.dir/src/string_util.cpp.o CMakeFiles/inchworm.dir/src/Fasta_reader.cpp.o CMakeFiles/inchworm.dir/src/stacktrace.cpp.o CMakeFiles/inchworm.dir/src/argProcessor.cpp.o -o inchworm [ 96%] Built target fastaToKmerCoverageStats make[4]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build' [ 96%] Built target inchworm [100%] Linking CXX executable FastaToDeBruijn /usr/bin/cmake -E cmake_link_script CMakeFiles/FastaToDeBruijn.dir/link.txt --verbose=1 /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/FastaToDeBruijn.dir/src/FastaToDeBruijn.cpp.o CMakeFiles/FastaToDeBruijn.dir/src/argProcessor.cpp.o CMakeFiles/FastaToDeBruijn.dir/src/Fasta_reader.cpp.o CMakeFiles/FastaToDeBruijn.dir/src/Fasta_entry.cpp.o CMakeFiles/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o CMakeFiles/FastaToDeBruijn.dir/src/string_util.cpp.o CMakeFiles/FastaToDeBruijn.dir/src/stacktrace.cpp.o CMakeFiles/FastaToDeBruijn.dir/src/DeBruijnGraph.cpp.o -o FastaToDeBruijn make[4]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build' [100%] Built target FastaToDeBruijn make[3]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build' /usr/bin/cmake -E cmake_progress_start /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build/CMakeFiles 0 make[2]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build' cd Chrysalis_build && make -j10 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis_build' /usr/bin/cmake -S/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -B/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis_build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis_build/CMakeFiles /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis_build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis_build' make -f CMakeFiles/CreateIwormFastaBundle.dir/build.make CMakeFiles/CreateIwormFastaBundle.dir/depend make -f CMakeFiles/BubbleUpClustering.dir/build.make CMakeFiles/BubbleUpClustering.dir/depend make -f CMakeFiles/ReadsToTranscripts.dir/build.make CMakeFiles/ReadsToTranscripts.dir/depend make -f CMakeFiles/QuantifyGraph.dir/build.make CMakeFiles/QuantifyGraph.dir/depend make -f CMakeFiles/GraphFromFasta.dir/build.make CMakeFiles/GraphFromFasta.dir/depend make[4]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis_build' cd /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis_build /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis_build /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis_build/CMakeFiles/CreateIwormFastaBundle.dir/DependInfo.cmake --color= make -f CMakeFiles/Chrysalis.dir/build.make CMakeFiles/Chrysalis.dir/depend make[4]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis_build' cd /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis 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/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/AACodons.cc /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/AACodons.cc /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/Chrysalis.dir/aligns/KmerAlignCore.cc.o -MF CMakeFiles/Chrysalis.dir/aligns/KmerAlignCore.cc.o.d -o CMakeFiles/Chrysalis.dir/aligns/KmerAlignCore.cc.o -c /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/aligns/KmerAlignCore.cc.o -MF CMakeFiles/GraphFromFasta.dir/aligns/KmerAlignCore.cc.o.d -o CMakeFiles/GraphFromFasta.dir/aligns/KmerAlignCore.cc.o -c /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/BubbleUpClustering.dir/analysis/AACodons.cc.o -MF CMakeFiles/BubbleUpClustering.dir/analysis/AACodons.cc.o.d -o CMakeFiles/BubbleUpClustering.dir/analysis/AACodons.cc.o -c /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/AACodons.cc /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function ‘void KmerAlignCore::AddData(const vecDNAVector&, const vecNumVector&, int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:79:49: warning: unused variable ‘t’ [-Wunused-variable] 79 | KmerAlignCoreRecordStoreTable & t = m_table; // not used? | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:49:9: warning: unused variable ‘i’ [-Wunused-variable] 49 | int i, j, k; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function ‘void KmerAlignCore::AddData(const DNAVector&, int, int, bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:128:9: warning: unused variable ‘i’ [-Wunused-variable] 128 | int i, j, k; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:128:12: warning: unused variable ‘j’ [-Wunused-variable] 128 | int i, j, k; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function ‘void KmerAlignCore::SortAll()’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:148:9: warning: unused variable ‘i’ [-Wunused-variable] 148 | int i, j; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function ‘const svec& KmerAlignCore::GetMatchesDirectly(const DNAVector&, int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:158:9: warning: unused variable ‘size’ [-Wunused-variable] 158 | int size = m_pTrans->GetSize(); | ^~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:159:9: warning: unused variable ‘i’ [-Wunused-variable] 159 | int i, j; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:159:12: warning: unused variable ‘j’ [-Wunused-variable] 159 | int i, j; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function ‘void KmerAlignCore::MergeSortFilter(svec&, const svec&, const svec&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:291:9: warning: unused variable ‘i’ [-Wunused-variable] 291 | int i; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function ‘void KmerAlignCore::AddData(const vecDNAVector&, const vecNumVector&, int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:79:49: warning: unused variable ‘t’ [-Wunused-variable] 79 | KmerAlignCoreRecordStoreTable & t = m_table; // not used? | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:49:9: warning: unused variable ‘i’ [-Wunused-variable] 49 | int i, j, k; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function ‘void KmerAlignCore::AddData(const DNAVector&, int, int, bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:128:9: warning: unused variable ‘i’ [-Wunused-variable] 128 | int i, j, k; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:128:12: warning: unused variable ‘j’ [-Wunused-variable] 128 | int i, j, k; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function ‘void KmerAlignCore::SortAll()’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:148:9: warning: unused variable ‘i’ [-Wunused-variable] 148 | int i, j; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function ‘const svec& KmerAlignCore::GetMatchesDirectly(const DNAVector&, int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:158:9: warning: unused variable ‘size’ [-Wunused-variable] 158 | int size = m_pTrans->GetSize(); | ^~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:159:9: warning: unused variable ‘i’ [-Wunused-variable] 159 | int i, j; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:159:12: warning: unused variable ‘j’ [-Wunused-variable] 159 | int i, j; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function ‘void KmerAlignCore::MergeSortFilter(svec&, const svec&, const svec&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:291:9: warning: unused variable ‘i’ [-Wunused-variable] 291 | int i; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc: In function ‘int main(int, char**)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc:181:17: warning: unused variable ‘num_iworm_contigs’ [-Wunused-variable] 181 | int num_iworm_contigs = parser.AsInt(2); | ^~~~~~~~~~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc:143:10: warning: unused variable ‘DEBUG’ [-Wunused-variable] 143 | bool DEBUG = P.GetBoolValueFor(debugCmmd); | ^~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc:166:12: warning: unused variable ‘pOut’ [-Wunused-variable] 166 | FILE * pOut = NULL; | ^~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function ‘void KmerAlignCore::AddData(const vecDNAVector&, const vecNumVector&, int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:79:49: warning: unused variable ‘t’ [-Wunused-variable] 79 | KmerAlignCoreRecordStoreTable & t = m_table; // not used? | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:49:9: warning: unused variable ‘i’ [-Wunused-variable] 49 | int i, j, k; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function ‘void KmerAlignCore::AddData(const DNAVector&, int, int, bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:128:9: warning: unused variable ‘i’ [-Wunused-variable] 128 | int i, j, k; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:128:12: warning: unused variable ‘j’ [-Wunused-variable] 128 | int i, j, k; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function ‘void KmerAlignCore::SortAll()’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:148:9: warning: unused variable ‘i’ [-Wunused-variable] 148 | int i, j; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function ‘const svec& KmerAlignCore::GetMatchesDirectly(const DNAVector&, int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:158:9: warning: unused variable ‘size’ [-Wunused-variable] 158 | int size = m_pTrans->GetSize(); | ^~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:159:9: warning: unused variable ‘i’ [-Wunused-variable] 159 | int i, j; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:159:12: warning: unused variable ‘j’ [-Wunused-variable] 159 | int i, j; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function ‘void KmerAlignCore::MergeSortFilter(svec&, const svec&, const svec&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:291:9: warning: unused variable ‘i’ [-Wunused-variable] 291 | int i; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function ‘void KmerAlignCore::AddData(const vecDNAVector&, const vecNumVector&, int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:79:49: warning: unused variable ‘t’ [-Wunused-variable] 79 | KmerAlignCoreRecordStoreTable & t = m_table; // not used? | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:49:9: warning: unused variable ‘i’ [-Wunused-variable] 49 | int i, j, k; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function ‘void KmerAlignCore::AddData(const DNAVector&, int, int, bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:128:9: warning: unused variable ‘i’ [-Wunused-variable] 128 | int i, j, k; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:128:12: warning: unused variable ‘j’ [-Wunused-variable] 128 | int i, j, k; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function ‘void KmerAlignCore::SortAll()’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:148:9: warning: unused variable ‘i’ [-Wunused-variable] 148 | int i, j; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function ‘const svec& KmerAlignCore::GetMatchesDirectly(const DNAVector&, int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:158:9: warning: unused variable ‘size’ [-Wunused-variable] 158 | int size = m_pTrans->GetSize(); | ^~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:159:9: warning: unused variable ‘i’ [-Wunused-variable] 159 | int i, j; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:159:12: warning: unused variable ‘j’ [-Wunused-variable] 159 | int i, j; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function ‘void KmerAlignCore::MergeSortFilter(svec&, const svec&, const svec&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/aligns/KmerAlignCore.cc:291:9: warning: unused variable ‘i’ [-Wunused-variable] 291 | int i; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/BubbleUpClustering.cc: In function ‘svec grow_prioritized_clusters(std::string&, std::map&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/BubbleUpClustering.cc: In function ‘svec sl_cluster_pools(std::map&, std::map&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/BubbleUpClustering.cc:19: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/Pool.h:24:5: note: because ‘Pool’ has user-provided ‘Pool::Pool(const Pool&)’ 24 | Pool(const Pool& p) { | ^~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/BubbleUpClustering.cc: In function ‘void populate_weld_reinforced_iworm_clusters(std::string&, std::map&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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; | ^ In file included from /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/BubbleUpClustering.cc:19: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/Pool.h:24:5: note: because ‘Pool’ has user-provided ‘Pool::Pool(const Pool&)’ 24 | Pool(const Pool& p) { | ^~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/BubbleUpClustering.cc: In function ‘int main(int, char**)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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++) { | ~~^~~~~~~~~~ [ 15%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/AACodons.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/analysis/AACodons.cc.o -MF CMakeFiles/GraphFromFasta.dir/analysis/AACodons.cc.o.d -o CMakeFiles/GraphFromFasta.dir/analysis/AACodons.cc.o -c /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/AACodons.cc [ 17%] Building CXX object CMakeFiles/Chrysalis.dir/analysis/AACodons.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/AACodons.cc [ 18%] Building CXX object CMakeFiles/Chrysalis.dir/analysis/Chrysalis.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/Chrysalis.cc [ 20%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/DNAVector.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/DNAVector.cc [ 21%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/DNAVector.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/DNAVector.cc [ 22%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/DeBruijnGraph.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/DeBruijnGraph.cc [ 24%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/DNAVector.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/DNAVector.cc /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/Chrysalis.cc: In function ‘int main(int, char**)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/Chrysalis.cc:582:21: warning: unused variable ‘num_iworm_contigs’ [-Wunused-variable] 582 | int num_iworm_contigs = parser.AsInt(2); | ^~~~~~~~~~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/Chrysalis.cc:570:16: warning: unused variable ‘pOut’ [-Wunused-variable] 570 | FILE * pOut = NULL; | ^~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/Chrysalis.cc:342:10: warning: unused variable ‘bSkip’ [-Wunused-variable] 342 | bool bSkip = P.GetBoolValueFor(skipCmmd); | ^~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/Chrysalis.cc:347:9: warning: unused variable ‘pairDist’ [-Wunused-variable] 347 | int pairDist = P.GetIntValueFor(distCmmd); | ^~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/Chrysalis.cc:354:10: warning: variable ‘bBreak’ set but not used [-Wunused-but-set-variable] 354 | bool bBreak = true; | ^~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/Chrysalis.cc:359:10: warning: unused variable ‘bButt’ [-Wunused-variable] 359 | bool bButt = P.GetBoolValueFor(buttCmmd); | ^~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/Chrysalis.cc:361:10: warning: unused variable ‘max_reads’ [-Wunused-variable] 361 | long max_reads = P.GetLongValueFor(maxReadsCmd); | ^~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/Chrysalis.cc:372:10: warning: unused variable ‘DEBUG’ [-Wunused-variable] 372 | bool DEBUG = P.GetBoolValueFor(debugCmmd); | ^~~~~ [ 25%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/KmerTable.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/KmerTable.cc /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function ‘void DeBruijnKmer::add_next_kmer(kmer_int_type_t, unsigned int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function ‘std::vector DeBruijnGraph::deconvolute_DS_mirror_graph()’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function ‘std::vector > DeBruijnGraph::get_candidate_weldmers(kmer_int_type_t, int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ [ 27%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/analysis/DNAVector.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/DNAVector.cc /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/KmerTable.cc: In member function ‘long long int KmerSequence::BasesToNumber(const DNAVector&, int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/KmerTable.cc:27:13: warning: unused variable ‘i’ [-Wunused-variable] 27 | long long i; | ^ [ 28%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/DNAVector.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/analysis/DNAVector.cc.o -MF CMakeFiles/GraphFromFasta.dir/analysis/DNAVector.cc.o.d -o CMakeFiles/GraphFromFasta.dir/analysis/DNAVector.cc.o -c /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/DNAVector.cc [ 30%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/DeBruijnGraph.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/analysis/DeBruijnGraph.cc.o -MF CMakeFiles/GraphFromFasta.dir/analysis/DeBruijnGraph.cc.o.d -o CMakeFiles/GraphFromFasta.dir/analysis/DeBruijnGraph.cc.o -c /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/DeBruijnGraph.cc [ 31%] Building CXX object CMakeFiles/Chrysalis.dir/analysis/DNAVector.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/DNAVector.cc [ 32%] Building CXX object CMakeFiles/Chrysalis.dir/analysis/TranscriptomeGraph.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc [ 34%] Building CXX object CMakeFiles/Chrysalis.dir/base/ErrorHandling.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/ErrorHandling.cc /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc: In member function ‘void KmerSequence::Setup()’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc:177:19: warning: unused variable ‘i’ [-Wunused-variable] 177 | long long i; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function ‘void DeBruijnKmer::add_next_kmer(kmer_int_type_t, unsigned int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc: In member function ‘void KmerSearch::Extend(long long int, DNAVector&, const svec&, DNAVector&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc:547:16: warning: unused variable ‘plusminus’ [-Wunused-variable] 547 | static int plusminus = 0; | ^~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc: In function ‘int TranscriptomeGraph(vecDNAVector&, FILE*, int, bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc:647:10: warning: unused variable ‘bAppend’ [-Wunused-variable] 647 | bool bAppend = true; | ^~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function ‘std::vector DeBruijnGraph::deconvolute_DS_mirror_graph()’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function ‘std::vector > DeBruijnGraph::get_candidate_weldmers(kmer_int_type_t, int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/ErrorHandling.cc: In function ‘void print_trace(FILE*, const char*, int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/ErrorHandling.cc:7:51: warning: unused parameter ‘line’ [-Wunused-parameter] 7 | void print_trace(FILE *out, const char *file, int line) | ~~~~^~~~ [ 35%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/base/ErrorHandling.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/ErrorHandling.cc /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc: At global scope: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc:547:16: warning: ‘plusminus’ defined but not used [-Wunused-variable] 547 | static int plusminus = 0; | ^~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/ErrorHandling.cc: In function ‘void print_trace(FILE*, const char*, int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/ErrorHandling.cc:7:51: warning: unused parameter ‘line’ [-Wunused-parameter] 7 | void print_trace(FILE *out, const char *file, int line) | ~~~~^~~~ [ 37%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/base/FileParser.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/FileParser.cc /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/FileParser.cc: In member function ‘bool StringParser::IsString(int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter ‘index’ [-Wunused-parameter] 50 | bool StringParser::IsString(int index) | ~~~~^~~~~ [ 38%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/NonRedKmerTable.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc [ 40%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/sequenceUtil.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/sequenceUtil.cc /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function ‘void NonRedKmerTable::SetUp(const vecDNAVector&, bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function ‘void NonRedKmerTable::AddData(const vecDNAVector&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function ‘void NonRedKmerTable::AddData(vecDNAVectorStream&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:125:9: warning: unused variable ‘i’ [-Wunused-variable] 125 | int i, j; | ^ [ 41%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/stacktrace.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/stacktrace.cc [ 42%] Building CXX object CMakeFiles/BubbleUpClustering.dir/base/ErrorHandling.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/ErrorHandling.cc /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function ‘bool contains_non_gatc(std::string)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/sequenceUtil.cc:33:26: warning: array subscript has type ‘char’ [-Wchar-subscripts] 33 | if (_base_to_int[c] > 3) | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function ‘kmer_int_type_t kmer_to_intval(std::string)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/sequenceUtil.cc:264:32: warning: array subscript has type ‘char’ [-Wchar-subscripts] 264 | int val = _base_to_int[c]; | ^ [ 44%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/KmerTable.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/KmerTable.cc [ 45%] Building CXX object CMakeFiles/Chrysalis.dir/base/FileParser.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/FileParser.cc [ 47%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/NonRedKmerTable.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/ErrorHandling.cc: In function ‘void print_trace(FILE*, const char*, int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/ErrorHandling.cc:7:51: warning: unused parameter ‘line’ [-Wunused-parameter] 7 | void print_trace(FILE *out, const char *file, int line) | ~~~~^~~~ [ 48%] Building CXX object CMakeFiles/Chrysalis.dir/base/StringUtil.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/StringUtil.cc [ 50%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/ReadsToTranscripts.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/ReadsToTranscripts.cc [ 51%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/sequenceUtil.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/sequenceUtil.cc [ 52%] Building CXX object CMakeFiles/BubbleUpClustering.dir/base/FileParser.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/FileParser.cc /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/FileParser.cc: In member function ‘bool StringParser::IsString(int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter ‘index’ [-Wunused-parameter] 50 | bool StringParser::IsString(int index) | ~~~~^~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/KmerTable.cc: In member function ‘long long int KmerSequence::BasesToNumber(const DNAVector&, int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/KmerTable.cc:27:13: warning: unused variable ‘i’ [-Wunused-variable] 27 | long long i; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function ‘bool contains_non_gatc(std::string)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/sequenceUtil.cc:33:26: warning: array subscript has type ‘char’ [-Wchar-subscripts] 33 | if (_base_to_int[c] > 3) | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function ‘kmer_int_type_t kmer_to_intval(std::string)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/sequenceUtil.cc:264:32: warning: array subscript has type ‘char’ [-Wchar-subscripts] 264 | int val = _base_to_int[c]; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function ‘void NonRedKmerTable::SetUp(const vecDNAVector&, bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function ‘void NonRedKmerTable::AddData(const vecDNAVector&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function ‘void NonRedKmerTable::AddData(vecDNAVectorStream&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:125:9: warning: unused variable ‘i’ [-Wunused-variable] 125 | int i, j; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/FileParser.cc: In member function ‘bool StringParser::IsString(int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter ‘index’ [-Wunused-parameter] 50 | bool StringParser::IsString(int index) | ~~~~^~~~~ [ 54%] Building CXX object CMakeFiles/BubbleUpClustering.dir/base/StringUtil.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/StringUtil.cc [ 55%] Building CXX object CMakeFiles/Chrysalis.dir/util/mutil.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc [ 57%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/base/StringUtil.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/StringUtil.cc [ 58%] Building CXX object CMakeFiles/BubbleUpClustering.dir/util/mutil.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In member function ‘virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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) { | ^~~~~~~ ~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:303:51: warning: unused parameter ‘pData’ [-Wunused-parameter] 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) | ~~~~~~~^~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:303:63: warning: unused parameter ‘lenInBytes’ [-Wunused-parameter] 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) | ~~~~~^~~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In member function ‘virtual bool CMAsciiReadFileStream::ReadString(CMString&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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) { | ^~~~~~~ ~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In member function ‘virtual bool CMAsciiWriteFileStream::WriteBlob(const void*, long int, long int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:526:65: warning: unused parameter ‘lenInElements’ [-Wunused-parameter] 526 | bool CMAsciiWriteFileStream::WriteBlob(const void * pData, long lenInElements, long elSize) | ~~~~~^~~~~~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In function ‘void MLog(const MCL_TCHAR*, bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:738:53: warning: unused parameter ‘bLineFeed’ [-Wunused-parameter] 738 | MDLLEXPORT void MLog(const MCL_TCHAR * szText, bool bLineFeed) | ~~~~~^~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In function ‘void MLog(const MCL_TCHAR*, long int, bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In function ‘void MLog(const MCL_TCHAR*, const MCL_TCHAR*, bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In function ‘void MCLSetUTF8Encode(bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:1288:39: warning: unused parameter ‘b’ [-Wunused-parameter] 1288 | MDLLEXPORT void MCLSetUTF8Encode(bool b) | ~~~~~^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In function ‘bool AddUTF8Sig(CMString&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:1688:16: warning: unused variable ‘p’ [-Wunused-variable] 1688 | const char * p = (const char*)string; | ^ [ 60%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/NonRedKmerTable.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In member function ‘virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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) { | ^~~~~~~ ~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:303:51: warning: unused parameter ‘pData’ [-Wunused-parameter] 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) | ~~~~~~~^~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:303:63: warning: unused parameter ‘lenInBytes’ [-Wunused-parameter] 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) | ~~~~~^~~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In member function ‘virtual bool CMAsciiReadFileStream::ReadString(CMString&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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) { | ^~~~~~~ ~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In member function ‘virtual bool CMAsciiWriteFileStream::WriteBlob(const void*, long int, long int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:526:65: warning: unused parameter ‘lenInElements’ [-Wunused-parameter] 526 | bool CMAsciiWriteFileStream::WriteBlob(const void * pData, long lenInElements, long elSize) | ~~~~~^~~~~~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In function ‘void MLog(const MCL_TCHAR*, bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:738:53: warning: unused parameter ‘bLineFeed’ [-Wunused-parameter] 738 | MDLLEXPORT void MLog(const MCL_TCHAR * szText, bool bLineFeed) | ~~~~~^~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In function ‘void MLog(const MCL_TCHAR*, long int, bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In function ‘void MLog(const MCL_TCHAR*, const MCL_TCHAR*, bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In function ‘void MCLSetUTF8Encode(bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:1288:39: warning: unused parameter ‘b’ [-Wunused-parameter] 1288 | MDLLEXPORT void MCLSetUTF8Encode(bool b) | ~~~~~^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In function ‘bool AddUTF8Sig(CMString&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:1688:16: warning: unused variable ‘p’ [-Wunused-variable] 1688 | const char * p = (const char*)string; | ^ [ 61%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/QuantifyGraph.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/QuantifyGraph.cc /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In member function ‘virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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:461, from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/string.h:26, from /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.h:19, from /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:9: /usr/include/stdio.h:410:12: note: by argument 2 of type ‘const char*’ to ‘int fscanf(FILE*, const char*, ...)’ declared here 410 | extern int __REDIRECT (fscanf, (FILE *__restrict __stream, | ^~~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:311:8: note: ‘szText’ declared here 311 | char szText[2048 * 10]; | ^~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In member function ‘virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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:461, from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/string.h:26, from /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.h:19, from /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:9: /usr/include/stdio.h:410:12: note: by argument 2 of type ‘const char*’ to ‘int fscanf(FILE*, const char*, ...)’ declared here 410 | extern int __REDIRECT (fscanf, (FILE *__restrict __stream, | ^~~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:311:8: note: ‘szText’ declared here 311 | char szText[2048 * 10]; | ^~~~~~ [ 62%] Building CXX object CMakeFiles/QuantifyGraph.dir/base/ErrorHandling.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/ErrorHandling.cc [ 64%] Building CXX object CMakeFiles/QuantifyGraph.dir/base/FileParser.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/FileParser.cc [ 65%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/stacktrace.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/stacktrace.cc /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function ‘void NonRedKmerTable::SetUp(const vecDNAVector&, bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function ‘void NonRedKmerTable::AddData(const vecDNAVector&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function ‘void NonRedKmerTable::AddData(vecDNAVectorStream&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:125:9: warning: unused variable ‘i’ [-Wunused-variable] 125 | int i, j; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/ErrorHandling.cc: In function ‘void print_trace(FILE*, const char*, int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/ErrorHandling.cc:7:51: warning: unused parameter ‘line’ [-Wunused-parameter] 7 | void print_trace(FILE *out, const char *file, int line) | ~~~~^~~~ [ 67%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/GraphFromFasta.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/analysis/GraphFromFasta.cc.o -MF CMakeFiles/GraphFromFasta.dir/analysis/GraphFromFasta.cc.o.d -o CMakeFiles/GraphFromFasta.dir/analysis/GraphFromFasta.cc.o -c /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/QuantifyGraph.cc:250:10: warning: ISO C++ forbids variable length array ‘kmerseq’ [-Wvla] 250 | char kmerseq [kmer_length + 1]; | ^~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/QuantifyGraph.cc: In function ‘int main(int, char**)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/QuantifyGraph.cc:372:29: warning: unused variable ‘prevNode’ [-Wunused-variable] 372 | int prevNode = parser.AsInt(1); | ^~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/QuantifyGraph.cc:409:13: warning: unused variable ‘node’ [-Wunused-variable] 409 | int node = parser.AsInt(0); | ^~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/QuantifyGraph.cc:412:30: warning: unused variable ‘p2’ [-Wunused-variable] 412 | const char * p2 = s.c_str(); | ^~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/QuantifyGraph.cc:337:16: warning: unused variable ‘j’ [-Wunused-variable] 337 | int i, j; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/QuantifyGraph.cc:350:16: warning: unused variable ‘m’ [-Wunused-variable] 350 | size_t m = kmers.size(); | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/FileParser.cc: In member function ‘bool StringParser::IsString(int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter ‘index’ [-Wunused-parameter] 50 | bool StringParser::IsString(int index) | ~~~~^~~~~ [ 68%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/KmerTable.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -MD -MT CMakeFiles/GraphFromFasta.dir/analysis/KmerTable.cc.o -MF CMakeFiles/GraphFromFasta.dir/analysis/KmerTable.cc.o.d -o CMakeFiles/GraphFromFasta.dir/analysis/KmerTable.cc.o -c /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/KmerTable.cc [ 70%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/NonRedKmerTable.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/NonRedKmerTable.cc [ 71%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/util/mutil.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc [ 72%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/sequenceUtil.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/sequenceUtil.cc [ 74%] Building CXX object CMakeFiles/QuantifyGraph.dir/base/StringUtil.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/StringUtil.cc /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function ‘bool SimpleHalves(const DNAVector&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function ‘float align_get_per_id(const DNAVector&, const DNAVector&, int, int, int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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) | ~~~~^ [ 75%] Linking CXX executable BubbleUpClustering /usr/bin/cmake -E cmake_link_script CMakeFiles/BubbleUpClustering.dir/link.txt --verbose=1 /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In member function ‘bool Welder::Weldable(const DNAVector&, int, const DNAVector&, int, int, std::string&, unsigned int&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:523:13: warning: unused variable ‘i’ [-Wunused-variable] 523 | int i; | ^ /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/BubbleUpClustering.dir/aligns/KmerAlignCore.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/AACodons.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/BubbleUpClustering.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/DNAVector.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/DeBruijnGraph.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/KmerTable.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/NonRedKmerTable.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/sequenceUtil.cc.o CMakeFiles/BubbleUpClustering.dir/analysis/stacktrace.cc.o CMakeFiles/BubbleUpClustering.dir/base/ErrorHandling.cc.o CMakeFiles/BubbleUpClustering.dir/base/FileParser.cc.o CMakeFiles/BubbleUpClustering.dir/base/StringUtil.cc.o CMakeFiles/BubbleUpClustering.dir/util/mutil.cc.o -o BubbleUpClustering /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function ‘void report_iworm_graph(std::map&, std::map&, std::map&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ [ 77%] Linking CXX executable Chrysalis /usr/bin/cmake -E cmake_link_script CMakeFiles/Chrysalis.dir/link.txt --verbose=1 /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function ‘svec sl_cluster_pools(std::map&, std::map&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:847:40: warning: implicitly-declared ‘Pool& Pool::operator=(const Pool&)’ is deprecated [-Wdeprecated-copy] 847 | pool_vec[oldpool_id] = tmp; | ^~~ In file included from /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:19: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/Pool.h:24:5: note: because ‘Pool’ has user-provided ‘Pool::Pool(const Pool&)’ 24 | Pool(const Pool& p) { | ^~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function ‘void add_scaffolds_to_clusters(std::map&, std::string, vecDNAVector&, int, float)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function ‘void add_iworm_link(std::map&, int, int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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; | ^ In file included from /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:19: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/Pool.h:24:5: note: because ‘Pool’ has user-provided ‘Pool::Pool(const Pool&)’ 24 | Pool(const Pool& p) { | ^~~~ /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/Chrysalis.dir/aligns/KmerAlignCore.cc.o CMakeFiles/Chrysalis.dir/analysis/AACodons.cc.o CMakeFiles/Chrysalis.dir/analysis/Chrysalis.cc.o CMakeFiles/Chrysalis.dir/analysis/DNAVector.cc.o CMakeFiles/Chrysalis.dir/analysis/TranscriptomeGraph.cc.o CMakeFiles/Chrysalis.dir/base/ErrorHandling.cc.o CMakeFiles/Chrysalis.dir/base/FileParser.cc.o CMakeFiles/Chrysalis.dir/base/StringUtil.cc.o CMakeFiles/Chrysalis.dir/util/mutil.cc.o -o Chrysalis /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function ‘int main(int, char**)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/GraphFromFasta.cc:1310:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1310 | for (i=0; i 3) | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function ‘kmer_int_type_t kmer_to_intval(std::string)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/sequenceUtil.cc:264:32: warning: array subscript has type ‘char’ [-Wchar-subscripts] 264 | int val = _base_to_int[c]; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/KmerTable.cc: In member function ‘long long int KmerSequence::BasesToNumber(const DNAVector&, int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/KmerTable.cc:27:13: warning: unused variable ‘i’ [-Wunused-variable] 27 | long long i; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In member function ‘virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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) { | ^~~~~~~ ~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:303:51: warning: unused parameter ‘pData’ [-Wunused-parameter] 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) | ~~~~~~~^~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:303:63: warning: unused parameter ‘lenInBytes’ [-Wunused-parameter] 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) | ~~~~~^~~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In member function ‘virtual bool CMAsciiReadFileStream::ReadString(CMString&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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) { | ^~~~~~~ ~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In member function ‘virtual bool CMAsciiWriteFileStream::WriteBlob(const void*, long int, long int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:526:65: warning: unused parameter ‘lenInElements’ [-Wunused-parameter] 526 | bool CMAsciiWriteFileStream::WriteBlob(const void * pData, long lenInElements, long elSize) | ~~~~~^~~~~~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:526:85: warning: unused parameter ‘elSize’ [-Wunused-parameter] 526 | bool CMAsciiWriteFileStream::WriteBlob(const void * pData, long lenInElements, long elSize) | ~~~~~^~~~~~ [ 81%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/sequenceUtil.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/sequenceUtil.cc /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In function ‘void MLog(const MCL_TCHAR*, bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:738:53: warning: unused parameter ‘bLineFeed’ [-Wunused-parameter] 738 | MDLLEXPORT void MLog(const MCL_TCHAR * szText, bool bLineFeed) | ~~~~~^~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In function ‘void MLog(const MCL_TCHAR*, long int, bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In function ‘void MLog(const MCL_TCHAR*, const MCL_TCHAR*, bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In function ‘void MCLSetUTF8Encode(bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:1288:39: warning: unused parameter ‘b’ [-Wunused-parameter] 1288 | MDLLEXPORT void MCLSetUTF8Encode(bool b) | ~~~~~^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In function ‘bool AddUTF8Sig(CMString&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:1688:16: warning: unused variable ‘p’ [-Wunused-variable] 1688 | const char * p = (const char*)string; | ^ [ 82%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/stacktrace.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/stacktrace.cc [ 84%] Building CXX object CMakeFiles/GraphFromFasta.dir/base/ErrorHandling.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/ErrorHandling.cc [ 85%] Building CXX object CMakeFiles/GraphFromFasta.dir/base/FileParser.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/FileParser.cc [ 87%] Linking CXX executable CreateIwormFastaBundle /usr/bin/cmake -E cmake_link_script CMakeFiles/CreateIwormFastaBundle.dir/link.txt --verbose=1 /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In member function ‘virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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:461, from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/string.h:26, from /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.h:19, from /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:9: /usr/include/stdio.h:410:12: note: by argument 2 of type ‘const char*’ to ‘int fscanf(FILE*, const char*, ...)’ declared here 410 | extern int __REDIRECT (fscanf, (FILE *__restrict __stream, | ^~~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:311:8: note: ‘szText’ declared here 311 | char szText[2048 * 10]; | ^~~~~~ /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/CreateIwormFastaBundle.dir/analysis/AACodons.cc.o CMakeFiles/CreateIwormFastaBundle.dir/analysis/CreateIwormFastaBundle.cc.o CMakeFiles/CreateIwormFastaBundle.dir/analysis/DNAVector.cc.o CMakeFiles/CreateIwormFastaBundle.dir/base/ErrorHandling.cc.o CMakeFiles/CreateIwormFastaBundle.dir/base/FileParser.cc.o CMakeFiles/CreateIwormFastaBundle.dir/base/StringUtil.cc.o CMakeFiles/CreateIwormFastaBundle.dir/util/mutil.cc.o -o CreateIwormFastaBundle /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/ErrorHandling.cc: In function ‘void print_trace(FILE*, const char*, int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/ErrorHandling.cc:7:51: warning: unused parameter ‘line’ [-Wunused-parameter] 7 | void print_trace(FILE *out, const char *file, int line) | ~~~~^~~~ [ 88%] Building CXX object CMakeFiles/GraphFromFasta.dir/base/StringUtil.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/StringUtil.cc /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function ‘bool contains_non_gatc(std::string)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/sequenceUtil.cc:33:26: warning: array subscript has type ‘char’ [-Wchar-subscripts] 33 | if (_base_to_int[c] > 3) | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function ‘kmer_int_type_t kmer_to_intval(std::string)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis_build' [ 88%] Built target CreateIwormFastaBundle [ 90%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/base/ErrorHandling.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/ErrorHandling.cc [ 91%] Building CXX object CMakeFiles/GraphFromFasta.dir/util/mutil.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc [ 92%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/base/FileParser.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/FileParser.cc /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/FileParser.cc: In member function ‘bool StringParser::IsString(int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter ‘index’ [-Wunused-parameter] 50 | bool StringParser::IsString(int index) | ~~~~^~~~~ [ 94%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/base/StringUtil.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/StringUtil.cc /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In member function ‘virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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) { | ^~~~~~~ ~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:303:51: warning: unused parameter ‘pData’ [-Wunused-parameter] 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) | ~~~~~~~^~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:303:63: warning: unused parameter ‘lenInBytes’ [-Wunused-parameter] 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) | ~~~~~^~~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In member function ‘virtual bool CMAsciiReadFileStream::ReadString(CMString&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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) { | ^~~~~~~ ~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In member function ‘virtual bool CMAsciiWriteFileStream::WriteBlob(const void*, long int, long int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:526:65: warning: unused parameter ‘lenInElements’ [-Wunused-parameter] 526 | bool CMAsciiWriteFileStream::WriteBlob(const void * pData, long lenInElements, long elSize) | ~~~~~^~~~~~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In function ‘void MLog(const MCL_TCHAR*, bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:738:53: warning: unused parameter ‘bLineFeed’ [-Wunused-parameter] 738 | MDLLEXPORT void MLog(const MCL_TCHAR * szText, bool bLineFeed) | ~~~~~^~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In function ‘void MLog(const MCL_TCHAR*, long int, bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In function ‘void MLog(const MCL_TCHAR*, const MCL_TCHAR*, bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In function ‘void MCLSetUTF8Encode(bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:1288:39: warning: unused parameter ‘b’ [-Wunused-parameter] 1288 | MDLLEXPORT void MCLSetUTF8Encode(bool b) | ~~~~~^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In function ‘bool AddUTF8Sig(CMString&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:1688:16: warning: unused variable ‘p’ [-Wunused-variable] 1688 | const char * p = (const char*)string; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/ErrorHandling.cc: In function ‘void print_trace(FILE*, const char*, int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In member function ‘virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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:461, from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/string.h:26, from /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.h:19, from /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:9: /usr/include/stdio.h:410:12: note: by argument 2 of type ‘const char*’ to ‘int fscanf(FILE*, const char*, ...)’ declared here 410 | extern int __REDIRECT (fscanf, (FILE *__restrict __stream, | ^~~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:311:8: note: ‘szText’ declared here 311 | char szText[2048 * 10]; | ^~~~~~ [ 95%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/util/mutil.cc.o /usr/bin/g++ -I/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/FileParser.cc: In member function ‘bool StringParser::IsString(int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter ‘index’ [-Wunused-parameter] 50 | bool StringParser::IsString(int index) | ~~~~^~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In member function ‘virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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) { | ^~~~~~~ ~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:303:51: warning: unused parameter ‘pData’ [-Wunused-parameter] 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) | ~~~~~~~^~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:303:63: warning: unused parameter ‘lenInBytes’ [-Wunused-parameter] 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) | ~~~~~^~~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In member function ‘virtual bool CMAsciiReadFileStream::ReadString(CMString&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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) { | ^~~~~~~ ~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In member function ‘virtual bool CMAsciiWriteFileStream::WriteBlob(const void*, long int, long int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:526:65: warning: unused parameter ‘lenInElements’ [-Wunused-parameter] 526 | bool CMAsciiWriteFileStream::WriteBlob(const void * pData, long lenInElements, long elSize) | ~~~~~^~~~~~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In function ‘void MLog(const MCL_TCHAR*, bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:738:53: warning: unused parameter ‘bLineFeed’ [-Wunused-parameter] 738 | MDLLEXPORT void MLog(const MCL_TCHAR * szText, bool bLineFeed) | ~~~~~^~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In function ‘void MLog(const MCL_TCHAR*, long int, bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In function ‘void MLog(const MCL_TCHAR*, const MCL_TCHAR*, bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In function ‘void MCLSetUTF8Encode(bool)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:1288:39: warning: unused parameter ‘b’ [-Wunused-parameter] 1288 | MDLLEXPORT void MCLSetUTF8Encode(bool b) | ~~~~~^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In function ‘bool AddUTF8Sig(CMString&)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:1688:16: warning: unused variable ‘p’ [-Wunused-variable] 1688 | const char * p = (const char*)string; | ^ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc: In member function ‘virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)’: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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:461, from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/string.h:26, from /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.h:19, from /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:9: /usr/include/stdio.h:410:12: note: by argument 2 of type ‘const char*’ to ‘int fscanf(FILE*, const char*, ...)’ declared here 410 | extern int __REDIRECT (fscanf, (FILE *__restrict __stream, | ^~~~~~~~~~ /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis/util/mutil.cc:311:8: note: ‘szText’ declared here 311 | char szText[2048 * 10]; | ^~~~~~ [ 97%] Linking CXX executable ReadsToTranscripts /usr/bin/cmake -E cmake_link_script CMakeFiles/ReadsToTranscripts.dir/link.txt --verbose=1 /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis_build' [ 98%] Linking CXX executable QuantifyGraph /usr/bin/cmake -E cmake_link_script CMakeFiles/QuantifyGraph.dir/link.txt --verbose=1 /usr/bin/g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/QuantifyGraph.dir/aligns/KmerAlignCore.cc.o CMakeFiles/QuantifyGraph.dir/analysis/AACodons.cc.o CMakeFiles/QuantifyGraph.dir/analysis/DNAVector.cc.o CMakeFiles/QuantifyGraph.dir/analysis/KmerTable.cc.o CMakeFiles/QuantifyGraph.dir/analysis/NonRedKmerTable.cc.o CMakeFiles/QuantifyGraph.dir/analysis/QuantifyGraph.cc.o CMakeFiles/QuantifyGraph.dir/base/ErrorHandling.cc.o CMakeFiles/QuantifyGraph.dir/base/FileParser.cc.o CMakeFiles/QuantifyGraph.dir/base/StringUtil.cc.o CMakeFiles/QuantifyGraph.dir/analysis/sequenceUtil.cc.o CMakeFiles/QuantifyGraph.dir/analysis/stacktrace.cc.o CMakeFiles/QuantifyGraph.dir/util/mutil.cc.o -o QuantifyGraph make[4]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis_build' [ 98%] Built target ReadsToTranscripts [ 98%] Built target QuantifyGraph [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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -lm -ldl -lrt -rdynamic CMakeFiles/GraphFromFasta.dir/aligns/KmerAlignCore.cc.o CMakeFiles/GraphFromFasta.dir/analysis/AACodons.cc.o CMakeFiles/GraphFromFasta.dir/analysis/DNAVector.cc.o CMakeFiles/GraphFromFasta.dir/analysis/DeBruijnGraph.cc.o CMakeFiles/GraphFromFasta.dir/analysis/GraphFromFasta.cc.o CMakeFiles/GraphFromFasta.dir/analysis/KmerTable.cc.o CMakeFiles/GraphFromFasta.dir/analysis/NonRedKmerTable.cc.o CMakeFiles/GraphFromFasta.dir/analysis/sequenceUtil.cc.o CMakeFiles/GraphFromFasta.dir/analysis/stacktrace.cc.o CMakeFiles/GraphFromFasta.dir/base/ErrorHandling.cc.o CMakeFiles/GraphFromFasta.dir/base/FileParser.cc.o CMakeFiles/GraphFromFasta.dir/base/StringUtil.cc.o CMakeFiles/GraphFromFasta.dir/util/mutil.cc.o -o GraphFromFasta make[4]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis_build' [100%] Built target GraphFromFasta make[3]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis_build' /usr/bin/cmake -E cmake_progress_start /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis_build/CMakeFiles 0 make[2]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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 -j10 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/slclust' X=`pwd`; \ for i in src; \ do echo '<<<' $i '>>>'; cd $X/$i; make all; done <<< src >>> make[3]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/slclust/src' g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -c -o slcluster.o slcluster.cpp g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -c -o graph.o graph.cpp g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -c -o graphnode.o graphnode.cpp g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cmd_line_opts.o cmd_line_opts.cpp g++ -Wl,-z,relro -Wl,-z,now slcluster.o graph.o graphnode.o cmd_line_opts.o -o slclust chmod 755 slclust make[3]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/slclust/src' make[2]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/slclust' cd trinity-plugins/scaffold_iworm_contigs && make -j10 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security ScaffoldIwormContigs.cpp error_checker.cpp -lhts -o scaffold_iworm_contigs make[2]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/scaffold_iworm_contigs' cd trinity-plugins/bamsifter && make -j10 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/bamsifter' g++ -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 make[2]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/bamsifter' cd trinity-plugins/seqtk-trinity && make -j10 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/seqtk-trinity' cc -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wno-unused-function -Wdate-time -D_FORTIFY_SOURCE=2 seqtk.c -o seqtk-trinity -lz -lm make[2]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/seqtk-trinity' make[1]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg' jh_build -a warning: [options] bootstrap class path not set in conjunction with -source 7 Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 1 warning Creating destination directory: "debian/_jh_build.javadoc/api/" ./Butterfly/Butterfly/src/src/My_DFS.java:30: warning - @param argument "roots" is not a parameter name. ./Butterfly/Butterfly/src/src/PairPath.java:124: warning - @param argument "isCircular" is not a parameter name. ./Butterfly/Butterfly/src/src/Read.java:18: warning - @param argument "toV" is not a parameter name. ./Butterfly/Butterfly/src/src/SeqVertex.java:80: warning - @param argument "nextID" is not a parameter name. ./Butterfly/Butterfly/src/src/SeqVertex.java:81: warning - @param argument "l" is not a parameter name. ./Butterfly/Butterfly/src/src/SeqVertex.java:155: warning - @param argument "_origButterflyID" is not a parameter name. ./Butterfly/Butterfly/src/src/SeqVertex.java:766: warning - @param argument "name" is not a parameter name. ./Butterfly/Butterfly/src/src/SeqVertex.java:767: warning - @param argument "weight" is not a parameter name. ./Butterfly/Butterfly/src/src/SeqVertex.java:768: warning - @param argument "name2" is not a parameter name. ./Butterfly/Butterfly/src/src/SeqVertex.java:769: warning - @param argument "weight2" is not a parameter name. ./Butterfly/Butterfly/src/src/TransAssembly_allProbPaths.java:15040: warning - @param argument "candidateNodes" is not a parameter name. ./Butterfly/Butterfly/src/src/TransAssembly_allProbPaths.java:15041: warning - @param argument "l" is not a parameter name. 12 warnings create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg' for target in Inchworm Chrysalis; do dh_auto_install \ --sourcedirectory=${target} --builddirectory=${target}_build; done cd Inchworm_build && make -j10 install DESTDIR=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build' /usr/bin/cmake -S/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm -B/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/debian/tmp/usr/bin/inchworm -- Installing: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/debian/tmp/usr/bin/FastaToDeBruijn -- Installing: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/debian/tmp/usr/bin/fastaToKmerCoverageStats make[2]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Inchworm_build' cd Chrysalis_build && make -j10 install DESTDIR=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis_build' /usr/bin/cmake -S/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis -B/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis_build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis_build' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/Chrysalis_build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/debian/tmp/usr/bin/Chrysalis -- Installing: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/debian/tmp/usr/bin/GraphFromFasta -- Installing: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/debian/tmp/usr/bin/QuantifyGraph -- Installing: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/debian/tmp/usr/bin/ReadsToTranscripts -- Installing: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/debian/tmp/usr/bin/BubbleUpClustering -- Installing: /build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/debian/tmp/usr/bin/CreateIwormFastaBundle make[2]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+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 -j10 install DESTDIR=/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/slclust' X=`pwd`; \ for i in src; \ do echo '<<<' $i '>>>'; cd $X/$i; make install; done <<< src >>> make[3]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/slclust/src' mv slclust ../bin/ make[3]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/slclust/src' make[2]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg/trinity-plugins/slclust' make[1]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg' debian/rules override_dh_install-arch make[1]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg' dh_install -a find debian/trinityrnaseq -name '*.p?' | xargs sed -i \ 's=^#!/usr/local/bin/perl=#!/usr/bin/perl=' chmod u+x \ debian/trinityrnaseq/usr/lib/trinityrnaseq/Analysis/DifferentialExpression/pairwise_summaries/class_to_separate_fpkm_matrices.pl \ debian/trinityrnaseq/usr/lib/trinityrnaseq/Analysis/FL_reconstruction_analysis/count_by_expression_quintile.pl \ debian/trinityrnaseq/usr/lib/trinityrnaseq/util/misc/capture_orig_n_unmapped_reads.pl \ debian/trinityrnaseq/usr/lib/trinityrnaseq/util/support_scripts/plugin_install_tests.sh \ debian/trinityrnaseq/usr/lib/trinityrnaseq/util/support_scripts/trinity_install_tests.sh chmod -R a-x debian/trinityrnaseq/usr/lib/trinityrnaseq/PerlLib/*.pm chmod -R a-x debian/trinityrnaseq/usr/lib/trinityrnaseq/PerlLib/*/*.pm find debian -name __pycache__ -type d | xargs rm -rf make[1]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg' jh_installjavadoc -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a jh_installlibs -a jh_classpath -a jh_manifest -a jh_exec -a jh_depends -a dh_strip_nondeterminism -a dh_compress -a debian/rules override_dh_fixperms make[1]: Entering directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg' dh_fixperms find debian -name genwig.sh -exec chmod +x \{\} \; for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/trinityrnaseq-GDdqzS/trinityrnaseq-2.13.2+dfsg' dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'trinityrnaseq-dbgsym' in '../trinityrnaseq-dbgsym_2.13.2+dfsg-3_amd64.deb'. dpkg-deb: building package 'trinityrnaseq' in '../trinityrnaseq_2.13.2+dfsg-3_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../trinityrnaseq_2.13.2+dfsg-3_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/trinityrnaseq-GDdqzS /tmp/trinityrnaseq-2.13.2+dfsg-3iw5i1yot I: cleaning package lists and apt cache... W: deleting files in /tmp: hsperfdata_root W: deleting files in /tmp: hsperfdata_builduser I: removing tempdir /tmp/mmdebstrap.t3ho_dzsWh... I: success in 1591.9644 seconds md5: trinityrnaseq-dbgsym_2.13.2+dfsg-3_amd64.deb: OK md5: trinityrnaseq_2.13.2+dfsg-3_amd64.deb: OK sha1: trinityrnaseq-dbgsym_2.13.2+dfsg-3_amd64.deb: OK sha1: trinityrnaseq_2.13.2+dfsg-3_amd64.deb: OK sha256: trinityrnaseq-dbgsym_2.13.2+dfsg-3_amd64.deb: OK sha256: trinityrnaseq_2.13.2+dfsg-3_amd64.deb: OK Checksums: OK