Diff of the two buildlogs: -- --- b1/build.log 2021-08-13 04:39:37.851204172 +0000 +++ b2/build.log 2021-08-13 05:53:29.506041781 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Aug 12 16:15:23 -12 2021 -I: pbuilder-time-stamp: 1628828123 +I: Current time: Fri Aug 13 18:39:51 +14 2021 +I: pbuilder-time-stamp: 1628829591 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 [./abyss_2.2.5+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.DIBDq1jj/trustedkeys.kbx': General error -gpgv: Signature made Fri Dec 4 01:53:32 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.aXcRAEqJ/trustedkeys.kbx': General error +gpgv: Signature made Sat Dec 5 03:53:32 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -29,135 +29,169 @@ dpkg-source: info: applying abyss-pe.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/10876/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/14388/tmp/hooks/D01_modify_environment starting +debug: Running on virt32b. +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/14388/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/14388/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=3' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=4' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='99101101b1314eeaa880f2cdad758465' - 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='10876' - PS1='# ' - PS2='> ' + INVOCATION_ID=756e5b808918444ebc7b7c6f4ab57e88 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=14388 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.jzu3foWQ5u/pbuilderrc_Rwjw --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.jzu3foWQ5u/b1 --logfile b1/build.log abyss_2.2.5+dfsg-1.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:8000/' + 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.jzu3foWQ5u/pbuilderrc_dLin --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.jzu3foWQ5u/b2 --logfile b2/build.log --extrapackages usrmerge abyss_2.2.5+dfsg-1.dsc' + SUDO_GID=112 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:8000/ I: uname -a - Linux virt64b 5.10.0-8-arm64 #1 SMP Debian 5.10.46-4 (2021-08-03) aarch64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-8-armmp-lpae #1 SMP Debian 5.10.46-4 (2021-08-03) armv7l GNU/Linux I: ls -l /bin total 3580 - -rwxr-xr-x 1 root root 816764 Aug 4 08:25 bash - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 26052 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 26052 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 9636 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 26668 Sep 22 2020 cat - -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown - -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp - -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash - -rwxr-xr-x 1 root root 75880 Sep 22 2020 date - -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd - -rwxr-xr-x 1 root root 59912 Sep 22 2020 df - -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir - -rwxr-xr-x 1 root root 55012 Jul 28 07:09 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 22508 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 22496 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 47492 Jul 28 07:09 findmnt - -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 124508 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe - -rwxr-xr-x 1 root root 64212 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln - -rwxr-xr-x 1 root root 35068 Feb 7 2020 login - -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls - -rwxr-xr-x 1 root root 99940 Jul 28 07:09 lsblk - -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 34408 Jul 28 07:09 more - -rwsr-xr-x 1 root root 34400 Jul 28 07:09 mount - -rwxr-xr-x 1 root root 9824 Jul 28 07:09 mountpoint - -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash - -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm - -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 10 21:24 sh -> dash - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty - -rwsr-xr-x 1 root root 46704 Jul 28 07:09 su - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync - -rwxr-xr-x 1 root root 340872 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch - -rwxr-xr-x 1 root root 22496 Sep 22 2020 true - -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Jul 28 07:09 umount - -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 38512 Jul 28 07:09 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless - -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew -I: user script /srv/workspace/pbuilder/10876/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 816764 Aug 5 10:25 bash + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 26052 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 26052 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 9636 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 26668 Sep 23 2020 cat + -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown + -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp + -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash + -rwxr-xr-x 1 root root 75880 Sep 23 2020 date + -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd + -rwxr-xr-x 1 root root 59912 Sep 23 2020 df + -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir + -rwxr-xr-x 1 root root 55012 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 22508 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 22496 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 47492 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 26076 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 124508 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 64212 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln + -rwxr-xr-x 1 root root 35068 Feb 8 2020 login + -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls + -rwxr-xr-x 1 root root 99940 Jul 29 09:09 lsblk + -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 34408 Jul 29 09:09 more + -rwsr-xr-x 1 root root 34400 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 9824 Jul 29 09:09 mountpoint + -rwxr-xr-x 1 root root 88524 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 26652 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash + -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm + -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Aug 13 18:41 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 11 23:26 sh.distrib -> dash + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty + -rwsr-xr-x 1 root root 46704 Jul 29 09:09 su + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync + -rwxr-xr-x 1 root root 340872 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch + -rwxr-xr-x 1 root root 22496 Sep 23 2020 true + -rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 38512 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/14388/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -310,7 +344,7 @@ Get: 101 http://deb.debian.org/debian bullseye/main armhf libtext-markdown-perl all 1.000031-3 [33.8 kB] Get: 102 http://deb.debian.org/debian bullseye/main armhf libtext-multimarkdown-perl all 1.000035-2 [28.6 kB] Get: 103 http://deb.debian.org/debian bullseye/main armhf pkg-config armhf 0.29.2-1 [62.4 kB] -Fetched 61.0 MB in 33s (1829 kB/s) +Fetched 61.0 MB in 6s (9645 kB/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 ... 19398 files and directories currently installed.) @@ -741,8 +775,45 @@ 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 armhf libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main armhf libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main armhf libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main armhf usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (545 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 ... 40749 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/abyss-2.2.5+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 > ../abyss_2.2.5+dfsg-1_source.changes +hostname: Name or service not known +I: Running cd /build/abyss-2.2.5+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 > ../abyss_2.2.5+dfsg-1_source.changes dpkg-buildpackage: info: source package abyss dpkg-buildpackage: info: source version 2.2.5+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -780,7 +851,7 @@ checking whether g++ supports C++11 features with -std=c++11... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes -checking for a thread-safe mkdir -p... /bin/mkdir -p +checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes @@ -803,8 +874,8 @@ checking for pandoc... no checking for ar... ar checking the archiver (ar) interface... ar -checking for grep that handles long lines and -e... /bin/grep -checking for egrep... /bin/grep -E +checking for grep that handles long lines and -e... /usr/bin/grep +checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes @@ -981,7 +1052,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/abyss-2.2.5+dfsg' dh_auto_build - make -j3 + make -j4 make[2]: Entering directory '/build/abyss-2.2.5+dfsg' make all-recursive make[3]: Entering directory '/build/abyss-2.2.5+dfsg' @@ -1001,6 +1072,9 @@ g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp +g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp +g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp +g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp In file included from /usr/include/c++/10/vector:72, from VectorUtil.h:4, from Histogram.h:6, @@ -1009,7 +1083,6 @@ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp In file included from /usr/include/c++/10/vector:67, from VectorUtil.h:4, from Histogram.h:6, @@ -1021,8 +1094,6 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp -g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-city.o `test -f 'city.cc' || echo './'`city.cc rm -f libcommon.a @@ -1047,19 +1118,19 @@ ar cru libdatalayer.a libdatalayer_a-FastaReader.o libdatalayer_a-FastaWriter.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdatalayer.a -g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm +g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/DataLayer' Making all in DataBase make[4]: Entering directory '/build/abyss-2.2.5+dfsg/DataBase' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_db_csv-DB.o `test -f 'DB.cc' || echo './'`DB.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_db_csv-db-csv.o `test -f 'db-csv.cc' || echo './'`db-csv.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc -g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm rm -f libdb.a ar cru libdb.a libdb_a-DB.o ../Common/libcommon.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdb.a +g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/DataBase' Making all in FMIndex make[4]: Entering directory '/build/abyss-2.2.5+dfsg/FMIndex' @@ -1075,7 +1146,7 @@ from BitArrays.h:4, from FMIndex.h:5, from DAWG.h:5, - from count.cc:2: + from abyss-dawg.cc:2: /usr/include/c++/10/bits/stl_uninitialized.h: In function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = wat_array::BitArray*; bool _TrivialValueTypes = false]': /usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 84 | __uninit_copy(_InputIterator __first, _InputIterator __last, @@ -1086,7 +1157,7 @@ from BitArrays.h:4, from FMIndex.h:5, from DAWG.h:5, - from abyss-dawg.cc:2: + from count.cc:2: /usr/include/c++/10/bits/stl_uninitialized.h: In function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = wat_array::BitArray*; bool _TrivialValueTypes = false]': /usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 84 | __uninit_copy(_InputIterator __first, _InputIterator __last, @@ -1097,7 +1168,7 @@ from BitArrays.h:4, from FMIndex.h:5, from DAWG.h:5, - from count.cc:2: + from abyss-dawg.cc:2: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > >}; _Tp = std::pair, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > >; _Alloc = std::allocator, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > > >]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > >, std::allocator, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > > > >::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: @@ -1111,7 +1182,7 @@ from BitArrays.h:4, from FMIndex.h:5, from DAWG.h:5, - from abyss-dawg.cc:2: + from count.cc:2: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > >}; _Tp = std::pair, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > >; _Alloc = std::allocator, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > > >]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > >, std::allocator, std::pair, std::pair > >, std::pair::out_edge_iterator, boost::graph_traits::out_edge_iterator> > > > >::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: @@ -1148,16 +1219,6 @@ | ~~~~~~~~~~~~~~~~~~ 150 | __uninit_copy(__first, __last, __result); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from bit_array.h:24, - from BitArrays.h:4, - from FMIndex.h:5, - from DAWG.h:5, - from count.cc:2: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void BitArrays::assign(It, It) [with It = __gnu_cxx::__normal_iterator >]': -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = wat_array::BitArray; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: @@ -1191,6 +1252,16 @@ from BitArrays.h:4, from FMIndex.h:5, from DAWG.h:5, + from count.cc:2: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void BitArrays::assign(It, It) [with It = __gnu_cxx::__normal_iterator >]': +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from bit_array.h:24, + from BitArrays.h:4, + from FMIndex.h:5, + from DAWG.h:5, from abyss-dawg.cc:2: /usr/include/c++/10/bits/stl_vector.h: In member function 'void BitArrays::assign(It, It) [with It = __gnu_cxx::__normal_iterator >]': /usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -1251,12 +1322,7 @@ gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o museq.o museq.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alig.o alig.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assemble.o assemble.c -alig.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined - 15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, - | ^~~~~~~~~~~~~~ -alig.c:13:20: warning: inline function 'calc_weight' declared but never defined - 13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, - | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o diag.o diag.c assemble.c:40:20: warning: inline function 'align_diag' declared but never defined 40 | extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); | ^~~~~~~~~~ @@ -1272,7 +1338,12 @@ assemble.c:13:20: warning: inline function 'calc_weight' declared but never defined 13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o diag.o diag.c +alig.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined + 15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, + | ^~~~~~~~~~~~~~ +alig.c:13:20: warning: inline function 'calc_weight' declared but never defined + 13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, + | ^~~~~~~~~~~ diag.c:1456:3: warning: 'real_calc_weight' is static but used in inline function 'find_diags_dyn' which is not static 1456 | real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn); | ^~~~~~~~~~~~~~~~ @@ -1364,6 +1435,7 @@ g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst_ssq-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp +g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst_ssq-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp In file included from /usr/include/c++/10/vector:72, from MLE.h:4, from MLE.cpp:1: @@ -1378,7 +1450,6 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst_ssq-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp In file included from /usr/include/c++/10/vector:72, from MLE.h:4, from MLE.cpp:1: @@ -1417,6 +1488,7 @@ g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_index-index.o `test -f 'index.cc' || echo './'`index.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_map-map.o `test -f 'map.cc' || echo './'`map.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -D SAM_SEQ_QUAL=1 -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_map_ssq-map.o `test -f 'map.cc' || echo './'`map.cc +g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo './'`overlap.cc In file included from /usr/include/c++/10/vector:66, from ../DataLayer/FastaIndex.h:11, from index.cc:3: @@ -1445,6 +1517,17 @@ 84 | __uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 +In file included from /usr/include/c++/10/vector:66, + from ../Common/Dictionary.h:10, + from ../Common/ContigID.h:5, + from ../Common/ContigNode.h:5, + from ../Common/ContigProperties.h:4, + from overlap.cc:10: +/usr/include/c++/10/bits/stl_uninitialized.h: In function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = wat_array::BitArray*; bool _TrivialValueTypes = false]': +/usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 + 84 | __uninit_copy(_InputIterator __first, _InputIterator __last, + | ^~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:72, from ../DataLayer/FastaIndex.h:11, from index.cc:3: @@ -1480,7 +1563,21 @@ /usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo './'`overlap.cc +g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-index abyss_index-index.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm +In file included from /usr/include/c++/10/vector:72, + from ../Common/Dictionary.h:10, + from ../Common/ContigID.h:5, + from ../Common/ContigNode.h:5, + from ../Common/ContigProperties.h:4, + from overlap.cc:10: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {FMIndex::Match}; _Tp = FMIndex::Match; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {FMIndex::Match}; _Tp = FMIndex::Match; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from ../FMIndex/bit_array.h:24, from ../FMIndex/BitArrays.h:4, @@ -1554,43 +1651,6 @@ | ~~~~~~~~~~~~~~~~~~ 150 | __uninit_copy(__first, __last, __result); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from ../FMIndex/bit_array.h:24, - from ../FMIndex/BitArrays.h:4, - from ../FMIndex/FMIndex.h:5, - from map.cc:3: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void BitArrays::assign(It, It) [with It = __gnu_cxx::__normal_iterator >]': -/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 960 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-index abyss_index-index.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm -g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-map abyss_map-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm -In file included from /usr/include/c++/10/vector:66, - from ../Common/Dictionary.h:10, - from ../Common/ContigID.h:5, - from ../Common/ContigNode.h:5, - from ../Common/ContigProperties.h:4, - from overlap.cc:10: -/usr/include/c++/10/bits/stl_uninitialized.h: In function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = wat_array::BitArray*; bool _TrivialValueTypes = false]': -/usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 - 84 | __uninit_copy(_InputIterator __first, _InputIterator __last, - | ^~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 -g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-map-ssq abyss_map_ssq-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm -In file included from /usr/include/c++/10/vector:72, - from ../Common/Dictionary.h:10, - from ../Common/ContigID.h:5, - from ../Common/ContigNode.h:5, - from ../Common/ContigProperties.h:4, - from overlap.cc:10: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {FMIndex::Match}; _Tp = FMIndex::Match; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {FMIndex::Match}; _Tp = FMIndex::Match; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = wat_array::BitArray; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: @@ -1620,6 +1680,15 @@ 150 | __uninit_copy(__first, __last, __result); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, + from ../FMIndex/bit_array.h:24, + from ../FMIndex/BitArrays.h:4, + from ../FMIndex/FMIndex.h:5, + from map.cc:3: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void BitArrays::assign(It, It) [with It = __gnu_cxx::__normal_iterator >]': +/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 960 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, from ../Common/Dictionary.h:10, from ../Common/ContigID.h:5, from ../Common/ContigNode.h:5, @@ -1629,6 +1698,8 @@ /usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-map abyss_map-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm +g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-map-ssq abyss_map_ssq-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-overlap abyss_overlap-overlap.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/Map' Making all in MergePaths @@ -1661,9 +1732,9 @@ g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fixmate-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fixmate_ssq-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo './'`ParseAligns.cpp +g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fixmate abyss_fixmate-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ParseAligns ParseAligns-ParseAligns.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fixmate-ssq abyss_fixmate_ssq-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm -g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fixmate abyss_fixmate-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/ParseAligns' Making all in PathOverlap make[4]: Entering directory '/build/abyss-2.2.5+dfsg/PathOverlap' @@ -1681,8 +1752,6 @@ g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_junction-junction.o `test -f 'junction.cc' || echo './'`junction.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_longseqdist-longseqdist.o `test -f 'longseqdist.cpp' || echo './'`longseqdist.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_drawgraph-drawgraph.o `test -f 'drawgraph.cc' || echo './'`drawgraph.cc -g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-junction abyss_junction-junction.o ../Common/libcommon.a -ldl -lm -g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-longseqdist abyss_longseqdist-longseqdist.o ../Common/libcommon.a -ldl -lm In file included from /usr/include/c++/10/algorithm:62, from /usr/include/boost/type_traits/is_nothrow_swappable.hpp:33, from /usr/include/boost/type_traits.hpp:122, @@ -1806,6 +1875,8 @@ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-junction abyss_junction-junction.o ../Common/libcommon.a -ldl -lm +g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-longseqdist abyss_longseqdist-longseqdist.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-drawgraph abyss_drawgraph-drawgraph.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-scaffold abyss_scaffold-scaffold.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/Scaffold' @@ -1858,7 +1929,7 @@ markdown README.md > README.html make[1]: Leaving directory '/build/abyss-2.2.5+dfsg' dh_auto_test - make -j3 check VERBOSE=1 + make -j4 check VERBOSE=1 make[1]: Entering directory '/build/abyss-2.2.5+dfsg' Making check in bin make[2]: Entering directory '/build/abyss-2.2.5+dfsg/bin' @@ -2060,17 +2131,6 @@ g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/MaskedKmerTest.o BloomDBG/MaskedKmerTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/SpacedSeedTest.o BloomDBG/SpacedSeedTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/arm-linux-gnueabihf/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/LightweightKmerTest.o BloomDBG/LightweightKmerTest.cpp -In file included from /usr/include/c++/10/unordered_map:46, - from ../vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:22, - from ../vendor/btl_bloomfilter/BloomFilter.hpp:13, - from ../BloomDBG/RollingBloomDBG.h:15, - from BloomDBG/RollingBloomDBGTest.cpp:1: -/usr/include/c++/10/bits/hashtable.h: In member function 'std::_Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal, _H1, _H2, _Hash, _RehashPolicy, _Traits>::iterator std::_Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal, _H1, _H2, _Hash, _RehashPolicy, _Traits>::erase(std::_Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal, _H1, _H2, _Hash, _RehashPolicy, _Traits>::const_iterator) [with _Key = RollingBloomDBGVertex; _Value = RollingBloomDBGVertex; _Alloc = std::allocator; _ExtractKey = std::__detail::_Identity; _Equal = std::equal_to; _H1 = std::hash; _H2 = std::__detail::_Mod_range_hashing; _Hash = std::__detail::_Default_ranged_hash; _RehashPolicy = std::__detail::_Prime_rehash_policy; _Traits = std::__detail::_Hashtable_traits]': -/usr/include/c++/10/bits/hashtable.h:1851:5: note: parameter passing for argument of type 'std::_Hashtable, std::__detail::_Identity, std::equal_to, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits >::const_iterator' {aka 'std::__detail::_Hashtable_base, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Hashtable_traits >::const_iterator'} changed in GCC 7.1 - 1851 | _Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1852 | _H1, _H2, _Hash, _RehashPolicy, _Traits>:: - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_stringutil Common/StringUtilTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_histogram Common/HistogramTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_bitutil Common/BitUtilTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm @@ -2081,30 +2141,25 @@ g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_sam_ssq Common/common_sam_ssq-SAM.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomFilter Konnector/BloomFilter-BloomFilter.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloom Konnector/DBGBloom-DBGBloomTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm -/usr/include/c++/10/bits/hashtable.h: In member function 'virtual void RollingBloomDBGTest_adjacency_iterator_Test::TestBody()': -/usr/include/c++/10/bits/hashtable.h:807:21: note: parameter passing for argument of type 'std::_Hashtable, std::__detail::_Identity, std::equal_to, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits >::const_iterator' {aka 'std::__detail::_Hashtable_base, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Hashtable_traits >::const_iterator'} changed in GCC 7.1 - 807 | { return erase(const_iterator(__it)); } - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloomAlgorithms Konnector/DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBFSVisitor Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm -/usr/include/c++/10/bits/hashtable.h: In member function 'virtual void RollingBloomDBGTest_out_edge_iterator_Test::TestBody()': -/usr/include/c++/10/bits/hashtable.h:807:21: note: parameter passing for argument of type 'std::_Hashtable, std::__detail::_Identity, std::equal_to, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits >::const_iterator' {aka 'std::__detail::_Hashtable_base, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Hashtable_traits >::const_iterator'} changed in GCC 7.1 - 807 | { return erase(const_iterator(__it)); } - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_BidirectionalBFS Graph/graph_BidirectionalBFS-BidirectionalBFSTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_AllPathsSearch Graph/graph_AllPathsSearch-AllPathsSearchTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm -/usr/include/c++/10/bits/hashtable.h: In member function 'virtual void RollingBloomDBGSpacedSeedTest_out_edge_iterator_Test::TestBody()': -/usr/include/c++/10/bits/hashtable.h:807:21: note: parameter passing for argument of type 'std::_Hashtable, std::__detail::_Identity, std::equal_to, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits >::const_iterator' {aka 'std::__detail::_Hashtable_base, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Hashtable_traits >::const_iterator'} changed in GCC 7.1 - 807 | { return erase(const_iterator(__it)); } - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_HashGraph Graph/graph_HashGraph-HashGraphTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBidiBFSVisitor Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ExtendPath Graph/graph_ExtendPath-ExtendPathTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm -/usr/include/c++/10/bits/hashtable.h: In member function 'virtual void RollingBloomDBGTest_in_edges_Test::TestBody()': -/usr/include/c++/10/bits/hashtable.h:807:21: note: parameter passing for argument of type 'std::_Hashtable, std::__detail::_Identity, std::equal_to, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits >::const_iterator' {aka 'std::__detail::_Hashtable_base, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Hashtable_traits >::const_iterator'} changed in GCC 7.1 - 807 | { return erase(const_iterator(__it)); } - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_DotIO Graph/graph_DotIO-DotIOTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm +In file included from /usr/include/c++/10/unordered_map:46, + from ../vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:22, + from ../vendor/btl_bloomfilter/BloomFilter.hpp:13, + from ../BloomDBG/RollingBloomDBG.h:15, + from BloomDBG/RollingBloomDBGTest.cpp:1: +/usr/include/c++/10/bits/hashtable.h: In member function 'std::_Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal, _H1, _H2, _Hash, _RehashPolicy, _Traits>::iterator std::_Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal, _H1, _H2, _Hash, _RehashPolicy, _Traits>::erase(std::_Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal, _H1, _H2, _Hash, _RehashPolicy, _Traits>::const_iterator) [with _Key = RollingBloomDBGVertex; _Value = RollingBloomDBGVertex; _Alloc = std::allocator; _ExtractKey = std::__detail::_Identity; _Equal = std::equal_to; _H1 = std::hash; _H2 = std::__detail::_Mod_range_hashing; _Hash = std::__detail::_Default_ranged_hash; _RehashPolicy = std::__detail::_Prime_rehash_policy; _Traits = std::__detail::_Hashtable_traits]': +/usr/include/c++/10/bits/hashtable.h:1851:5: note: parameter passing for argument of type 'std::_Hashtable, std::__detail::_Identity, std::equal_to, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits >::const_iterator' {aka 'std::__detail::_Hashtable_base, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Hashtable_traits >::const_iterator'} changed in GCC 7.1 + 1851 | _Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1852 | _H1, _H2, _Hash, _RehashPolicy, _Traits>:: + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_UndirectedGraph Graph/UndirectedGraphTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DBG_LoadAlgorithm DBG/LoadAlgorithm-LoadAlgorithmTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_LoadAlgorithm PairedDBG/LoadAlgorithm-LoadAlgorithmTest.o ../PairedDBG/libpaireddbg.a ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm @@ -2116,31 +2171,47 @@ g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHashIterator BloomDBG/RollingHashIteratorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_HashAgnosticCascadingBloom BloomDBG/HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_CountingBloomFilter BloomDBG/CountingBloomFilter-CountingBloomFilterTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm -g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingBloomDBG BloomDBG/RollingBloomDBG-RollingBloomDBGTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_MaskedKmer BloomDBG/MaskedKmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_SpacedSeed BloomDBG/SpacedSeedTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_LightweightKmer BloomDBG/LightweightKmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm +/usr/include/c++/10/bits/hashtable.h: In member function 'virtual void RollingBloomDBGTest_adjacency_iterator_Test::TestBody()': +/usr/include/c++/10/bits/hashtable.h:807:21: note: parameter passing for argument of type 'std::_Hashtable, std::__detail::_Identity, std::equal_to, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits >::const_iterator' {aka 'std::__detail::_Hashtable_base, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Hashtable_traits >::const_iterator'} changed in GCC 7.1 + 807 | { return erase(const_iterator(__it)); } + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/hashtable.h: In member function 'virtual void RollingBloomDBGTest_out_edge_iterator_Test::TestBody()': +/usr/include/c++/10/bits/hashtable.h:807:21: note: parameter passing for argument of type 'std::_Hashtable, std::__detail::_Identity, std::equal_to, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits >::const_iterator' {aka 'std::__detail::_Hashtable_base, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Hashtable_traits >::const_iterator'} changed in GCC 7.1 + 807 | { return erase(const_iterator(__it)); } + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/hashtable.h: In member function 'virtual void RollingBloomDBGSpacedSeedTest_out_edge_iterator_Test::TestBody()': +/usr/include/c++/10/bits/hashtable.h:807:21: note: parameter passing for argument of type 'std::_Hashtable, std::__detail::_Identity, std::equal_to, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits >::const_iterator' {aka 'std::__detail::_Hashtable_base, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Hashtable_traits >::const_iterator'} changed in GCC 7.1 + 807 | { return erase(const_iterator(__it)); } + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/hashtable.h: In member function 'virtual void RollingBloomDBGTest_in_edges_Test::TestBody()': +/usr/include/c++/10/bits/hashtable.h:807:21: note: parameter passing for argument of type 'std::_Hashtable, std::__detail::_Identity, std::equal_to, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits >::const_iterator' {aka 'std::__detail::_Hashtable_base, std::hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Hashtable_traits >::const_iterator'} changed in GCC 7.1 + 807 | { return erase(const_iterator(__it)); } + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ +g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingBloomDBG BloomDBG/RollingBloomDBG-RollingBloomDBGTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/Unittest' make check-TESTS make[3]: Entering directory '/build/abyss-2.2.5+dfsg/Unittest' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Unittest' PASS: common_stringutil -PASS: common_histogram PASS: common_bitutil -PASS: common_KmerIterator PASS: common_kmer +PASS: common_histogram PASS: common_sequence -PASS: common_sam +PASS: common_KmerIterator PASS: BloomFilter -PASS: common_sam_ssq +PASS: common_sam PASS: Konnector_DBGBloom +PASS: common_sam_ssq PASS: Konnector_DBGBloomAlgorithms PASS: graph_ConstrainedBFSVisitor PASS: graph_BidirectionalBFS -PASS: graph_AllPathsSearch PASS: graph_HashGraph -PASS: graph_ConstrainedBidiBFSVisitor PASS: graph_ExtendPath +PASS: graph_ConstrainedBidiBFSVisitor +PASS: graph_AllPathsSearch PASS: graph_DotIO PASS: graph_UndirectedGraph PASS: Konnector_konnector @@ -2151,8 +2222,8 @@ PASS: BloomDBG_RollingHash PASS: BloomDBG_RollingHashIterator PASS: BloomDBG_HashAgnosticCascadingBloom -PASS: BloomDBG_CountingBloomFilter PASS: BloomDBG_RollingBloomDBG +PASS: BloomDBG_CountingBloomFilter PASS: BloomDBG_MaskedKmer PASS: BloomDBG_SpacedSeed PASS: BloomDBG_LightweightKmer @@ -2180,13 +2251,13 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/abyss-2.2.5+dfsg' dh_auto_install --destdir=debian/tmp - make -j3 install DESTDIR=/build/abyss-2.2.5\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no + make -j4 install DESTDIR=/build/abyss-2.2.5\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/abyss-2.2.5+dfsg' Making install in bin make[3]: Entering directory '/build/abyss-2.2.5+dfsg/bin' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/bin' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-bowtie abyss-bowtie2 abyss-bwa abyss-bwasw abyss-bwamem abyss-fatoagp abyss-kaligner abyss-pe abyss-samtoafg abyss-tabtomd abyss-bloom-dist.mk abyss-dida abyss-stack-size '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/bin' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/bin' @@ -2194,8 +2265,8 @@ make[3]: Entering directory '/build/abyss-2.2.5+dfsg/doc' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/doc' make[4]: Nothing to be done for 'install-exec-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/share/doc/abyss' - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/share/man/man1' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/share/doc/abyss' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 flowchart.pdf flowchart_simplified.pdf '/build/abyss-2.2.5+dfsg/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 ABYSS.1 abyss-pe.1 abyss-tofastq.1 '/build/abyss-2.2.5+dfsg/debian/tmp/usr/share/man/man1' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/doc' @@ -2210,8 +2281,8 @@ Making install in Graph make[3]: Entering directory '/build/abyss-2.2.5+dfsg/Graph' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Graph' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-gc abyss-todot '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/Graph' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/Graph' @@ -2219,18 +2290,18 @@ make[3]: Entering directory '/build/abyss-2.2.5+dfsg/DataLayer' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/DataLayer' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-fac abyss-tofastq '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/DataLayer' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/DataLayer' Making install in DataBase make[3]: Entering directory '/build/abyss-2.2.5+dfsg/DataBase' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/DataBase' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' - /usr/bin/install -c abyss-db-txt '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-csv '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' + /usr/bin/install -c abyss-db-txt '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/DataBase' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/DataBase' Making install in FMIndex @@ -2258,7 +2329,7 @@ make[3]: Entering directory '/build/abyss-2.2.5+dfsg/Align' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Align' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-align abyss-mergepairs '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/Align' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/Align' @@ -2266,15 +2337,15 @@ make[3]: Entering directory '/build/abyss-2.2.5+dfsg/ABYSS' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/ABYSS' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c ABYSS '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/ABYSS' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/ABYSS' Making install in Parallel make[3]: Entering directory '/build/abyss-2.2.5+dfsg/Parallel' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Parallel' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c ABYSS-P abyss-paired-dbg-mpi '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/Parallel' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/Parallel' @@ -2282,15 +2353,15 @@ make[3]: Entering directory '/build/abyss-2.2.5+dfsg/Bloom' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Bloom' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/Bloom' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/Bloom' Making install in BloomDBG make[3]: Entering directory '/build/abyss-2.2.5+dfsg/BloomDBG' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/BloomDBG' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom-dbg '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/BloomDBG' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/BloomDBG' @@ -2298,7 +2369,7 @@ make[3]: Entering directory '/build/abyss-2.2.5+dfsg/Konnector' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Konnector' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c konnector '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/Konnector' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/Konnector' @@ -2306,31 +2377,31 @@ make[3]: Entering directory '/build/abyss-2.2.5+dfsg/Consensus' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Consensus' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c Consensus '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/Consensus' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/Consensus' Making install in DAssembler make[3]: Entering directory '/build/abyss-2.2.5+dfsg/DAssembler' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/DAssembler' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c DAssembler '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/DAssembler' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/DAssembler' Making install in DistanceEst make[3]: Entering directory '/build/abyss-2.2.5+dfsg/DistanceEst' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/DistanceEst' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c DistanceEst DistanceEst-ssq '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/DistanceEst' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/DistanceEst' Making install in KAligner make[3]: Entering directory '/build/abyss-2.2.5+dfsg/KAligner' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/KAligner' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c KAligner '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/KAligner' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/KAligner' @@ -2338,7 +2409,7 @@ make[3]: Entering directory '/build/abyss-2.2.5+dfsg/Layout' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Layout' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-layout '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/Layout' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/Layout' @@ -2346,14 +2417,14 @@ make[3]: Entering directory '/build/abyss-2.2.5+dfsg/LogKmerCount' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/LogKmerCount' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c logcounter '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/LogKmerCount' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/LogKmerCount' Making install in Map make[3]: Entering directory '/build/abyss-2.2.5+dfsg/Map' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Map' - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-index abyss-map abyss-map-ssq abyss-overlap '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/Map' @@ -2361,8 +2432,8 @@ Making install in MergePaths make[3]: Entering directory '/build/abyss-2.2.5+dfsg/MergePaths' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/MergePaths' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c MergePaths MergeContigs PathConsensus '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/MergePaths' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/MergePaths' @@ -2370,7 +2441,7 @@ make[3]: Entering directory '/build/abyss-2.2.5+dfsg/Overlap' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Overlap' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c Overlap '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/Overlap' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/Overlap' @@ -2378,47 +2449,47 @@ make[3]: Entering directory '/build/abyss-2.2.5+dfsg/PairedDBG' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/PairedDBG' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-paired-dbg '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/PairedDBG' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/PairedDBG' Making install in ParseAligns make[3]: Entering directory '/build/abyss-2.2.5+dfsg/ParseAligns' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/ParseAligns' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-fixmate abyss-fixmate-ssq ParseAligns '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/ParseAligns' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/ParseAligns' Making install in PathOverlap make[3]: Entering directory '/build/abyss-2.2.5+dfsg/PathOverlap' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/PathOverlap' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c PathOverlap '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/PathOverlap' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/PathOverlap' Making install in PopBubbles make[3]: Entering directory '/build/abyss-2.2.5+dfsg/PopBubbles' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/PopBubbles' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c PopBubbles '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/PopBubbles' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/PopBubbles' Making install in Scaffold make[3]: Entering directory '/build/abyss-2.2.5+dfsg/Scaffold' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Scaffold' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-scaffold abyss-junction abyss-longseqdist '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/Scaffold' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/Scaffold' Making install in SimpleGraph make[3]: Entering directory '/build/abyss-2.2.5+dfsg/SimpleGraph' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/SimpleGraph' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c SimpleGraph '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/SimpleGraph' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/SimpleGraph' @@ -2433,14 +2504,14 @@ make[3]: Entering directory '/build/abyss-2.2.5+dfsg/FilterGraph' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/FilterGraph' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-filtergraph '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/FilterGraph' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/FilterGraph' Making install in GapFiller make[3]: Entering directory '/build/abyss-2.2.5+dfsg/GapFiller' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/GapFiller' - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-gapfill '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/GapFiller' @@ -2448,15 +2519,15 @@ Making install in Sealer make[3]: Entering directory '/build/abyss-2.2.5+dfsg/Sealer' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Sealer' - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-sealer '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/Sealer' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/Sealer' Making install in AdjList make[3]: Entering directory '/build/abyss-2.2.5+dfsg/AdjList' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/AdjList' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c AdjList '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/AdjList' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/AdjList' @@ -2484,15 +2555,15 @@ make[3]: Entering directory '/build/abyss-2.2.5+dfsg' make[4]: Entering directory '/build/abyss-2.2.5+dfsg' make[4]: Nothing to be done for 'install-exec-am'. - /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/share/doc/abyss' + /usr/bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 ChangeLog CITATION.bib CITATION.md COPYRIGHT LICENSE README.md '/build/abyss-2.2.5+dfsg/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg' make[2]: Leaving directory '/build/abyss-2.2.5+dfsg' -PATH=debian/tmp/usr/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games help2man --no-info \ +PATH=debian/tmp/usr/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path help2man --no-info \ -n "Estimate distances between contigs using paired-end alignments." \ DistanceEst > debian/tmp/usr/share/man/man1/DistanceEst.1 -PATH=debian/tmp/usr/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games help2man --no-info \ +PATH=debian/tmp/usr/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path help2man --no-info \ -n "Fill the paired-end fields of SAM alignments" abyss-fixmate \ > debian/tmp/usr/share/man/man1/abyss-fixmate.1 make[1]: Leaving directory '/build/abyss-2.2.5+dfsg' @@ -2516,56 +2587,56 @@ dh_strip -a dh_makeshlibs -a dh_shlibdeps -a -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-align contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-scaffold contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/ABYSS-P contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-map contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-layout contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/PathConsensus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/PathOverlap contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/MergePaths contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/DistanceEst contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/ABYSS contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-overlap contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-junction contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/ParseAligns contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-fixmate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-sealer contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/ABYSS-P contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/AdjList contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/konnector contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-index contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-tofastq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-junction contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/MergeContigs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-fac contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/Overlap contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-gapfill contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-mergepairs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/SimpleGraph contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-tofastq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/KAligner contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-db-csv contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-paired-dbg contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-map contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/bin/DistanceEst contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/PopBubbles contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-overlap contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/KAligner contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-longseqdist contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-paired-dbg-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-todot contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/DistanceEst contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-paired-dbg contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/logcounter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-fixmate-ssq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-map-ssq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-bloom contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/DistanceEst-ssq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-filtergraph contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/SimpleGraph contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-bloom-dbg contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/PathOverlap contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/bin/abyss-fixmate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-layout contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/Consensus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-todot contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-align contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/bin/abyss-fixmate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-fixmate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/ParseAligns contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/DistanceEst-ssq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-bloom contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-fixmate-ssq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-scaffold contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-db-csv contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/DAssembler contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/MergePaths contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/bin/DistanceEst contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-sealer contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/MergeContigs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-gapfill contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-paired-dbg-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-filtergraph contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/konnector contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-map-ssq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-index contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/abyss-gc contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/PathConsensus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/abyss/usr/lib/abyss/Overlap contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'abyss-dbgsym' in '../abyss-dbgsym_2.2.5+dfsg-1_armhf.deb'. dpkg-deb: building package 'abyss' in '../abyss_2.2.5+dfsg-1_armhf.deb'. +dpkg-deb: building package 'abyss-dbgsym' in '../abyss-dbgsym_2.2.5+dfsg-1_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../abyss_2.2.5+dfsg-1_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2573,12 +2644,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/14388/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/14388/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/10876 and its subdirectories -I: Current time: Thu Aug 12 16:38:25 -12 2021 -I: pbuilder-time-stamp: 1628829505 +I: removing directory /srv/workspace/pbuilder/14388 and its subdirectories +I: Current time: Fri Aug 13 19:50:49 +14 2021 +I: pbuilder-time-stamp: 1628833849