Diff of the two buildlogs: -- --- b1/build.log 2021-07-19 19:29:15.668361534 +0000 +++ b2/build.log 2021-07-19 19:34:43.667973414 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Aug 21 13:46:52 -12 2022 -I: pbuilder-time-stamp: 1661132812 +I: Current time: Tue Jul 20 09:29:19 +14 2021 +I: pbuilder-time-stamp: 1626722959 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Thu Dec 13 06:44:54 2018 -12 +gpgv: Signature made Fri Dec 14 08:44:54 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -30,136 +30,170 @@ dpkg-source: info: applying disable-version-check.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/40023/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/7456/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/7456/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/7456/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='6f59675229d94786aad7637bde74b85f' - 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='40023' - PS1='# ' - PS2='> ' + INVOCATION_ID=b4259675e00e47e7a66bfb077a8b8a5b + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=7456 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.YkONjuJpzg/pbuilderrc_KeXd --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.YkONjuJpzg/b1 --logfile b1/build.log salmon_0.12.0+ds1-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.YkONjuJpzg/pbuilderrc_UbYD --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.YkONjuJpzg/b2 --logfile b2/build.log salmon_0.12.0+ds1-1.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos15-amd64 5.10.0-0.bpo.7-amd64 #1 SMP Debian 5.10.40-1~bpo10+1 (2021-06-04) x86_64 GNU/Linux + Linux i-capture-the-hostname 4.19.0-17-amd64 #1 SMP Debian 4.19.194-2 (2021-06-21) x86_64 GNU/Linux I: ls -l /bin total 5116 - -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat - -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown - -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp - -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash - -rwxr-xr-x 1 root root 109408 Feb 28 2019 date - -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93744 Feb 28 2019 df - -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir - -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 35424 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln - -rwxr-xr-x 1 root root 56760 Jul 26 2018 login - -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 43008 Jan 9 2019 more - -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm - -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 9 02:47 sh -> dash - -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty - -rwsr-xr-x 1 root root 63568 Jan 9 2019 su - -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync - -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar - -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch - -rwxr-xr-x 1 root root 35424 Feb 28 2019 true - -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount - -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/40023/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat + -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown + -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp + -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash + -rwxr-xr-x 1 root root 109408 Mar 1 2019 date + -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93744 Mar 1 2019 df + -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir + -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 35424 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln + -rwxr-xr-x 1 root root 56760 Jul 27 2018 login + -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 43008 Jan 10 2019 more + -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm + -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 20 09:29 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 7 22:24 sh.distrib -> dash + -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty + -rwsr-xr-x 1 root root 63568 Jan 10 2019 su + -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync + -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar + -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch + -rwxr-xr-x 1 root root 35424 Mar 1 2019 true + -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount + -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/7456/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -417,7 +451,7 @@ Get: 162 http://deb.debian.org/debian buster/main amd64 python3-sphinx-rtd-theme all 0.4.3+dfsg-1 [9696 B] Get: 163 http://deb.debian.org/debian buster/main amd64 rapmap-dev all 0.12.0+dfsg-3 [191 kB] Get: 164 http://deb.debian.org/debian buster/main amd64 sphinx-doc all 1.8.4-1 [1106 kB] -Fetched 77.9 MB in 1s (75.9 MB/s) +Fetched 77.9 MB in 1s (64.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19195 files and directories currently installed.) @@ -1126,7 +1160,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/salmon-0.12.0+ds1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/salmon-0.12.0+ds1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package salmon dpkg-buildpackage: info: source version 0.12.0+ds1-1 dpkg-buildpackage: info: source distribution unstable @@ -1252,7 +1286,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/salmon-0.12.0+ds1' dh_auto_build - cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j15 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/salmon-0.12.0+ds1 -B/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/CMakeFiles /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/CMakeFiles/progress.marks @@ -1262,122 +1296,122 @@ make -f src/CMakeFiles/ksw2pp_sse4.dir/build.make src/CMakeFiles/ksw2pp_sse4.dir/depend make -f src/CMakeFiles/ksw2pp_sse2.dir/build.make src/CMakeFiles/ksw2pp_sse2.dir/depend make -f CMakeFiles/libstadenio.dir/build.make CMakeFiles/libstadenio.dir/depend +make -f CMakeFiles/libcereal.dir/build.make CMakeFiles/libcereal.dir/depend make -f CMakeFiles/libdivsufsort.dir/build.make CMakeFiles/libdivsufsort.dir/depend make -f CMakeFiles/libgff.dir/build.make CMakeFiles/libgff.dir/depend make[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1/src /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/ksw2pp_basic.dir/DependInfo.cmake --color= -make -f CMakeFiles/libcereal.dir/build.make CMakeFiles/libcereal.dir/depend -make[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1/src /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/ksw2pp_sse4.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/CMakeFiles/libdivsufsort.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/CMakeFiles/libgff.dir/DependInfo.cmake --color= +cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/CMakeFiles/libstadenio.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1/src /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/ksw2pp_sse2.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/CMakeFiles/libstadenio.dir/DependInfo.cmake --color= +cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1/src /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/ksw2pp_basic.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/CMakeFiles/libcereal.dir/DependInfo.cmake --color= -Scanning dependencies of target ksw2pp_basic -make[4]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -Scanning dependencies of target ksw2pp_sse4 +make[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' +cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/CMakeFiles/libdivsufsort.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' +cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/CMakeFiles/libgff.dir/DependInfo.cmake --color= Scanning dependencies of target libgff -make -f src/CMakeFiles/ksw2pp_basic.dir/build.make src/CMakeFiles/ksw2pp_basic.dir/build -Scanning dependencies of target libdivsufsort -Scanning dependencies of target libcereal -Scanning dependencies of target libstadenio make[4]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -make -f src/CMakeFiles/ksw2pp_sse4.dir/build.make src/CMakeFiles/ksw2pp_sse4.dir/build +make -f CMakeFiles/libgff.dir/build.make CMakeFiles/libgff.dir/build +Scanning dependencies of target libstadenio make[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -Scanning dependencies of target ksw2pp_sse2 +make[4]: Nothing to be done for 'CMakeFiles/libgff.dir/build'. make[4]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' +make -f CMakeFiles/libstadenio.dir/build.make CMakeFiles/libstadenio.dir/build +Scanning dependencies of target libdivsufsort +make[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'CMakeFiles/libstadenio.dir/build'. make[4]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -make -f CMakeFiles/libgff.dir/build.make CMakeFiles/libgff.dir/build -make -f CMakeFiles/libdivsufsort.dir/build.make CMakeFiles/libdivsufsort.dir/build +Scanning dependencies of target libcereal make[4]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -make -f CMakeFiles/libstadenio.dir/build.make CMakeFiles/libstadenio.dir/build +make -f CMakeFiles/libdivsufsort.dir/build.make CMakeFiles/libdivsufsort.dir/build make[4]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make -f CMakeFiles/libcereal.dir/build.make CMakeFiles/libcereal.dir/build +Scanning dependencies of target ksw2pp_basic make[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -make -f src/CMakeFiles/ksw2pp_sse2.dir/build.make src/CMakeFiles/ksw2pp_sse2.dir/build -make[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'CMakeFiles/libgff.dir/build'. -make[4]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'CMakeFiles/libstadenio.dir/build'. +make[4]: Nothing to be done for 'CMakeFiles/libdivsufsort.dir/build'. make[4]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'CMakeFiles/libcereal.dir/build'. make[4]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' +make -f src/CMakeFiles/ksw2pp_basic.dir/build.make src/CMakeFiles/ksw2pp_basic.dir/build +Scanning dependencies of target ksw2pp_sse4 +Scanning dependencies of target ksw2pp_sse2 make[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'CMakeFiles/libdivsufsort.dir/build'. make[4]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' +make -f src/CMakeFiles/ksw2pp_sse4.dir/build.make src/CMakeFiles/ksw2pp_sse4.dir/build +make -f src/CMakeFiles/ksw2pp_sse2.dir/build.make src/CMakeFiles/ksw2pp_sse2.dir/build make[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -[ 1%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -[ 2%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -[ 2%] Built target libstadenio -[ 4%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -[ 5%] Built target libgff -[ 5%] Building CXX object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -[ 7%] Building C object src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o -[ 8%] Building C object src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-0.12.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -c /build/salmon-0.12.0+ds1/src/ksw2pp/ksw2_gg2.c -[ 10%] Building C object src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o +make[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' +[ 0%] Built target libgff +[ 0%] Built target libstadenio make -f src/CMakeFiles/alevin_core.dir/build.make src/CMakeFiles/alevin_core.dir/depend -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-0.12.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -c /build/salmon-0.12.0+ds1/src/ksw2pp/ksw2_gg.c -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-0.12.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -c /build/salmon-0.12.0+ds1/src/ksw2pp/ksw2_gg2_sse.c +[ 0%] Built target libdivsufsort +[ 0%] Built target libcereal make[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1/src /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/alevin_core.dir/DependInfo.cmake --color= -[ 13%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -[ 13%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-0.12.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse4.1 -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o -c /build/salmon-0.12.0+ds1/src/ksw2pp/ksw2_extd2_sse.c -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-0.12.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -c /build/salmon-0.12.0+ds1/src/ksw2pp/KSW2Aligner.cpp -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-0.12.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -c /build/salmon-0.12.0+ds1/src/ksw2pp/kalloc.c +[ 2%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o +[ 5%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o +[ 5%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o +[ 2%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-0.12.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -c /build/salmon-0.12.0+ds1/src/ksw2pp/ksw2_extd.c -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-0.12.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse4.1 -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -c /build/salmon-0.12.0+ds1/src/ksw2pp/ksw2_extz2_sse.c -[ 14%] Building C object src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse2 -mno-sse4.1 -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -c /build/salmon-0.12.0+ds1/src/ksw2pp/ksw2_extd2_sse.c -[ 14%] Built target libdivsufsort -[ 15%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -[ 15%] Built target libcereal -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-0.12.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse4.1 -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o -c /build/salmon-0.12.0+ds1/src/ksw2pp/ksw2_extf2_sse.c -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-0.12.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -c /build/salmon-0.12.0+ds1/src/ksw2pp/ksw2_extz.c make -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/depend +[ 7%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o +[ 8%] Building C object src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o +cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-0.12.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -c /build/salmon-0.12.0+ds1/src/ksw2pp/kalloc.c +cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-0.12.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -c /build/salmon-0.12.0+ds1/src/ksw2pp/ksw2_extz.c +cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-0.12.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -c /build/salmon-0.12.0+ds1/src/ksw2pp/ksw2_gg.c make[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1/src /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/salmon_core.dir/DependInfo.cmake --color= -[ 17%] Building C object src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -[ 18%] Building C object src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o +cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse2 -mno-sse4.1 -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -c /build/salmon-0.12.0+ds1/src/ksw2pp/ksw2_extd2_sse.c +[ 10%] Building CXX object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o +[ 11%] Building C object src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o +cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-0.12.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -c /build/salmon-0.12.0+ds1/src/ksw2pp/ksw2_gg2_sse.c +cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-0.12.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse4.1 -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o -c /build/salmon-0.12.0+ds1/src/ksw2pp/ksw2_extd2_sse.c +cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-0.12.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -c /build/salmon-0.12.0+ds1/src/ksw2pp/KSW2Aligner.cpp +[ 13%] Building C object src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o +[ 14%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse2 -mno-sse4.1 -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -c /build/salmon-0.12.0+ds1/src/ksw2pp/ksw2_extf2_sse.c +cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-0.12.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -c /build/salmon-0.12.0+ds1/src/ksw2pp/ksw2_gg2.c +[ 15%] Building C object src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o +[ 17%] Building C object src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse2 -mno-sse4.1 -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -c /build/salmon-0.12.0+ds1/src/ksw2pp/ksw2_extz2_sse.c +cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-0.12.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse4.1 -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -c /build/salmon-0.12.0+ds1/src/ksw2pp/ksw2_extz2_sse.c +[ 18%] Building C object src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o +cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/salmon-0.12.0+ds1/include -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse4.1 -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o -c /build/salmon-0.12.0+ds1/src/ksw2pp/ksw2_extf2_sse.c +Scanning dependencies of target salmon_core +make[4]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' +make -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/build Scanning dependencies of target alevin_core make[4]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/alevin_core.dir/build.make src/CMakeFiles/alevin_core.dir/build make[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' [ 20%] Building CXX object src/CMakeFiles/alevin_core.dir/edlib.cpp.o cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security 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CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o -c /build/salmon-0.12.0+ds1/src/AlevinUtils.cpp -make[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -[ 23%] Building CXX object src/CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o +[ 21%] Building CXX object src/CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o -c /build/salmon-0.12.0+ds1/src/jellyfish/mer_dna.cc +[ 23%] Building CXX object src/CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o +cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o -c /build/salmon-0.12.0+ds1/src/AlevinUtils.cpp [ 24%] Building C object src/CMakeFiles/salmon_core.dir/xxhash.c.o cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/salmon_core.dir/xxhash.c.o -c /build/salmon-0.12.0+ds1/src/xxhash.c [ 26%] Building CXX object src/CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o -[ 27%] Building CXX object src/CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o -c /build/salmon-0.12.0+ds1/src/TranscriptGroup.cpp -[ 28%] Building CXX object src/CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o -c /build/salmon-0.12.0+ds1/src/EffectiveLengthStats.cpp +[ 27%] Building CXX object src/CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o +[ 28%] Building CXX object src/CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o -c /build/salmon-0.12.0+ds1/src/LibraryFormat.cpp +cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o -c /build/salmon-0.12.0+ds1/src/EffectiveLengthStats.cpp [ 30%] Building CXX object src/CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o -c /build/salmon-0.12.0+ds1/src/GenomicFeature.cpp [ 31%] Building CXX object src/CMakeFiles/salmon_core.dir/VersionChecker.cpp.o -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/VersionChecker.cpp.o -c /build/salmon-0.12.0+ds1/src/VersionChecker.cpp [ 33%] Building CXX object src/CMakeFiles/salmon_core.dir/SBModel.cpp.o +cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/VersionChecker.cpp.o -c /build/salmon-0.12.0+ds1/src/VersionChecker.cpp cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/SBModel.cpp.o -c /build/salmon-0.12.0+ds1/src/SBModel.cpp [ 34%] Building CXX object src/CMakeFiles/salmon_core.dir/FastxParser.cpp.o cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/FastxParser.cpp.o -c /build/salmon-0.12.0+ds1/src/FastxParser.cpp @@ -1386,32 +1420,32 @@ [ 37%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o -c /build/salmon-0.12.0+ds1/src/SalmonUtils.cpp [ 39%] Building CXX object src/CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o +make[4]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o -c /build/salmon-0.12.0+ds1/src/DistributionUtils.cpp +[ 39%] Built target ksw2pp_basic [ 40%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o -c /build/salmon-0.12.0+ds1/src/SalmonExceptions.cpp [ 42%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o -c /build/salmon-0.12.0+ds1/src/SalmonStringUtils.cpp make[4]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -[ 42%] Built target ksw2pp_basic [ 43%] Building CXX object src/CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o +[ 43%] Built target ksw2pp_sse2 cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o -c /build/salmon-0.12.0+ds1/src/SimplePosBias.cpp [ 44%] Building CXX object src/CMakeFiles/salmon_core.dir/SGSmooth.cpp.o cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/SGSmooth.cpp.o -c /build/salmon-0.12.0+ds1/src/SGSmooth.cpp make[4]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' [ 44%] Built target ksw2pp_sse4 -[ 44%] Built target ksw2pp_sse2 make -f src/CMakeFiles/ksw2pp.dir/build.make src/CMakeFiles/ksw2pp.dir/depend -[ 46%] Building CXX object src/CMakeFiles/salmon_core.dir/metro/metrohash64.cpp.o make[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1/src /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/ksw2pp.dir/DependInfo.cmake --color= -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/metro/metrohash64.cpp.o -c /build/salmon-0.12.0+ds1/src/metro/metrohash64.cpp Scanning dependencies of target ksw2pp make[4]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/ksw2pp.dir/build.make src/CMakeFiles/ksw2pp.dir/build make[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -[ 47%] Linking CXX static library libksw2pp.a +[ 46%] Linking CXX static library libksw2pp.a cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/ksw2pp.dir/cmake_clean_target.cmake +[ 47%] Building CXX object src/CMakeFiles/salmon_core.dir/metro/metrohash64.cpp.o +cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/metro/metrohash64.cpp.o -c /build/salmon-0.12.0+ds1/src/metro/metrohash64.cpp cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ksw2pp.dir/link.txt --verbose=1 /usr/bin/ar qc libksw2pp.a CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o /usr/bin/ranlib libksw2pp.a @@ -1438,14 +1472,14 @@ make[4]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/unitTests.dir/build.make src/CMakeFiles/unitTests.dir/build make[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -[ 52%] Building CXX object src/CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o -c /build/salmon-0.12.0+ds1/src/FragmentLengthDistribution.cpp -[ 53%] Building CXX object src/CMakeFiles/unitTests.dir/__/tests/UnitTests.cpp.o -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/unitTests.dir/__/tests/UnitTests.cpp.o -c /build/salmon-0.12.0+ds1/tests/UnitTests.cpp +[ 52%] Building CXX object src/CMakeFiles/unitTests.dir/__/tests/UnitTests.cpp.o [ 55%] Building CXX object src/CMakeFiles/unitTests.dir/__/external/install/src/rapmap/rank9b.cpp.o +[ 55%] Building CXX object src/CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o [ 56%] Building C object src/CMakeFiles/unitTests.dir/__/external/install/src/rapmap/bit_array.c.o -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/unitTests.dir/__/external/install/src/rapmap/rank9b.cpp.o -c /build/salmon-0.12.0+ds1/external/install/src/rapmap/rank9b.cpp +cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/unitTests.dir/__/tests/UnitTests.cpp.o -c /build/salmon-0.12.0+ds1/tests/UnitTests.cpp cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -o CMakeFiles/unitTests.dir/__/external/install/src/rapmap/bit_array.c.o -c /build/salmon-0.12.0+ds1/external/install/src/rapmap/bit_array.c +cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o -c /build/salmon-0.12.0+ds1/src/FragmentLengthDistribution.cpp +cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/unitTests.dir/__/external/install/src/rapmap/rank9b.cpp.o -c /build/salmon-0.12.0+ds1/external/install/src/rapmap/rank9b.cpp [ 57%] Linking CXX executable unitTests cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/unitTests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/unitTests.dir/__/tests/UnitTests.cpp.o CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o CMakeFiles/unitTests.dir/__/external/install/src/rapmap/rank9b.cpp.o CMakeFiles/unitTests.dir/__/external/install/src/rapmap/bit_array.c.o -o unitTests -L/build/salmon-0.12.0+ds1/lib -L/build/salmon-0.12.0+ds1/external/install/lib -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/../../lib:\$ORIGIN/:\$ORIGIN/../../external/install/lib" libsalmon_core.a libalevin_core.a -lgff -lboost_iostreams -lboost_filesystem -lboost_system -lboost_timer -lboost_chrono -lboost_program_options -lboost_regex -lstaden-read -lz -ldivsufsort -ldivsufsort64 -lm 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src/CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/salmon.dir/__/external/install/src/rapmap/RapMapSAIndex.cpp.o -c /build/salmon-0.12.0+ds1/external/install/src/rapmap/RapMapSAIndex.cpp -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-0.12.0+ds1/include 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cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -o CMakeFiles/salmon.dir/__/external/install/src/rapmap/bit_array.c.o -c /build/salmon-0.12.0+ds1/external/install/src/rapmap/bit_array.c -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external 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-I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/salmon.dir/Salmon.cpp.o -c /build/salmon-0.12.0+ds1/src/Salmon.cpp cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o -c /build/salmon-0.12.0+ds1/src/BuildSalmonIndex.cpp -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/salmon.dir/Graph.cpp.o -c /build/salmon-0.12.0+ds1/src/Graph.cpp -[ 79%] Building CXX object src/CMakeFiles/salmon.dir/DedupUMI.cpp.o +cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/salmon.dir/DedupUMI.cpp.o -c /build/salmon-0.12.0+ds1/src/DedupUMI.cpp [ 81%] Building CXX object src/CMakeFiles/salmon.dir/Alevin.cpp.o cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/salmon.dir/Alevin.cpp.o -c /build/salmon-0.12.0+ds1/src/Alevin.cpp -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/salmon.dir/DedupUMI.cpp.o -c /build/salmon-0.12.0+ds1/src/DedupUMI.cpp [ 82%] Building CXX object src/CMakeFiles/salmon.dir/SalmonAlevin.cpp.o cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/salmon.dir/SalmonAlevin.cpp.o -c /build/salmon-0.12.0+ds1/src/SalmonAlevin.cpp -[ 84%] Building CXX object src/CMakeFiles/salmon.dir/WhiteList.cpp.o -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/salmon.dir/WhiteList.cpp.o -c /build/salmon-0.12.0+ds1/src/WhiteList.cpp In file included from /build/salmon-0.12.0+ds1/include/pcg_random.hpp:104, from /build/salmon-0.12.0+ds1/src/CollapsedGibbsSampler.cpp:22: /build/salmon-0.12.0+ds1/include/pcg_extras.hpp:563:51: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] @@ -1504,6 +1536,8 @@ /build/salmon-0.12.0+ds1/include/pcg_extras.hpp:563:60: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] fnv(IntType(2166136261U ^ sizeof(IntType)), __DATE__ __TIME__ __FILE__); ^~~~~~~~ +[ 84%] Building CXX object src/CMakeFiles/salmon.dir/WhiteList.cpp.o +cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/salmon.dir/WhiteList.cpp.o -c /build/salmon-0.12.0+ds1/src/WhiteList.cpp [ 85%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantify.cpp.o cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/build/salmon-0.12.0+ds1/external -I/build/salmon-0.12.0+ds1/external/cereal/include -I/build/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -ffile-prefix-map=/build/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/salmon.dir/SalmonQuantify.cpp.o -c /build/salmon-0.12.0+ds1/src/SalmonQuantify.cpp [ 86%] Building CXX object src/CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o @@ -1691,13 +1725,13 @@ /usr/bin/ctest --force-new-ctest-process -j1 Test project /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu Start 1: unit_tests -1/2 Test #1: unit_tests ....................... Passed 0.17 sec +1/2 Test #1: unit_tests ....................... Passed 0.16 sec Start 2: salmon_read_test_quasi -2/2 Test #2: salmon_read_test_quasi ........... Passed 1.63 sec +2/2 Test #2: salmon_read_test_quasi ........... Passed 0.96 sec 100% tests passed, 0 tests failed out of 2 -Total Test time (real) = 1.80 sec +Total Test time (real) = 1.13 sec make[2]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/salmon-0.12.0+ds1' create-stamp debian/debhelper-build-stamp @@ -1706,7 +1740,7 @@ dh_testroot dh_prep dh_auto_install - cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/salmon-0.12.0\+ds1/debian/salmon AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j15 install DESTDIR=/build/salmon-0.12.0\+ds1/debian/salmon AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/salmon-0.12.0+ds1 -B/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/CMakeFiles /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/CMakeFiles/progress.marks @@ -1716,70 +1750,70 @@ make -f src/CMakeFiles/ksw2pp_sse4.dir/build.make src/CMakeFiles/ksw2pp_sse4.dir/depend make -f src/CMakeFiles/ksw2pp_sse2.dir/build.make src/CMakeFiles/ksw2pp_sse2.dir/depend make -f CMakeFiles/libstadenio.dir/build.make CMakeFiles/libstadenio.dir/depend +make -f CMakeFiles/libcereal.dir/build.make CMakeFiles/libcereal.dir/depend make -f CMakeFiles/libdivsufsort.dir/build.make CMakeFiles/libdivsufsort.dir/depend make -f CMakeFiles/libgff.dir/build.make CMakeFiles/libgff.dir/depend -make -f CMakeFiles/libcereal.dir/build.make CMakeFiles/libcereal.dir/depend -make[3]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1/src /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/ksw2pp_sse2.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/CMakeFiles/libstadenio.dir/DependInfo.cmake --color= +cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1/src /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/ksw2pp_sse4.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1/src /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/ksw2pp_basic.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/CMakeFiles/libcereal.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1/src 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'/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/CMakeFiles/libdivsufsort.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/CMakeFiles/libgff.dir/DependInfo.cmake --color= +cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1/src /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/ksw2pp_sse2.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -make -f src/CMakeFiles/ksw2pp_sse2.dir/build.make src/CMakeFiles/ksw2pp_sse2.dir/build -make[3]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -make[3]: Nothing to be done for 'src/CMakeFiles/ksw2pp_sse2.dir/build'. +make -f CMakeFiles/libdivsufsort.dir/build.make CMakeFiles/libdivsufsort.dir/build make[3]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -make -f CMakeFiles/libcereal.dir/build.make CMakeFiles/libcereal.dir/build +make -f CMakeFiles/libstadenio.dir/build.make CMakeFiles/libstadenio.dir/build make[3]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' +make -f src/CMakeFiles/ksw2pp_sse2.dir/build.make src/CMakeFiles/ksw2pp_sse2.dir/build +make -f CMakeFiles/libcereal.dir/build.make CMakeFiles/libcereal.dir/build +make[3]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -make -f CMakeFiles/libstadenio.dir/build.make CMakeFiles/libstadenio.dir/build -make -f CMakeFiles/libdivsufsort.dir/build.make CMakeFiles/libdivsufsort.dir/build +make[3]: Nothing to be done for 'CMakeFiles/libstadenio.dir/build'. make[3]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -make -f src/CMakeFiles/ksw2pp_basic.dir/build.make src/CMakeFiles/ksw2pp_basic.dir/build +make -f CMakeFiles/libgff.dir/build.make CMakeFiles/libgff.dir/build make[3]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -make[3]: Nothing to be done for 'CMakeFiles/libcereal.dir/build'. +make[3]: Nothing to be done for 'CMakeFiles/libdivsufsort.dir/build'. make[3]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/ksw2pp_sse4.dir/build.make src/CMakeFiles/ksw2pp_sse4.dir/build make[3]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -make[3]: Nothing to be done for 'CMakeFiles/libstadenio.dir/build'. +make[3]: Nothing to be done for 'CMakeFiles/libgff.dir/build'. make[3]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -make[3]: Nothing to be done for 'CMakeFiles/libdivsufsort.dir/build'. +make[3]: Nothing to be done for 'CMakeFiles/libcereal.dir/build'. make[3]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -make[3]: Nothing to be done for 'src/CMakeFiles/ksw2pp_basic.dir/build'. +make[3]: Nothing to be done for 'src/CMakeFiles/ksw2pp_sse2.dir/build'. make[3]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'src/CMakeFiles/ksw2pp_sse4.dir/build'. make[3]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -make -f CMakeFiles/libgff.dir/build.make CMakeFiles/libgff.dir/build +make -f src/CMakeFiles/ksw2pp_basic.dir/build.make src/CMakeFiles/ksw2pp_basic.dir/build make[3]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' -make[3]: Nothing to be done for 'CMakeFiles/libgff.dir/build'. +make[3]: Nothing to be done for 'src/CMakeFiles/ksw2pp_basic.dir/build'. make[3]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' +[ 0%] Built target libdivsufsort [ 4%] Built target ksw2pp_sse2 [ 4%] Built target libstadenio [ 4%] Built target libcereal make -f src/CMakeFiles/alevin_core.dir/build.make src/CMakeFiles/alevin_core.dir/depend -[ 4%] Built target libdivsufsort -[ 14%] Built target ksw2pp_basic +[ 8%] Built target ksw2pp_sse4 make[3]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1/src /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/alevin_core.dir/DependInfo.cmake --color= -[ 18%] Built target ksw2pp_sse4 -[ 18%] Built target libgff -make -f src/CMakeFiles/ksw2pp.dir/build.make src/CMakeFiles/ksw2pp.dir/depend +[ 8%] Built target libgff make -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/depend +[ 18%] Built target ksw2pp_basic +make -f src/CMakeFiles/ksw2pp.dir/build.make src/CMakeFiles/ksw2pp.dir/depend make[3]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/salmon-0.12.0+ds1 /build/salmon-0.12.0+ds1/src /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/ksw2pp.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' @@ -1791,9 +1825,9 @@ make[3]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/alevin_core.dir/build.make src/CMakeFiles/alevin_core.dir/build +[ 20%] Built target ksw2pp make[3]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/build -[ 20%] Built target ksw2pp make[3]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'src/CMakeFiles/alevin_core.dir/build'. make[3]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' @@ -1854,15 +1888,15 @@ dh_strip dh_makeshlibs dh_shlibdeps -dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/salmon/usr/bin/salmon was not linked against libboost_chrono.so.1.67.0 (it uses none of the library's symbols) +dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/salmon/usr/bin/salmon was not linked against libboost_timer.so.1.67.0 (it uses none of the library's symbols) +dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/salmon/usr/bin/salmon was not linked against libgomp.so.1 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/salmon/usr/bin/salmon was not linked against libdl.so.2 (it uses none of the library's symbols) -dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/salmon/usr/bin/salmon was not linked against liblzma.so.5 (it uses none of the library's symbols) +dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/salmon/usr/bin/salmon was not linked against libbz2.so.1.0 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/salmon/usr/bin/salmon was not linked against libboost_regex.so.1.67.0 (it uses none of the library's symbols) -dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/salmon/usr/bin/salmon was not linked against librt.so.1 (it uses none of the library's symbols) -dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/salmon/usr/bin/salmon was not linked against libgomp.so.1 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/salmon/usr/bin/salmon was not linked against libtbbmalloc.so.2 (it uses none of the library's symbols) -dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/salmon/usr/bin/salmon was not linked against libbz2.so.1.0 (it uses none of the library's symbols) -dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/salmon/usr/bin/salmon was not linked against libboost_timer.so.1.67.0 (it uses none of the library's symbols) +dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/salmon/usr/bin/salmon was not linked against librt.so.1 (it uses none of the library's symbols) +dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/salmon/usr/bin/salmon was not linked against liblzma.so.5 (it uses none of the library's symbols) +dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/salmon/usr/bin/salmon was not linked against libboost_chrono.so.1.67.0 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package salmon: substitution variable ${sphinxdoc:Built-Using} unused, but is defined @@ -1877,12 +1911,14 @@ dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/7456/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/7456/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/40023 and its subdirectories -I: Current time: Sun Aug 21 13:52:16 -12 2022 -I: pbuilder-time-stamp: 1661133136 +I: removing directory /srv/workspace/pbuilder/7456 and its subdirectories +I: Current time: Tue Jul 20 09:34:43 +14 2021 +I: pbuilder-time-stamp: 1626723283