Diff of the two buildlogs: -- --- b1/build.log 2021-12-17 08:42:12.432760557 +0000 +++ b2/build.log 2021-12-17 08:47:59.469951473 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jan 19 03:01:59 -12 2023 -I: pbuilder-time-stamp: 1674140519 +I: Current time: Fri Dec 17 22:42:21 +14 2021 +I: pbuilder-time-stamp: 1639730541 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Thu Jan 3 23:44:59 2019 -12 +gpgv: Signature made Sat Jan 5 01:44:59 2019 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./trinityrnaseq_2.6.6+dfsg-6.dsc @@ -42,136 +42,170 @@ dpkg-source: info: applying unfix_num_of_cores I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2854445/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2846764/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +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/2846764/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2846764/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='d68b02edebf44193a1251584761a24c1' - 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='2854445' - PS1='# ' - PS2='> ' + INVOCATION_ID=404d251a5c1e45a0a2b397f332b7e266 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2846764 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.Q5O2GxgM62/pbuilderrc_zLRm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Q5O2GxgM62/b1 --logfile b1/build.log trinityrnaseq_2.6.6+dfsg-6.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + 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.Q5O2GxgM62/pbuilderrc_SwSV --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Q5O2GxgM62/b2 --logfile b2/build.log trinityrnaseq_2.6.6+dfsg-6.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos15-amd64 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-9-amd64 #1 SMP Debian 5.10.70-1 (2021-09-30) x86_64 GNU/Linux I: ls -l /bin total 5116 - -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat - -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown - -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp - -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash - -rwxr-xr-x 1 root root 109408 Feb 28 2019 date - -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93744 Feb 28 2019 df - -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir - -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 35424 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln - -rwxr-xr-x 1 root root 56760 Jul 26 2018 login - -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 43008 Jan 9 2019 more - -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm - -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Dec 10 16:20 sh -> dash - -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty - -rwsr-xr-x 1 root root 63568 Jan 9 2019 su - -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync - -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar - -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch - -rwxr-xr-x 1 root root 35424 Feb 28 2019 true - -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount - -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/2854445/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat + -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown + -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp + -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash + -rwxr-xr-x 1 root root 109408 Mar 1 2019 date + -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93744 Mar 1 2019 df + -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir + -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 35424 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln + -rwxr-xr-x 1 root root 56760 Jul 27 2018 login + -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 43008 Jan 10 2019 more + -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm + -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Dec 17 22:42 sh -> bash + lrwxrwxrwx 1 root root 4 Nov 8 11:58 sh.distrib -> dash + -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty + -rwsr-xr-x 1 root root 63568 Jan 10 2019 su + -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync + -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar + -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch + -rwxr-xr-x 1 root root 35424 Mar 1 2019 true + -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount + -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/2846764/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -466,7 +500,7 @@ Get: 233 http://deb.debian.org/debian buster/main amd64 parafly amd64 0.0.2013.01.21-4 [15.8 kB] Get: 234 http://deb.debian.org/debian buster/main amd64 sphinx-rtd-theme-common all 0.4.3+dfsg-1 [1021 kB] Get: 235 http://deb.debian.org/debian buster/main amd64 salmon amd64 0.12.0+ds1-1+b1 [1354 kB] -Fetched 351 MB in 5s (73.0 MB/s) +Fetched 351 MB in 8s (42.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19195 files and directories currently installed.) @@ -1619,7 +1653,8 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/trinityrnaseq-2.6.6+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_2.6.6+dfsg-6_source.changes +hostname: Name or service not known +I: Running cd /build/trinityrnaseq-2.6.6+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_2.6.6+dfsg-6_source.changes dpkg-buildpackage: info: source package trinityrnaseq dpkg-buildpackage: info: source version 2.6.6+dfsg-6 dpkg-buildpackage: info: source distribution unstable @@ -1632,7 +1667,7 @@ make[1]: Entering directory '/build/trinityrnaseq-2.6.6+dfsg' for target in Inchworm Chrysalis trinity-plugins/*Fastool* trinity-plugins/slclust trinity-plugins/scaffold_iworm_contigs; do dh_auto_clean \ --sourcedirectory=${target}; done - cd Chrysalis && make -j16 clean + cd Chrysalis && make -j15 clean make[2]: Entering directory '/build/trinityrnaseq-2.6.6+dfsg/Chrysalis' Makefile:80: ---------------------------------------------------------- Makefile:81: using g++ version 8 @@ -1646,7 +1681,7 @@ rm -f lib_*_temp.a make[2]: Leaving directory '/build/trinityrnaseq-2.6.6+dfsg/Chrysalis' dh_auto_clean: invalid or non-existing path to the source directory: trinity-plugins/*Fastool* - cd trinity-plugins/slclust && make -j16 clean + cd trinity-plugins/slclust && make -j15 clean make[2]: Entering directory '/build/trinityrnaseq-2.6.6+dfsg/trinity-plugins/slclust' X=`pwd`; \ for i in src; \ @@ -1657,7 +1692,7 @@ ../bin/slclust make[3]: Leaving directory '/build/trinityrnaseq-2.6.6+dfsg/trinity-plugins/slclust/src' make[2]: Leaving directory '/build/trinityrnaseq-2.6.6+dfsg/trinity-plugins/slclust' - cd trinity-plugins/scaffold_iworm_contigs && make -j16 clean + cd trinity-plugins/scaffold_iworm_contigs && make -j15 clean make[2]: Entering directory '/build/trinityrnaseq-2.6.6+dfsg/trinity-plugins/scaffold_iworm_contigs' rm -f scaffold_iworm_contigs make[2]: Leaving directory '/build/trinityrnaseq-2.6.6+dfsg/trinity-plugins/scaffold_iworm_contigs' @@ -1684,9 +1719,7 @@ make[4]: Leaving directory '/build/trinityrnaseq-2.6.6+dfsg/trinity-plugins/slclust/src' make[3]: Leaving directory '/build/trinityrnaseq-2.6.6+dfsg/trinity-plugins/slclust' cd COLLECTL && rm -rf "collectl-4.1.0" && rm -f collectl - - -** Done cleaning plugins area ** +\n\n** Done cleaning plugins area ** make[2]: Leaving directory '/build/trinityrnaseq-2.6.6+dfsg/trinity-plugins' make[1]: Leaving directory '/build/trinityrnaseq-2.6.6+dfsg' jh_clean @@ -1749,7 +1782,7 @@ make[1]: Entering directory '/build/trinityrnaseq-2.6.6+dfsg' for target in Inchworm Chrysalis trinity-plugins/*Fastool* trinity-plugins/slclust trinity-plugins/scaffold_iworm_contigs trinity-plugins/seqtk-trinity-*; do dh_auto_build \ -O--sourcedirectory=${target}; done - cd Inchworm && make -j16 + cd Inchworm && make -j15 make[2]: Entering directory '/build/trinityrnaseq-2.6.6+dfsg/Inchworm' make all-recursive make[3]: Entering directory '/build/trinityrnaseq-2.6.6+dfsg/Inchworm' @@ -1793,7 +1826,7 @@ make[4]: Leaving directory '/build/trinityrnaseq-2.6.6+dfsg/Inchworm' make[3]: Leaving directory '/build/trinityrnaseq-2.6.6+dfsg/Inchworm' make[2]: Leaving directory '/build/trinityrnaseq-2.6.6+dfsg/Inchworm' - cd Chrysalis && make -j16 "INSTALL=install --strip-program=true" + cd Chrysalis && make -j15 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/trinityrnaseq-2.6.6+dfsg/Chrysalis' Makefile:80: ---------------------------------------------------------- Makefile:81: using g++ version 8 @@ -1827,30 +1860,21 @@ ~~~~~~~~~~~~~~~~~~~~^~ ( CompareSubstring( filename, filename.size() - 2, 2, ".h" ) == 0 ) || ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.14.0-0.bpo.2-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./aligns/KmerAlignCore.cc -o obj/aligns/KmerAlignCore.o -g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.14.0-0.bpo.2-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./analysis/AACodons.cc -o obj/analysis/AACodons.o -g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.14.0-0.bpo.2-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./analysis/BreakTransByPairs.cc -o obj/analysis/BreakTransByPairs.o -g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.14.0-0.bpo.2-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./analysis/DNAVector.cc -o obj/analysis/DNAVector.o -g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.14.0-0.bpo.2-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./analysis/KmerTable.cc -o obj/analysis/KmerTable.o -g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.14.0-0.bpo.2-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./analysis/NonRedKmerTable.cc -o obj/analysis/NonRedKmerTable.o -g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.14.0-0.bpo.2-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./base/ErrorHandling.cc -o obj/base/ErrorHandling.o -g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.14.0-0.bpo.2-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./base/FileParser.cc -o obj/base/FileParser.o -g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.14.0-0.bpo.2-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./base/StringUtil.cc -o obj/base/StringUtil.o -g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.14.0-0.bpo.2-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./util/mutil.cc -o obj/util/mutil.o -g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.14.0-0.bpo.2-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./analysis/BubbleUpClustering.cc -o obj/analysis/BubbleUpClustering.o -g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.14.0-0.bpo.2-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./analysis/DeBruijnGraph.cc -o obj/analysis/DeBruijnGraph.o -g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.14.0-0.bpo.2-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./analysis/sequenceUtil.cc -o obj/analysis/sequenceUtil.o -g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.14.0-0.bpo.2-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./analysis/stacktrace.cc -o obj/analysis/stacktrace.o -g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.14.0-0.bpo.2-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./analysis/Chrysalis.cc -o obj/analysis/Chrysalis.o -g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.14.0-0.bpo.2-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./analysis/TranscriptomeGraph.cc -o obj/analysis/TranscriptomeGraph.o -./util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': -./util/mutil.cc:313:14: warning: passing argument 1 to restrict-qualified parameter aliases with argument 4 [-Wrestrict] - if (fscanf(m_pFile, szText, sizeof(szText), m_pFile) == EOF) { - ^~~~~~~ ~~~~~~~ -./util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadString(CMString&)': -./util/mutil.cc:436:14: warning: passing argument 1 to restrict-qualified parameter aliases with argument 4 [-Wrestrict] - if (fscanf(m_pFile, pData, len, m_pFile) == EOF) { - ^~~~~~~ ~~~~~~~ +g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.10.0-9-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./aligns/KmerAlignCore.cc -o obj/aligns/KmerAlignCore.o +g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.10.0-9-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./analysis/AACodons.cc -o obj/analysis/AACodons.o +g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.10.0-9-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./analysis/BreakTransByPairs.cc -o obj/analysis/BreakTransByPairs.o +g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.10.0-9-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./analysis/DNAVector.cc -o obj/analysis/DNAVector.o +g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.10.0-9-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./analysis/KmerTable.cc -o obj/analysis/KmerTable.o +g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.10.0-9-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./analysis/NonRedKmerTable.cc -o obj/analysis/NonRedKmerTable.o +g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.10.0-9-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./base/ErrorHandling.cc -o obj/base/ErrorHandling.o +g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.10.0-9-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./base/FileParser.cc -o obj/base/FileParser.o +g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.10.0-9-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./base/StringUtil.cc -o obj/base/StringUtil.o +g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.10.0-9-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./util/mutil.cc -o obj/util/mutil.o +g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.10.0-9-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./analysis/BubbleUpClustering.cc -o obj/analysis/BubbleUpClustering.o +g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.10.0-9-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./analysis/DeBruijnGraph.cc -o obj/analysis/DeBruijnGraph.o +g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.10.0-9-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./analysis/sequenceUtil.cc -o obj/analysis/sequenceUtil.o +g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.10.0-9-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./analysis/stacktrace.cc -o obj/analysis/stacktrace.o +g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.10.0-9-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./analysis/Chrysalis.cc -o obj/analysis/Chrysalis.o ./analysis/NonRedKmerTable.cc: In member function 'void NonRedKmerTable::SetUp(const vecDNAVector&, bool)': ./analysis/NonRedKmerTable.cc:46:20: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for (j=0; j<=d.size()-m_k; j++) { @@ -1865,27 +1889,20 @@ ./analysis/NonRedKmerTable.cc:109:16: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for (j=0; j<= d.isize()-m_k; j++) { ~^~~~~~~~~~~~~~~~ -g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.14.0-0.bpo.2-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./analysis/CreateIwormFastaBundle.cc -o obj/analysis/CreateIwormFastaBundle.o -g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.14.0-0.bpo.2-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./analysis/GraphFromFasta.cc -o obj/analysis/GraphFromFasta.o -./analysis/sequenceUtil.cc: In function 'bool contains_non_gatc(std::__cxx11::string)': -./analysis/sequenceUtil.cc:33:20: warning: array subscript has type 'char' [-Wchar-subscripts] - if (_base_to_int[c] > 3) - ^ -./analysis/sequenceUtil.cc: In function 'kmer_int_type_t kmer_to_intval(std::__cxx11::string)': -./analysis/sequenceUtil.cc:264:26: warning: array subscript has type 'char' [-Wchar-subscripts] - int val = _base_to_int[c]; - ^ +g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.10.0-9-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./analysis/TranscriptomeGraph.cc -o obj/analysis/TranscriptomeGraph.o +./util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadSimpleType(void*, long int)': +./util/mutil.cc:313:14: warning: passing argument 1 to restrict-qualified parameter aliases with argument 4 [-Wrestrict] + if (fscanf(m_pFile, szText, sizeof(szText), m_pFile) == EOF) { + ^~~~~~~ ~~~~~~~ +./util/mutil.cc: In member function 'virtual bool CMAsciiReadFileStream::ReadString(CMString&)': +./util/mutil.cc:436:14: warning: passing argument 1 to restrict-qualified parameter aliases with argument 4 [-Wrestrict] + if (fscanf(m_pFile, pData, len, m_pFile) == EOF) { + ^~~~~~~ ~~~~~~~ +g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.10.0-9-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./analysis/CreateIwormFastaBundle.cc -o obj/analysis/CreateIwormFastaBundle.o ./analysis/BreakTransByPairs.cc: In function 'int main(int, char**)': ./analysis/BreakTransByPairs.cc:105:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for (i=0; i > DeBruijnGraph::get_candidate_weldmers(kmer_int_type_t, int)': ./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] for (int i = 0; i < left_extensions.size(); i++) { @@ -1893,10 +1910,6 @@ ./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] for (int j = 0; j < right_extensions.size(); j++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~ -./analysis/TranscriptomeGraph.cc: In function 'int TranscriptomeGraph(vecDNAVector&, FILE*, int, bool)': -./analysis/TranscriptomeGraph.cc:668:20: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - for (i=0; i<=d.isize()-k; i++) { - ~^~~~~~~~~~~~~ ./analysis/DeBruijnGraph.cc: In member function 'void DeBruijnGraph::recursively_construct_kmer_extensions(kmer_int_type_t, std::vector&, std::vector >&, char, std::map&, int)': ./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] for (int i = 0; i < adjacent_kmers.size(); i++) { @@ -1904,10 +1917,31 @@ ./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] if (kmer_extension_chars.size() == flank_extension_length) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +./analysis/sequenceUtil.cc: In function 'bool contains_non_gatc(std::__cxx11::string)': +./analysis/sequenceUtil.cc:33:20: warning: array subscript has type 'char' [-Wchar-subscripts] + if (_base_to_int[c] > 3) + ^ +./analysis/sequenceUtil.cc: In function 'kmer_int_type_t kmer_to_intval(std::__cxx11::string)': +./analysis/sequenceUtil.cc:264:26: warning: array subscript has type 'char' [-Wchar-subscripts] + int val = _base_to_int[c]; + ^ +./analysis/BubbleUpClustering.cc: In function 'int main(int, char**)': +./analysis/BubbleUpClustering.cc:692:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + for (size_t j = 0; j < p.size(); j++) { + ~~^~~~~~~~~~ +./analysis/BubbleUpClustering.cc:705:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + for (size_t j = 0; j < p.size(); j++) { + ~~^~~~~~~~~~ +g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.10.0-9-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./analysis/GraphFromFasta.cc -o obj/analysis/GraphFromFasta.o ./analysis/Chrysalis.cc: In function 'int main(int, char**)': ./analysis/Chrysalis.cc:384:11: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(command.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~ +./analysis/TranscriptomeGraph.cc: In function 'int TranscriptomeGraph(vecDNAVector&, FILE*, int, bool)': +./analysis/TranscriptomeGraph.cc:668:20: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + for (i=0; i<=d.isize()-k; i++) { + ~^~~~~~~~~~~~~ +g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.10.0-9-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./GraphFromFasta_MPI.cc -o obj/GraphFromFasta_MPI.o ./analysis/GraphFromFasta.cc: In function 'bool SimpleHalves(const DNAVector&)': ./analysis/GraphFromFasta.cc:255:15: warning: suggest parentheses around '&&' within '||' [-Wparentheses] ( (! DISABLE_REPEAT_CHECK) @@ -1930,8 +1964,7 @@ ./analysis/GraphFromFasta.cc:1294:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for (i=0; i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j = 0; j < m_index.size(); j++) { @@ -1981,6 +2014,7 @@ ./GraphFromFasta_MPI.cc:2496:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for (size_t j = 0; j < p.size(); j++) { ~~^~~~~~~~~~ +g++ -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -DMAKE_DATE='""""' -DMAKE_OS_RELEASE='"5.10.0-9-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread -ftemplate-depth-30 -fno-strict-aliasing -iquote . -ISpines -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c ./analysis/JoinTransByPairs.cc -o obj/analysis/JoinTransByPairs.o ./analysis/IsoformAugment.cc: In function 'int main(int, char**)': ./analysis/IsoformAugment.cc:87:16: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for (j=0; j../trinityrnaseq_2.6.6+dfsg-6_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -11805,12 +11838,14 @@ 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/2846764/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2846764/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/2854445 and its subdirectories -I: Current time: Thu Jan 19 03:05:16 -12 2023 -I: pbuilder-time-stamp: 1674140716 +I: removing directory /srv/workspace/pbuilder/2846764 and its subdirectories +I: Current time: Fri Dec 17 22:47:58 +14 2021 +I: pbuilder-time-stamp: 1639730878