Mon Jul 19 19:23:50 UTC 2021 I: starting to build salmon/buster/amd64 on jenkins on '2021-07-19 19:23' Mon Jul 19 19:23:50 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_20/73554/console.log Mon Jul 19 19:23:50 UTC 2021 I: Downloading source for buster/salmon=0.12.0+ds1-1 --2021-07-19 19:23:50-- http://deb.debian.org/debian/pool/main/s/salmon/salmon_0.12.0+ds1-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2506 (2.4K) Saving to: ‘salmon_0.12.0+ds1-1.dsc’ 0K .. 100% 247M=0s 2021-07-19 19:23:50 (247 MB/s) - ‘salmon_0.12.0+ds1-1.dsc’ saved [2506/2506] Mon Jul 19 19:23:50 UTC 2021 I: salmon_0.12.0+ds1-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: salmon Binary: salmon Architecture: any Version: 0.12.0+ds1-1 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Kevin Murray Homepage: https://github.com/COMBINE-lab/salmon Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/salmon Vcs-Git: https://salsa.debian.org/med-team/salmon.git Build-Depends: debhelper (>= 11~), cmake, libboost-filesystem-dev, libboost-system-dev, libboost-iostreams-dev, libboost-thread-dev, libboost-program-options-dev, libboost-timer-dev, libjellyfish-2.0-dev (>> 2.2.3-2), libpthread-stubs0-dev, libsparsehash-dev, libdivsufsort-dev, libbwa-dev, pkg-config, libjemalloc-dev, libcereal-dev, libtbb-dev, libgff-dev, libstaden-read-dev, libspdlog-dev, libtclap-dev, help2man, sphinx-doc, python3-sphinx, python3-sphinx-rtd-theme, zlib1g-dev, libeigen3-dev, libbz2-dev, liblzma-dev, rapmap-dev (>= 0.12.0~) Package-List: salmon deb science optional arch=any Checksums-Sha1: a78a9d85908853eff813c1f4a1eaa33e3f678db1 6551816 salmon_0.12.0+ds1.orig.tar.xz 7147ca23586050dcddc621d35187d9135b17e807 8872 salmon_0.12.0+ds1-1.debian.tar.xz Checksums-Sha256: 79c1eb664567ff63416364f63832b075e3dc2939bdcd1a20f4725f224eb4324c 6551816 salmon_0.12.0+ds1.orig.tar.xz 402582021e594e9f7b21f7b699918df6d6ffb6f8c7d1aafaa0ae4f8e390dd4c1 8872 salmon_0.12.0+ds1-1.debian.tar.xz Files: 1cedbf2dfe6c8a4285ed9135e72a78ba 6551816 salmon_0.12.0+ds1.orig.tar.xz d46b4c07b9305f8550421fc46e21d04e 8872 salmon_0.12.0+ds1-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlwSqKYRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEKtA/+NL4arFM/TcmYHpVVpjOh5GlKjcSu+hHv htDa+XZmiEY3e7RL/8jFXbQ9hJndIRlz33cfEMnWIPFLdFE30P5HPS/RH/0MfFNP ++ZEy+GFwQkVLh8MUNJol9Mux8DGxGHaM8WUXZC6+rd4/iSs1tMm98gtpMAphlkj v8zxILpGm2M1b2NxIXFDXbz1rjFqDOdMayrsrBMdVUvrNvqCjWt6SD+vBHk8iD8w xhYiTfCJMkivsV9weICZEzXABJVHfaJiUEC9ivYzvNQmQdDaiqvffYp+L/riMNxD kz17ZilpLhqrs3B3/85EUSINYiEOg/qt99hjeefFcstWiwfz1/+47zAGSET6NL6N cKZaTqTDQlVHIqrji5YQUw5lu5u54PrAIziOG8afPCdvG1uEj1FNtooqTdJeoXT+ oa2f9UgqoGlXP/YMFO/jagiORe+7DYiuLpXndqOk/POp+lG0p109SlNj1fVQyv1S WFM34KJODxrCr2eRX3gxXiyUKePEctmAIh98XvXhwvrqxz3gjj+k/oEA8ftFlCCp eLFLGo70ruhubzyOiF+hpGPQTh7QbdQfpk167McbkFUoSLB2ZllLV0ejnJAm/ZUl s7gnL1yUn4pa82m20VunJrhHNqnMONAtUPT9c38GTraQiDNc++4dr2+KFIDdi8Bh ZZrT3PEG24M= =Dfea -----END PGP SIGNATURE----- Mon Jul 19 19:23:50 UTC 2021 I: Checking whether the package is not for us Mon Jul 19 19:23:50 UTC 2021 I: Starting 1st build on remote node ionos15-amd64.debian.net. Mon Jul 19 19:23:50 UTC 2021 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Mon Jul 19 19:29:17 UTC 2021 I: Deleting $TMPDIR on ionos15-amd64.debian.net. 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: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [salmon_0.12.0+ds1-1.dsc] I: copying [./salmon_0.12.0+ds1.orig.tar.xz] I: copying [./salmon_0.12.0+ds1-1.debian.tar.xz] 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: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./salmon_0.12.0+ds1-1.dsc dpkg-source: info: extracting salmon in salmon-0.12.0+ds1 dpkg-source: info: unpacking salmon_0.12.0+ds1.orig.tar.xz dpkg-source: info: unpacking salmon_0.12.0+ds1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libs.patch 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: 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' 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='> ' 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' 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 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 -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), cmake, libboost-filesystem-dev, libboost-system-dev, libboost-iostreams-dev, libboost-thread-dev, libboost-program-options-dev, libboost-timer-dev, libjellyfish-2.0-dev (>> 2.2.3-2), libpthread-stubs0-dev, libsparsehash-dev, libdivsufsort-dev, libbwa-dev, pkg-config, libjemalloc-dev, libcereal-dev, libtbb-dev, libgff-dev, libstaden-read-dev, libspdlog-dev, libtclap-dev, help2man, sphinx-doc, python3-sphinx, python3-sphinx-rtd-theme, zlib1g-dev, libeigen3-dev, libbz2-dev, liblzma-dev, rapmap-dev (>= 0.12.0~) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libboost-filesystem-dev; however: Package libboost-filesystem-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-system-dev; however: Package libboost-system-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-thread-dev; however: Package libboost-thread-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-timer-dev; however: Package libboost-timer-dev is not installed. pbuilder-satisfydepends-dummy depends on libjellyfish-2.0-dev (>> 2.2.3-2); however: Package libjellyfish-2.0-dev is not installed. pbuilder-satisfydepends-dummy depends on libpthread-stubs0-dev; however: Package libpthread-stubs0-dev is not installed. pbuilder-satisfydepends-dummy depends on libsparsehash-dev; however: Package libsparsehash-dev is not installed. pbuilder-satisfydepends-dummy depends on libdivsufsort-dev; however: Package libdivsufsort-dev is not installed. pbuilder-satisfydepends-dummy depends on libbwa-dev; however: Package libbwa-dev is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on libjemalloc-dev; however: Package libjemalloc-dev is not installed. pbuilder-satisfydepends-dummy depends on libcereal-dev; however: Package libcereal-dev is not installed. pbuilder-satisfydepends-dummy depends on libtbb-dev; however: Package libtbb-dev is not installed. pbuilder-satisfydepends-dummy depends on libgff-dev; however: Package libgff-dev is not installed. pbuilder-satisfydepends-dummy depends on libstaden-read-dev; however: Package libstaden-read-dev is not installed. pbuilder-satisfydepends-dummy depends on libspdlog-dev; however: Package libspdlog-dev is not installed. pbuilder-satisfydepends-dummy depends on libtclap-dev; however: Package libtclap-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on sphinx-doc; however: Package sphinx-doc is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-rtd-theme; however: Package python3-sphinx-rtd-theme is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libeigen3-dev; however: Package libeigen3-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on rapmap-dev (>= 0.12.0~); however: Package rapmap-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} ca-certificates{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} docutils-common{a} docutils-doc{a} dwz{a} file{a} fonts-font-awesome{a} fonts-lato{a} fonts-roboto-slab{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libboost-atomic1.67-dev{a} libboost-atomic1.67.0{a} libboost-chrono1.67-dev{a} libboost-chrono1.67.0{a} libboost-date-time1.67-dev{a} libboost-date-time1.67.0{a} libboost-filesystem-dev{a} libboost-filesystem1.67-dev{a} libboost-filesystem1.67.0{a} libboost-iostreams-dev{a} libboost-iostreams1.67-dev{a} libboost-program-options-dev{a} libboost-program-options1.67-dev{a} libboost-program-options1.67.0{a} libboost-regex1.67-dev{a} libboost-regex1.67.0{a} libboost-serialization1.67-dev{a} libboost-serialization1.67.0{a} libboost-system-dev{a} libboost-system1.67-dev{a} libboost-thread-dev{a} libboost-thread1.67-dev{a} libboost-thread1.67.0{a} libboost-timer-dev{a} libboost-timer1.67-dev{a} libboost-timer1.67.0{a} libboost1.67-dev{a} libbsd0{a} libbwa-dev{a} libbz2-dev{a} libcereal-dev{a} libcroco3{a} libcurl3-gnutls{a} libcurl4{a} libcurl4-gnutls-dev{a} libdivsufsort-dev{a} libdivsufsort3{a} libeigen3-dev{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgff-dev{a} libglib2.0-0{a} libgssapi-krb5-2{a} libicu-dev{a} libicu63{a} libjellyfish-2.0-2{a} libjellyfish-2.0-dev{a} libjemalloc-dev{a} libjemalloc2{a} libjs-jquery{a} libjs-modernizr{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp1{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.4-2{a} libldap-common{a} liblocale-gettext-perl{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libmpdec2{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libprocps7{a} libpsl5{a} libpthread-stubs0-dev{a} libpython3-stdlib{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} libreadline7{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsparsehash-dev{a} libspdlog-dev{a} libssh2-1{a} libssl1.1{a} libstaden-read-dev{a} libstaden-read13{a} libtbb-dev{a} libtbb2{a} libtclap-dev{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} lsb-base{a} m4{a} man-db{a} mime-support{a} openssl{a} pkg-config{a} po-debconf{a} procps{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-distutils{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-jinja2{a} python3-lib2to3{a} python3-markupsafe{a} python3-minimal{a} python3-packaging{a} python3-pkg-resources{a} python3-pygments{a} python3-pyparsing{a} python3-requests{a} python3-roman{a} python3-six{a} python3-sphinx{a} python3-sphinx-rtd-theme{a} python3-tz{a} python3-urllib3{a} python3.7{a} python3.7-minimal{a} rapmap-dev{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-doc{a} sphinx-rtd-theme-common{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl javascript-common krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules lynx psmisc publicsuffix python3-pil shared-mime-info wget xdg-user-dirs 0 packages upgraded, 164 newly installed, 0 to remove and 0 not upgraded. Need to get 77.9 MB of archives. After unpacking 452 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 fonts-lato all 2.0-2 [2698 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u6 [1539 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 libpython3.7-minimal amd64 3.7.3-2+deb10u3 [589 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 python3.7-minimal amd64 3.7.3-2+deb10u3 [1737 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 python3-minimal amd64 3.7.3-1 [36.6 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libpython3.7-stdlib amd64 3.7.3-2+deb10u3 [1734 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 python3.7 amd64 3.7.3-2+deb10u3 [330 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 libpython3-stdlib amd64 3.7.3-1 [20.0 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 python3 amd64 3.7.3-1 [61.5 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 sgml-base all 1.29 [14.8 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 libprocps7 amd64 2:3.3.15-2 [61.7 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 lsb-base all 10.2019051400 [28.4 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 procps amd64 2:3.3.15-2 [259 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 openssl amd64 1.1.1d-0+deb10u6 [844 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 ca-certificates all 20200601~deb10u2 [166 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 cmake-data all 3.13.4-1 [1476 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libarchive13 amd64 3.3.3-4+deb10u1 [313 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u1 [65.8 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u1 [122 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u1 [369 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u1 [158 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u1 [69.1 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u1 [106 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 [224 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 libcurl4 amd64 7.64.0-4+deb10u2 [332 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 libjsoncpp1 amd64 1.7.4-3 [75.6 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 librhash0 amd64 1.3.8-1 [122 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 libuv1 amd64 1.24.1-1 [110 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 cmake amd64 3.13.4-1 [3480 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 docutils-common all 0.14+dfsg-4 [167 kB] Get: 77 http://deb.debian.org/debian buster/main amd64 docutils-doc all 0.14+dfsg-4 [924 kB] Get: 78 http://deb.debian.org/debian buster/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-1 [515 kB] Get: 79 http://deb.debian.org/debian buster/main amd64 fonts-roboto-slab all 1.100263+20170512-1 [207 kB] Get: 80 http://deb.debian.org/debian buster/main amd64 help2man amd64 1.47.8 [177 kB] Get: 81 http://deb.debian.org/debian buster/main amd64 icu-devtools amd64 63.1-6+deb10u1 [189 kB] Get: 82 http://deb.debian.org/debian buster/main amd64 libboost1.67-dev amd64 1.67.0-13+deb10u1 [8388 kB] Get: 83 http://deb.debian.org/debian buster/main amd64 libboost-atomic1.67.0 amd64 1.67.0-13+deb10u1 [226 kB] Get: 84 http://deb.debian.org/debian buster/main amd64 libboost-atomic1.67-dev amd64 1.67.0-13+deb10u1 [225 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 libboost-chrono1.67.0 amd64 1.67.0-13+deb10u1 [234 kB] Get: 86 http://deb.debian.org/debian buster/main amd64 libboost-chrono1.67-dev amd64 1.67.0-13+deb10u1 [236 kB] Get: 87 http://deb.debian.org/debian buster/main amd64 libboost-date-time1.67.0 amd64 1.67.0-13+deb10u1 [239 kB] Get: 88 http://deb.debian.org/debian buster/main amd64 libboost-serialization1.67.0 amd64 1.67.0-13+deb10u1 [319 kB] Get: 89 http://deb.debian.org/debian buster/main amd64 libboost-serialization1.67-dev amd64 1.67.0-13+deb10u1 [359 kB] Get: 90 http://deb.debian.org/debian buster/main amd64 libboost-date-time1.67-dev amd64 1.67.0-13+deb10u1 [248 kB] Get: 91 http://deb.debian.org/debian buster/main amd64 libboost-filesystem1.67.0 amd64 1.67.0-13+deb10u1 [261 kB] Get: 92 http://deb.debian.org/debian buster/main amd64 libboost-system1.67-dev amd64 1.67.0-13+deb10u1 [231 kB] Get: 93 http://deb.debian.org/debian buster/main amd64 libboost-filesystem1.67-dev amd64 1.67.0-13+deb10u1 [269 kB] Get: 94 http://deb.debian.org/debian buster/main amd64 libboost-filesystem-dev amd64 1.67.0.1 [3684 B] Get: 95 http://deb.debian.org/debian buster/main amd64 libboost-regex1.67.0 amd64 1.67.0-13+deb10u1 [485 kB] Get: 96 http://deb.debian.org/debian buster/main amd64 libicu-dev amd64 63.1-6+deb10u1 [9186 kB] Get: 97 http://deb.debian.org/debian buster/main amd64 libboost-regex1.67-dev amd64 1.67.0-13+deb10u1 [539 kB] Get: 98 http://deb.debian.org/debian buster/main amd64 libboost-iostreams1.67-dev amd64 1.67.0-13+deb10u1 [255 kB] Get: 99 http://deb.debian.org/debian buster/main amd64 libboost-iostreams-dev amd64 1.67.0.1 [3632 B] Get: 100 http://deb.debian.org/debian buster/main amd64 libboost-program-options1.67.0 amd64 1.67.0-13+deb10u1 [357 kB] Get: 101 http://deb.debian.org/debian buster/main amd64 libboost-program-options1.67-dev amd64 1.67.0-13+deb10u1 [385 kB] Get: 102 http://deb.debian.org/debian buster/main amd64 libboost-program-options-dev amd64 1.67.0.1 [3656 B] Get: 103 http://deb.debian.org/debian buster/main amd64 libboost-system-dev amd64 1.67.0.1 [3788 B] Get: 104 http://deb.debian.org/debian buster/main amd64 libboost-thread1.67.0 amd64 1.67.0-13+deb10u1 [268 kB] Get: 105 http://deb.debian.org/debian buster/main amd64 libboost-thread1.67-dev amd64 1.67.0-13+deb10u1 [270 kB] Get: 106 http://deb.debian.org/debian buster/main amd64 libboost-thread-dev amd64 1.67.0.1 [3672 B] Get: 107 http://deb.debian.org/debian buster/main amd64 libboost-timer1.67.0 amd64 1.67.0-13+deb10u1 [231 kB] Get: 108 http://deb.debian.org/debian buster/main amd64 libboost-timer1.67-dev amd64 1.67.0-13+deb10u1 [231 kB] Get: 109 http://deb.debian.org/debian buster/main amd64 libboost-timer-dev amd64 1.67.0.1 [3772 B] Get: 110 http://deb.debian.org/debian buster/main amd64 libbwa-dev amd64 0.7.17-3 [130 kB] Get: 111 http://deb.debian.org/debian buster/main amd64 libbz2-dev amd64 1.0.6-9.2~deb10u1 [30.2 kB] Get: 112 http://deb.debian.org/debian buster/main amd64 libcereal-dev amd64 1.2.2-3 [258 kB] Get: 113 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get: 114 http://deb.debian.org/debian buster/main amd64 libcurl4-gnutls-dev amd64 7.64.0-4+deb10u2 [418 kB] Get: 115 http://deb.debian.org/debian buster/main amd64 libdivsufsort3 amd64 2.0.1-4 [44.5 kB] Get: 116 http://deb.debian.org/debian buster/main amd64 libdivsufsort-dev amd64 2.0.1-4 [27.4 kB] Get: 117 http://deb.debian.org/debian buster/main amd64 pkg-config amd64 0.29-6 [63.5 kB] Get: 118 http://deb.debian.org/debian buster/main amd64 libeigen3-dev all 3.3.7-1 [850 kB] Get: 119 http://deb.debian.org/debian buster/main amd64 libgff-dev amd64 1.0-2 [138 kB] Get: 120 http://deb.debian.org/debian buster/main amd64 libjellyfish-2.0-2 amd64 2.2.10-2 [64.6 kB] Get: 121 http://deb.debian.org/debian buster/main amd64 libjellyfish-2.0-dev amd64 2.2.10-2 [135 kB] Get: 122 http://deb.debian.org/debian buster/main amd64 libjemalloc2 amd64 5.1.0-3 [225 kB] Get: 123 http://deb.debian.org/debian buster/main amd64 libjemalloc-dev amd64 5.1.0-3 [403 kB] Get: 124 http://deb.debian.org/debian buster/main amd64 libjs-jquery all 3.3.1~dfsg-3+deb10u1 [332 kB] Get: 125 http://deb.debian.org/debian buster/main amd64 libjs-modernizr all 2.6.2+ds1-3 [46.7 kB] Get: 126 http://deb.debian.org/debian buster/main amd64 libjs-underscore all 1.9.1~dfsg-1+deb10u1 [100.0 kB] Get: 127 http://deb.debian.org/debian buster/main amd64 libjs-sphinxdoc all 1.8.4-1 [95.9 kB] Get: 128 http://deb.debian.org/debian buster/main amd64 liblzma-dev amd64 5.2.4-1 [210 kB] Get: 129 http://deb.debian.org/debian buster/main amd64 libpthread-stubs0-dev amd64 0.4-1 [5344 B] Get: 130 http://deb.debian.org/debian buster/main amd64 libsparsehash-dev all 2.0.2-1 [76.9 kB] Get: 131 http://deb.debian.org/debian buster/main amd64 libspdlog-dev amd64 1:1.3.1-1 [176 kB] Get: 132 http://deb.debian.org/debian buster/main amd64 libstaden-read13 amd64 1.14.11-6 [280 kB] Get: 133 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] Get: 134 http://deb.debian.org/debian buster/main amd64 libstaden-read-dev amd64 1.14.11-6 [361 kB] Get: 135 http://deb.debian.org/debian buster/main amd64 libtbb2 amd64 2018~U6-4 [147 kB] Get: 136 http://deb.debian.org/debian buster/main amd64 libtbb-dev amd64 2018~U6-4 [286 kB] Get: 137 http://deb.debian.org/debian buster/main amd64 libtclap-dev amd64 1.2.2-1 [139 kB] Get: 138 http://deb.debian.org/debian buster/main amd64 python-babel-localedata all 2.6.0+dfsg.1-1 [4083 kB] Get: 139 http://deb.debian.org/debian buster/main amd64 python3-alabaster all 0.7.8-1 [18.4 kB] Get: 140 http://deb.debian.org/debian buster/main amd64 python3-pkg-resources all 40.8.0-1 [153 kB] Get: 141 http://deb.debian.org/debian buster/main amd64 python3-tz all 2019.1-1 [27.1 kB] Get: 142 http://deb.debian.org/debian buster/main amd64 python3-babel all 2.6.0+dfsg.1-1 [96.7 kB] Get: 143 http://deb.debian.org/debian buster/main amd64 python3-certifi all 2018.8.24-1 [140 kB] Get: 144 http://deb.debian.org/debian buster/main amd64 python3-chardet all 3.0.4-3 [80.5 kB] Get: 145 http://deb.debian.org/debian buster/main amd64 python3-lib2to3 all 3.7.3-1 [76.7 kB] Get: 146 http://deb.debian.org/debian buster/main amd64 python3-distutils all 3.7.3-1 [142 kB] Get: 147 http://deb.debian.org/debian buster/main amd64 python3-roman all 2.0.0-3 [8768 B] Get: 148 http://deb.debian.org/debian buster/main amd64 python3-docutils all 0.14+dfsg-4 [378 kB] Get: 149 http://deb.debian.org/debian buster/main amd64 python3-idna all 2.6-1 [34.3 kB] Get: 150 http://deb.debian.org/debian buster/main amd64 python3-imagesize all 1.0.0-1 [4960 B] Get: 151 http://deb.debian.org/debian buster/main amd64 python3-markupsafe amd64 1.1.0-1 [14.8 kB] Get: 152 http://deb.debian.org/debian buster/main amd64 python3-jinja2 all 2.10-2 [106 kB] Get: 153 http://deb.debian.org/debian buster/main amd64 python3-pyparsing all 2.2.0+dfsg1-2 [89.6 kB] Get: 154 http://deb.debian.org/debian buster/main amd64 python3-six all 1.12.0-1 [15.7 kB] Get: 155 http://deb.debian.org/debian buster/main amd64 python3-packaging all 19.0-1 [20.5 kB] Get: 156 http://deb.debian.org/debian buster/main amd64 python3-pygments all 2.3.1+dfsg-1+deb10u2 [594 kB] Get: 157 http://deb.debian.org/debian buster/main amd64 python3-urllib3 all 1.24.1-1 [97.1 kB] Get: 158 http://deb.debian.org/debian buster/main amd64 python3-requests all 2.21.0-1 [66.9 kB] Get: 159 http://deb.debian.org/debian buster/main amd64 sphinx-common all 1.8.4-1 [500 kB] Get: 160 http://deb.debian.org/debian buster/main amd64 python3-sphinx all 1.8.4-1 [481 kB] Get: 161 http://deb.debian.org/debian buster/main amd64 sphinx-rtd-theme-common all 0.4.3+dfsg-1 [1021 kB] 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) 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.) Preparing to unpack .../00-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3+deb10u1_amd64.deb ... Unpacking groff-base (1.22.4-3+deb10u1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_amd64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package fonts-lato. Preparing to unpack .../06-fonts-lato_2.0-2_all.deb ... Unpacking fonts-lato (2.0-2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../07-liblocale-gettext-perl_1.07-3+b4_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../08-libssl1.1_1.1.1d-0+deb10u6_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1d-0+deb10u6) ... Selecting previously unselected package libpython3.7-minimal:amd64. Preparing to unpack .../09-libpython3.7-minimal_3.7.3-2+deb10u3_amd64.deb ... Unpacking libpython3.7-minimal:amd64 (3.7.3-2+deb10u3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../10-libexpat1_2.2.6-2+deb10u1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.6-2+deb10u1) ... Selecting previously unselected package python3.7-minimal. Preparing to unpack .../11-python3.7-minimal_3.7.3-2+deb10u3_amd64.deb ... Unpacking python3.7-minimal (3.7.3-2+deb10u3) ... Setting up libssl1.1:amd64 (1.1.1d-0+deb10u6) ... Setting up libpython3.7-minimal:amd64 (3.7.3-2+deb10u3) ... Setting up libexpat1:amd64 (2.2.6-2+deb10u1) ... Setting up python3.7-minimal (3.7.3-2+deb10u3) ... Selecting previously unselected package python3-minimal. (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 ... 20131 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.7.3-1_amd64.deb ... Unpacking python3-minimal (3.7.3-1) ... Selecting previously unselected package mime-support. Preparing to unpack .../1-mime-support_3.62_all.deb ... Unpacking mime-support (3.62) ... Selecting previously unselected package libmpdec2:amd64. Preparing to unpack .../2-libmpdec2_2.4.2-2_amd64.deb ... Unpacking libmpdec2:amd64 (2.4.2-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../3-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package libreadline7:amd64. Preparing to unpack .../4-libreadline7_7.0-5_amd64.deb ... Unpacking libreadline7:amd64 (7.0-5) ... Selecting previously unselected package libpython3.7-stdlib:amd64. Preparing to unpack .../5-libpython3.7-stdlib_3.7.3-2+deb10u3_amd64.deb ... Unpacking libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... Selecting previously unselected package python3.7. Preparing to unpack .../6-python3.7_3.7.3-2+deb10u3_amd64.deb ... Unpacking python3.7 (3.7.3-2+deb10u3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../7-libpython3-stdlib_3.7.3-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.7.3-1) ... Setting up python3-minimal (3.7.3-1) ... Selecting previously unselected package python3. (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 ... 20592 files and directories currently installed.) Preparing to unpack .../000-python3_3.7.3-1_amd64.deb ... Unpacking python3 (3.7.3-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.29_all.deb ... Unpacking sgml-base (1.29) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../002-libncurses6_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package libprocps7:amd64. Preparing to unpack .../003-libprocps7_2%3a3.3.15-2_amd64.deb ... Unpacking libprocps7:amd64 (2:3.3.15-2) ... Selecting previously unselected package lsb-base. Preparing to unpack .../004-lsb-base_10.2019051400_all.deb ... Unpacking lsb-base (10.2019051400) ... Selecting previously unselected package procps. Preparing to unpack .../005-procps_2%3a3.3.15-2_amd64.deb ... Unpacking procps (2:3.3.15-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../006-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../007-libmagic-mgc_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../008-libmagic1_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4+deb10u2) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking file (1:5.35-4+deb10u2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../011-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../012-m4_1.4.18-2_amd64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../013-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../014-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../015-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../016-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package openssl. Preparing to unpack .../017-openssl_1.1.1d-0+deb10u6_amd64.deb ... Unpacking openssl (1.1.1d-0+deb10u6) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../018-ca-certificates_20200601~deb10u2_all.deb ... Unpacking ca-certificates (20200601~deb10u2) ... Selecting previously unselected package cmake-data. Preparing to unpack .../019-cmake-data_3.13.4-1_all.deb ... Unpacking cmake-data (3.13.4-1) ... Selecting previously unselected package libicu63:amd64. Preparing to unpack .../020-libicu63_63.1-6+deb10u1_amd64.deb ... Unpacking libicu63:amd64 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../021-libxml2_2.9.4+dfsg1-7+deb10u2_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Selecting previously unselected package libarchive13:amd64. Preparing to unpack .../022-libarchive13_3.3.3-4+deb10u1_amd64.deb ... Unpacking libarchive13:amd64 (3.3.3-4+deb10u1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../023-libkeyutils1_1.6-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6-6) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../024-libkrb5support0_1.17-3+deb10u1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.17-3+deb10u1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../025-libk5crypto3_1.17-3+deb10u1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.17-3+deb10u1) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../026-libkrb5-3_1.17-3+deb10u1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.17-3+deb10u1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../027-libgssapi-krb5-2_1.17-3+deb10u1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.17-3+deb10u1) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../028-libsasl2-modules-db_2.1.27+dfsg-1+deb10u1_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u1) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../029-libsasl2-2_2.1.27+dfsg-1+deb10u1_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u1) ... Selecting previously unselected package libldap-common. Preparing to unpack .../030-libldap-common_2.4.47+dfsg-3+deb10u6_all.deb ... Unpacking libldap-common (2.4.47+dfsg-3+deb10u6) ... Selecting previously unselected package libldap-2.4-2:amd64. Preparing to unpack .../031-libldap-2.4-2_2.4.47+dfsg-3+deb10u6_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u6) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../032-libnghttp2-14_1.36.0-2+deb10u1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../033-libpsl5_0.20.2-2_amd64.deb ... Unpacking libpsl5:amd64 (0.20.2-2) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../034-librtmp1_2.4+20151223.gitfa8646d.1-2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../035-libssh2-1_1.8.0-2.1_amd64.deb ... Unpacking libssh2-1:amd64 (1.8.0-2.1) ... Selecting previously unselected package libcurl4:amd64. Preparing to unpack .../036-libcurl4_7.64.0-4+deb10u2_amd64.deb ... Unpacking libcurl4:amd64 (7.64.0-4+deb10u2) ... Selecting previously unselected package libjsoncpp1:amd64. Preparing to unpack .../037-libjsoncpp1_1.7.4-3_amd64.deb ... Unpacking libjsoncpp1:amd64 (1.7.4-3) ... Selecting previously unselected package librhash0:amd64. Preparing to unpack .../038-librhash0_1.3.8-1_amd64.deb ... Unpacking librhash0:amd64 (1.3.8-1) ... Selecting previously unselected package libuv1:amd64. Preparing to unpack .../039-libuv1_1.24.1-1_amd64.deb ... Unpacking libuv1:amd64 (1.24.1-1) ... Selecting previously unselected package cmake. Preparing to unpack .../040-cmake_3.13.4-1_amd64.deb ... Unpacking cmake (3.13.4-1) ... Selecting previously unselected package libtool. Preparing to unpack .../041-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../042-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../043-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../044-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../045-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../046-libelf1_0.176-1.1_amd64.deb ... Unpacking libelf1:amd64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../047-dwz_0.12-3_amd64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../048-libglib2.0-0_2.58.3-2+deb10u3_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../049-libcroco3_0.6.12-3_amd64.deb ... Unpacking libcroco3:amd64 (0.6.12-3) ... Selecting previously unselected package gettext. Preparing to unpack .../050-gettext_0.19.8.1-9_amd64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../051-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../052-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../053-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package xml-core. Preparing to unpack .../054-xml-core_0.18+nmu1_all.deb ... Unpacking xml-core (0.18+nmu1) ... Selecting previously unselected package docutils-common. Preparing to unpack .../055-docutils-common_0.14+dfsg-4_all.deb ... Unpacking docutils-common (0.14+dfsg-4) ... Selecting previously unselected package docutils-doc. Preparing to unpack .../056-docutils-doc_0.14+dfsg-4_all.deb ... Unpacking docutils-doc (0.14+dfsg-4) ... Selecting previously unselected package fonts-font-awesome. Preparing to unpack .../057-fonts-font-awesome_5.0.10+really4.7.0~dfsg-1_all.deb ... Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-1) ... Selecting previously unselected package fonts-roboto-slab. Preparing to unpack .../058-fonts-roboto-slab_1.100263+20170512-1_all.deb ... Unpacking fonts-roboto-slab (1.100263+20170512-1) ... Selecting previously unselected package help2man. Preparing to unpack .../059-help2man_1.47.8_amd64.deb ... Unpacking help2man (1.47.8) ... Selecting previously unselected package icu-devtools. Preparing to unpack .../060-icu-devtools_63.1-6+deb10u1_amd64.deb ... Unpacking icu-devtools (63.1-6+deb10u1) ... Selecting previously unselected package libboost1.67-dev:amd64. Preparing to unpack .../061-libboost1.67-dev_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost1.67-dev:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-atomic1.67.0:amd64. Preparing to unpack .../062-libboost-atomic1.67.0_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-atomic1.67.0:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-atomic1.67-dev:amd64. Preparing to unpack .../063-libboost-atomic1.67-dev_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-atomic1.67-dev:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-chrono1.67.0:amd64. Preparing to unpack .../064-libboost-chrono1.67.0_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-chrono1.67.0:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-chrono1.67-dev:amd64. Preparing to unpack .../065-libboost-chrono1.67-dev_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-chrono1.67-dev:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-date-time1.67.0:amd64. Preparing to unpack .../066-libboost-date-time1.67.0_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-date-time1.67.0:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-serialization1.67.0:amd64. Preparing to unpack .../067-libboost-serialization1.67.0_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-serialization1.67.0:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-serialization1.67-dev:amd64. Preparing to unpack .../068-libboost-serialization1.67-dev_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-serialization1.67-dev:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-date-time1.67-dev:amd64. Preparing to unpack .../069-libboost-date-time1.67-dev_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-date-time1.67-dev:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-filesystem1.67.0:amd64. Preparing to unpack .../070-libboost-filesystem1.67.0_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-filesystem1.67.0:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-system1.67-dev:amd64. Preparing to unpack .../071-libboost-system1.67-dev_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-system1.67-dev:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-filesystem1.67-dev:amd64. Preparing to unpack .../072-libboost-filesystem1.67-dev_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-filesystem1.67-dev:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-filesystem-dev:amd64. Preparing to unpack .../073-libboost-filesystem-dev_1.67.0.1_amd64.deb ... Unpacking libboost-filesystem-dev:amd64 (1.67.0.1) ... Selecting previously unselected package libboost-regex1.67.0:amd64. Preparing to unpack .../074-libboost-regex1.67.0_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-regex1.67.0:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libicu-dev:amd64. Preparing to unpack .../075-libicu-dev_63.1-6+deb10u1_amd64.deb ... Unpacking libicu-dev:amd64 (63.1-6+deb10u1) ... Selecting previously unselected package libboost-regex1.67-dev:amd64. Preparing to unpack .../076-libboost-regex1.67-dev_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-regex1.67-dev:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-iostreams1.67-dev:amd64. Preparing to unpack .../077-libboost-iostreams1.67-dev_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-iostreams1.67-dev:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-iostreams-dev:amd64. Preparing to unpack .../078-libboost-iostreams-dev_1.67.0.1_amd64.deb ... Unpacking libboost-iostreams-dev:amd64 (1.67.0.1) ... Selecting previously unselected package libboost-program-options1.67.0:amd64. Preparing to unpack .../079-libboost-program-options1.67.0_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-program-options1.67.0:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-program-options1.67-dev:amd64. Preparing to unpack .../080-libboost-program-options1.67-dev_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-program-options1.67-dev:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-program-options-dev:amd64. Preparing to unpack .../081-libboost-program-options-dev_1.67.0.1_amd64.deb ... Unpacking libboost-program-options-dev:amd64 (1.67.0.1) ... Selecting previously unselected package libboost-system-dev:amd64. Preparing to unpack .../082-libboost-system-dev_1.67.0.1_amd64.deb ... Unpacking libboost-system-dev:amd64 (1.67.0.1) ... Selecting previously unselected package libboost-thread1.67.0:amd64. Preparing to unpack .../083-libboost-thread1.67.0_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-thread1.67.0:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-thread1.67-dev:amd64. Preparing to unpack .../084-libboost-thread1.67-dev_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-thread1.67-dev:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-thread-dev:amd64. Preparing to unpack .../085-libboost-thread-dev_1.67.0.1_amd64.deb ... Unpacking libboost-thread-dev:amd64 (1.67.0.1) ... Selecting previously unselected package libboost-timer1.67.0:amd64. Preparing to unpack .../086-libboost-timer1.67.0_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-timer1.67.0:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-timer1.67-dev:amd64. Preparing to unpack .../087-libboost-timer1.67-dev_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-timer1.67-dev:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-timer-dev:amd64. Preparing to unpack .../088-libboost-timer-dev_1.67.0.1_amd64.deb ... Unpacking libboost-timer-dev:amd64 (1.67.0.1) ... Selecting previously unselected package libbwa-dev. Preparing to unpack .../089-libbwa-dev_0.7.17-3_amd64.deb ... Unpacking libbwa-dev (0.7.17-3) ... Selecting previously unselected package libbz2-dev:amd64. Preparing to unpack .../090-libbz2-dev_1.0.6-9.2~deb10u1_amd64.deb ... Unpacking libbz2-dev:amd64 (1.0.6-9.2~deb10u1) ... Selecting previously unselected package libcereal-dev. Preparing to unpack .../091-libcereal-dev_1.2.2-3_amd64.deb ... Unpacking libcereal-dev (1.2.2-3) ... Selecting previously unselected package libcurl3-gnutls:amd64. Preparing to unpack .../092-libcurl3-gnutls_7.64.0-4+deb10u2_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Selecting previously unselected package libcurl4-gnutls-dev:amd64. Preparing to unpack .../093-libcurl4-gnutls-dev_7.64.0-4+deb10u2_amd64.deb ... Unpacking libcurl4-gnutls-dev:amd64 (7.64.0-4+deb10u2) ... Selecting previously unselected package libdivsufsort3:amd64. Preparing to unpack .../094-libdivsufsort3_2.0.1-4_amd64.deb ... Unpacking libdivsufsort3:amd64 (2.0.1-4) ... Selecting previously unselected package libdivsufsort-dev:amd64. Preparing to unpack .../095-libdivsufsort-dev_2.0.1-4_amd64.deb ... Unpacking libdivsufsort-dev:amd64 (2.0.1-4) ... Selecting previously unselected package pkg-config. Preparing to unpack .../096-pkg-config_0.29-6_amd64.deb ... Unpacking pkg-config (0.29-6) ... Selecting previously unselected package libeigen3-dev. Preparing to unpack .../097-libeigen3-dev_3.3.7-1_all.deb ... Unpacking libeigen3-dev (3.3.7-1) ... Selecting previously unselected package libgff-dev. Preparing to unpack .../098-libgff-dev_1.0-2_amd64.deb ... Unpacking libgff-dev (1.0-2) ... Selecting previously unselected package libjellyfish-2.0-2:amd64. Preparing to unpack .../099-libjellyfish-2.0-2_2.2.10-2_amd64.deb ... Unpacking libjellyfish-2.0-2:amd64 (2.2.10-2) ... Selecting previously unselected package libjellyfish-2.0-dev:amd64. Preparing to unpack .../100-libjellyfish-2.0-dev_2.2.10-2_amd64.deb ... Unpacking libjellyfish-2.0-dev:amd64 (2.2.10-2) ... Selecting previously unselected package libjemalloc2:amd64. Preparing to unpack .../101-libjemalloc2_5.1.0-3_amd64.deb ... Unpacking libjemalloc2:amd64 (5.1.0-3) ... Selecting previously unselected package libjemalloc-dev. Preparing to unpack .../102-libjemalloc-dev_5.1.0-3_amd64.deb ... Unpacking libjemalloc-dev (5.1.0-3) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../103-libjs-jquery_3.3.1~dfsg-3+deb10u1_all.deb ... Unpacking libjs-jquery (3.3.1~dfsg-3+deb10u1) ... Selecting previously unselected package libjs-modernizr. Preparing to unpack .../104-libjs-modernizr_2.6.2+ds1-3_all.deb ... Unpacking libjs-modernizr (2.6.2+ds1-3) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../105-libjs-underscore_1.9.1~dfsg-1+deb10u1_all.deb ... Unpacking libjs-underscore (1.9.1~dfsg-1+deb10u1) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../106-libjs-sphinxdoc_1.8.4-1_all.deb ... Unpacking libjs-sphinxdoc (1.8.4-1) ... Selecting previously unselected package liblzma-dev:amd64. Preparing to unpack .../107-liblzma-dev_5.2.4-1_amd64.deb ... Unpacking liblzma-dev:amd64 (5.2.4-1) ... Selecting previously unselected package libpthread-stubs0-dev:amd64. Preparing to unpack .../108-libpthread-stubs0-dev_0.4-1_amd64.deb ... Unpacking libpthread-stubs0-dev:amd64 (0.4-1) ... Selecting previously unselected package libsparsehash-dev. Preparing to unpack .../109-libsparsehash-dev_2.0.2-1_all.deb ... Unpacking libsparsehash-dev (2.0.2-1) ... Selecting previously unselected package libspdlog-dev:amd64. Preparing to unpack .../110-libspdlog-dev_1%3a1.3.1-1_amd64.deb ... Unpacking libspdlog-dev:amd64 (1:1.3.1-1) ... Selecting previously unselected package libstaden-read13:amd64. Preparing to unpack .../111-libstaden-read13_1.14.11-6_amd64.deb ... Unpacking libstaden-read13:amd64 (1.14.11-6) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../112-zlib1g-dev_1%3a1.2.11.dfsg-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.11.dfsg-1) ... Selecting previously unselected package libstaden-read-dev. Preparing to unpack .../113-libstaden-read-dev_1.14.11-6_amd64.deb ... Unpacking libstaden-read-dev (1.14.11-6) ... Selecting previously unselected package libtbb2:amd64. Preparing to unpack .../114-libtbb2_2018~U6-4_amd64.deb ... Unpacking libtbb2:amd64 (2018~U6-4) ... Selecting previously unselected package libtbb-dev:amd64. Preparing to unpack .../115-libtbb-dev_2018~U6-4_amd64.deb ... Unpacking libtbb-dev:amd64 (2018~U6-4) ... Selecting previously unselected package libtclap-dev. Preparing to unpack .../116-libtclap-dev_1.2.2-1_amd64.deb ... Unpacking libtclap-dev (1.2.2-1) ... Selecting previously unselected package python-babel-localedata. Preparing to unpack .../117-python-babel-localedata_2.6.0+dfsg.1-1_all.deb ... Unpacking python-babel-localedata (2.6.0+dfsg.1-1) ... Selecting previously unselected package python3-alabaster. Preparing to unpack .../118-python3-alabaster_0.7.8-1_all.deb ... Unpacking python3-alabaster (0.7.8-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../119-python3-pkg-resources_40.8.0-1_all.deb ... Unpacking python3-pkg-resources (40.8.0-1) ... Selecting previously unselected package python3-tz. Preparing to unpack .../120-python3-tz_2019.1-1_all.deb ... Unpacking python3-tz (2019.1-1) ... Selecting previously unselected package python3-babel. Preparing to unpack .../121-python3-babel_2.6.0+dfsg.1-1_all.deb ... Unpacking python3-babel (2.6.0+dfsg.1-1) ... Selecting previously unselected package python3-certifi. Preparing to unpack .../122-python3-certifi_2018.8.24-1_all.deb ... Unpacking python3-certifi (2018.8.24-1) ... Selecting previously unselected package python3-chardet. Preparing to unpack .../123-python3-chardet_3.0.4-3_all.deb ... Unpacking python3-chardet (3.0.4-3) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../124-python3-lib2to3_3.7.3-1_all.deb ... Unpacking python3-lib2to3 (3.7.3-1) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../125-python3-distutils_3.7.3-1_all.deb ... Unpacking python3-distutils (3.7.3-1) ... Selecting previously unselected package python3-roman. Preparing to unpack .../126-python3-roman_2.0.0-3_all.deb ... Unpacking python3-roman (2.0.0-3) ... Selecting previously unselected package python3-docutils. Preparing to unpack .../127-python3-docutils_0.14+dfsg-4_all.deb ... Unpacking python3-docutils (0.14+dfsg-4) ... Selecting previously unselected package python3-idna. Preparing to unpack .../128-python3-idna_2.6-1_all.deb ... Unpacking python3-idna (2.6-1) ... Selecting previously unselected package python3-imagesize. Preparing to unpack .../129-python3-imagesize_1.0.0-1_all.deb ... Unpacking python3-imagesize (1.0.0-1) ... Selecting previously unselected package python3-markupsafe. Preparing to unpack .../130-python3-markupsafe_1.1.0-1_amd64.deb ... Unpacking python3-markupsafe (1.1.0-1) ... Selecting previously unselected package python3-jinja2. Preparing to unpack .../131-python3-jinja2_2.10-2_all.deb ... Unpacking python3-jinja2 (2.10-2) ... Selecting previously unselected package python3-pyparsing. Preparing to unpack .../132-python3-pyparsing_2.2.0+dfsg1-2_all.deb ... Unpacking python3-pyparsing (2.2.0+dfsg1-2) ... Selecting previously unselected package python3-six. Preparing to unpack .../133-python3-six_1.12.0-1_all.deb ... Unpacking python3-six (1.12.0-1) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../134-python3-packaging_19.0-1_all.deb ... Unpacking python3-packaging (19.0-1) ... Selecting previously unselected package python3-pygments. Preparing to unpack .../135-python3-pygments_2.3.1+dfsg-1+deb10u2_all.deb ... Unpacking python3-pygments (2.3.1+dfsg-1+deb10u2) ... Selecting previously unselected package python3-urllib3. Preparing to unpack .../136-python3-urllib3_1.24.1-1_all.deb ... Unpacking python3-urllib3 (1.24.1-1) ... Selecting previously unselected package python3-requests. Preparing to unpack .../137-python3-requests_2.21.0-1_all.deb ... Unpacking python3-requests (2.21.0-1) ... Selecting previously unselected package sphinx-common. Preparing to unpack .../138-sphinx-common_1.8.4-1_all.deb ... Unpacking sphinx-common (1.8.4-1) ... Selecting previously unselected package python3-sphinx. Preparing to unpack .../139-python3-sphinx_1.8.4-1_all.deb ... Unpacking python3-sphinx (1.8.4-1) ... Selecting previously unselected package sphinx-rtd-theme-common. Preparing to unpack .../140-sphinx-rtd-theme-common_0.4.3+dfsg-1_all.deb ... Unpacking sphinx-rtd-theme-common (0.4.3+dfsg-1) ... Selecting previously unselected package python3-sphinx-rtd-theme. Preparing to unpack .../141-python3-sphinx-rtd-theme_0.4.3+dfsg-1_all.deb ... Unpacking python3-sphinx-rtd-theme (0.4.3+dfsg-1) ... Selecting previously unselected package rapmap-dev. Preparing to unpack .../142-rapmap-dev_0.12.0+dfsg-3_all.deb ... Unpacking rapmap-dev (0.12.0+dfsg-3) ... Selecting previously unselected package sphinx-doc. Preparing to unpack .../143-sphinx-doc_1.8.4-1_all.deb ... Unpacking sphinx-doc (1.8.4-1) ... Setting up libboost1.67-dev:amd64 (1.67.0-13+deb10u1) ... Setting up libboost-program-options1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up libpipeline1:amd64 (1.5.1-2) ... Setting up lsb-base (10.2019051400) ... Setting up libkeyutils1:amd64 (1.6-6) ... Setting up libpsl5:amd64 (0.20.2-2) ... Setting up libboost-chrono1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up fonts-lato (2.0-2) ... Setting up docutils-doc (0.14+dfsg-4) ... Setting up mime-support (3.62) ... Setting up libmagic-mgc (1:5.35-4+deb10u2) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libboost-program-options1.67-dev:amd64 (1.67.0-13+deb10u1) ... Setting up libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... No schema files found: doing nothing. Setting up libprocps7:amd64 (2:3.3.15-2) ... Setting up libtbb2:amd64 (2018~U6-4) ... Setting up libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Setting up libmagic1:amd64 (1:5.35-4+deb10u2) ... Setting up fonts-roboto-slab (1.100263+20170512-1) ... Setting up libcereal-dev (1.2.2-3) ... Setting up gettext-base (0.19.8.1-9) ... Setting up libboost-date-time1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up file (1:5.35-4+deb10u2) ... Setting up libjemalloc2:amd64 (5.1.0-3) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u6) ... Setting up libspdlog-dev:amd64 (1:1.3.1-1) ... Setting up libjs-modernizr (2.6.2+ds1-3) ... Setting up libsparsehash-dev (2.0.2-1) ... Setting up libpthread-stubs0-dev:amd64 (0.4-1) ... Setting up libicu63:amd64 (63.1-6+deb10u1) ... Setting up python-babel-localedata (2.6.0+dfsg.1-1) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u1) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up libjellyfish-2.0-2:amd64 (2.2.10-2) ... Setting up libjemalloc-dev (5.1.0-3) ... Setting up libboost-chrono1.67-dev:amd64 (1.67.0-13+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up libuv1:amd64 (1.24.1-1) ... Setting up libgff-dev (1.0-2) ... Setting up libboost-program-options-dev:amd64 (1.67.0.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up icu-devtools (63.1-6+deb10u1) ... Setting up pkg-config (0.29-6) ... Setting up libk5crypto3:amd64 (1.17-3+deb10u1) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up libbwa-dev (0.7.17-3) ... Setting up libtclap-dev (1.2.2-1) ... Setting up liblzma-dev:amd64 (5.2.4-1) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up librhash0:amd64 (1.3.8-1) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libboost-timer1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up procps (2:3.3.15-2) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode Setting up libboost-filesystem1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up libboost-atomic1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up sgml-base (1.29) ... Setting up cmake-data (3.13.4-1) ... Setting up libboost-system1.67-dev:amd64 (1.67.0-13+deb10u1) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u1) ... Setting up libtbb-dev:amd64 (2018~U6-4) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up libjs-jquery (3.3.1~dfsg-3+deb10u1) ... Setting up libdivsufsort3:amd64 (2.0.1-4) ... Setting up libboost-serialization1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up openssl (1.1.1d-0+deb10u6) ... Setting up libbsd0:amd64 (0.9.1-2+deb10u1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up rapmap-dev (0.12.0+dfsg-3) ... Setting up readline-common (7.0-5) ... Setting up libicu-dev:amd64 (63.1-6+deb10u1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-1) ... Setting up sphinx-rtd-theme-common (0.4.3+dfsg-1) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up libjsoncpp1:amd64 (1.7.4-3) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libjs-underscore (1.9.1~dfsg-1+deb10u1) ... Setting up libdivsufsort-dev:amd64 (2.0.1-4) ... Setting up libbz2-dev:amd64 (1.0.6-9.2~deb10u1) ... Setting up libboost-atomic1.67-dev:amd64 (1.67.0-13+deb10u1) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libboost-serialization1.67-dev:amd64 (1.67.0-13+deb10u1) ... Setting up libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... Setting up libboost-regex1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up libboost-filesystem1.67-dev:amd64 (1.67.0-13+deb10u1) ... Setting up libjellyfish-2.0-dev:amd64 (2.2.10-2) ... Setting up libboost-thread1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up libtool (2.4.6-9) ... Setting up libarchive13:amd64 (3.3.3-4+deb10u1) ... Setting up libboost-regex1.67-dev:amd64 (1.67.0-13+deb10u1) ... Setting up libboost-system-dev:amd64 (1.67.0.1) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u6) ... Setting up m4 (1.4.18-2) ... Setting up help2man (1.47.8) ... Setting up ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 137 added, 0 removed; done. Setting up libboost-date-time1.67-dev:amd64 (1.67.0-13+deb10u1) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libeigen3-dev (3.3.7-1) ... Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u1) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up libjs-sphinxdoc (1.8.4-1) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up libboost-timer1.67-dev:amd64 (1.67.0-13+deb10u1) ... Setting up groff-base (1.22.4-3+deb10u1) ... Setting up xml-core (0.18+nmu1) ... Setting up libcurl4:amd64 (7.64.0-4+deb10u2) ... Setting up libboost-iostreams1.67-dev:amd64 (1.67.0-13+deb10u1) ... Setting up libboost-timer-dev:amd64 (1.67.0.1) ... Setting up libboost-filesystem-dev:amd64 (1.67.0.1) ... Setting up libpython3-stdlib:amd64 (3.7.3-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up sphinx-doc (1.8.4-1) ... Setting up python3.7 (3.7.3-2+deb10u3) ... Setting up gettext (0.19.8.1-9) ... Setting up libboost-thread1.67-dev:amd64 (1.67.0-13+deb10u1) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Setting up python3 (3.7.3-1) ... Setting up libboost-iostreams-dev:amd64 (1.67.0.1) ... Setting up libcurl4-gnutls-dev:amd64 (7.64.0-4+deb10u2) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-markupsafe (1.1.0-1) ... Setting up python3-tz (2019.1-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-six (1.12.0-1) ... Setting up python3-roman (2.0.0-3) ... Setting up python3-jinja2 (2.10-2) ... Setting up python3-pygments (2.3.1+dfsg-1+deb10u2) ... Setting up python3-pyparsing (2.2.0+dfsg1-2) ... Setting up python3-certifi (2018.8.24-1) ... Setting up sphinx-common (1.8.4-1) ... Setting up python3-idna (2.6-1) ... Setting up python3-urllib3 (1.24.1-1) ... Setting up cmake (3.13.4-1) ... Setting up python3-lib2to3 (3.7.3-1) ... Setting up libstaden-read13:amd64 (1.14.11-6) ... Setting up libboost-thread-dev:amd64 (1.67.0.1) ... Setting up python3-imagesize (1.0.0-1) ... Setting up python3-pkg-resources (40.8.0-1) ... Setting up python3-distutils (3.7.3-1) ... Setting up python3-babel (2.6.0+dfsg.1-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-alabaster (0.7.8-1) ... Setting up po-debconf (1.0.21) ... Setting up libstaden-read-dev (1.14.11-6) ... Setting up python3-packaging (19.0-1) ... Setting up python3-chardet (3.0.4-3) ... Setting up python3-requests (2.21.0-1) ... Setting up dh-autoreconf (19) ... Setting up debhelper (12.1.1) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Processing triggers for sgml-base (1.29) ... Setting up docutils-common (0.14+dfsg-4) ... Processing triggers for sgml-base (1.29) ... Setting up python3-docutils (0.14+dfsg-4) ... update-alternatives: using /usr/share/docutils/scripts/python3/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode Setting up python3-sphinx (1.8.4-1) ... update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-apidoc to provide /usr/bin/sphinx-apidoc (sphinx-apidoc) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-autogen to provide /usr/bin/sphinx-autogen (sphinx-autogen) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-build to provide /usr/bin/sphinx-build (sphinx-build) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-quickstart to provide /usr/bin/sphinx-quickstart (sphinx-quickstart) in auto mode Setting up python3-sphinx-rtd-theme (0.4.3+dfsg-1) ... Processing triggers for ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... 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 dpkg-buildpackage: info: source package salmon dpkg-buildpackage: info: source version 0.12.0+ds1-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with sphinxdoc debian/rules override_dh_auto_clean make[1]: Entering directory '/build/salmon-0.12.0+ds1' dh_auto_clean rm -rf external rm -f debian/*.1 rm -Rf sample_data cd doc && /usr/bin/make clean make[2]: Entering directory '/build/salmon-0.12.0+ds1/doc' rm -rf build/* make[2]: Leaving directory '/build/salmon-0.12.0+ds1/doc' make[1]: Leaving directory '/build/salmon-0.12.0+ds1' dh_clean debian/rules build dh build --with sphinxdoc dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/salmon-0.12.0+ds1' # See here # https://github.com/COMBINE-lab/salmon/issues/87 # for a discussion with upstream why it is necessary to include rapmap source mkdir -p /build/salmon-0.12.0+ds1/external/install/src/rapmap cp -av /usr/share/rapmap/src/* /build/salmon-0.12.0+ds1/external/install/src/rapmap '/usr/share/rapmap/src/HitManager.cpp' -> '/build/salmon-0.12.0+ds1/external/install/src/rapmap/HitManager.cpp' '/usr/share/rapmap/src/RapMapFileSystem.cpp' -> '/build/salmon-0.12.0+ds1/external/install/src/rapmap/RapMapFileSystem.cpp' '/usr/share/rapmap/src/RapMapSAIndex.cpp' -> '/build/salmon-0.12.0+ds1/external/install/src/rapmap/RapMapSAIndex.cpp' '/usr/share/rapmap/src/RapMapSAIndexer.cpp' -> '/build/salmon-0.12.0+ds1/external/install/src/rapmap/RapMapSAIndexer.cpp' '/usr/share/rapmap/src/RapMapUtils.cpp' -> '/build/salmon-0.12.0+ds1/external/install/src/rapmap/RapMapUtils.cpp' '/usr/share/rapmap/src/bit_array.c' -> '/build/salmon-0.12.0+ds1/external/install/src/rapmap/bit_array.c' '/usr/share/rapmap/src/rank9b.cpp' -> '/build/salmon-0.12.0+ds1/external/install/src/rapmap/rank9b.cpp' dh_auto_configure -- -DDEBIAN_BUILD=1 -DCONDA_BUILD=1 -DFETCHED_RAPMAP=1 -DBZIP2_LIBRARIES=-lbz2 -DBZIP2_INCLUDE_DIR=/usr/include -DLIBLZMA_INCLUDE_DIR=/usr/include/ -DLIBLZMA_LIBRARY=lzma -DLIBLZMA_HAS_AUTO_DECODER=1 -DLIBLZMA_HAS_EASY_ENCODER=1 -DLIBLZMA_HAS_LZMA_PRESET=1 -DCMAKE_MODULE_PATH=/usr/share/cmake/Modules -DTBB_WILL_RECONFIGURE=FALSE -DBOOST_WILL_RECONFIGURE=FALSE cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DDEBIAN_BUILD=1 -DCONDA_BUILD=1 -DFETCHED_RAPMAP=1 -DBZIP2_LIBRARIES=-lbz2 -DBZIP2_INCLUDE_DIR=/usr/include -DLIBLZMA_INCLUDE_DIR=/usr/include/ -DLIBLZMA_LIBRARY=lzma -DLIBLZMA_HAS_AUTO_DECODER=1 -DLIBLZMA_HAS_EASY_ENCODER=1 -DLIBLZMA_HAS_LZMA_PRESET=1 -DCMAKE_MODULE_PATH=/usr/share/cmake/Modules -DTBB_WILL_RECONFIGURE=FALSE -DBOOST_WILL_RECONFIGURE=FALSE .. CC: gcc CC version: -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done version: 0.12.0 -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Check if compiler accepts -pthread -- Check if compiler accepts -pthread - yes -- Found Threads: TRUE Building with CONDA_BUILD flag Making Default build type -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.a (found version "1.2.11") -- Found LibLZMA: /usr/include (found version "5.2.4") Found liblzma library: /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/lzma =========================================== -- Found BZip2: -lbz2 (found version "1.0.6") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found Found libbz2 library: -lbz2 =========================================== -- Boost version: 1.67.0 -- Found the following Boost libraries: -- iostreams -- filesystem -- system -- timer -- chrono -- program_options -- regex BOOST_INCLUDEDIR = BOOST_LIBRARYDIR = Boost_FOUND = 1 BOOST ROOT = BOOST INCLUDE DIR = /usr/include BOOST INCLUDE DIRS = /usr/include BOOST LIB DIR = /usr/lib/x86_64-linux-gnu BOOST LIBRARIES = /usr/lib/x86_64-linux-gnu/libboost_iostreams.a;/usr/lib/x86_64-linux-gnu/libboost_filesystem.a;/usr/lib/x86_64-linux-gnu/libboost_system.a;/usr/lib/x86_64-linux-gnu/libboost_timer.a;/usr/lib/x86_64-linux-gnu/libboost_chrono.a;/usr/lib/x86_64-linux-gnu/libboost_program_options.a;/usr/lib/x86_64-linux-gnu/libboost_regex.a Use Debian packaged libdivsufsort ================================= -- Performing Test TBB_without_pthread -- Performing Test TBB_without_pthread - Failed -- Performing Test TBB_with_pthread -- Performing Test TBB_with_pthread - Success -- Found Intel TBB TBB_LIBRARIES = optimized;/usr/lib/x86_64-linux-gnu/libtbb.so;debug;/usr/lib/x86_64-linux-gnu/libtbb.so;optimized;/usr/lib/x86_64-linux-gnu/libtbbmalloc.so;debug;/usr/lib/x86_64-linux-gnu/libtbbmalloc.so;general;-pthread Use Debian packaged Staden IOLib ================================ -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29") -- Found Jemalloc: /usr/lib/x86_64-linux-gnu/libjemalloc.a (found version "5.1.0-0-g61efbda7098de6fe64c362d309824864308c36d4") Found Jemalloc library --- using this memory allocator CPACK_SOURCE_IGNORE_FILES = /src/PCA.cpp;/src/PCAUtils.cpp;/build/;/scripts/AggregateToGeneLevel.py;/scripts/ExpressionTools.py;/scripts/GenerateExpressionFiles.sh;/scripts/ParseSoftFile.py;/scripts/PlotCorrelation.py;/scripts/junk;/scripts/sfstrace.log;/scripts/SFPipeline.py;/bin/;/lib/;/sample_data/;PublishREADMEToWebsite.sh;/external/;/src/obsolete/;/include/obsolete/;WebsiteHeader.txt;/experimental_configs/;.git/ TBB_LIBRARIES = optimized;/usr/lib/x86_64-linux-gnu/libtbb.so;debug;/usr/lib/x86_64-linux-gnu/libtbb.so;optimized;/usr/lib/x86_64-linux-gnu/libtbbmalloc.so;debug;/usr/lib/x86_64-linux-gnu/libtbbmalloc.so;general;-pthread -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR DEBIAN_BUILD -- Build files have been written to: /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/salmon-0.12.0+ds1' 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" 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 make -f CMakeFiles/Makefile2 all make[3]: Entering 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/depend 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/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= 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= 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 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[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' Scanning dependencies of target ksw2pp_sse2 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[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 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[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 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]: 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]: 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]: 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 -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 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 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 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_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 -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 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' [ 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 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/alevin_core.dir/edlib.cpp.o -c /build/salmon-0.12.0+ds1/src/edlib.cpp Scanning dependencies of target salmon_core [ 21%] Building CXX object src/CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o 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 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 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 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 [ 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 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 [ 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/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 [ 36%] Building CXX object src/CMakeFiles/salmon_core.dir/StadenUtils.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/StadenUtils.cpp.o -c /build/salmon-0.12.0+ds1/src/StadenUtils.cpp [ 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 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 [ 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 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 cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/ksw2pp.dir/cmake_clean_target.cmake 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 make[4]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' [ 47%] Built target ksw2pp [ 49%] Linking CXX static library libalevin_core.a cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/alevin_core.dir/cmake_clean_target.cmake cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/alevin_core.dir/link.txt --verbose=1 /usr/bin/ar qc libalevin_core.a CMakeFiles/alevin_core.dir/edlib.cpp.o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o /usr/bin/ranlib libalevin_core.a make[4]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' [ 49%] Built target alevin_core [ 50%] Linking CXX static library libsalmon_core.a cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/salmon_core.dir/cmake_clean_target.cmake cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/salmon_core.dir/link.txt --verbose=1 /usr/bin/ar qc libsalmon_core.a CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o CMakeFiles/salmon_core.dir/xxhash.c.o CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o CMakeFiles/salmon_core.dir/VersionChecker.cpp.o CMakeFiles/salmon_core.dir/SBModel.cpp.o CMakeFiles/salmon_core.dir/FastxParser.cpp.o CMakeFiles/salmon_core.dir/StadenUtils.cpp.o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o CMakeFiles/salmon_core.dir/SGSmooth.cpp.o CMakeFiles/salmon_core.dir/metro/metrohash64.cpp.o /usr/bin/ranlib libsalmon_core.a make[4]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' [ 50%] Built target salmon_core make -f src/CMakeFiles/unitTests.dir/build.make src/CMakeFiles/unitTests.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/unitTests.dir/DependInfo.cmake --color= Scanning dependencies of target unitTests 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 [ 55%] Building CXX object src/CMakeFiles/unitTests.dir/__/external/install/src/rapmap/rank9b.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/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 [ 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 -llzma -lbz2 -ltbb -ltbbmalloc -lgomp -lrt -ldl -pthread Copying unitTests cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E copy /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src/unitTests /build/salmon-0.12.0+ds1/tests/unitTests make[4]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' [ 57%] Built target unitTests make -f src/CMakeFiles/salmon.dir/build.make src/CMakeFiles/salmon.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/salmon.dir/DependInfo.cmake --color= Scanning dependencies of target salmon make[4]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/salmon.dir/build.make src/CMakeFiles/salmon.dir/build make[4]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' [ 59%] Building CXX object src/CMakeFiles/salmon.dir/__/external/install/src/rapmap/RapMapUtils.cpp.o [ 60%] Building CXX object src/CMakeFiles/salmon.dir/__/external/install/src/rapmap/RapMapFileSystem.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/RapMapFileSystem.cpp.o -c /build/salmon-0.12.0+ds1/external/install/src/rapmap/RapMapFileSystem.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/__/external/install/src/rapmap/RapMapUtils.cpp.o -c /build/salmon-0.12.0+ds1/external/install/src/rapmap/RapMapUtils.cpp [ 62%] Building CXX object src/CMakeFiles/salmon.dir/__/external/install/src/rapmap/RapMapSAIndex.cpp.o [ 65%] Building CXX object src/CMakeFiles/salmon.dir/__/external/install/src/rapmap/RapMapSAIndexer.cpp.o [ 65%] Building CXX object src/CMakeFiles/salmon.dir/__/external/install/src/rapmap/HitManager.cpp.o [ 66%] Building CXX object src/CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o [ 68%] Building CXX object src/CMakeFiles/salmon.dir/__/external/install/src/rapmap/rank9b.cpp.o [ 69%] Building CXX object src/CMakeFiles/salmon.dir/EMUtils.cpp.o [ 71%] Building C object src/CMakeFiles/salmon.dir/__/external/install/src/rapmap/bit_array.c.o [ 72%] Building CXX object src/CMakeFiles/salmon.dir/Graph.cpp.o [ 73%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o [ 75%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o [ 78%] Building CXX object src/CMakeFiles/salmon.dir/Salmon.cpp.o [ 78%] Building CXX object 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/RapMapSAIndexer.cpp.o -c /build/salmon-0.12.0+ds1/external/install/src/rapmap/RapMapSAIndexer.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/__/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 -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/HitManager.cpp.o -c /build/salmon-0.12.0+ds1/external/install/src/rapmap/HitManager.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/__/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/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 -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/EMUtils.cpp.o -c /build/salmon-0.12.0+ds1/src/EMUtils.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/CollapsedEMOptimizer.cpp.o -c /build/salmon-0.12.0+ds1/src/CollapsedEMOptimizer.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/CollapsedCellOptimizer.cpp.o -c /build/salmon-0.12.0+ds1/src/CollapsedCellOptimizer.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/CollapsedGibbsSampler.cpp.o -c /build/salmon-0.12.0+ds1/src/CollapsedGibbsSampler.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/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 [ 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] fnv(IntType(2166136261U ^ sizeof(IntType)), __DATE__ __TIME__ __FILE__); ^~~~~~~~ /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__); ^~~~~~~~ [ 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 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/FragmentLengthDistribution.cpp.o -c /build/salmon-0.12.0+ds1/src/FragmentLengthDistribution.cpp [ 88%] Building CXX object src/CMakeFiles/salmon.dir/FragmentStartPositionDistribution.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/FragmentStartPositionDistribution.cpp.o -c /build/salmon-0.12.0+ds1/src/FragmentStartPositionDistribution.cpp [ 89%] Building CXX object src/CMakeFiles/salmon.dir/SequenceBiasModel.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/SequenceBiasModel.cpp.o -c /build/salmon-0.12.0+ds1/src/SequenceBiasModel.cpp [ 91%] Building CXX object src/CMakeFiles/salmon.dir/GZipWriter.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/GZipWriter.cpp.o -c /build/salmon-0.12.0+ds1/src/GZipWriter.cpp [ 92%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantMerge.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/SalmonQuantMerge.cpp.o -c /build/salmon-0.12.0+ds1/src/SalmonQuantMerge.cpp [ 94%] Building CXX object src/CMakeFiles/salmon.dir/ProgramOptionsGenerator.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/ProgramOptionsGenerator.cpp.o -c /build/salmon-0.12.0+ds1/src/ProgramOptionsGenerator.cpp [ 95%] Building CXX object src/CMakeFiles/salmon.dir/FASTAParser.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/FASTAParser.cpp.o -c /build/salmon-0.12.0+ds1/src/FASTAParser.cpp [ 97%] Building CXX object src/CMakeFiles/salmon.dir/AlignmentModel.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/AlignmentModel.cpp.o -c /build/salmon-0.12.0+ds1/src/AlignmentModel.cpp [ 98%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantifyAlignments.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/SalmonQuantifyAlignments.cpp.o -c /build/salmon-0.12.0+ds1/src/SalmonQuantifyAlignments.cpp [100%] Linking CXX executable salmon cd /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/salmon.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/salmon.dir/__/external/install/src/rapmap/RapMapFileSystem.cpp.o CMakeFiles/salmon.dir/__/external/install/src/rapmap/RapMapSAIndexer.cpp.o CMakeFiles/salmon.dir/__/external/install/src/rapmap/RapMapSAIndex.cpp.o CMakeFiles/salmon.dir/__/external/install/src/rapmap/RapMapUtils.cpp.o CMakeFiles/salmon.dir/__/external/install/src/rapmap/HitManager.cpp.o CMakeFiles/salmon.dir/__/external/install/src/rapmap/rank9b.cpp.o CMakeFiles/salmon.dir/__/external/install/src/rapmap/bit_array.c.o CMakeFiles/salmon.dir/EMUtils.cpp.o CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o CMakeFiles/salmon.dir/Salmon.cpp.o CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o CMakeFiles/salmon.dir/Graph.cpp.o CMakeFiles/salmon.dir/DedupUMI.cpp.o CMakeFiles/salmon.dir/Alevin.cpp.o CMakeFiles/salmon.dir/SalmonAlevin.cpp.o CMakeFiles/salmon.dir/WhiteList.cpp.o CMakeFiles/salmon.dir/SalmonQuantify.cpp.o CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o CMakeFiles/salmon.dir/SequenceBiasModel.cpp.o CMakeFiles/salmon.dir/GZipWriter.cpp.o CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o CMakeFiles/salmon.dir/FASTAParser.cpp.o CMakeFiles/salmon.dir/AlignmentModel.cpp.o CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o -o salmon -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 -llzma -lbz2 -ltbb -ltbbmalloc -lgomp -ljemalloc -lrt libksw2pp.a -ldl -pthread make[4]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' [100%] Built target salmon make[3]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' mv doc/source/license.rst doc/ # unused PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -bhtml doc/source doc/build/html Running Sphinx v1.8.4 making output directory... building [mo]: targets for 0 po files that are out of date building [html]: targets for 6 source files that are out of date updating environment: 6 added, 0 changed, 0 removed reading sources... [ 16%] alevin reading sources... [ 33%] building reading sources... [ 50%] file_formats reading sources... [ 66%] index reading sources... [ 83%] library_type reading sources... [100%] salmon /build/salmon-0.12.0+ds1/doc/source/alevin.rst:32: WARNING: Title underline too short. Providing multiple read files to Alevin ------------ /build/salmon-0.12.0+ds1/doc/source/alevin.rst:32: WARNING: Title underline too short. Providing multiple read files to Alevin ------------ /build/salmon-0.12.0+ds1/doc/source/alevin.rst:52: WARNING: Explicit markup ends without a blank line; unexpected unindent. /build/salmon-0.12.0+ds1/doc/source/alevin.rst:75: WARNING: Block quote ends without a blank line; unexpected unindent. /build/salmon-0.12.0+ds1/doc/source/alevin.rst:79: WARNING: Title overline too short. """""""""""" ``--whitelist`` """""""""""" /build/salmon-0.12.0+ds1/doc/source/alevin.rst:79: WARNING: Title overline too short. """""""""""" ``--whitelist`` """""""""""" /build/salmon-0.12.0+ds1/doc/source/alevin.rst:89: WARNING: Title overline too short. """""""""""" ``--noQuant`` """""""""""" /build/salmon-0.12.0+ds1/doc/source/alevin.rst:89: WARNING: Title overline too short. """""""""""" ``--noQuant`` """""""""""" /build/salmon-0.12.0+ds1/doc/source/alevin.rst:95: WARNING: Title overline too short. """""""""""" ``--noDedup`` """""""""""" /build/salmon-0.12.0+ds1/doc/source/alevin.rst:95: WARNING: Title overline too short. """""""""""" ``--noDedup`` """""""""""" /build/salmon-0.12.0+ds1/doc/source/alevin.rst:114: WARNING: Title overline too short. """""""""""" ``--useCorrelation`` """""""""""" /build/salmon-0.12.0+ds1/doc/source/alevin.rst:114: WARNING: Title overline too short. """""""""""" ``--useCorrelation`` """""""""""" /build/salmon-0.12.0+ds1/doc/source/alevin.rst:127: WARNING: Title overline too short. """""""""""" ``--dumpBfh`` """""""""""" /build/salmon-0.12.0+ds1/doc/source/alevin.rst:127: WARNING: Title overline too short. """""""""""" ``--dumpBfh`` """""""""""" /build/salmon-0.12.0+ds1/doc/source/alevin.rst:133: WARNING: Title overline too short. """""""""""" ``--dumpFeatures`` """""""""""" /build/salmon-0.12.0+ds1/doc/source/alevin.rst:133: WARNING: Title overline too short. """""""""""" ``--dumpFeatures`` """""""""""" /build/salmon-0.12.0+ds1/doc/source/alevin.rst:139: WARNING: Title overline too short. """""""""""" ``--dumpCsvCounts`` """""""""""" /build/salmon-0.12.0+ds1/doc/source/alevin.rst:139: WARNING: Title overline too short. """""""""""" ``--dumpCsvCounts`` """""""""""" /build/salmon-0.12.0+ds1/doc/source/alevin.rst:155: WARNING: Title overline too short. """""""""""""""""""""" ``--numCellBootstraps`` """""""""""""""""""""" /build/salmon-0.12.0+ds1/doc/source/alevin.rst:155: WARNING: Title overline too short. """""""""""""""""""""" ``--numCellBootstraps`` """""""""""""""""""""" /build/salmon-0.12.0+ds1/doc/source/alevin.rst:215: WARNING: Footnote [#] is not referenced. /build/salmon-0.12.0+ds1/doc/source/alevin.rst:217: WARNING: Footnote [#] is not referenced. /build/salmon-0.12.0+ds1/doc/source/alevin.rst:219: WARNING: Footnote [#] is not referenced. /build/salmon-0.12.0+ds1/doc/source/alevin.rst:221: WARNING: Footnote [#] is not referenced. /build/salmon-0.12.0+ds1/doc/source/alevin.rst:223: WARNING: Footnote [#] is not referenced. /build/salmon-0.12.0+ds1/doc/source/salmon.rst:73: WARNING: Title underline too short. Preparing transcriptome indices (Quasi-index and FMD-index-based modes) ---------------------------------------------------------- /build/salmon-0.12.0+ds1/doc/source/salmon.rst:73: WARNING: Title underline too short. Preparing transcriptome indices (Quasi-index and FMD-index-based modes) ---------------------------------------------------------- /build/salmon-0.12.0+ds1/doc/source/salmon.rst:271: WARNING: Block quote ends without a blank line; unexpected unindent. looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 16%] alevin writing output... [ 33%] building writing output... [ 50%] file_formats writing output... [ 66%] index writing output... [ 83%] library_type writing output... [100%] salmon generating indices... genindex writing additional pages... search copying images... [100%] ReadLibraryIllustration.png copying static files... WARNING: html_static_path entry '/build/salmon-0.12.0+ds1/doc/source/_static' does not exist done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 29 warnings. The HTML pages are in doc/build/html. mv doc/license.rst doc/source/ cd obj*/src && \ help2man --no-discard-stderr --no-info --name="highly-accurate, transcript-level quantification estimates from RNA-seq data"\ ./salmon > ../../debian/salmon.1 && \ for option in index quant swim; do help2man --no-discard-stderr \ --version-string="0.12.0+ds1" --no-info "./salmon --no-version-check ${option}" \ --include=../../debian/salmon-${option}-man-include \ > ../../debian/salmon-${option}.1; done make[1]: Leaving directory '/build/salmon-0.12.0+ds1' debian/rules override_dh_auto_test make[1]: Entering directory '/build/salmon-0.12.0+ds1' DEB_BUILD_OPTIONS="parallel=1" dh_auto_test cd obj-x86_64-linux-gnu && make -j1 test ARGS\+=-j1 make[2]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' Running tests... /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 Start 2: salmon_read_test_quasi 2/2 Test #2: salmon_read_test_quasi ........... Passed 1.63 sec 100% tests passed, 0 tests failed out of 2 Total Test time (real) = 1.80 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 fakeroot debian/rules binary dh binary --with sphinxdoc 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" 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 make -f CMakeFiles/Makefile2 all make[2]: Entering 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/depend 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/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= 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 /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 /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= 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[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[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/libstadenio.dir/build.make CMakeFiles/libstadenio.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 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/libcereal.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]: 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]: 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]: 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[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]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' [ 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 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 make -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.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' 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= make[3]: 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[3]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'src/CMakeFiles/ksw2pp.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/alevin_core.dir/build.make src/CMakeFiles/alevin_core.dir/build 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' make[3]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'src/CMakeFiles/salmon_core.dir/build'. make[3]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' [ 24%] Built target alevin_core [ 50%] Built target salmon_core make -f src/CMakeFiles/unitTests.dir/build.make src/CMakeFiles/unitTests.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/unitTests.dir/DependInfo.cmake --color= make[3]: 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[3]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'src/CMakeFiles/unitTests.dir/build'. make[3]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' [ 57%] Built target unitTests make -f src/CMakeFiles/salmon.dir/build.make src/CMakeFiles/salmon.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/salmon.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/salmon.dir/build.make src/CMakeFiles/salmon.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/salmon.dir/build'. make[3]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' [100%] Built target salmon make[2]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/salmon-0.12.0+ds1/debian/salmon/usr/bin/salmon -- Installing: /build/salmon-0.12.0+ds1/debian/salmon/usr/lib/libsalmon_core.a Installation complete. Please ensure the following paths are set properly. ========================================================================== Please add /usr/bin to your PATH Please add /usr/lib to your LD_LIBRARY_PATH ========================================================================== make[1]: Leaving directory '/build/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' dh_installdocs dh_sphinxdoc dh_sphinxdoc: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/js/modernizr.min.js dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing 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 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 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) dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package salmon: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dpkg-gencontrol: warning: package salmon: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'salmon-dbgsym' in '../salmon-dbgsym_0.12.0+ds1-1_amd64.deb'. dpkg-deb: building package 'salmon' in '../salmon_0.12.0+ds1-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../salmon_0.12.0+ds1-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration 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 Mon Jul 19 19:29:17 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Mon Jul 19 19:29:17 UTC 2021 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Mon Jul 19 19:34:44 UTC 2021 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Mon Jul 19 19:34:44 UTC 2021 I: salmon_0.12.0+ds1-1_amd64.changes: Format: 1.8 Date: Thu, 13 Dec 2018 18:21:38 +0100 Source: salmon Binary: salmon salmon-dbgsym Architecture: amd64 Version: 0.12.0+ds1-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: salmon - wicked-fast transcript quantification from RNA-seq data Closes: 909767 Changes: salmon (0.12.0+ds1-1) unstable; urgency=medium . * Team upload. * New upstream version Closes: #909767 * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 * Remove debian/gbp.conf * Build-Depends: libbz2-dev, liblzma-dev * Use python3-sphinx exclusively * Do not parse d/changelog Checksums-Sha1: e7b6ab79fecf5052209994f3068ea90073e388a8 38964068 salmon-dbgsym_0.12.0+ds1-1_amd64.deb b539cb6868cb6fbc56ea3285558754ce0d555011 9702 salmon_0.12.0+ds1-1_amd64.buildinfo 0bbd0a720217ebf2b24946e37b1168ddf7151602 1386616 salmon_0.12.0+ds1-1_amd64.deb Checksums-Sha256: e18be64c90210e3cfe687cdcb4c079e2c6d1365a37df1bf91f5a5610c94c6b4c 38964068 salmon-dbgsym_0.12.0+ds1-1_amd64.deb 725eae4938dd6e7c06adafbceab603ced7f261224c5727e61cb1c84a52e74931 9702 salmon_0.12.0+ds1-1_amd64.buildinfo b0a0b73bb8a86e29d780c7547c65f0aa38cf3bb5f8ccc0bec972244193fb37dd 1386616 salmon_0.12.0+ds1-1_amd64.deb Files: 9785b0e9ec1bdcc5cfa0cab795b2a31d 38964068 debug optional salmon-dbgsym_0.12.0+ds1-1_amd64.deb acdde318b42285b0a4bf26b5922a095e 9702 science optional salmon_0.12.0+ds1-1_amd64.buildinfo b2a4d76b5988f01254487eb6a894332f 1386616 science optional salmon_0.12.0+ds1-1_amd64.deb Mon Jul 19 19:34:46 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.YkONjuJpzg/salmon_0.12.0+ds1-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.YkONjuJpzg/salmon_0.12.0+ds1-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.YkONjuJpzg/salmon_0.12.0+ds1-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.YkONjuJpzg/b1/salmon_0.12.0+ds1-1_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.YkONjuJpzg/b2/salmon_0.12.0+ds1-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.676s) 0.676s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.434s) 0.433s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Mon Jul 19 19:45:23 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Mon Jul 19 19:45:23 UTC 2021 I: salmon from buster built successfully and reproducibly on amd64. Mon Jul 19 19:45:38 UTC 2021 I: Submitting .buildinfo files to external archives: Mon Jul 19 19:45:38 UTC 2021 I: Submitting 12K b1/salmon_0.12.0+ds1-1_amd64.buildinfo.asc Mon Jul 19 19:45:39 UTC 2021 I: Submitting 12K b2/salmon_0.12.0+ds1-1_amd64.buildinfo.asc Mon Jul 19 19:45:40 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Jul 19 19:45:40 UTC 2021 I: Done submitting .buildinfo files. Mon Jul 19 19:45:40 UTC 2021 I: Removing signed salmon_0.12.0+ds1-1_amd64.buildinfo.asc files: removed './b1/salmon_0.12.0+ds1-1_amd64.buildinfo.asc' removed './b2/salmon_0.12.0+ds1-1_amd64.buildinfo.asc'