Diff of the two buildlogs: -- --- b1/build.log 2021-08-12 18:33:41.951935420 +0000 +++ b2/build.log 2021-08-12 18:48:19.343078798 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Sep 14 12:38:53 -12 2022 -I: pbuilder-time-stamp: 1663202333 +I: Current time: Fri Aug 13 08:34:40 +14 2021 +I: pbuilder-time-stamp: 1628793280 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.O_Y6KEbl/trustedkeys.kbx': General error -gpgv: Signature made Tue Jan 19 01:18:29 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.fuuTFA_m/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/20980/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/9603/tmp/hooks/D01_modify_environment starting +debug: Running on codethink16-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +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/9603/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/9603/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='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' - DISTRIBUTION='' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='20980' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=9603 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.87geXlNEUG/pbuilderrc_QlPe --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.87geXlNEUG/b1 --logfile b1/build.log trinityrnaseq_2.11.0+dfsg-6.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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.87geXlNEUG/pbuilderrc_xxj1 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.87geXlNEUG/b2 --logfile b2/build.log --extrapackages usrmerge trinityrnaseq_2.11.0+dfsg-6.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink11-arm64 4.15.0-153-generic #160-Ubuntu SMP Thu Jul 29 07:06:07 UTC 2021 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-153-generic #160-Ubuntu SMP Thu Jul 29 07:06:07 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 - -rwxr-xr-x 1 root root 1282512 Aug 4 2021 bash - -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 34808 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 34808 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 14264 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 39832 Sep 22 2020 cat - -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown - -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp - -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash - -rwxr-xr-x 1 root root 101384 Sep 22 2020 date - -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd - -rwxr-xr-x 1 root root 89824 Sep 22 2020 df - -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir - -rwxr-xr-x 1 root root 76152 Jul 28 2021 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 35632 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 31512 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 64856 Jul 28 2021 findmnt - -rwsr-xr-x 1 root root 34824 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 178400 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 93744 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln - -rwxr-xr-x 1 root root 52720 Feb 7 2020 login - -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls - -rwxr-xr-x 1 root root 161960 Jul 28 2021 lsblk - -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 51368 Jul 28 2021 more - -rwsr-xr-x 1 root root 51360 Jul 28 2021 mount - -rwxr-xr-x 1 root root 14496 Jul 28 2021 mountpoint - -rwxr-xr-x 1 root root 134808 Sep 22 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 35720 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash - -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm - -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Sep 14 03:47 sh -> dash - -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty - -rwsr-xr-x 1 root root 67776 Jul 28 2021 su - -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync - -rwxr-xr-x 1 root root 535768 Feb 16 2021 tar - -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch - -rwxr-xr-x 1 root root 31512 Sep 22 2020 true - -rwxr-xr-x 1 root root 14264 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 30880 Jul 28 2021 umount - -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 59584 Jul 28 2021 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/20980/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1282512 Aug 5 10:25 bash + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 34808 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 34808 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 14264 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 39832 Sep 23 2020 cat + -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown + -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp + -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash + -rwxr-xr-x 1 root root 101384 Sep 23 2020 date + -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd + -rwxr-xr-x 1 root root 89824 Sep 23 2020 df + -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir + -rwxr-xr-x 1 root root 76152 Jul 29 09:09 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 35632 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 31512 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 64856 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 34824 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 178400 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 93744 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln + -rwxr-xr-x 1 root root 52720 Feb 8 2020 login + -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls + -rwxr-xr-x 1 root root 161960 Jul 29 09:09 lsblk + -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 51368 Jul 29 09:09 more + -rwsr-xr-x 1 root root 51360 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 14496 Jul 29 09:09 mountpoint + -rwxr-xr-x 1 root root 134808 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 35720 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash + -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm + -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Aug 13 08:35 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 12 23:25 sh.distrib -> dash + -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty + -rwsr-xr-x 1 root root 67776 Jul 29 09:09 su + -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync + -rwxr-xr-x 1 root root 535768 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch + -rwxr-xr-x 1 root root 31512 Sep 23 2020 true + -rwxr-xr-x 1 root root 14264 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 30880 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 59584 Jul 29 09:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/9603/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -782,7 +816,7 @@ Get: 493 http://deb.debian.org/debian bullseye/main arm64 salmon arm64 1.4.0+ds1-1+b4 [2046 kB] Get: 494 http://deb.debian.org/debian bullseye/main arm64 subread arm64 2.0.1+dfsg-1 [635 kB] Get: 495 http://deb.debian.org/debian bullseye/main arm64 tabix arm64 1.11-4 [316 kB] -Fetched 696 MB in 60s (11.6 MB/s) +Fetched 696 MB in 36s (19.5 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 ... 19646 files and directories currently installed.) @@ -2965,8 +2999,45 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main arm64 libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main arm64 libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main arm64 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main arm64 usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (2024 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(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 ... 62678 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. 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: Temporary failure in name resolution +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 @@ -3023,8 +3094,8 @@ 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 @@ -3112,47 +3183,47 @@ 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 -f CMakeFiles/FastaToDeBruijn.dir/build.make CMakeFiles/FastaToDeBruijn.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/FastaToDeBruijn.dir/DependInfo.cmake --color= -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/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". Scanning dependencies of target FastaToDeBruijn +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". make[4]: Leaving 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' -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". Scanning dependencies of target fastaToKmerCoverageStats -[ 3%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/FastaToDeBruijn.cpp.o +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/CMakeDirectoryInformation.cmake" is newer than depender "/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build/CMakeFiles/inchworm.dir/depend.internal". make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build' make -f CMakeFiles/fastaToKmerCoverageStats.dir/build.make CMakeFiles/fastaToKmerCoverageStats.dir/build make[4]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build' -/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 -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/CMakeDirectoryInformation.cmake" is newer than depender "/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build/CMakeFiles/inchworm.dir/depend.internal". -[ 7%] 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/FastaToDeBruijn.dir/src/Fasta_reader.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/Fasta_reader.cpp -[ 10%] 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 Scanning dependencies of target inchworm -[ 14%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/fastaToKmerCoverageStats.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 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' -[ 17%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.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/fastaToKmerCoverageStats.dir/src/argProcessor.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/argProcessor.cpp -[ 21%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o -[ 25%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/argProcessor.cpp.o +[ 3%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/argProcessor.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/FastaToDeBruijn.dir/src/FastaToDeBruijn.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/FastaToDeBruijn.cpp +[ 10%] Building CXX object CMakeFiles/FastaToDeBruijn.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/FastaToDeBruijn.dir/src/argProcessor.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/argProcessor.cpp +[ 17%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/string_util.cpp.o +[ 21%] Building CXX object CMakeFiles/FastaToDeBruijn.dir/src/Fasta_entry.cpp.o +[ 14%] 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/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/FastaToDeBruijn.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/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/sequenceUtil.cpp -[ 28%] Building CXX object CMakeFiles/inchworm.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/string_util.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/string_util.cpp +[ 25%] Building CXX object CMakeFiles/inchworm.dir/src/Fasta_entry.cpp.o +[ 28%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.dir/src/fastaToKmerCoverageStats.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/inchworm.dir/src/Fasta_entry.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/Fasta_entry.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, @@ -3163,12 +3234,8 @@ | ^~~~~~~ [ 32%] 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/IRKE_run.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/IRKE_run.cpp -[ 35%] 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 -/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) - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +[ 35%] 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 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, @@ -3176,54 +3243,32 @@ /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 \ | ^~~~~~~ +[ 39%] 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/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) + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /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(); | ^~~~~~~~~~~ -[ 39%] 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 -[ 42%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.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/Fasta_reader.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/Fasta_reader.cpp -[ 46%] 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 -[ 50%] 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/fastaToKmerCoverageStats.dir/src/Fasta_entry.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/Fasta_entry.cpp -[ 53%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.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 -[ 57%] 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/string_util.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/string_util.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) - | ^~~ +[ 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/inchworm.dir/src/sequenceUtil.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/sequenceUtil.cpp +[ 46%] 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/IRKE.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/IRKE.cpp +[ 50%] 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 /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++) { | ~~^~~~~~~~~~~~~~~~~~~~~ -/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++) { - | ~~^~~~~~~~~~~~~~~~~~~ -/build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/DeBruijnGraph.cpp:494:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 494 | for (int i=0; i < next_kmers.size(); i++) { - | ~~^~~~~~~~~~~~~~~~~~~ -[ 60%] 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 -/build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/DeBruijnGraph.cpp: In member function 'std::string DeBruijnGraph::toChrysalisFormat(int, bool)': -/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++) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~ -[ 64%] 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 \ | ^~~~~~~ -[ 67%] 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/inchworm.dir/src/sequenceUtil.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/sequenceUtil.cpp -[ 71%] 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/IRKE.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/IRKE.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, @@ -3231,37 +3276,63 @@ /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/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 +/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++) { + | ~~^~~~~~~~~~~~~~~~~~~ +/build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/DeBruijnGraph.cpp:494:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 494 | for (int i=0; i < next_kmers.size(); i++) { + | ~~^~~~~~~~~~~~~~~~~~~ +/build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/DeBruijnGraph.cpp: In member function 'std::string DeBruijnGraph::toChrysalisFormat(int, bool)': +/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) + | ^~~ +[ 53%] 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 +[ 57%] 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 +[ 60%] 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 +[ 64%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.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/fastaToKmerCoverageStats.dir/src/argProcessor.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/argProcessor.cpp +[ 67%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.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/Fasta_reader.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/Fasta_reader.cpp +[ 71%] 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 +[ 75%] 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/fastaToKmerCoverageStats.dir/src/Fasta_entry.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/Fasta_entry.cpp +[ 78%] Building CXX object CMakeFiles/fastaToKmerCoverageStats.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 +[ 82%] 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/string_util.cpp.o -c /build/trinityrnaseq-2.11.0+dfsg/Inchworm/src/string_util.cpp +[ 85%] 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 +[ 89%] 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 \ | ^~~~~~~ -[ 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 -[ 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 -[ 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 -make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build' -[ 92%] Built target fastaToKmerCoverageStats -[ 96%] Linking CXX executable inchworm +[ 92%] Linking CXX executable inchworm /usr/bin/cmake -E cmake_link_script CMakeFiles/inchworm.dir/link.txt --verbose=1 /usr/bin/g++ -g -O2 -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/inchworm.dir/src/Fasta_entry.cpp.o CMakeFiles/inchworm.dir/src/IRKE_run.cpp.o CMakeFiles/inchworm.dir/src/sequenceUtil.cpp.o CMakeFiles/inchworm.dir/src/IRKE.cpp.o CMakeFiles/inchworm.dir/src/KmerCounter.cpp.o CMakeFiles/inchworm.dir/src/string_util.cpp.o CMakeFiles/inchworm.dir/src/Fasta_reader.cpp.o CMakeFiles/inchworm.dir/src/stacktrace.cpp.o CMakeFiles/inchworm.dir/src/argProcessor.cpp.o -o inchworm make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build' -[ 96%] Built target inchworm -[100%] Linking CXX executable FastaToDeBruijn +[ 92%] Built target inchworm +[ 96%] Linking CXX executable FastaToDeBruijn /usr/bin/cmake -E cmake_link_script CMakeFiles/FastaToDeBruijn.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/FastaToDeBruijn.dir/src/FastaToDeBruijn.cpp.o CMakeFiles/FastaToDeBruijn.dir/src/argProcessor.cpp.o CMakeFiles/FastaToDeBruijn.dir/src/Fasta_reader.cpp.o CMakeFiles/FastaToDeBruijn.dir/src/Fasta_entry.cpp.o CMakeFiles/FastaToDeBruijn.dir/src/sequenceUtil.cpp.o CMakeFiles/FastaToDeBruijn.dir/src/string_util.cpp.o CMakeFiles/FastaToDeBruijn.dir/src/stacktrace.cpp.o CMakeFiles/FastaToDeBruijn.dir/src/DeBruijnGraph.cpp.o -o FastaToDeBruijn make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build' -[100%] Built target FastaToDeBruijn +[ 96%] Built target FastaToDeBruijn +[100%] 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 +make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Inchworm_build' +[100%] Built target fastaToKmerCoverageStats 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' @@ -3272,9 +3343,9 @@ make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' make -f CMakeFiles/CreateIwormFastaBundle.dir/build.make CMakeFiles/CreateIwormFastaBundle.dir/depend +make -f CMakeFiles/BubbleUpClustering.dir/build.make CMakeFiles/BubbleUpClustering.dir/depend make[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/BubbleUpClustering.dir/build.make CMakeFiles/BubbleUpClustering.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/BubbleUpClustering.dir/DependInfo.cmake --color= make -f CMakeFiles/ReadsToTranscripts.dir/build.make CMakeFiles/ReadsToTranscripts.dir/depend @@ -3291,56 +3362,60 @@ 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/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". -Scanning dependencies of target CreateIwormFastaBundle 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 CreateIwormFastaBundle +Dependee "/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles/QuantifyGraph.dir/DependInfo.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/CMakeDirectoryInformation.cmake" is newer than depender "/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles/QuantifyGraph.dir/depend.internal". make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' make -f CMakeFiles/CreateIwormFastaBundle.dir/build.make CMakeFiles/CreateIwormFastaBundle.dir/build +Scanning dependencies of target QuantifyGraph +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]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' +Scanning dependencies of target BubbleUpClustering make[4]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' Dependee "/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles/ReadsToTranscripts.dir/DependInfo.cmake" is newer than depender "/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles/ReadsToTranscripts.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/ReadsToTranscripts.dir/depend.internal". -Scanning dependencies of target BubbleUpClustering -Dependee "/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles/QuantifyGraph.dir/DependInfo.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/GraphFromFasta.dir/DependInfo.cmake" is newer than depender "/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles/GraphFromFasta.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/QuantifyGraph.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/GraphFromFasta.dir/depend.internal". make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' -make -f CMakeFiles/BubbleUpClustering.dir/build.make CMakeFiles/BubbleUpClustering.dir/build -Scanning dependencies of target ReadsToTranscripts Dependee "/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles/Chrysalis.dir/DependInfo.cmake" is newer than depender "/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles/Chrysalis.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/Chrysalis.dir/depend.internal". +make -f CMakeFiles/BubbleUpClustering.dir/build.make CMakeFiles/BubbleUpClustering.dir/build +Dependee "/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles/GraphFromFasta.dir/DependInfo.cmake" is newer than depender "/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build/CMakeFiles/GraphFromFasta.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/GraphFromFasta.dir/depend.internal". make[4]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' -Scanning dependencies of target QuantifyGraph -make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' -make -f CMakeFiles/ReadsToTranscripts.dir/build.make CMakeFiles/ReadsToTranscripts.dir/build [ 1%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/analysis/AACodons.cc.o -make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' -make[4]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' -make -f CMakeFiles/QuantifyGraph.dir/build.make CMakeFiles/QuantifyGraph.dir/build +[ 2%] Building CXX object CMakeFiles/QuantifyGraph.dir/aligns/KmerAlignCore.cc.o Scanning dependencies of target Chrysalis -Scanning dependencies of target GraphFromFasta /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/analysis/AACodons.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/AACodons.cc make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' +/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/aligns/KmerAlignCore.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc make -f CMakeFiles/Chrysalis.dir/build.make CMakeFiles/Chrysalis.dir/build make[4]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' +[ 4%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/analysis/CreateIwormFastaBundle.cc.o +Scanning dependencies of target ReadsToTranscripts +/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/analysis/CreateIwormFastaBundle.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.cc +make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' +make -f CMakeFiles/ReadsToTranscripts.dir/build.make CMakeFiles/ReadsToTranscripts.dir/build make[4]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' +Scanning dependencies of target GraphFromFasta make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' make -f CMakeFiles/GraphFromFasta.dir/build.make CMakeFiles/GraphFromFasta.dir/build -[ 2%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/analysis/DNAVector.cc.o make[4]: Entering directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' -/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/analysis/DNAVector.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/DNAVector.cc -[ 4%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/analysis/CreateIwormFastaBundle.cc.o -[ 5%] Building CXX object CMakeFiles/ReadsToTranscripts.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/CreateIwormFastaBundle.dir/analysis/CreateIwormFastaBundle.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/CreateIwormFastaBundle.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/AACodons.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/AACodons.cc -[ 8%] Building CXX object CMakeFiles/Chrysalis.dir/aligns/KmerAlignCore.cc.o -[ 10%] Building CXX object CMakeFiles/QuantifyGraph.dir/aligns/KmerAlignCore.cc.o -[ 7%] Building CXX object CMakeFiles/BubbleUpClustering.dir/aligns/KmerAlignCore.cc.o +[ 5%] Building CXX object CMakeFiles/BubbleUpClustering.dir/aligns/KmerAlignCore.cc.o +[ 7%] 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 /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/aligns/KmerAlignCore.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc +[ 8%] 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 -/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/aligns/KmerAlignCore.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc -[ 11%] Building CXX object CMakeFiles/GraphFromFasta.dir/aligns/KmerAlignCore.cc.o +[ 10%] Building CXX object CMakeFiles/GraphFromFasta.dir/aligns/KmerAlignCore.cc.o +[ 11%] Building CXX object CMakeFiles/ReadsToTranscripts.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/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/ReadsToTranscripts.dir/analysis/AACodons.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/AACodons.cc +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/AACodons.cc: In static member function 'static const string& AACodons::GetBases(char, int)': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/AACodons.cc:152:9: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 152 | if (aa < 0) { + | ~~~^~~ In file included from /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc:6: /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberExact::BasesToNumber(const DNAVector&, int) const': /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:52:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] @@ -3386,23 +3461,6 @@ /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/AACodons.cc: In static member function 'static const string& AACodons::GetBases(char, int)': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/AACodons.cc:152:9: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 152 | if (aa < 0) { - | ~~~^~~ -In file included from /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc:6: -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberExact::BasesToNumber(const DNAVector&, int) const': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:52:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 52 | if (v == -1 || v == 4) - | ~~^~~~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberProtein::BasesToNumber(const DNAVector&, int) const': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:93:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 93 | if (v == -1) - | ~~^~~~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberDoubleComb::BasesToNumber(const DNAVector&, int) const': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:126:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 126 | if (v == -1 || v == 4) - | ~~^~~~~ /build/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); @@ -3458,6 +3516,14 @@ /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/AACodons.cc: In static member function 'static const string& AACodons::GetBases(char, int)': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/AACodons.cc:152:9: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 152 | if (aa < 0) { + | ~~~^~~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/AACodons.cc: In static member function 'static const string& AACodons::GetBases(char, int)': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/AACodons.cc:152:9: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 152 | if (aa < 0) { + | ~~~^~~ In file included from /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc:6: /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberExact::BasesToNumber(const DNAVector&, int) const': /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:52:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] @@ -3467,14 +3533,27 @@ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:93:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] 93 | if (v == -1) | ~~^~~~~ -/build/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? - | ^ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberDoubleComb::BasesToNumber(const DNAVector&, int) const': /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:126:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] 126 | if (v == -1 || v == 4) | ~~^~~~~ +In file included from /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc:6: +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberExact::BasesToNumber(const DNAVector&, int) const': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:52:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 52 | if (v == -1 || v == 4) + | ~~^~~~~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberProtein::BasesToNumber(const DNAVector&, int) const': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:93:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 93 | if (v == -1) + | ~~^~~~~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberDoubleComb::BasesToNumber(const DNAVector&, int) const': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:126:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 126 | if (v == -1 || v == 4) + | ~~^~~~~ +/build/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? + | ^ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc:49:9: warning: unused variable 'i' [-Wunused-variable] 49 | int i, j, k; | ^ @@ -3489,10 +3568,6 @@ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc:148:9: warning: unused variable 'i' [-Wunused-variable] 148 | int i, j; | ^ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/AACodons.cc: In static member function 'static const string& AACodons::GetBases(char, int)': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/AACodons.cc:152:9: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 152 | if (aa < 0) { - | ~~~^~~ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc: In member function 'const svec& KmerAlignCore::GetMatchesDirectly(const DNAVector&, int)': /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc:158:9: warning: unused variable 'size' [-Wunused-variable] 158 | int size = m_pTrans->GetSize(); @@ -3503,14 +3578,14 @@ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc:159:12: warning: unused variable 'j' [-Wunused-variable] 159 | int i, j; | ^ -/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/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? | ^ +/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/aligns/KmerAlignCore.cc:49:9: warning: unused variable 'i' [-Wunused-variable] 49 | int i, j, k; | ^ @@ -3539,14 +3614,14 @@ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc:291:9: warning: unused variable 'i' [-Wunused-variable] 291 | int i; | ^ -[ 13%] 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 -[ 14%] 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 -[ 16%] Building CXX object CMakeFiles/Chrysalis.dir/analysis/AACodons.cc.o +[ 13%] 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 -[ 17%] Building CXX object CMakeFiles/GraphFromFasta.dir/analysis/AACodons.cc.o +[ 14%] 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 +[ 16%] 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 +[ 17%] 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/analysis/AACodons.cc: In static member function 'static const string& AACodons::GetBases(char, int)': /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/AACodons.cc:152:9: warning: comparison is always false due to limited range of data type [-Wtype-limits] 152 | if (aa < 0) { @@ -3559,14 +3634,31 @@ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/AACodons.cc:152:9: warning: comparison is always false due to limited range of data type [-Wtype-limits] 152 | if (aa < 0) { | ~~~^~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/AACodons.cc: In static member function 'static const string& AACodons::GetBases(char, int)': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/AACodons.cc:152:9: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 152 | if (aa < 0) { - | ~~~^~~ -[ 19%] Building CXX object CMakeFiles/CreateIwormFastaBundle.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/CreateIwormFastaBundle.dir/base/ErrorHandling.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/ErrorHandling.cc +[ 19%] 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 [ 20%] Building CXX object CMakeFiles/ReadsToTranscripts.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/ReadsToTranscripts.dir/analysis/DNAVector.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/DNAVector.cc +[ 22%] Building CXX object CMakeFiles/CreateIwormFastaBundle.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/CreateIwormFastaBundle.dir/analysis/DNAVector.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/DNAVector.cc +In file included from /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/KmerTable.cc:1: +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberExact::BasesToNumber(const DNAVector&, int) const': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:52:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 52 | if (v == -1 || v == 4) + | ~~^~~~~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberProtein::BasesToNumber(const DNAVector&, int) const': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:93:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 93 | if (v == -1) + | ~~^~~~~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberDoubleComb::BasesToNumber(const DNAVector&, int) const': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:126:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 126 | if (v == -1 || v == 4) + | ~~^~~~~ +/build/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; + | ^ +[ 23%] Building CXX object CMakeFiles/CreateIwormFastaBundle.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/CreateIwormFastaBundle.dir/base/ErrorHandling.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/base/ErrorHandling.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) @@ -3577,26 +3669,112 @@ /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) | ~~~~^~~~ -[ 22%] Building CXX object CMakeFiles/CreateIwormFastaBundle.dir/base/FileParser.cc.o +[ 25%] 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 -[ 23%] 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/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 +[ 27%] Building CXX object CMakeFiles/ReadsToTranscripts.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/ReadsToTranscripts.dir/analysis/NonRedKmerTable.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/NonRedKmerTable.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) | ~~~~^~~~~ -[ 25%] 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 -[ 26%] 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 -[ 27%] 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 -[ 29%] 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 -[ 30%] Building CXX object CMakeFiles/Chrysalis.dir/analysis/Chrysalis.cc.o -[ 32%] 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/Chrysalis.dir/analysis/Chrysalis.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/Chrysalis.cc +[ 29%] 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 +[ 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 +/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/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/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()); + | ~~~~~~^~~~~~~~~~~~~~~~~ +[ 32%] 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 +In file included from /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/BubbleUpClustering.cc:10: +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberExact::BasesToNumber(const DNAVector&, int) const': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:52:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 52 | if (v == -1 || v == 4) + | ~~^~~~~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberProtein::BasesToNumber(const DNAVector&, int) const': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:93:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 93 | if (v == -1) + | ~~^~~~~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberDoubleComb::BasesToNumber(const DNAVector&, int) const': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:126:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 126 | if (v == -1 || v == 4) + | ~~^~~~~ +/build/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) { + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/BubbleUpClustering.cc: In function 'svec sl_cluster_pools(std::map&, std::map&)': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/BubbleUpClustering.cc:326:40: warning: implicitly-declared 'Pool& Pool::operator=(const Pool&)' is deprecated [-Wdeprecated-copy] + 326 | pool_vec[oldpool_id] = tmp; + | ^~~ +In file included from /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/BubbleUpClustering.cc:19: +/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) { + | ^~~~ +/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; + | ^ +In file included from /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/BubbleUpClustering.cc:19: +/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) { + | ^~~~ +/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++) { + | ~~^~~~~~~~~~ +/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++) { + | ~~^~~~~~~~~~ +[ 33%] 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 +[ 35%] 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 /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) { @@ -3641,106 +3819,163 @@ /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; | ^ -In file included from /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/KmerTable.cc:1: -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberExact::BasesToNumber(const DNAVector&, int) const': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:52:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 52 | if (v == -1 || v == 4) - | ~~^~~~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberProtein::BasesToNumber(const DNAVector&, int) const': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:93:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 93 | if (v == -1) - | ~~^~~~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberDoubleComb::BasesToNumber(const DNAVector&, int) const': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:126:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 126 | if (v == -1 || v == 4) - | ~~^~~~~ -/build/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; - | ^ -In file included from /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/BubbleUpClustering.cc:10: -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberExact::BasesToNumber(const DNAVector&, int) const': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:52:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 52 | if (v == -1 || v == 4) - | ~~^~~~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberProtein::BasesToNumber(const DNAVector&, int) const': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:93:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 93 | if (v == -1) - | ~~^~~~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberDoubleComb::BasesToNumber(const DNAVector&, int) const': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:126:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 126 | if (v == -1 || v == 4) - | ~~^~~~~ -/build/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) { - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/BubbleUpClustering.cc: In function 'svec sl_cluster_pools(std::map&, std::map&)': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/BubbleUpClustering.cc:326:40: warning: implicitly-declared 'Pool& Pool::operator=(const Pool&)' is deprecated [-Wdeprecated-copy] - 326 | pool_vec[oldpool_id] = tmp; - | ^~~ -In file included from /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/BubbleUpClustering.cc:19: -/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) { - | ^~~~ -/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; - | ^ -In file included from /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/BubbleUpClustering.cc:19: -/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) { - | ^~~~ -/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/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++) { - | ~~^~~~~~~~~~ -/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++) { - | ~~^~~~~~~~~~ -/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/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()); - | ~~~~~~^~~~~~~~~~~~~~~~~ -[ 33%] 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 -[ 35%] Linking CXX executable CreateIwormFastaBundle +[ 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/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/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; + | ^ +[ 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/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 +[ 42%] 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 -[ 36%] 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/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) + | ~~~~^~~~ +make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' +[ 42%] Built target CreateIwormFastaBundle +[ 44%] 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 +[ 45%] 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 +[ 47%] 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 +[ 48%] 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/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/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; + | ^ +[ 50%] 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 +[ 51%] 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 +[ 52%] 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/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(); + | ^ +[ 54%] Building CXX object CMakeFiles/BubbleUpClustering.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/BubbleUpClustering.dir/analysis/DeBruijnGraph.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/DeBruijnGraph.cc +[ 55%] 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 /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) { | ~~~~~~~~~~~~~^~~~~~~~~~~ -make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' -[ 36%] Built target CreateIwormFastaBundle -[ 38%] 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/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 '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/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/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; @@ -3759,6 +3994,32 @@ /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) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +[ 57%] 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 +In file included from /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/KmerTable.cc:1: +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberExact::BasesToNumber(const DNAVector&, int) const': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:52:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 52 | if (v == -1 || v == 4) + | ~~^~~~~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberProtein::BasesToNumber(const DNAVector&, int) const': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:93:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 93 | if (v == -1) + | ~~^~~~~ +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberDoubleComb::BasesToNumber(const DNAVector&, int) const': +/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:126:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 126 | if (v == -1 || v == 4) + | ~~^~~~~ +[ 58%] 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 +/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; + | ^ +make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' +[ 58%] Built target ReadsToTranscripts +[ 60%] 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/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++) { @@ -3777,6 +4038,38 @@ /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]; + | ^ +[ 61%] 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 +[ 63%] 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 +[ 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 +[ 66%] 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 +/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) + | ~~~~^~~~ +[ 67%] 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 +[ 69%] 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 +[ 70%] 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 In file included from /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/GraphFromFasta.cc:10: /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberExact::BasesToNumber(const DNAVector&, int) const': /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:52:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] @@ -3790,6 +4083,54 @@ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:126:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] 126 | if (v == -1 || v == 4) | ~~^~~~~ +/build/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/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/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) @@ -3840,16 +4181,6 @@ /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/GraphFromFasta.cc:1442:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1442 | for (i=0; i&, 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/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/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) @@ -3941,30 +4276,27 @@ /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) | ~~~~^~~~ -[ 51%] 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 -[ 52%] 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 -/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]; - | ^ +[ 77%] 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 +/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; + | ^~~~~~~~~ +[ 79%] 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 +[ 80%] 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 +[ 82%] 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 +[ 83%] 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 +[ 85%] 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/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) | ~~~~^~~~~ -[ 54%] 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 -[ 55%] 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 -[ 57%] 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 -[ 58%] 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/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) @@ -3975,120 +4307,12 @@ /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) | ~~~~^~~~ -[ 60%] 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/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) - | ~~~~^~~~~ -[ 61%] 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 -/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) - | ~~~~~^~~~~~~~~ -[ 63%] Building CXX object CMakeFiles/ReadsToTranscripts.dir/analysis/sequenceUtil.cc.o -/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) - | ~~~~~^~~~~~~~~ -/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/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; - | ^ -[ 64%] 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 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; - | ^ -[ 66%] 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 -/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]; - | ^ -[ 67%] 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 -[ 69%] 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 +make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' +[ 85%] Built target BubbleUpClustering +[ 86%] Building CXX object CMakeFiles/Chrysalis.dir/util/mutil.cc.o +[ 88%] 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 +/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 /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) @@ -4099,17 +4323,8 @@ /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/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 -[ 72%] 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 -[ 73%] 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 -/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/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 /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) { @@ -4154,78 +4369,20 @@ /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; | ^ -make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' -[ 73%] Built target QuantifyGraph -[ 75%] 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 -[ 76%] 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' -[ 76%] Built target GraphFromFasta -[ 77%] 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 -[ 79%] 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 -[ 80%] 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 -In file included from /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/TranscriptomeGraph.cc:9: -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberExact::BasesToNumber(const DNAVector&, int) const': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:52:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 52 | if (v == -1 || v == 4) - | ~~^~~~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberProtein::BasesToNumber(const DNAVector&, int) const': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:93:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 93 | if (v == -1) - | ~~^~~~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberDoubleComb::BasesToNumber(const DNAVector&, int) const': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:126:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 126 | if (v == -1 || v == 4) - | ~~^~~~~ -/build/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/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/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) - | ~~~~^~~~ -[ 82%] Building CXX object CMakeFiles/BubbleUpClustering.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/BubbleUpClustering.dir/analysis/DeBruijnGraph.cc.o -c /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/DeBruijnGraph.cc -[ 83%] 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 +[ 91%] 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 +[ 92%] 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/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) + | ~~~~^~~~~ +[ 94%] 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) | ~~~~^~~~~ -/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; - | ^~~~~~~~~ -[ 85%] 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 -[ 86%] 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 -[ 88%] 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 /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) { @@ -4270,99 +4427,8 @@ /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; | ^ -make[4]: Leaving directory '/build/trinityrnaseq-2.11.0+dfsg/Chrysalis_build' -[ 88%] Built target ReadsToTranscripts -[ 89%] 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 -[ 91%] 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/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/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) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/trinityrnaseq-2.11.0+dfsg/Chrysalis/analysis/KmerTable.cc:1: -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberExact::BasesToNumber(const DNAVector&, int) const': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:52:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 52 | if (v == -1 || v == 4) - | ~~^~~~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberProtein::BasesToNumber(const DNAVector&, int) const': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:93:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 93 | if (v == -1) - | ~~^~~~~ -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h: In member function 'virtual int TranslateBasesToNumberDoubleComb::BasesToNumber(const DNAVector&, int) const': -/build/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h:126:13: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 126 | if (v == -1 || v == 4) - | ~~^~~~~ -/build/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; - | ^ -[ 92%] 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/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; - | ^ -[ 94%] 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 -/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/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/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/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) - | ~~~~^~~~~ -[ 97%] 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 +[ 95%] 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 /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) { @@ -4407,16 +4473,21 @@ /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; | ^ -[ 98%] Linking CXX executable Chrysalis +[ 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' -[ 98%] Built target Chrysalis -[100%] 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 +[ 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 BubbleUpClustering +[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' @@ -13513,13 +13584,13 @@ -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 -Sep 14, 2022 12:50:15 PM jaligner.NeedlemanWunschGotoh construct +Aug 13, 2021 8:43:27 AM jaligner.NeedlemanWunschGotoh construct INFO: Started... -Sep 14, 2022 12:50:16 PM jaligner.NeedlemanWunschGotoh construct +Aug 13, 2021 8:43:27 AM jaligner.NeedlemanWunschGotoh construct INFO: Finished. -Sep 14, 2022 12:50:16 PM jaligner.NeedlemanWunschGotoh traceback +Aug 13, 2021 8:43:27 AM jaligner.NeedlemanWunschGotoh traceback INFO: Started... -Sep 14, 2022 12:50:16 PM jaligner.NeedlemanWunschGotoh traceback +Aug 13, 2021 8:43:27 AM jaligner.NeedlemanWunschGotoh traceback INFO: Finished. A 1 GGCCACACGATGGCTTATCACGTCCACATTTCTACTGGCTACAAACAGAC 50 .|..||||||..|.| @@ -14149,9 +14220,9 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'trinityrnaseq-examples' in '../trinityrnaseq-examples_2.11.0+dfsg-6_all.deb'. -dpkg-deb: building package 'trinityrnaseq-dbgsym' in '../trinityrnaseq-dbgsym_2.11.0+dfsg-6_arm64.deb'. dpkg-deb: building package 'trinityrnaseq' in '../trinityrnaseq_2.11.0+dfsg-6_arm64.deb'. +dpkg-deb: building package 'trinityrnaseq-dbgsym' in '../trinityrnaseq-dbgsym_2.11.0+dfsg-6_arm64.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_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -14159,12 +14230,14 @@ 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/9603/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/9603/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/20980 and its subdirectories -I: Current time: Wed Sep 14 12:56:40 -12 2022 -I: pbuilder-time-stamp: 1663203400 +I: removing directory /srv/workspace/pbuilder/9603 and its subdirectories +I: Current time: Fri Aug 13 08:48:18 +14 2021 +I: pbuilder-time-stamp: 1628794098