Diff of the two buildlogs: -- --- b1/build.log 2022-01-11 20:06:34.748814539 +0000 +++ b2/build.log 2022-01-11 20:10:58.708653542 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jan 11 07:19:22 -12 2022 -I: pbuilder-time-stamp: 1641928762 +I: Current time: Tue Feb 14 16:29:45 +14 2023 +I: pbuilder-time-stamp: 1676341785 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./trinityrnaseq_2.11.0+dfsg-6.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.7i03qiSi/trustedkeys.kbx': General error -gpgv: Signature made Tue Jan 19 01:18:29 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.aujeB0j2/trustedkeys.kbx': General error +gpgv: Signature made Wed Jan 20 03:18:29 2021 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./trinityrnaseq_2.11.0+dfsg-6.dsc @@ -49,135 +49,169 @@ dpkg-source: info: applying strip_m64 I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/30135/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2587150/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/2587150/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2587150/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='d44adf9d3c7d476c9efa33ef7585d414' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='30135' - PS1='# ' - PS2='> ' + INVOCATION_ID=078cd1ea39a64a7dbdd30b802a533034 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2587150 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.LFq8pEDwdJ/pbuilderrc_bV2Z --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.LFq8pEDwdJ/b1 --logfile b1/build.log trinityrnaseq_2.11.0+dfsg-6.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.LFq8pEDwdJ/pbuilderrc_F1E6 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.LFq8pEDwdJ/b2 --logfile b2/build.log trinityrnaseq_2.11.0+dfsg-6.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos11-amd64 5.10.0-10-amd64 #1 SMP Debian 5.10.84-1 (2021-12-08) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Aug 4 08:25 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Jul 28 07:09 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 69032 Jul 28 07:09 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 98048 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Jul 28 07:09 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Jul 28 07:09 more - -rwsr-xr-x 1 root root 55528 Jul 28 07:09 mount - -rwxr-xr-x 1 root root 18664 Jul 28 07:09 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jan 6 21:24 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Jul 28 07:09 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Jul 28 07:09 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Jul 28 07:09 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/30135/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Aug 5 2021 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Jul 29 2021 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 69032 Jul 29 2021 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 98048 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Jul 29 2021 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Jul 29 2021 more + -rwsr-xr-x 1 root root 55528 Jul 29 2021 mount + -rwxr-xr-x 1 root root 18664 Jul 29 2021 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 2021 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Feb 14 16:30 sh -> bash + lrwxrwxrwx 1 root root 4 Feb 10 05:47 sh.distrib -> dash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Jul 29 2021 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Jul 29 2021 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Jul 29 2021 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/2587150/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -784,7 +818,7 @@ Get: 495 http://deb.debian.org/debian bullseye/main amd64 salmon amd64 1.4.0+ds1-1+b4 [2221 kB] Get: 496 http://deb.debian.org/debian bullseye/main amd64 subread amd64 2.0.1+dfsg-1 [667 kB] Get: 497 http://deb.debian.org/debian bullseye/main amd64 tabix amd64 1.11-4 [339 kB] -Fetched 726 MB in 49s (14.8 MB/s) +Fetched 726 MB in 11s (68.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19655 files and directories currently installed.) @@ -2976,7 +3010,8 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/trinityrnaseq-2.11.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../trinityrnaseq_2.11.0+dfsg-6_source.changes +hostname: Name or service not known +I: Running cd /build/trinityrnaseq-2.11.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../trinityrnaseq_2.11.0+dfsg-6_source.changes dpkg-buildpackage: info: source package trinityrnaseq dpkg-buildpackage: info: source version 2.11.0+dfsg-6 dpkg-buildpackage: info: source distribution unstable @@ -2991,7 +3026,7 @@ --sourcedirectory=${target} --builddirectory=${target}_build; done for target in trinity-plugins/slclust trinity-plugins/scaffold_iworm_contigs trinity-plugins/bamsifter; do dh_auto_clean \ --sourcedirectory=${target}; done - cd trinity-plugins/slclust && make -j15 clean + cd trinity-plugins/slclust && make -j16 clean make[2]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/trinity-plugins/slclust' X=`pwd`; \ for i in src; \ @@ -3002,7 +3037,7 @@ ../bin/slclust make[3]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/trinity-plugins/slclust/src' make[2]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/trinity-plugins/slclust' - cd trinity-plugins/scaffold_iworm_contigs && make -j15 clean + cd trinity-plugins/scaffold_iworm_contigs && make -j16 clean make[2]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/trinity-plugins/scaffold_iworm_contigs' rm -f scaffold_iworm_contigs make[2]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/trinity-plugins/scaffold_iworm_contigs' @@ -3033,8 +3068,8 @@ make[3]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/trinity-plugins/slclust' cd COLLECTL && rm -rf "collectl-4.1.0" && rm -f collectl cd htslib && /usr/bin/make clean -/bin/sh: 1: cd: can't cd to htslib -make[2]: *** [Makefile:55: clean] Error 2 +/bin/sh: line 1: cd: htslib: No such file or directory +make[2]: *** [Makefile:55: clean] Error 1 make[2]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/trinity-plugins' make[1]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg' jh_clean @@ -3115,87 +3150,85 @@ make[1]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg' for target in Inchworm Chrysalis; do dh_auto_build \ --sourcedirectory=${target} --builddirectory=${target}_build; done - cd Inchworm_build && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 + cd Inchworm_build && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build' /usr/bin/cmake -S/build/trinityrnaseq-2.11.0+dfsg/Inchworm -B/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/trinityrnaseq-2.11.0+dfsg/Inchworm_build/CMakeFiles /build/trinityrnaseq-2.11.0+dfsg/Inchworm_build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build' make -f CMakeFiles/fastaToKmerCoverageStats.dir/build.make CMakeFiles/fastaToKmerCoverageStats.dir/depend -make[4]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build' -cd /build/trinityrnaseq-2.11.0+dfsg/Inchworm_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/trinityrnaseq-2.11.0+dfsg/Inchworm /build/trinityrnaseq-2.11.0+dfsg/Inchworm /build/trinityrnaseq-2.11.0+dfsg/Inchworm_build /build/trinityrnaseq-2.11.0+dfsg/Inchworm_build /build/trinityrnaseq-2.11.0+dfsg/Inchworm_build/CMakeFiles/fastaToKmerCoverageStats.dir/DependInfo.cmake --color= 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-2.11.0+dfsg/Inchworm_build' +cd /build/trinityrnaseq-2.11.0+dfsg/Inchworm_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/trinityrnaseq-2.11.0+dfsg/Inchworm /build/trinityrnaseq-2.11.0+dfsg/Inchworm /build/trinityrnaseq-2.11.0+dfsg/Inchworm_build /build/trinityrnaseq-2.11.0+dfsg/Inchworm_build /build/trinityrnaseq-2.11.0+dfsg/Inchworm_build/CMakeFiles/fastaToKmerCoverageStats.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build' cd /build/trinityrnaseq-2.11.0+dfsg/Inchworm_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/trinityrnaseq-2.11.0+dfsg/Inchworm /build/trinityrnaseq-2.11.0+dfsg/Inchworm /build/trinityrnaseq-2.11.0+dfsg/Inchworm_build /build/trinityrnaseq-2.11.0+dfsg/Inchworm_build /build/trinityrnaseq-2.11.0+dfsg/Inchworm_build/CMakeFiles/FastaToDeBruijn.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build' cd /build/trinityrnaseq-2.11.0+dfsg/Inchworm_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/trinityrnaseq-2.11.0+dfsg/Inchworm /build/trinityrnaseq-2.11.0+dfsg/Inchworm /build/trinityrnaseq-2.11.0+dfsg/Inchworm_build /build/trinityrnaseq-2.11.0+dfsg/Inchworm_build /build/trinityrnaseq-2.11.0+dfsg/Inchworm_build/CMakeFiles/inchworm.dir/DependInfo.cmake --color= -Dependee "/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build/CMakeFiles/FastaToDeBruijn.dir/DependInfo.cmake" is newer than depender "/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build/CMakeFiles/FastaToDeBruijn.dir/depend.internal". -Dependee "/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build/CMakeFiles/FastaToDeBruijn.dir/depend.internal". Dependee "/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build/CMakeFiles/fastaToKmerCoverageStats.dir/DependInfo.cmake" is newer than depender "/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build/CMakeFiles/fastaToKmerCoverageStats.dir/depend.internal". Dependee "/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build/CMakeFiles/fastaToKmerCoverageStats.dir/depend.internal". Dependee "/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build/CMakeFiles/inchworm.dir/DependInfo.cmake" is newer than depender "/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build/CMakeFiles/inchworm.dir/depend.internal". +Dependee "/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build/CMakeFiles/FastaToDeBruijn.dir/DependInfo.cmake" is newer than depender "/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build/CMakeFiles/FastaToDeBruijn.dir/depend.internal". +Dependee "/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build/CMakeFiles/FastaToDeBruijn.dir/depend.internal". Dependee "/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build/CMakeFiles/inchworm.dir/depend.internal". Scanning dependencies of target fastaToKmerCoverageStats Scanning dependencies of target FastaToDeBruijn +Scanning dependencies of target inchworm make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build' make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build' -Scanning dependencies of target inchworm make -f CMakeFiles/fastaToKmerCoverageStats.dir/build.make CMakeFiles/fastaToKmerCoverageStats.dir/build +make -f CMakeFiles/FastaToDeBruijn.dir/build.make CMakeFiles/FastaToDeBruijn.dir/build make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build' +make -f CMakeFiles/inchworm.dir/build.make CMakeFiles/inchworm.dir/build make[4]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build' -make -f CMakeFiles/FastaToDeBruijn.dir/build.make CMakeFiles/FastaToDeBruijn.dir/build make[4]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build' -make -f CMakeFiles/inchworm.dir/build.make CMakeFiles/inchworm.dir/build make[4]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build' -[ 3%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/fastaToKmerCoverageStats.cpp.o -[ 7%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/FastaToDeBruijn.cpp.o -/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/fastaToKmerCoverageStats.dir/src/fastaToKmerCoverageStats.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp -[ 10%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/argProcessor.cpp.o +[ 3%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/FastaToDeBruijn.cpp.o +[ 14%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/fastaToKmerCoverageStats.cpp.o [ 14%] Building CXX object CMakeFiles/inchworm.dir/src/Fasta_entry.cpp.o +[ 14%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/sequenceUtil.cpp.o +[ 17%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/argProcessor.cpp.o +[ 25%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/argProcessor.cpp.o +[ 25%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/Fasta_entry.cpp.o +[ 28%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_reader.cpp.o +[ 32%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/string_util.cpp.o +/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/fastaToKmerCoverageStats.dir/src/fastaToKmerCoverageStats.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp /usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/fastaToKmerCoverageStats.dir/src/argProcessor.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/argProcessor.cpp -/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/inchworm.dir/src/Fasta_entry.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/Fasta_entry.cpp +/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_reader.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/Fasta_reader.cpp /usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/FastaToDeBruijn.dir/src/FastaToDeBruijn.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/FastaToDeBruijn.cpp -[ 21%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/Fasta_reader.cpp.o -[ 21%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/argProcessor.cpp.o -[ 25%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_reader.cpp.o -[ 28%] Building CXX object CMakeFiles/inchworm.dir/src/IRKE_run.cpp.o +/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/inchworm.dir/src/Fasta_entry.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/Fasta_entry.cpp +/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/fastaToKmerCoverageStats.dir/src/sequenceUtil.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/sequenceUtil.cpp +[ 35%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/Fasta_reader.cpp.o +/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/fastaToKmerCoverageStats.dir/src/string_util.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/string_util.cpp /usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/FastaToDeBruijn.dir/src/argProcessor.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/argProcessor.cpp -/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_reader.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/Fasta_reader.cpp -/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/inchworm.dir/src/IRKE_run.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/IRKE_run.cpp -[ 32%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_entry.cpp.o /usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/FastaToDeBruijn.dir/src/Fasta_reader.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/Fasta_reader.cpp -/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_entry.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/Fasta_entry.cpp -[ 35%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o -[ 39%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/sequenceUtil.cpp.o -[ 42%] Building CXX object CMakeFiles/inchworm.dir/src/sequenceUtil.cpp.o -/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/fastaToKmerCoverageStats.dir/src/sequenceUtil.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/sequenceUtil.cpp -[ 46%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/Fasta_entry.cpp.o /usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/FastaToDeBruijn.dir/src/Fasta_entry.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/Fasta_entry.cpp +[ 39%] Building CXX object CMakeFiles/inchworm.dir/src/sequenceUtil.cpp.o +[ 42%] Building CXX object CMakeFiles/inchworm.dir/src/IRKE.cpp.o /usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/inchworm.dir/src/sequenceUtil.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/sequenceUtil.cpp -[ 50%] Building CXX object CMakeFiles/inchworm.dir/src/IRKE.cpp.o -[ 53%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/string_util.cpp.o -/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/sequenceUtil.cpp -/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/fastaToKmerCoverageStats.dir/src/string_util.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/string_util.cpp /usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/inchworm.dir/src/IRKE.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/IRKE.cpp +[ 46%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_entry.cpp.o +[ 50%] Building CXX object CMakeFiles/inchworm.dir/src/IRKE_run.cpp.o +/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/fastaToKmerCoverageStats.dir/src/Fasta_entry.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/Fasta_entry.cpp +/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/inchworm.dir/src/IRKE_run.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/IRKE_run.cpp +[ 57%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o +[ 57%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/stacktrace.cpp.o +/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/fastaToKmerCoverageStats.dir/src/stacktrace.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/stacktrace.cpp +/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/sequenceUtil.cpp In file included from /usr/include/c++/10/ext/hash_map:60, from /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/KmerCounter.hpp:53, from /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/IRKE.hpp:7, - from /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/IRKE_run.cpp:11: + from /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp:20: /usr/include/c++/10/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++/10/ext/hash_map:60, from /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/KmerCounter.hpp:53, from /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/IRKE.hpp:7, - from /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp:20: + from /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/IRKE_run.cpp:11: /usr/include/c++/10/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-2.11.0+dfsg/Inchworm/src/FastaToDeBruijn.cpp: In function 'void createGraphPerRecord(std::vector >, int, bool, ArgProcessor)': -/build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/FastaToDeBruijn.cpp:215:39: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 215 | if (seq_region.size() < kmer_length) { continue; } // can be encountered in jaccard-clip mode (rarely) - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ In file included from /usr/include/c++/10/ext/hash_map:60, from /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/KmerCounter.hpp:53, from /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/IRKE.hpp:7, @@ -3203,25 +3236,25 @@ /usr/include/c++/10/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ +[ 60%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/KmerCounter.cpp.o +/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/fastaToKmerCoverageStats.dir/src/KmerCounter.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/KmerCounter.cpp +[ 64%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/string_util.cpp.o +/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/FastaToDeBruijn.dir/src/string_util.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/string_util.cpp +[ 67%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/stacktrace.cpp.o +/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/FastaToDeBruijn.dir/src/stacktrace.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/stacktrace.cpp +[ 71%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/DeBruijnGraph.cpp.o +/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/FastaToDeBruijn.dir/src/DeBruijnGraph.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/DeBruijnGraph.cpp /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp: In function 'void populate_kmer_counter_from_reads(KmerCounter&, std::string&)': /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp:231:18: warning: unused variable 'kmer_length' [-Wunused-variable] 231 | unsigned int kmer_length = kcounter.get_kmer_length(); | ^~~~~~~~~~~ -[ 57%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/stacktrace.cpp.o -/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/fastaToKmerCoverageStats.dir/src/stacktrace.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/stacktrace.cpp -[ 60%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/string_util.cpp.o -/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/FastaToDeBruijn.dir/src/string_util.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/string_util.cpp -[ 64%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/stacktrace.cpp.o -/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/FastaToDeBruijn.dir/src/stacktrace.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/stacktrace.cpp -[ 67%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/KmerCounter.cpp.o -/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/fastaToKmerCoverageStats.dir/src/KmerCounter.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/KmerCounter.cpp In file included from /usr/include/c++/10/ext/hash_map:60, from /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/KmerCounter.hpp:53, from /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/KmerCounter.cpp:1: /usr/include/c++/10/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 \ | ^~~~~~~ -[ 71%] Building CXX object CMakeFiles/inchworm.dir/src/KmerCounter.cpp.o +[ 75%] Building CXX object CMakeFiles/inchworm.dir/src/KmerCounter.cpp.o /usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/inchworm.dir/src/KmerCounter.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/KmerCounter.cpp In file included from /usr/include/c++/10/ext/hash_map:60, from /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/KmerCounter.hpp:53, @@ -3229,23 +3262,22 @@ /usr/include/c++/10/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ -[ 75%] Building CXX object CMakeFiles/inchworm.dir/src/string_util.cpp.o +/build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/FastaToDeBruijn.cpp: In function 'void createGraphPerRecord(std::vector >, int, bool, ArgProcessor)': +/build/trinityrnaseq-2.11.0+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) + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +[ 78%] Building CXX object CMakeFiles/inchworm.dir/src/string_util.cpp.o /usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/inchworm.dir/src/string_util.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/string_util.cpp -[ 78%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/DeBruijnGraph.cpp.o -/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/FastaToDeBruijn.dir/src/DeBruijnGraph.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/DeBruijnGraph.cpp [ 82%] Building CXX object CMakeFiles/inchworm.dir/src/Fasta_reader.cpp.o /usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/inchworm.dir/src/Fasta_reader.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/Fasta_reader.cpp [ 85%] Building CXX object CMakeFiles/inchworm.dir/src/stacktrace.cpp.o /usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/inchworm.dir/src/stacktrace.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/stacktrace.cpp -[ 89%] Building CXX object CMakeFiles/inchworm.dir/src/argProcessor.cpp.o -/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/inchworm.dir/src/argProcessor.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/argProcessor.cpp -/build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp:250:9: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized] - 250 | #pragma omp parallel private (myTid) - | ^~~ /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/DeBruijnGraph.cpp: In member function 'std::string DeBruijnKmer::get_annotations_string()': /build/trinityrnaseq-2.11.0+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++) { | ~~^~~~~~~~~~~~~~~~~~~~~ +[ 89%] Building CXX object CMakeFiles/inchworm.dir/src/argProcessor.cpp.o +/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -o CMakeFiles/inchworm.dir/src/argProcessor.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/argProcessor.cpp /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/DeBruijnGraph.cpp: In member function 'std::string DeBruijnGraph::toDOT(bool)': /build/trinityrnaseq-2.11.0+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++) { @@ -3257,6 +3289,9 @@ /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/DeBruijnGraph.cpp:725:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 725 | for (int i = 0; i < collected_kmers.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~ +/build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp:250:9: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized] + 250 | #pragma omp parallel private (myTid) + | ^~~ [ 92%] Linking CXX executable fastaToKmerCoverageStats /usr/bin/cmake -E cmake_link_script CMakeFiles/fastaToKmerCoverageStats.dir/link.txt --verbose=1 /usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+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 @@ -3275,7 +3310,7 @@ make[3]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build' /usr/bin/cmake -E cmake_progress_start /build/trinityrnaseq-2.11.0+dfsg/Inchworm_build/CMakeFiles 0 make[2]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build' - cd Chrysalis_build && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 + cd Chrysalis_build && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' /usr/bin/cmake -S/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -B/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build//CMakeFiles/progress.marks @@ -3286,85 +3321,87 @@ 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 -f CMakeFiles/Chrysalis.dir/build.make CMakeFiles/Chrysalis.dir/depend make[4]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' cd /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/trinityrnaseq-2.11.0+dfsg/Chrysalis /build/trinityrnaseq-2.11.0+dfsg/Chrysalis /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build /build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis_build' -cd /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/trinityrnaseq-2.11.0+dfsg/Chrysalis /build/trinityrnaseq-2.11.0+dfsg/Chrysalis /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles/ReadsToTranscripts.dir/DependInfo.cmake --color= +cd /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/trinityrnaseq-2.11.0+dfsg/Chrysalis /build/trinityrnaseq-2.11.0+dfsg/Chrysalis /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles/BubbleUpClustering.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' -cd /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/trinityrnaseq-2.11.0+dfsg/Chrysalis /build/trinityrnaseq-2.11.0+dfsg/Chrysalis /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles/GraphFromFasta.dir/DependInfo.cmake --color= +cd /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/trinityrnaseq-2.11.0+dfsg/Chrysalis /build/trinityrnaseq-2.11.0+dfsg/Chrysalis /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles/ReadsToTranscripts.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' cd /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/trinityrnaseq-2.11.0+dfsg/Chrysalis /build/trinityrnaseq-2.11.0+dfsg/Chrysalis /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles/QuantifyGraph.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' -cd /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/trinityrnaseq-2.11.0+dfsg/Chrysalis /build/trinityrnaseq-2.11.0+dfsg/Chrysalis /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build 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/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles/Chrysalis.dir/DependInfo.cmake --color= +Dependee "/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles/CreateIwormFastaBundle.dir/DependInfo.cmake" is newer than depender "/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles/CreateIwormFastaBundle.dir/depend.internal". +Dependee "/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles/CreateIwormFastaBundle.dir/depend.internal". 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Dependee "/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles/QuantifyGraph.dir/depend.internal". -Dependee "/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles/BubbleUpClustering.dir/DependInfo.cmake" is newer than depender "/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles/BubbleUpClustering.dir/depend.internal". -Dependee "/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles/BubbleUpClustering.dir/depend.internal". -Scanning dependencies of target QuantifyGraph -Scanning dependencies of target BubbleUpClustering -make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' -make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' -Scanning dependencies of target ReadsToTranscripts 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make[4]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' -make -f CMakeFiles/Chrysalis.dir/build.make CMakeFiles/Chrysalis.dir/build +Scanning dependencies of target Chrysalis +Scanning dependencies of target QuantifyGraph +Scanning dependencies of target BubbleUpClustering +make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' Scanning dependencies of target GraphFromFasta -make[4]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' +make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' +make -f CMakeFiles/QuantifyGraph.dir/build.make CMakeFiles/QuantifyGraph.dir/build +make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' +make -f CMakeFiles/BubbleUpClustering.dir/build.make CMakeFiles/BubbleUpClustering.dir/build make -f CMakeFiles/GraphFromFasta.dir/build.make 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CMakeFiles/ReadsToTranscripts.dir/analysis/DNAVector.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/DNAVector.cc +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/ReadsToTranscripts.dir/analysis/NonRedKmerTable.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/CreateIwormFastaBundle.dir/base/StringUtil.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/StringUtil.cc +[ 14%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/ReadsToTranscripts.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/ReadsToTranscripts.dir/analysis/AACodons.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/AACodons.cc +[ 16%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/util/mutil.cc.o +[ 19%] Building CXX object CMakeFiles/QuantifyGraph.dir/aligns/KmerAlignCore.cc.o +[ 19%] Building CXX object CMakeFiles/BubbleUpClustering.dir/aligns/KmerAlignCore.cc.o +[ 20%] Building CXX object CMakeFiles/GraphFromFasta.dir/aligns/KmerAlignCore.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o 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-I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/GraphFromFasta.dir/aligns/KmerAlignCore.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/CreateIwormFastaBundle.dir/util/mutil.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/ReadsToTranscripts.dir/analysis/ReadsToTranscripts.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/ReadsToTranscripts.cc +[ 22%] Building CXX object CMakeFiles/Chrysalis.dir/aligns/KmerAlignCore.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/Chrysalis.dir/aligns/KmerAlignCore.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc +[ 23%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/sequenceUtil.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/ReadsToTranscripts.dir/analysis/sequenceUtil.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/ErrorHandling.cc: In function 'void print_trace(FILE*, const char*, int)': /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/ErrorHandling.cc:7:24: warning: unused parameter 'out' [-Wunused-parameter] 7 | void print_trace(FILE *out, const char *file, int line) @@ -3375,8 +3412,56 @@ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/ErrorHandling.cc:7:51: warning: unused parameter 'line' [-Wunused-parameter] 7 | void print_trace(FILE *out, const char *file, int line) | ~~~~^~~~ -[ 23%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/base/FileParser.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/CreateIwormFastaBundle.dir/base/FileParser.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/FileParser.cc +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': +/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/util/mutil.cc:303:51: warning: unused parameter 'pData' [-Wunused-parameter] + 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) + | ~~~~~~~^~~~~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc:303:63: warning: unused parameter 'lenInBytes' [-Wunused-parameter] + 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) + | ~~~~~^~~~~~~~~~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadString(CMString&)': +/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiWriteFileStream::WriteBlob(const void*, long int, long int)': +/build/trinityrnaseq-2.11.0+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-2.11.0+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-2.11.0+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-2.11.0+dfsg/Chrysalis/util/mutil.cc: In function 'void MLog(const MCL_TCHAR*, bool)': +/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/util/mutil.cc: In function 'void MLog(const MCL_TCHAR*, long int, bool)': +/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/util/mutil.cc: In function 'void MLog(const MCL_TCHAR*, const MCL_TCHAR*, bool)': +/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/util/mutil.cc: In function 'void MCLSetUTF8Encode(bool)': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc:1288:39: warning: unused parameter 'b' [-Wunused-parameter] + 1288 | MDLLEXPORT void MCLSetUTF8Encode(bool b) + | ~~~~~^ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc: In function 'bool AddUTF8Sig(CMString&)': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc:1688:16: warning: unused variable 'p' [-Wunused-variable] + 1688 | const char * p = (const char*)string; + | ^ +[ 25%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/AACodons.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/BubbleUpClustering.dir/analysis/AACodons.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/AACodons.cc +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/FileParser.cc: In member function 'bool StringParser::IsString(int)': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter 'index' [-Wunused-parameter] + 50 | bool StringParser::IsString(int index) + | ~~~~^~~~~ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function 'void KmerAlignCore::AddData(const vecDNAVector&, const vecNumVector&, int)': /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc:79:49: warning: unused variable 't' [-Wunused-variable] 79 | KmerAlignCoreRecordStoreTable & t = m_table; // not used? @@ -3409,28 +3494,6 @@ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc:291:9: warning: unused variable 'i' [-Wunused-variable] 291 | int i; | ^ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'void DeBruijnKmer::add_next_kmer(kmer_int_type_t, unsigned int)': -/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::SetUp(const vecDNAVector&, bool)': -/build/trinityrnaseq-2.11.0+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-2.11.0+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-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::AddData(const vecDNAVector&)': -/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::AddData(vecDNAVectorStream&)': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:125:9: warning: unused variable 'i' [-Wunused-variable] - 125 | int i, j; - | ^ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function 'void KmerAlignCore::AddData(const vecDNAVector&, const vecNumVector&, int)': /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc:79:49: warning: unused variable 't' [-Wunused-variable] 79 | KmerAlignCoreRecordStoreTable & t = m_table; // not used? @@ -3463,28 +3526,44 @@ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc:291:9: warning: unused variable 'i' [-Wunused-variable] 291 | int i; | ^ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'std::vector DeBruijnGraph::deconvolute_DS_mirror_graph()': -/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'std::vector > DeBruijnGraph::get_candidate_weldmers(kmer_int_type_t, int)': -/build/trinityrnaseq-2.11.0+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-2.11.0+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-2.11.0+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-2.11.0+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-2.11.0+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-2.11.0+dfsg/Chrysalis/base/FileParser.cc: In member function 'bool StringParser::IsString(int)': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter 'index' [-Wunused-parameter] - 50 | bool StringParser::IsString(int index) - | ~~~~^~~~~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc: In function 'int main(int, char**)': +/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc:143:10: warning: unused variable 'DEBUG' [-Wunused-variable] + 143 | bool DEBUG = P.GetBoolValueFor(debugCmmd); + | ^~~~~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc:166:12: warning: unused variable 'pOut' [-Wunused-variable] + 166 | FILE * pOut = NULL; + | ^~~~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::SetUp(const vecDNAVector&, bool)': +/build/trinityrnaseq-2.11.0+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-2.11.0+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-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::AddData(const vecDNAVector&)': +/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::AddData(vecDNAVectorStream&)': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:125:9: warning: unused variable 'i' [-Wunused-variable] + 125 | int i, j; + | ^ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'bool contains_non_gatc(std::string)': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc:33:19: warning: array subscript has type 'char' [-Wchar-subscripts] + 33 | if (_base_to_int[c] > 3) + | ^ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'kmer_int_type_t kmer_to_intval(std::string)': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc:264:25: warning: array subscript has type 'char' [-Wchar-subscripts] + 264 | int val = _base_to_int[c]; + | ^ +[ 26%] Building CXX object CMakeFiles/Chrysalis.dir/analysis/AACodons.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/Chrysalis.dir/analysis/AACodons.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/AACodons.cc /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function 'void KmerAlignCore::AddData(const vecDNAVector&, const vecNumVector&, int)': /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc:79:49: warning: unused variable 't' [-Wunused-variable] 79 | KmerAlignCoreRecordStoreTable & t = m_table; // not used? @@ -3513,20 +3592,12 @@ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc:159:12: warning: unused variable 'j' [-Wunused-variable] 159 | int i, j; | ^ +[ 27%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/AACodons.cc.o /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function 'void KmerAlignCore::MergeSortFilter(svec&, const svec&, const svec&)': /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc:291:9: warning: unused variable 'i' [-Wunused-variable] 291 | int i; | ^ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc: In function 'int main(int, char**)': -/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc:143:10: warning: unused variable 'DEBUG' [-Wunused-variable] - 143 | bool DEBUG = P.GetBoolValueFor(debugCmmd); - | ^~~~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc:166:12: warning: unused variable 'pOut' [-Wunused-variable] - 166 | FILE * pOut = NULL; - | ^~~~ +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/GraphFromFasta.dir/analysis/AACodons.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/AACodons.cc /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function 'void KmerAlignCore::AddData(const vecDNAVector&, const vecNumVector&, int)': /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc:79:49: warning: unused variable 't' [-Wunused-variable] 79 | KmerAlignCoreRecordStoreTable & t = m_table; // not used? @@ -3559,6 +3630,28 @@ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc:291:9: warning: unused variable 'i' [-Wunused-variable] 291 | int i; | ^ +[ 29%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/stacktrace.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/ReadsToTranscripts.dir/analysis/stacktrace.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/stacktrace.cc +[ 30%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/BubbleUpClustering.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/BubbleUpClustering.dir/analysis/BubbleUpClustering.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/BubbleUpClustering.cc +[ 32%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/AACodons.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/QuantifyGraph.dir/analysis/AACodons.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/AACodons.cc +[ 33%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/DNAVector.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/QuantifyGraph.dir/analysis/DNAVector.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/DNAVector.cc +[ 35%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/base/ErrorHandling.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/ReadsToTranscripts.dir/base/ErrorHandling.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/ErrorHandling.cc +[ 36%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/base/FileParser.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/ReadsToTranscripts.dir/base/FileParser.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/FileParser.cc +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/ErrorHandling.cc: In function 'void print_trace(FILE*, const char*, int)': +/build/trinityrnaseq-2.11.0+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-2.11.0+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-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/BubbleUpClustering.cc: In function 'svec grow_prioritized_clusters(std::string&, std::map&)': /build/trinityrnaseq-2.11.0+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) { @@ -3571,6 +3664,9 @@ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/Pool.h:24:5: note: because 'Pool' has user-provided 'Pool::Pool(const Pool&)' 24 | Pool(const Pool& p) { | ^~~~ +[ 38%] Building CXX object CMakeFiles/Chrysalis.dir/analysis/Chrysalis.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/Chrysalis.dir/analysis/Chrysalis.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/Chrysalis.cc +[ 39%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/base/StringUtil.cc.o /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/BubbleUpClustering.cc: In function 'void populate_weld_reinforced_iworm_clusters(std::string&, std::map&)': /build/trinityrnaseq-2.11.0+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; @@ -3579,6 +3675,7 @@ /build/trinityrnaseq-2.11.0+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++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/ReadsToTranscripts.dir/base/StringUtil.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/StringUtil.cc /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/BubbleUpClustering.cc: In function 'int main(int, char**)': /build/trinityrnaseq-2.11.0+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++) { @@ -3586,200 +3683,41 @@ /build/trinityrnaseq-2.11.0+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++) { | ~~^~~~~~~~~~ -[ 25%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/base/StringUtil.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/CreateIwormFastaBundle.dir/base/StringUtil.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/StringUtil.cc -[ 26%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/AACodons.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/QuantifyGraph.dir/analysis/AACodons.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/AACodons.cc -[ 27%] Building CXX object CMakeFiles/Chrysalis.dir/analysis/AACodons.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/Chrysalis.dir/analysis/AACodons.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/AACodons.cc -[ 29%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/AACodons.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/GraphFromFasta.dir/analysis/AACodons.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/AACodons.cc -[ 30%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/util/mutil.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/CreateIwormFastaBundle.dir/util/mutil.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc -[ 32%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/KmerTable.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/BubbleUpClustering.dir/analysis/KmerTable.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/KmerTable.cc -[ 33%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/ReadsToTranscripts.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/ReadsToTranscripts.dir/analysis/ReadsToTranscripts.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/ReadsToTranscripts.cc -[ 35%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/NonRedKmerTable.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/BubbleUpClustering.dir/analysis/NonRedKmerTable.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc -[ 36%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/sequenceUtil.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/ReadsToTranscripts.dir/analysis/sequenceUtil.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc -[ 38%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/sequenceUtil.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/BubbleUpClustering.dir/analysis/sequenceUtil.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': -/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/util/mutil.cc:303:51: warning: unused parameter 'pData' [-Wunused-parameter] - 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) - | ~~~~~~~^~~~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc:303:63: warning: unused parameter 'lenInBytes' [-Wunused-parameter] - 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) - | ~~~~~^~~~~~~~~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadString(CMString&)': -/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiWriteFileStream::WriteBlob(const void*, long int, long int)': -/build/trinityrnaseq-2.11.0+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-2.11.0+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-2.11.0+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-2.11.0+dfsg/Chrysalis/util/mutil.cc: In function 'void MLog(const MCL_TCHAR*, bool)': -/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/util/mutil.cc: In function 'void MLog(const MCL_TCHAR*, long int, bool)': -/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/util/mutil.cc: In function 'void MLog(const MCL_TCHAR*, const MCL_TCHAR*, bool)': -/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/util/mutil.cc: In function 'void MCLSetUTF8Encode(bool)': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc:1288:39: warning: unused parameter 'b' [-Wunused-parameter] - 1288 | MDLLEXPORT void MCLSetUTF8Encode(bool b) - | ~~~~~^ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc: In function 'bool AddUTF8Sig(CMString&)': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc:1688:16: warning: unused variable 'p' [-Wunused-variable] - 1688 | const char * p = (const char*)string; - | ^ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/KmerTable.cc: In member function 'long long int KmerSequence::BasesToNumber(const DNAVector&, int)': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/KmerTable.cc:27:13: warning: unused variable 'i' [-Wunused-variable] - 27 | long long i; - | ^ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::SetUp(const vecDNAVector&, bool)': -/build/trinityrnaseq-2.11.0+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-2.11.0+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-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::AddData(const vecDNAVector&)': -/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::AddData(vecDNAVectorStream&)': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:125:9: warning: unused variable 'i' [-Wunused-variable] - 125 | int i, j; - | ^ -[ 39%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/stacktrace.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/ReadsToTranscripts.dir/analysis/stacktrace.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/stacktrace.cc -[ 41%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/stacktrace.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/BubbleUpClustering.dir/analysis/stacktrace.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/stacktrace.cc -[ 42%] Building CXX object CMakeFiles/BubbleUpClustering.dir/base/ErrorHandling.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/BubbleUpClustering.dir/base/ErrorHandling.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/ErrorHandling.cc -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'bool contains_non_gatc(std::string)': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc:33:19: warning: array subscript has type 'char' [-Wchar-subscripts] - 33 | if (_base_to_int[c] > 3) - | ^ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'kmer_int_type_t kmer_to_intval(std::string)': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc:264:25: warning: array subscript has type 'char' [-Wchar-subscripts] - 264 | int val = _base_to_int[c]; - | ^ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'bool contains_non_gatc(std::string)': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc:33:19: warning: array subscript has type 'char' [-Wchar-subscripts] - 33 | if (_base_to_int[c] > 3) - | ^ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'kmer_int_type_t kmer_to_intval(std::string)': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc:264:25: warning: array subscript has type 'char' [-Wchar-subscripts] - 264 | int val = _base_to_int[c]; - | ^ -[ 44%] Building CXX object CMakeFiles/BubbleUpClustering.dir/base/FileParser.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/BubbleUpClustering.dir/base/FileParser.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/FileParser.cc -[ 45%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/base/ErrorHandling.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/ReadsToTranscripts.dir/base/ErrorHandling.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/ErrorHandling.cc -[ 47%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/base/FileParser.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/ReadsToTranscripts.dir/base/FileParser.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/FileParser.cc -[ 48%] Building CXX object CMakeFiles/BubbleUpClustering.dir/base/StringUtil.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/BubbleUpClustering.dir/base/StringUtil.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/StringUtil.cc -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/ErrorHandling.cc: In function 'void print_trace(FILE*, const char*, int)': -/build/trinityrnaseq-2.11.0+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-2.11.0+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-2.11.0+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-2.11.0+dfsg/Chrysalis/base/ErrorHandling.cc: In function 'void print_trace(FILE*, const char*, int)': -/build/trinityrnaseq-2.11.0+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-2.11.0+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-2.11.0+dfsg/Chrysalis/base/ErrorHandling.cc:7:51: warning: unused parameter 'line' [-Wunused-parameter] - 7 | void print_trace(FILE *out, const char *file, int line) - | ~~~~^~~~ +[ 41%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/DNAVector.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/GraphFromFasta.dir/analysis/DNAVector.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/DNAVector.cc /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/FileParser.cc: In member function 'bool StringParser::IsString(int)': /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter 'index' [-Wunused-parameter] 50 | bool StringParser::IsString(int index) | ~~~~^~~~~ -[ 50%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/base/StringUtil.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/ReadsToTranscripts.dir/base/StringUtil.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/StringUtil.cc -[ 51%] Building CXX object CMakeFiles/BubbleUpClustering.dir/util/mutil.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/BubbleUpClustering.dir/util/mutil.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc -[ 52%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/util/mutil.cc.o +[ 42%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/DNAVector.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/BubbleUpClustering.dir/analysis/DNAVector.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/DNAVector.cc +[ 44%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/util/mutil.cc.o /usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/ReadsToTranscripts.dir/util/mutil.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc -[ 54%] Building CXX object CMakeFiles/Chrysalis.dir/analysis/Chrysalis.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/Chrysalis.dir/analysis/Chrysalis.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/Chrysalis.cc -[ 55%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/DNAVector.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/GraphFromFasta.dir/analysis/DNAVector.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/DNAVector.cc -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': -/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/util/mutil.cc:303:51: warning: unused parameter 'pData' [-Wunused-parameter] - 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) - | ~~~~~~~^~~~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc:303:63: warning: unused parameter 'lenInBytes' [-Wunused-parameter] - 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) - | ~~~~~^~~~~~~~~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadString(CMString&)': -/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiWriteFileStream::WriteBlob(const void*, long int, long int)': -/build/trinityrnaseq-2.11.0+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-2.11.0+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-2.11.0+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-2.11.0+dfsg/Chrysalis/util/mutil.cc: In function 'void MLog(const MCL_TCHAR*, bool)': -/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/util/mutil.cc: In function 'void MLog(const MCL_TCHAR*, long int, bool)': -/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/util/mutil.cc: In function 'void MLog(const MCL_TCHAR*, const MCL_TCHAR*, bool)': -/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/util/mutil.cc: In function 'void MCLSetUTF8Encode(bool)': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc:1288:39: warning: unused parameter 'b' [-Wunused-parameter] - 1288 | MDLLEXPORT void MCLSetUTF8Encode(bool b) - | ~~~~~^ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc: In function 'bool AddUTF8Sig(CMString&)': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc:1688:16: warning: unused variable 'p' [-Wunused-variable] - 1688 | const char * p = (const char*)string; - | ^ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/Chrysalis.cc: In function 'int main(int, char**)': +/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/Chrysalis.cc:570:16: warning: unused variable 'pOut' [-Wunused-variable] + 570 | FILE * pOut = NULL; + | ^~~~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/Chrysalis.cc:342:10: warning: unused variable 'bSkip' [-Wunused-variable] + 342 | bool bSkip = P.GetBoolValueFor(skipCmmd); + | ^~~~~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/Chrysalis.cc:347:9: warning: unused variable 'pairDist' [-Wunused-variable] + 347 | int pairDist = P.GetIntValueFor(distCmmd); + | ^~~~~~~~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/Chrysalis.cc:354:10: warning: variable 'bBreak' set but not used [-Wunused-but-set-variable] + 354 | bool bBreak = true; + | ^~~~~~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/Chrysalis.cc:359:10: warning: unused variable 'bButt' [-Wunused-variable] + 359 | bool bButt = P.GetBoolValueFor(buttCmmd); + | ^~~~~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/Chrysalis.cc:361:10: warning: unused variable 'max_reads' [-Wunused-variable] + 361 | long max_reads = P.GetLongValueFor(maxReadsCmd); + | ^~~~~~~~~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/Chrysalis.cc:372:10: warning: unused variable 'DEBUG' [-Wunused-variable] + 372 | bool DEBUG = P.GetBoolValueFor(debugCmmd); + | ^~~~~ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': /build/trinityrnaseq-2.11.0+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) { @@ -3790,6 +3728,7 @@ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc:303:63: warning: unused parameter 'lenInBytes' [-Wunused-parameter] 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) | ~~~~~^~~~~~~~~~ +[ 45%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/DeBruijnGraph.cc.o /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadString(CMString&)': /build/trinityrnaseq-2.11.0+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) { @@ -3816,64 +3755,36 @@ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc:787:80: warning: unused parameter 'bLineFeed' [-Wunused-parameter] 787 | MDLLEXPORT void MLog(const MCL_TCHAR * szText, const MCL_TCHAR * szText2, bool bLineFeed) | ~~~~~^~~~~~~~~ +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/BubbleUpClustering.dir/analysis/DeBruijnGraph.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/DeBruijnGraph.cc +/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/util/mutil.cc: In function 'void MCLSetUTF8Encode(bool)': /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc:1288:39: warning: unused parameter 'b' [-Wunused-parameter] 1288 | MDLLEXPORT void MCLSetUTF8Encode(bool b) | ~~~~~^ +[ 47%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/DeBruijnGraph.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/GraphFromFasta.dir/analysis/DeBruijnGraph.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/DeBruijnGraph.cc /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc: In function 'bool AddUTF8Sig(CMString&)': /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc:1688:16: warning: unused variable 'p' [-Wunused-variable] 1688 | const char * p = (const char*)string; | ^ -[ 57%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/DeBruijnGraph.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/GraphFromFasta.dir/analysis/DeBruijnGraph.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/DeBruijnGraph.cc -[ 58%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/DNAVector.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/QuantifyGraph.dir/analysis/DNAVector.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/DNAVector.cc -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/FileParser.cc: In member function 'bool StringParser::IsString(int)': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter 'index' [-Wunused-parameter] - 50 | bool StringParser::IsString(int index) - | ~~~~^~~~~ -[ 60%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/KmerTable.cc.o +[ 48%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/KmerTable.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/BubbleUpClustering.dir/analysis/KmerTable.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/KmerTable.cc +[ 50%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/KmerTable.cc.o /usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/QuantifyGraph.dir/analysis/KmerTable.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/KmerTable.cc -[ 61%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/NonRedKmerTable.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/QuantifyGraph.dir/analysis/NonRedKmerTable.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/Chrysalis.cc: In function 'int main(int, char**)': -/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/Chrysalis.cc:570:16: warning: unused variable 'pOut' [-Wunused-variable] - 570 | FILE * pOut = NULL; - | ^~~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/Chrysalis.cc:342:10: warning: unused variable 'bSkip' [-Wunused-variable] - 342 | bool bSkip = P.GetBoolValueFor(skipCmmd); - | ^~~~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/Chrysalis.cc:347:9: warning: unused variable 'pairDist' [-Wunused-variable] - 347 | int pairDist = P.GetIntValueFor(distCmmd); - | ^~~~~~~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/Chrysalis.cc:354:10: warning: variable 'bBreak' set but not used [-Wunused-but-set-variable] - 354 | bool bBreak = true; - | ^~~~~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/Chrysalis.cc:359:10: warning: unused variable 'bButt' [-Wunused-variable] - 359 | bool bButt = P.GetBoolValueFor(buttCmmd); - | ^~~~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/Chrysalis.cc:361:10: warning: unused variable 'max_reads' [-Wunused-variable] - 361 | long max_reads = P.GetLongValueFor(maxReadsCmd); - | ^~~~~~~~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/Chrysalis.cc:372:10: warning: unused variable 'DEBUG' [-Wunused-variable] - 372 | bool DEBUG = P.GetBoolValueFor(debugCmmd); - | ^~~~~ +[ 51%] Building CXX object CMakeFiles/Chrysalis.dir/analysis/DNAVector.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/Chrysalis.dir/analysis/DNAVector.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/DNAVector.cc /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'void DeBruijnKmer::add_next_kmer(kmer_int_type_t, unsigned int)': /build/trinityrnaseq-2.11.0+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-2.11.0+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()); - | ~~~~~~^~~~~~~~~~~~~~~~~ +[ 52%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/GraphFromFasta.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/GraphFromFasta.dir/analysis/GraphFromFasta.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/GraphFromFasta.cc /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/KmerTable.cc: In member function 'long long int KmerSequence::BasesToNumber(const DNAVector&, int)': /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/KmerTable.cc:27:13: warning: unused variable 'i' [-Wunused-variable] 27 | long long i; | ^ -[ 63%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/QuantifyGraph.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/QuantifyGraph.dir/analysis/QuantifyGraph.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/QuantifyGraph.cc /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'std::vector DeBruijnGraph::deconvolute_DS_mirror_graph()': /build/trinityrnaseq-2.11.0+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; @@ -3892,97 +3803,34 @@ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/DeBruijnGraph.cc:527:41: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 527 | if (kmer_extension_chars.size() == flank_extension_length) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 64%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/GraphFromFasta.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/GraphFromFasta.dir/analysis/GraphFromFasta.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/GraphFromFasta.cc -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::SetUp(const vecDNAVector&, bool)': -/build/trinityrnaseq-2.11.0+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-2.11.0+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-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::AddData(const vecDNAVector&)': -/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::AddData(vecDNAVectorStream&)': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:125:9: warning: unused variable 'i' [-Wunused-variable] - 125 | int i, j; - | ^ -[ 66%] Building CXX object CMakeFiles/QuantifyGraph.dir/base/ErrorHandling.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/QuantifyGraph.dir/base/ErrorHandling.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/ErrorHandling.cc -[ 67%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/KmerTable.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/GraphFromFasta.dir/analysis/KmerTable.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/KmerTable.cc -[ 69%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/NonRedKmerTable.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/GraphFromFasta.dir/analysis/NonRedKmerTable.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc -[ 70%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/sequenceUtil.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/GraphFromFasta.dir/analysis/sequenceUtil.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/ErrorHandling.cc: In function 'void print_trace(FILE*, const char*, int)': -/build/trinityrnaseq-2.11.0+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-2.11.0+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-2.11.0+dfsg/Chrysalis/base/ErrorHandling.cc:7:51: warning: unused parameter 'line' [-Wunused-parameter] - 7 | void print_trace(FILE *out, const char *file, int line) - | ~~~~^~~~ -[ 72%] Building CXX object CMakeFiles/QuantifyGraph.dir/base/FileParser.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/QuantifyGraph.dir/base/FileParser.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/FileParser.cc -[ 73%] Building CXX object CMakeFiles/QuantifyGraph.dir/base/StringUtil.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/QuantifyGraph.dir/base/StringUtil.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/StringUtil.cc -[ 75%] Linking CXX executable CreateIwormFastaBundle -/usr/bin/cmake -E cmake_link_script CMakeFiles/CreateIwormFastaBundle.dir/link.txt --verbose=1 -/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/QuantifyGraph.cc: In function 'int main(int, char**)': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/QuantifyGraph.cc:348:8: warning: unused variable 'prevNode' [-Wunused-variable] - 348 | int prevNode = parser.AsInt(1); - | ^~~~~~~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/QuantifyGraph.cc:380:7: warning: unused variable 'node' [-Wunused-variable] - 380 | int node = parser.AsInt(0); - | ^~~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/QuantifyGraph.cc:383:16: warning: unused variable 'p2' [-Wunused-variable] - 383 | const char * p2 = s.c_str(); - | ^~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/QuantifyGraph.cc:313:9: warning: unused variable 'j' [-Wunused-variable] - 313 | int i, j; - | ^ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/QuantifyGraph.cc:326:9: warning: unused variable 'm' [-Wunused-variable] - 326 | size_t m = kmers.size(); - | ^ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::SetUp(const vecDNAVector&, bool)': -/build/trinityrnaseq-2.11.0+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-2.11.0+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-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::AddData(const vecDNAVector&)': -/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::AddData(vecDNAVectorStream&)': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:125:9: warning: unused variable 'i' [-Wunused-variable] - 125 | int i, j; - | ^ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'void DeBruijnKmer::add_next_kmer(kmer_int_type_t, unsigned int)': +/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/KmerTable.cc: In member function 'long long int KmerSequence::BasesToNumber(const DNAVector&, int)': /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/KmerTable.cc:27:13: warning: unused variable 'i' [-Wunused-variable] 27 | long long i; | ^ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'bool contains_non_gatc(std::string)': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc:33:19: warning: array subscript has type 'char' [-Wchar-subscripts] - 33 | if (_base_to_int[c] > 3) - | ^ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'kmer_int_type_t kmer_to_intval(std::string)': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc:264:25: warning: array subscript has type 'char' [-Wchar-subscripts] - 264 | int val = _base_to_int[c]; - | ^ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'std::vector DeBruijnGraph::deconvolute_DS_mirror_graph()': +/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/DeBruijnGraph.cc: In member function 'std::vector > DeBruijnGraph::get_candidate_weldmers(kmer_int_type_t, int)': +/build/trinityrnaseq-2.11.0+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-2.11.0+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-2.11.0+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-2.11.0+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-2.11.0+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) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +[ 54%] Building CXX object CMakeFiles/QuantifyGraph.dir/analysis/NonRedKmerTable.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/QuantifyGraph.dir/analysis/NonRedKmerTable.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'bool SimpleHalves(const DNAVector&)': /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/GraphFromFasta.cc:272:15: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 271 | ( (! DISABLE_REPEAT_CHECK) @@ -4023,8 +3871,6 @@ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/Pool.h:24:5: note: because 'Pool' has user-provided 'Pool::Pool(const Pool&)' 24 | Pool(const Pool& p) { | ^~~~ -[ 76%] Linking CXX executable BubbleUpClustering -/usr/bin/cmake -E cmake_link_script CMakeFiles/BubbleUpClustering.dir/link.txt --verbose=1 /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/GraphFromFasta.cc: In function 'int main(int, char**)': /build/trinityrnaseq-2.11.0+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&, DNAVector&)': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc:547:16: warning: unused variable 'plusminus' [-Wunused-variable] + 547 | static int plusminus = 0; + | ^~~~~~~~~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc: In function 'int TranscriptomeGraph(vecDNAVector&, FILE*, int, bool)': +/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc:647:10: warning: unused variable 'bAppend' [-Wunused-variable] + 647 | bool bAppend = true; + | ^~~~~~~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::SetUp(const vecDNAVector&, bool)': +/build/trinityrnaseq-2.11.0+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-2.11.0+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-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::AddData(const vecDNAVector&)': +/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::AddData(vecDNAVectorStream&)': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:125:9: warning: unused variable 'i' [-Wunused-variable] + 125 | int i, j; + | ^ +[ 63%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/NonRedKmerTable.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/GraphFromFasta.dir/analysis/NonRedKmerTable.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc +[ 64%] Linking CXX executable CreateIwormFastaBundle +/usr/bin/cmake -E cmake_link_script CMakeFiles/CreateIwormFastaBundle.dir/link.txt --verbose=1 +/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/QuantifyGraph.cc: In function 'int main(int, char**)': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/QuantifyGraph.cc:348:8: warning: unused variable 'prevNode' [-Wunused-variable] + 348 | int prevNode = parser.AsInt(1); + | ^~~~~~~~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/QuantifyGraph.cc:380:7: warning: unused variable 'node' [-Wunused-variable] + 380 | int node = parser.AsInt(0); + | ^~~~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/QuantifyGraph.cc:383:16: warning: unused variable 'p2' [-Wunused-variable] + 383 | const char * p2 = s.c_str(); + | ^~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/QuantifyGraph.cc:313:9: warning: unused variable 'j' [-Wunused-variable] + 313 | int i, j; + | ^ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/QuantifyGraph.cc:326:9: warning: unused variable 'm' [-Wunused-variable] + 326 | size_t m = kmers.size(); + | ^ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc: At global scope: +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc:547:16: warning: 'plusminus' defined but not used [-Wunused-variable] + 547 | static int plusminus = 0; + | ^~~~~~~~~ +[ 66%] Linking CXX executable ReadsToTranscripts +/usr/bin/cmake -E cmake_link_script CMakeFiles/ReadsToTranscripts.dir/link.txt --verbose=1 +/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+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 +[ 67%] Building CXX object CMakeFiles/QuantifyGraph.dir/base/ErrorHandling.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/QuantifyGraph.dir/base/ErrorHandling.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/ErrorHandling.cc +make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' +[ 67%] Built target CreateIwormFastaBundle +[ 69%] Building CXX object CMakeFiles/BubbleUpClustering.dir/analysis/stacktrace.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/BubbleUpClustering.dir/analysis/stacktrace.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/stacktrace.cc +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'bool contains_non_gatc(std::string)': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc:33:19: warning: array subscript has type 'char' [-Wchar-subscripts] + 33 | if (_base_to_int[c] > 3) + | ^ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'kmer_int_type_t kmer_to_intval(std::string)': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc:264:25: warning: array subscript has type 'char' [-Wchar-subscripts] + 264 | int val = _base_to_int[c]; + | ^ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::SetUp(const vecDNAVector&, bool)': +/build/trinityrnaseq-2.11.0+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-2.11.0+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-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::AddData(const vecDNAVector&)': +/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::AddData(vecDNAVectorStream&)': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.cc:125:9: warning: unused variable 'i' [-Wunused-variable] + 125 | int i, j; + | ^ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/ErrorHandling.cc: In function 'void print_trace(FILE*, const char*, int)': +/build/trinityrnaseq-2.11.0+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-2.11.0+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-2.11.0+dfsg/Chrysalis/base/ErrorHandling.cc:7:51: warning: unused parameter 'line' [-Wunused-parameter] + 7 | void print_trace(FILE *out, const char *file, int line) + | ~~~~^~~~ +[ 70%] Building CXX object CMakeFiles/QuantifyGraph.dir/base/FileParser.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/QuantifyGraph.dir/base/FileParser.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/FileParser.cc +make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' +[ 70%] Built target ReadsToTranscripts +[ 72%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/sequenceUtil.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/GraphFromFasta.dir/analysis/sequenceUtil.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc +[ 73%] Building CXX object CMakeFiles/BubbleUpClustering.dir/base/ErrorHandling.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/BubbleUpClustering.dir/base/ErrorHandling.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/ErrorHandling.cc +[ 75%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/stacktrace.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/GraphFromFasta.dir/analysis/stacktrace.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/stacktrace.cc +[ 76%] Building CXX object CMakeFiles/BubbleUpClustering.dir/base/FileParser.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/BubbleUpClustering.dir/base/FileParser.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/FileParser.cc +[ 77%] Building CXX object CMakeFiles/BubbleUpClustering.dir/base/StringUtil.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/BubbleUpClustering.dir/base/StringUtil.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/StringUtil.cc +[ 79%] Building CXX object CMakeFiles/BubbleUpClustering.dir/util/mutil.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/BubbleUpClustering.dir/util/mutil.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/FileParser.cc: In member function 'bool StringParser::IsString(int)': /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter 'index' [-Wunused-parameter] 50 | bool StringParser::IsString(int index) | ~~~~^~~~~ -make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' -[ 76%] Built target CreateIwormFastaBundle -[ 77%] Building CXX object CMakeFiles/QuantifyGraph.dir/util/mutil.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/QuantifyGraph.dir/util/mutil.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc -[ 79%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/stacktrace.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/GraphFromFasta.dir/analysis/stacktrace.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/stacktrace.cc -make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' -[ 79%] Built target BubbleUpClustering +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/ErrorHandling.cc: In function 'void print_trace(FILE*, const char*, int)': +/build/trinityrnaseq-2.11.0+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-2.11.0+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-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'bool contains_non_gatc(std::string)': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc:33:19: warning: array subscript has type 'char' [-Wchar-subscripts] + 33 | if (_base_to_int[c] > 3) + | ^ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc: In function 'kmer_int_type_t kmer_to_intval(std::string)': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/sequenceUtil.cc:264:25: warning: array subscript has type 'char' [-Wchar-subscripts] + 264 | int val = _base_to_int[c]; + | ^ [ 80%] Building CXX object CMakeFiles/GraphFromFasta.dir/base/ErrorHandling.cc.o /usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/GraphFromFasta.dir/base/ErrorHandling.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/ErrorHandling.cc [ 82%] Building CXX object CMakeFiles/GraphFromFasta.dir/base/FileParser.cc.o /usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/GraphFromFasta.dir/base/FileParser.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/FileParser.cc -[ 83%] Building CXX object CMakeFiles/GraphFromFasta.dir/base/StringUtil.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/GraphFromFasta.dir/base/StringUtil.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/StringUtil.cc /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': /build/trinityrnaseq-2.11.0+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) { @@ -4100,12 +4104,14 @@ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc:1288:39: warning: unused parameter 'b' [-Wunused-parameter] 1288 | MDLLEXPORT void MCLSetUTF8Encode(bool b) | ~~~~~^ -[ 85%] Building CXX object CMakeFiles/GraphFromFasta.dir/util/mutil.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/GraphFromFasta.dir/util/mutil.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc: In function 'bool AddUTF8Sig(CMString&)': /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc:1688:16: warning: unused variable 'p' [-Wunused-variable] 1688 | const char * p = (const char*)string; | ^ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/FileParser.cc: In member function 'bool StringParser::IsString(int)': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter 'index' [-Wunused-parameter] + 50 | bool StringParser::IsString(int index) + | ~~~~^~~~~ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/ErrorHandling.cc: In function 'void print_trace(FILE*, const char*, int)': /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/ErrorHandling.cc:7:24: warning: unused parameter 'out' [-Wunused-parameter] 7 | void print_trace(FILE *out, const char *file, int line) @@ -4116,18 +4122,23 @@ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/ErrorHandling.cc:7:51: warning: unused parameter 'line' [-Wunused-parameter] 7 | void print_trace(FILE *out, const char *file, int line) | ~~~~^~~~ -[ 86%] Building CXX object CMakeFiles/Chrysalis.dir/analysis/DNAVector.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/Chrysalis.dir/analysis/DNAVector.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/DNAVector.cc -[ 88%] Building CXX object CMakeFiles/Chrysalis.dir/analysis/TranscriptomeGraph.cc.o -/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/Chrysalis.dir/analysis/TranscriptomeGraph.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc -[ 89%] Building CXX object CMakeFiles/Chrysalis.dir/base/ErrorHandling.cc.o +[ 83%] Building CXX object CMakeFiles/GraphFromFasta.dir/base/StringUtil.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/GraphFromFasta.dir/base/StringUtil.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/StringUtil.cc +[ 85%] Building CXX object CMakeFiles/GraphFromFasta.dir/util/mutil.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/GraphFromFasta.dir/util/mutil.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc +[ 86%] Building CXX object CMakeFiles/Chrysalis.dir/base/ErrorHandling.cc.o /usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/Chrysalis.dir/base/ErrorHandling.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/ErrorHandling.cc +[ 88%] Building CXX object CMakeFiles/QuantifyGraph.dir/base/StringUtil.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/QuantifyGraph.dir/base/StringUtil.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/StringUtil.cc +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/FileParser.cc: In member function 'bool StringParser::IsString(int)': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter 'index' [-Wunused-parameter] + 50 | bool StringParser::IsString(int index) + | ~~~~^~~~~ +[ 89%] Building CXX object CMakeFiles/QuantifyGraph.dir/util/mutil.cc.o +/usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/QuantifyGraph.dir/util/mutil.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc [ 91%] Building CXX object CMakeFiles/Chrysalis.dir/base/FileParser.cc.o /usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/Chrysalis.dir/base/FileParser.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/FileParser.cc -[ 92%] Linking CXX executable ReadsToTranscripts -/usr/bin/cmake -E cmake_link_script CMakeFiles/ReadsToTranscripts.dir/link.txt --verbose=1 -/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+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 -[ 94%] Building CXX object CMakeFiles/Chrysalis.dir/base/StringUtil.cc.o +[ 92%] Building CXX object CMakeFiles/Chrysalis.dir/base/StringUtil.cc.o /usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/Chrysalis.dir/base/StringUtil.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/StringUtil.cc /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc:313:14: warning: passing argument 1 to 'restrict'-qualified parameter aliases with argument 4 [-Wrestrict] @@ -4153,6 +4164,16 @@ /build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/base/ErrorHandling.cc: In function 'void print_trace(FILE*, const char*, int)': +/build/trinityrnaseq-2.11.0+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-2.11.0+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-2.11.0+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-2.11.0+dfsg/Chrysalis/util/mutil.cc: In function 'void MLog(const MCL_TCHAR*, bool)': /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc:738:53: warning: unused parameter 'bLineFeed' [-Wunused-parameter] 738 | MDLLEXPORT void MLog(const MCL_TCHAR * szText, bool bLineFeed) @@ -4173,24 +4194,52 @@ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc:1688:16: warning: unused variable 'p' [-Wunused-variable] 1688 | const char * p = (const char*)string; | ^ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/FileParser.cc: In member function 'bool StringParser::IsString(int)': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter 'index' [-Wunused-parameter] - 50 | bool StringParser::IsString(int index) - | ~~~~^~~~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/ErrorHandling.cc: In function 'void print_trace(FILE*, const char*, int)': -/build/trinityrnaseq-2.11.0+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-2.11.0+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-2.11.0+dfsg/Chrysalis/base/ErrorHandling.cc:7:51: warning: unused parameter 'line' [-Wunused-parameter] - 7 | void print_trace(FILE *out, const char *file, int line) - | ~~~~^~~~ -[ 95%] Building CXX object CMakeFiles/Chrysalis.dir/util/mutil.cc.o +[ 94%] Building CXX object CMakeFiles/Chrysalis.dir/util/mutil.cc.o /usr/bin/g++ -I/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pipe -W -Wall -Wpedantic -fopenmp -pthread -o CMakeFiles/Chrysalis.dir/util/mutil.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc -make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' -[ 95%] Built target ReadsToTranscripts +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': +/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/util/mutil.cc:303:51: warning: unused parameter 'pData' [-Wunused-parameter] + 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) + | ~~~~~~~^~~~~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc:303:63: warning: unused parameter 'lenInBytes' [-Wunused-parameter] + 303 | bool CMAsciiReadFileStream::ReadSimpleType(void * pData, long lenInBytes) + | ~~~~~^~~~~~~~~~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadString(CMString&)': +/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/util/mutil.cc: In member function 'virtual bool CMAsciiWriteFileStream::WriteBlob(const void*, long int, long int)': +/build/trinityrnaseq-2.11.0+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-2.11.0+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-2.11.0+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-2.11.0+dfsg/Chrysalis/util/mutil.cc: In function 'void MLog(const MCL_TCHAR*, bool)': +/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/util/mutil.cc: In function 'void MLog(const MCL_TCHAR*, long int, bool)': +/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/util/mutil.cc: In function 'void MLog(const MCL_TCHAR*, const MCL_TCHAR*, bool)': +/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/util/mutil.cc: In function 'void MCLSetUTF8Encode(bool)': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc:1288:39: warning: unused parameter 'b' [-Wunused-parameter] + 1288 | MDLLEXPORT void MCLSetUTF8Encode(bool b) + | ~~~~~^ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc: In function 'bool AddUTF8Sig(CMString&)': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc:1688:16: warning: unused variable 'p' [-Wunused-variable] + 1688 | const char * p = (const char*)string; + | ^ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/FileParser.cc: In member function 'bool StringParser::IsString(int)': /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/FileParser.cc:50:33: warning: unused parameter 'index' [-Wunused-parameter] 50 | bool StringParser::IsString(int index) @@ -4227,10 +4276,6 @@ /build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc: In member function 'void KmerSequence::Setup()': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc:177:19: warning: unused variable 'i' [-Wunused-variable] - 177 | long long i; - | ^ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc: In function 'void MLog(const MCL_TCHAR*, const MCL_TCHAR*, bool)': /build/trinityrnaseq-2.11.0+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) @@ -4243,42 +4288,32 @@ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc:1688:16: warning: unused variable 'p' [-Wunused-variable] 1688 | const char * p = (const char*)string; | ^ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc: In member function 'void KmerSearch::Extend(long long int, DNAVector&, const svec&, DNAVector&)': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc:547:16: warning: unused variable 'plusminus' [-Wunused-variable] - 547 | static int plusminus = 0; - | ^~~~~~~~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc: In function 'int TranscriptomeGraph(vecDNAVector&, FILE*, int, bool)': -/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc:647:10: warning: unused variable 'bAppend' [-Wunused-variable] - 647 | bool bAppend = true; - | ^~~~~~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc: At global scope: -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc:547:16: warning: 'plusminus' defined but not used [-Wunused-variable] - 547 | static int plusminus = 0; - | ^~~~~~~~~ -[ 97%] Linking CXX executable QuantifyGraph -/usr/bin/cmake -E cmake_link_script CMakeFiles/QuantifyGraph.dir/link.txt --verbose=1 -/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+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/util/mutil.cc.o -o QuantifyGraph +[ 95%] Linking CXX executable BubbleUpClustering +/usr/bin/cmake -E cmake_link_script CMakeFiles/BubbleUpClustering.dir/link.txt --verbose=1 +/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+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 make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' -[ 97%] Built target QuantifyGraph -[ 98%] Linking CXX executable Chrysalis +[ 95%] Built target BubbleUpClustering +[ 97%] Linking CXX executable Chrysalis /usr/bin/cmake -E cmake_link_script CMakeFiles/Chrysalis.dir/link.txt --verbose=1 /usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+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 +make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' +[ 97%] Built target Chrysalis +[ 98%] Linking CXX executable QuantifyGraph +/usr/bin/cmake -E cmake_link_script CMakeFiles/QuantifyGraph.dir/link.txt --verbose=1 +/usr/bin/g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+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/util/mutil.cc.o -o QuantifyGraph +make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' +[ 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 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/Chrysalis_build' -[100%] Built target Chrysalis -make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' [100%] Built target GraphFromFasta make[3]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' /usr/bin/cmake -E cmake_progress_start /build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles 0 make[2]: Leaving directory '/build/trinityrnaseq-2.11.0+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 -j15 "INSTALL=install --strip-program=true" + cd trinity-plugins/slclust && make -j16 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/trinity-plugins/slclust' X=`pwd`; \ for i in src; \ @@ -4293,15 +4328,15 @@ chmod 755 slclust make[3]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/trinity-plugins/slclust/src' make[2]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/trinity-plugins/slclust' - cd trinity-plugins/scaffold_iworm_contigs && make -j15 "INSTALL=install --strip-program=true" + cd trinity-plugins/scaffold_iworm_contigs && make -j16 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/trinityrnaseq-2.11.0+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 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security ScaffoldIwormContigs.cpp error_checker.cpp -lhts -o scaffold_iworm_contigs make[2]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/trinity-plugins/scaffold_iworm_contigs' - cd trinity-plugins/bamsifter && make -j15 "INSTALL=install --strip-program=true" + cd trinity-plugins/bamsifter && make -j16 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/trinity-plugins/bamsifter' g++ -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/trinity-plugins/bamsifter' - cd trinity-plugins/seqtk-trinity && make -j15 "INSTALL=install --strip-program=true" + cd trinity-plugins/seqtk-trinity && make -j16 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/trinity-plugins/seqtk-trinity' cc -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/trinityrnaseq-2.11.0+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-2.11.0+dfsg/trinity-plugins/seqtk-trinity' @@ -13352,13 +13387,13 @@ -no shared node, alignment not cached, computing: [-1, 380, 982, 440] to [-1, 945] -path1s length: 94, path2s length: 59 -running Needleman-Wunsch alignment of path sequences -Jan 11, 2022 7:52:41 AM jaligner.NeedlemanWunschGotoh construct +Feb 14, 2023 4:32:46 PM jaligner.NeedlemanWunschGotoh construct INFO: Started... -Jan 11, 2022 7:52:42 AM jaligner.NeedlemanWunschGotoh construct +Feb 14, 2023 4:32:46 PM jaligner.NeedlemanWunschGotoh construct INFO: Finished. -Jan 11, 2022 7:52:42 AM jaligner.NeedlemanWunschGotoh traceback +Feb 14, 2023 4:32:46 PM jaligner.NeedlemanWunschGotoh traceback INFO: Started... -Jan 11, 2022 7:52:42 AM jaligner.NeedlemanWunschGotoh traceback +Feb 14, 2023 4:32:46 PM jaligner.NeedlemanWunschGotoh traceback INFO: Finished. A 1 GGCCACACGATGGCTTATCACGTCCACATTTCTACTGGCTACAAACAGAC 50 .|..||||||..|.| @@ -13889,7 +13924,7 @@ make[1]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg' for target in Inchworm Chrysalis; do dh_auto_install \ --sourcedirectory=${target} --builddirectory=${target}_build; done - cd Inchworm_build && make -j15 install DESTDIR=/build/trinityrnaseq-2.11.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd Inchworm_build && make -j16 install DESTDIR=/build/trinityrnaseq-2.11.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build' /usr/bin/cmake -S/build/trinityrnaseq-2.11.0+dfsg/Inchworm -B/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -13903,7 +13938,7 @@ -- Installing: /build/trinityrnaseq-2.11.0+dfsg/debian/tmp/usr/bin/FastaToDeBruijn -- Installing: /build/trinityrnaseq-2.11.0+dfsg/debian/tmp/usr/bin/fastaToKmerCoverageStats make[2]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build' - cd Chrysalis_build && make -j15 install DESTDIR=/build/trinityrnaseq-2.11.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd Chrysalis_build && make -j16 install DESTDIR=/build/trinityrnaseq-2.11.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' /usr/bin/cmake -S/build/trinityrnaseq-2.11.0+dfsg/Chrysalis -B/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -13922,7 +13957,7 @@ make[2]: Leaving directory '/build/trinityrnaseq-2.11.0+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 -j15 install DESTDIR=/build/trinityrnaseq-2.11.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd trinity-plugins/slclust && make -j16 install DESTDIR=/build/trinityrnaseq-2.11.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/trinity-plugins/slclust' X=`pwd`; \ for i in src; \ @@ -13989,8 +14024,8 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'trinityrnaseq-dbgsym' in '../trinityrnaseq-dbgsym_2.11.0+dfsg-6_amd64.deb'. -dpkg-deb: building package 'trinityrnaseq-examples' in '../trinityrnaseq-examples_2.11.0+dfsg-6_all.deb'. dpkg-deb: building package 'trinityrnaseq' in '../trinityrnaseq_2.11.0+dfsg-6_amd64.deb'. +dpkg-deb: building package 'trinityrnaseq-examples' in '../trinityrnaseq-examples_2.11.0+dfsg-6_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../trinityrnaseq_2.11.0+dfsg-6_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -13998,12 +14033,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2587150/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2587150/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/30135 and its subdirectories -I: Current time: Tue Jan 11 08:06:31 -12 2022 -I: pbuilder-time-stamp: 1641931591 +I: removing directory /srv/workspace/pbuilder/2587150 and its subdirectories +I: Current time: Tue Feb 14 16:33:59 +14 2023 +I: pbuilder-time-stamp: 1676342039