Tue Aug 17 09:16:23 UTC 2021 I: starting to build kallisto/bullseye/i386 on jenkins on '2021-08-17 09:16' Tue Aug 17 09:16:23 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_1/439/console.log Tue Aug 17 09:16:23 UTC 2021 I: Downloading source for bullseye/kallisto=0.46.2+dfsg-2 --2021-08-17 09:16:23-- http://cdn-fastly.deb.debian.org/debian/pool/main/k/kallisto/kallisto_0.46.2+dfsg-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2111 (2.1K) Saving to: ‘kallisto_0.46.2+dfsg-2.dsc’ 0K .. 100% 142M=0s 2021-08-17 09:16:23 (142 MB/s) - ‘kallisto_0.46.2+dfsg-2.dsc’ saved [2111/2111] Tue Aug 17 09:16:24 UTC 2021 I: kallisto_0.46.2+dfsg-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: kallisto Binary: kallisto, kallisto-examples Architecture: any all Version: 0.46.2+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://pachterlab.github.io/kallisto Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/kallisto Vcs-Git: https://salsa.debian.org/med-team/kallisto.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 12), cmake, libhdf5-dev, libhts-dev Package-List: kallisto deb science optional arch=any kallisto-examples deb science optional arch=all Checksums-Sha1: 9cd6f32f91c9b65e54f0d86de9f67ce1c988d1ae 1076104 kallisto_0.46.2+dfsg.orig.tar.xz d9eabef16e3666afa5b07d9f96c25c575869bf81 6324 kallisto_0.46.2+dfsg-2.debian.tar.xz Checksums-Sha256: b92d212294147e371fc9e77190e6384b3101045af1f832d144101285791b29db 1076104 kallisto_0.46.2+dfsg.orig.tar.xz 536a062673108723ebd7158464448fbd996af60e7764b64977a19ba4108b39af 6324 kallisto_0.46.2+dfsg-2.debian.tar.xz Files: 0e8ff786acae328e36281ad930529f98 1076104 kallisto_0.46.2+dfsg.orig.tar.xz 0829a5b73df3c7816698e4d6b32bce93 6324 kallisto_0.46.2+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl6/eWoRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFprQ//WF28hxL9KqPfL3r8KtA80yr6oTjxdnnT io51YJaKS1tSb70+oi7ZIy6RSZlwnvRhJAFlsn7GnfualVsle1ycyB/2YLYOKEhQ Ew1x1DGUdLqg8t8R7Cna+l2/iy5TINzyiA2OKF+MFlQ4B8o6+i3rhhmgnPkCOorJ rGBTt9b4LOcIpJhvS8PIN05Msbf2AhcOLZJwqA9wEBbOONDXWMls21AkjRIRzyXf 3RJ/PqAhizlj3tuexpAkfbTHUvOahH802JDpG49X8zy9c4i4A7cusp6MRjEDubud smV77fc+geayNRpUvsLBmgR92PmjYvfbUqFTC7KC+gpL7AXoi7ACttNMianGMluO Y/UEv98iKTAgUr7ml0NplAXBkveS5ZooyzBERSkGDhYifElpc6woQ1V1LSFHbPGN pYCTsM7KuZUT5ezcrqS0kWmLMTnNU3duhuKTsLshMaZ7ix4e8S75BS/8NODWQasq 1spJ1r0TS06AAeqkVllubpaWMUuQOT23xQnjaEOl+II7YBGUeynmducWxgiCjHCf sOCUZL0HqVUuWe7l6hoXMeM1maDO2eSI2OeOfyLoCxmP/xMgJ+341x5N/gojI+LN MOzBz+91SSYDptkYKqNrFLOu8uJtQx0L/SIj2wz5h2kArybR6g2/HjSgEvSvrlGd jmZbokRFzls= =PcMa -----END PGP SIGNATURE----- Tue Aug 17 09:16:24 UTC 2021 I: Checking whether the package is not for us Tue Aug 17 09:16:24 UTC 2021 I: Starting 1st build on remote node ionos2-i386.debian.net. Tue Aug 17 09:16:24 UTC 2021 I: Preparing to do remote build '1' on ionos2-i386.debian.net. Tue Aug 17 09:21:12 UTC 2021 I: Deleting $TMPDIR on ionos2-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Aug 16 21:16:28 -12 2021 I: pbuilder-time-stamp: 1629191788 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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: using eatmydata during job I: Copying source file I: copying [kallisto_0.46.2+dfsg-2.dsc] I: copying [./kallisto_0.46.2+dfsg.orig.tar.xz] I: copying [./kallisto_0.46.2+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.1ZrdoXVl/trustedkeys.kbx': General error gpgv: Signature made Fri May 15 17:26:02 2020 -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 ./kallisto_0.46.2+dfsg-2.dsc dpkg-source: info: extracting kallisto in kallisto-0.46.2+dfsg dpkg-source: info: unpacking kallisto_0.46.2+dfsg.orig.tar.xz dpkg-source: info: unpacking kallisto_0.46.2+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_htslib.patch dpkg-source: info: applying spelling dpkg-source: info: applying htslib1.3 dpkg-source: info: applying Check_busOptions.seq_length_before_accessing.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/27037/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='d0fcb68ab2584b61842042bbe1654e8e' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='27037' 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.TlK0Y14zgc/pbuilderrc_N5TB --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.TlK0Y14zgc/b1 --logfile b1/build.log kallisto_0.46.2+dfsg-2.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos2-i386 4.19.0-17-686-pae #1 SMP Debian 4.19.194-3 (2021-07-18) i686 GNU/Linux I: ls -l /bin total 5776 -rwxr-xr-x 1 root root 1367848 Aug 4 08:25 bash -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash -rwxr-xr-x 1 root root 124904 Sep 22 2020 date -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd -rwxr-xr-x 1 root root 100752 Sep 22 2020 df -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir -rwxr-xr-x 1 root root 83644 Jul 28 07:09 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 34664 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 71928 Jul 28 07:09 findmnt -rwsr-xr-x 1 root root 30112 Feb 26 04:12 fusermount -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe -rwxr-xr-x 1 root root 100952 Mar 2 11:30 gzip -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln -rwxr-xr-x 1 root root 55572 Feb 7 2020 login -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls -rwxr-xr-x 1 root root 153124 Jul 28 07:09 lsblk -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 58920 Jul 28 07:09 more -rwsr-xr-x 1 root root 50720 Jul 28 07:09 mount -rwxr-xr-x 1 root root 13856 Jul 28 07:09 mountpoint -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 15 21:25 sh -> dash -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty -rwsr-xr-x 1 root root 79396 Jul 28 07:09 su -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync -rwxr-xr-x 1 root root 602584 Feb 16 21:55 tar -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch -rwxr-xr-x 1 root root 34664 Sep 22 2020 true -rwxr-xr-x 1 root root 17768 Feb 26 04:12 ulockmgr_server -rwsr-xr-x 1 root root 30236 Jul 28 07:09 umount -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir -rwxr-xr-x 1 root root 63024 Jul 28 07:09 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew I: user script /srv/workspace/pbuilder/27037/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: i386 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-compat (= 12), cmake, libhdf5-dev, libhts-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19675 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-compat (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libhdf5-dev; however: Package libhdf5-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-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} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} hdf5-helpers{a} intltool-debian{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarchive13{a} libbrotli1{a} libcurl3-gnutls{a} libcurl4{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libhdf5-103-1{a} libhdf5-cpp-103-1{a} libhdf5-dev{a} libhdf5-fortran-102{a} libhdf5-hl-100{a} libhdf5-hl-cpp-100{a} libhdf5-hl-fortran-100{a} libhts-dev{a} libhts3{a} libicu67{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjsoncpp24{a} libldap-2.4-2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libprocps8{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libsub-override-perl{a} libsz2{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} m4{a} man-db{a} po-debconf{a} procps{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget 0 packages upgraded, 73 newly installed, 0 to remove and 0 not upgraded. Need to get 41.3 MB of archives. After unpacking 141 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-8 [149 kB] Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB] Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB] Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB] Get: 6 http://deb.debian.org/debian bullseye/main i386 libncurses6 i386 6.2+20201114-2 [110 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libprocps8 i386 2:3.3.17-5 [64.2 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 procps i386 2:3.3.17-5 [501 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3 [273 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3 [133 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3 [69.0 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 cmake-data all 3.18.4-2 [1725 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-7 [8775 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7 [728 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 libarchive13 i386 3.4.3-2+b1 [384 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 libbrotli1 i386 1.0.9-2+b2 [286 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 libsasl2-modules-db i386 2.1.27+dfsg-2.1 [70.0 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 libsasl2-2 i386 2.1.27+dfsg-2.1 [110 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 libldap-2.4-2 i386 2.4.57+dfsg-3 [244 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 libnghttp2-14 i386 1.43.0-1 [85.7 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 libpsl5 i386 0.21.0-1.2 [57.9 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 libssh2-1 i386 1.9.0-2 [164 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 libcurl4 i386 7.74.0-1.3+b1 [372 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 libexpat1 i386 2.2.10-2 [98.8 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 libjsoncpp24 i386 1.9.4-4 [86.1 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 librhash0 i386 1.4.1-2 [144 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 libuv1 i386 1.40.0-2 [139 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 cmake i386 3.18.4-2 [7029 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 42 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 51 http://deb.debian.org/debian bullseye/main i386 hdf5-helpers i386 1.10.6+repack-4 [40.4 kB] Get: 52 http://deb.debian.org/debian bullseye/main i386 libaec0 i386 1.0.4-1 [22.6 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 libsz2 i386 1.0.4-1 [6820 B] Get: 54 http://deb.debian.org/debian bullseye/main i386 libaec-dev i386 1.0.4-1 [21.5 kB] Get: 55 http://deb.debian.org/debian bullseye/main i386 libcurl3-gnutls i386 7.74.0-1.3+b1 [368 kB] Get: 56 http://deb.debian.org/debian bullseye/main i386 libcurl4-gnutls-dev i386 7.74.0-1.3+b1 [471 kB] Get: 57 http://deb.debian.org/debian bullseye/main i386 libdeflate0 i386 1.7-1 [48.4 kB] Get: 58 http://deb.debian.org/debian bullseye/main i386 libdeflate-dev i386 1.7-1 [44.4 kB] Get: 59 http://deb.debian.org/debian bullseye/main i386 libgfortran5 i386 10.2.1-6 [643 kB] Get: 60 http://deb.debian.org/debian bullseye/main i386 libhdf5-103-1 i386 1.10.6+repack-4 [1156 kB] Get: 61 http://deb.debian.org/debian bullseye/main i386 libhdf5-cpp-103-1 i386 1.10.6+repack-4 [148 kB] Get: 62 http://deb.debian.org/debian bullseye/main i386 libhdf5-fortran-102 i386 1.10.6+repack-4 [114 kB] Get: 63 http://deb.debian.org/debian bullseye/main i386 libhdf5-hl-100 i386 1.10.6+repack-4 [93.2 kB] Get: 64 http://deb.debian.org/debian bullseye/main i386 libhdf5-hl-fortran-100 i386 1.10.6+repack-4 [58.3 kB] Get: 65 http://deb.debian.org/debian bullseye/main i386 libhdf5-hl-cpp-100 i386 1.10.6+repack-4 [38.1 kB] Get: 66 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2 [194 kB] Get: 67 http://deb.debian.org/debian bullseye/main i386 libjpeg62-turbo i386 1:2.0.6-4 [160 kB] Get: 68 http://deb.debian.org/debian bullseye/main i386 libjpeg62-turbo-dev i386 1:2.0.6-4 [299 kB] Get: 69 http://deb.debian.org/debian bullseye/main i386 libjpeg-dev i386 1:2.0.6-4 [67.8 kB] Get: 70 http://deb.debian.org/debian bullseye/main i386 libhdf5-dev i386 1.10.6+repack-4 [2586 kB] Get: 71 http://deb.debian.org/debian bullseye/main i386 libhts3 i386 1.11-4 [408 kB] Get: 72 http://deb.debian.org/debian bullseye/main i386 liblzma-dev i386 5.2.5-2 [240 kB] Get: 73 http://deb.debian.org/debian bullseye/main i386 libhts-dev i386 1.11-4 [3817 kB] Fetched 41.3 MB in 8s (5450 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19675 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8_i386.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../01-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_i386.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../03-libpipeline1_1.5.3-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_i386.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libncurses6:i386. Preparing to unpack .../05-libncurses6_6.2+20201114-2_i386.deb ... Unpacking libncurses6:i386 (6.2+20201114-2) ... Selecting previously unselected package libprocps8:i386. Preparing to unpack .../06-libprocps8_2%3a3.3.17-5_i386.deb ... Unpacking libprocps8:i386 (2:3.3.17-5) ... Selecting previously unselected package procps. Preparing to unpack .../07-procps_2%3a3.3.17-5_i386.deb ... Unpacking procps (2:3.3.17-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../08-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../09-libmagic-mgc_1%3a5.39-3_i386.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../10-libmagic1_1%3a5.39-3_i386.deb ... Unpacking libmagic1:i386 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../11-file_1%3a5.39-3_i386.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../12-gettext-base_0.21-4_i386.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../13-libsigsegv2_2.13-1_i386.deb ... Unpacking libsigsegv2:i386 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../14-m4_1.4.18-5_i386.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../15-autoconf_2.69-14_all.deb ... 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Preparing to unpack .../27-libnghttp2-14_1.43.0-1_i386.deb ... Unpacking libnghttp2-14:i386 (1.43.0-1) ... Selecting previously unselected package libpsl5:i386. Preparing to unpack .../28-libpsl5_0.21.0-1.2_i386.deb ... Unpacking libpsl5:i386 (0.21.0-1.2) ... Selecting previously unselected package librtmp1:i386. Preparing to unpack .../29-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_i386.deb ... Unpacking librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:i386. Preparing to unpack .../30-libssh2-1_1.9.0-2_i386.deb ... Unpacking libssh2-1:i386 (1.9.0-2) ... Selecting previously unselected package libcurl4:i386. Preparing to unpack .../31-libcurl4_7.74.0-1.3+b1_i386.deb ... Unpacking libcurl4:i386 (7.74.0-1.3+b1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../32-libexpat1_2.2.10-2_i386.deb ... Unpacking libexpat1:i386 (2.2.10-2) ... Selecting previously unselected package libjsoncpp24:i386. 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Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package gettext. Preparing to unpack .../46-gettext_0.21-4_i386.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../47-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 .../48-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../49-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package hdf5-helpers. Preparing to unpack .../50-hdf5-helpers_1.10.6+repack-4_i386.deb ... Unpacking hdf5-helpers (1.10.6+repack-4) ... Selecting previously unselected package libaec0:i386. Preparing to unpack .../51-libaec0_1.0.4-1_i386.deb ... Unpacking libaec0:i386 (1.0.4-1) ... 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Selecting previously unselected package libgfortran5:i386. Preparing to unpack .../58-libgfortran5_10.2.1-6_i386.deb ... Unpacking libgfortran5:i386 (10.2.1-6) ... Selecting previously unselected package libhdf5-103-1:i386. Preparing to unpack .../59-libhdf5-103-1_1.10.6+repack-4_i386.deb ... Unpacking libhdf5-103-1:i386 (1.10.6+repack-4) ... Selecting previously unselected package libhdf5-cpp-103-1:i386. Preparing to unpack .../60-libhdf5-cpp-103-1_1.10.6+repack-4_i386.deb ... Unpacking libhdf5-cpp-103-1:i386 (1.10.6+repack-4) ... Selecting previously unselected package libhdf5-fortran-102:i386. Preparing to unpack .../61-libhdf5-fortran-102_1.10.6+repack-4_i386.deb ... Unpacking libhdf5-fortran-102:i386 (1.10.6+repack-4) ... Selecting previously unselected package libhdf5-hl-100:i386. Preparing to unpack .../62-libhdf5-hl-100_1.10.6+repack-4_i386.deb ... Unpacking libhdf5-hl-100:i386 (1.10.6+repack-4) ... Selecting previously unselected package libhdf5-hl-fortran-100:i386. 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Unpacking libjpeg-dev:i386 (1:2.0.6-4) ... Selecting previously unselected package libhdf5-dev. Preparing to unpack .../69-libhdf5-dev_1.10.6+repack-4_i386.deb ... Unpacking libhdf5-dev (1.10.6+repack-4) ... Selecting previously unselected package libhts3:i386. Preparing to unpack .../70-libhts3_1.11-4_i386.deb ... Unpacking libhts3:i386 (1.11-4) ... Selecting previously unselected package liblzma-dev:i386. Preparing to unpack .../71-liblzma-dev_5.2.5-2_i386.deb ... Unpacking liblzma-dev:i386 (5.2.5-2) ... Selecting previously unselected package libhts-dev:i386. Preparing to unpack .../72-libhts-dev_1.11-4_i386.deb ... Unpacking libhts-dev:i386 (1.11-4) ... Setting up libexpat1:i386 (2.2.10-2) ... Setting up libpipeline1:i386 (1.5.3-1) ... Setting up libpsl5:i386 (0.21.0-1.2) ... Setting up bsdextrautils (2.36.1-8) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up hdf5-helpers (1.10.6+repack-4) ... Setting up libicu67:i386 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:i386 (1.0.9-2+b2) ... Setting up libnghttp2-14:i386 (1.43.0-1) ... Setting up libmagic1:i386 (1:5.39-3) ... Setting up libdeflate0:i386 (1.7-1) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libaec0:i386 (1.0.4-1) ... Setting up libsasl2-modules-db:i386 (2.1.27+dfsg-2.1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libuv1:i386 (1.40.0-2) ... Setting up libjpeg62-turbo:i386 (1:2.0.6-4) ... Setting up libjpeg62-turbo-dev:i386 (1:2.0.6-4) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:i386 (6.2+20201114-2) ... Setting up libsigsegv2:i386 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up libsasl2-2:i386 (2.1.27+dfsg-2.1) ... Setting up libgfortran5:i386 (10.2.1-6) ... Setting up libjsoncpp24:i386 (1.9.4-4) ... Setting up liblzma-dev:i386 (5.2.5-2) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.14) ... Setting up librhash0:i386 (1.4.1-2) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:i386 (1.9.0-2) ... Setting up cmake-data (3.18.4-2) ... Setting up libdeflate-dev:i386 (1.7-1) ... Setting up libelf1:i386 (0.183-1) ... Setting up libxml2:i386 (2.9.10+dfsg-6.7) ... Setting up libprocps8:i386 (2:3.3.17-5) ... Setting up libsz2:i386 (1.0.4-1) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libarchive13:i386 (3.4.3-2+b1) ... Setting up libaec-dev:i386 (1.0.4-1) ... Setting up libjpeg-dev:i386 (1:2.0.6-4) ... Setting up libldap-2.4-2:i386 (2.4.57+dfsg-3) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:i386 (7.74.0-1.3+b1) ... Setting up libcurl4-gnutls-dev:i386 (7.74.0-1.3+b1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up libhdf5-103-1:i386 (1.10.6+repack-4) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up procps (2:3.3.17-5) ... Setting up libhdf5-cpp-103-1:i386 (1.10.6+repack-4) ... Setting up libcurl4:i386 (7.74.0-1.3+b1) ... Setting up libhdf5-hl-100:i386 (1.10.6+repack-4) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libhts3:i386 (1.11-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhts-dev:i386 (1.11-4) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up libhdf5-hl-cpp-100:i386 (1.10.6+repack-4) ... Setting up libhdf5-fortran-102:i386 (1.10.6+repack-4) ... Setting up cmake (3.18.4-2) ... Setting up libhdf5-hl-fortran-100:i386 (1.10.6+repack-4) ... Setting up debhelper (13.3.4) ... Setting up libhdf5-dev (1.10.6+repack-4) ... update-alternatives: using /usr/lib/i386-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/i386-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Processing triggers for libc-bin (2.31-13) ... 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 I: Building the package I: Running cd /build/kallisto-0.46.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package kallisto dpkg-buildpackage: info: source version 0.46.2+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pranav Ballaney dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/kallisto-0.46.2+dfsg' dh_auto_configure -- -DDEBIAN_BUILD=1 -DLINK=shared cd obj-i686-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/i386-linux-gnu -DDEBIAN_BUILD=1 -DLINK=shared .. -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done shared build -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Found ZLIB: /usr/lib/i386-linux-gnu/libz.so (found version "1.2.11") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY -- Build files have been written to: /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu make[1]: Leaving directory '/build/kallisto-0.46.2+dfsg' dh_auto_build cd obj-i686-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/kallisto-0.46.2+dfsg -B/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/CMakeFiles /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu' make -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/depend make[3]: Entering directory '/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu' cd /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kallisto-0.46.2+dfsg /build/kallisto-0.46.2+dfsg/src /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src/CMakeFiles/kallisto_core.dir/DependInfo.cmake --color= Dependee "/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src/CMakeFiles/kallisto_core.dir/DependInfo.cmake" is newer than depender "/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src/CMakeFiles/kallisto_core.dir/depend.internal". Dependee "/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src/CMakeFiles/kallisto_core.dir/depend.internal". Scanning dependencies of target kallisto_core make[3]: Leaving directory '/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu' make -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/build make[3]: Entering directory '/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu' [ 4%] Building CXX object src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o [ 9%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o [ 19%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o [ 19%] Building CXX object src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o [ 23%] Building CXX object src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o cd /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/BUSData.cpp.o -c /build/kallisto-0.46.2+dfsg/src/BUSData.cpp cd /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/BUSTools.cpp.o -c /build/kallisto-0.46.2+dfsg/src/BUSTools.cpp cd /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/H5Writer.cpp.o -c /build/kallisto-0.46.2+dfsg/src/H5Writer.cpp cd /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -c /build/kallisto-0.46.2+dfsg/src/Bootstrap.cpp [ 28%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o cd /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/GeneModel.cpp.o -c /build/kallisto-0.46.2+dfsg/src/GeneModel.cpp [ 33%] Building CXX object src/CMakeFiles/kallisto_core.dir/Kmer.cpp.o cd /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o -c /build/kallisto-0.46.2+dfsg/src/KmerIndex.cpp [ 38%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o cd /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/Kmer.cpp.o -c /build/kallisto-0.46.2+dfsg/src/Kmer.cpp cd /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o -c /build/kallisto-0.46.2+dfsg/src/KmerIterator.cpp [ 42%] Building CXX object src/CMakeFiles/kallisto_core.dir/Merge.cpp.o cd /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/Merge.cpp.o -c /build/kallisto-0.46.2+dfsg/src/Merge.cpp [ 47%] Building CXX object src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o cd /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/MinCollector.cpp.o -c /build/kallisto-0.46.2+dfsg/src/MinCollector.cpp [ 52%] Building CXX object src/CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o cd /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o -c /build/kallisto-0.46.2+dfsg/src/PlaintextWriter.cpp In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /build/kallisto-0.46.2+dfsg/src/GeneModel.h:10, from /build/kallisto-0.46.2+dfsg/src/GeneModel.cpp:1: /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable::rndup(size_t)': /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /build/kallisto-0.46.2+dfsg/src/KmerIndex.cpp:1: /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable::rndup(size_t)': /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /build/kallisto-0.46.2+dfsg/src/Bootstrap.h:7, from /build/kallisto-0.46.2+dfsg/src/Bootstrap.cpp:1: /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable::rndup(size_t)': /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ In file included from /build/kallisto-0.46.2+dfsg/src/GeneModel.cpp:1: /build/kallisto-0.46.2+dfsg/src/GeneModel.h: In member function 'std::size_t std::hash >::operator()(const std::pair&) const': /build/kallisto-0.46.2+dfsg/src/GeneModel.h:66:105: warning: left shift count >= width of type [-Wshift-count-overflow] 66 | return std::hash()(x.first) ^ (std::hash()(x.second)<<32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 57%] Building CXX object src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o cd /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o -c /build/kallisto-0.46.2+dfsg/src/ProcessReads.cpp In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /build/kallisto-0.46.2+dfsg/src/GeneModel.h:10, from /build/kallisto-0.46.2+dfsg/src/GeneModel.cpp:1: /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]': /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:125:13: required from 'void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]' /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:92:5: required from 'KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]' /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:96:106: required from here /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ In file included from /build/kallisto-0.46.2+dfsg/src/PlaintextWriter.h:13, from /build/kallisto-0.46.2+dfsg/src/Bootstrap.cpp:2: /build/kallisto-0.46.2+dfsg/src/GeneModel.h: In member function 'std::size_t std::hash >::operator()(const std::pair&) const': /build/kallisto-0.46.2+dfsg/src/GeneModel.h:66:105: warning: left shift count >= width of type [-Wshift-count-overflow] 66 | return std::hash()(x.first) ^ (std::hash()(x.second)<<32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /build/kallisto-0.46.2+dfsg/src/Merge.cpp:11: /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable::rndup(size_t)': /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /build/kallisto-0.46.2+dfsg/src/Bootstrap.h:7, from /build/kallisto-0.46.2+dfsg/src/Bootstrap.cpp:1: /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]': /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:125:13: required from 'void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]' /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:92:5: required from 'KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]' /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:96:106: required from here /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /build/kallisto-0.46.2+dfsg/src/PlaintextWriter.h:12, from /build/kallisto-0.46.2+dfsg/src/PlaintextWriter.cpp:1: /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable::rndup(size_t)': /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]': /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:218:13: required from 'void KmerHashTable::reserve(size_t, bool) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]' /build/kallisto-0.46.2+dfsg/src/KmerIndex.cpp:848:32: required from here /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]': /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:125:13: required from 'void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]' /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:92:5: required from 'KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]' /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:96:106: required from here /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] In file included from /build/kallisto-0.46.2+dfsg/src/PlaintextWriter.h:13, from /build/kallisto-0.46.2+dfsg/src/PlaintextWriter.cpp:1: /build/kallisto-0.46.2+dfsg/src/GeneModel.h: In member function 'std::size_t std::hash >::operator()(const std::pair&) const': /build/kallisto-0.46.2+dfsg/src/GeneModel.h:66:105: warning: left shift count >= width of type [-Wshift-count-overflow] 66 | return std::hash()(x.first) ^ (std::hash()(x.second)<<32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /build/kallisto-0.46.2+dfsg/src/MinCollector.h:11, from /build/kallisto-0.46.2+dfsg/src/MinCollector.cpp:1: /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable::rndup(size_t)': /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ [ 61%] Building CXX object src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o cd /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o -c /build/kallisto-0.46.2+dfsg/src/PseudoBam.cpp In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /build/kallisto-0.46.2+dfsg/src/PlaintextWriter.h:12, from /build/kallisto-0.46.2+dfsg/src/PlaintextWriter.cpp:1: /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]': /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:125:13: required from 'void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]' /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:92:5: required from 'KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]' /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:96:106: required from here /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]': /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:125:13: required from 'void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]' /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:92:5: required from 'KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]' /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:96:106: required from here /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /build/kallisto-0.46.2+dfsg/src/MinCollector.h:11, from /build/kallisto-0.46.2+dfsg/src/ProcessReads.h:18, from /build/kallisto-0.46.2+dfsg/src/ProcessReads.cpp:22: /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable::rndup(size_t)': /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ In file included from /build/kallisto-0.46.2+dfsg/src/PseudoBam.h:13, from /build/kallisto-0.46.2+dfsg/src/ProcessReads.h:21, from /build/kallisto-0.46.2+dfsg/src/ProcessReads.cpp:22: /build/kallisto-0.46.2+dfsg/src/GeneModel.h: In member function 'std::size_t std::hash >::operator()(const std::pair&) const': /build/kallisto-0.46.2+dfsg/src/GeneModel.h:66:105: warning: left shift count >= width of type [-Wshift-count-overflow] 66 | return std::hash()(x.first) ^ (std::hash()(x.second)<<32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /build/kallisto-0.46.2+dfsg/src/PseudoBam.h:12, from /build/kallisto-0.46.2+dfsg/src/PseudoBam.cpp:3: /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable::rndup(size_t)': /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ In file included from /build/kallisto-0.46.2+dfsg/src/PseudoBam.h:13, from /build/kallisto-0.46.2+dfsg/src/PseudoBam.cpp:3: /build/kallisto-0.46.2+dfsg/src/GeneModel.h: In member function 'std::size_t std::hash >::operator()(const std::pair&) const': /build/kallisto-0.46.2+dfsg/src/GeneModel.h:66:105: warning: left shift count >= width of type [-Wshift-count-overflow] 66 | return std::hash()(x.first) ^ (std::hash()(x.second)<<32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /build/kallisto-0.46.2+dfsg/src/PseudoBam.h:12, from /build/kallisto-0.46.2+dfsg/src/PseudoBam.cpp:3: /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]': /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:125:13: required from 'void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]' /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:92:5: required from 'KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]' /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:96:106: required from here /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /build/kallisto-0.46.2+dfsg/src/MinCollector.h:11, from /build/kallisto-0.46.2+dfsg/src/ProcessReads.h:18, from /build/kallisto-0.46.2+dfsg/src/ProcessReads.cpp:22: /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]': /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:125:13: required from 'void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]' /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:92:5: required from 'KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]' /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:96:106: required from here /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ [ 66%] Building CXX object src/CMakeFiles/kallisto_core.dir/common.cpp.o cd /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/common.cpp.o -c /build/kallisto-0.46.2+dfsg/src/common.cpp [ 71%] Building CXX object src/CMakeFiles/kallisto_core.dir/h5utils.cpp.o cd /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/h5utils.cpp.o -c /build/kallisto-0.46.2+dfsg/src/h5utils.cpp [ 76%] Building CXX object src/CMakeFiles/kallisto_core.dir/hash.cpp.o cd /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/hash.cpp.o -c /build/kallisto-0.46.2+dfsg/src/hash.cpp [ 80%] Building CXX object src/CMakeFiles/kallisto_core.dir/main.cpp.o cd /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/main.cpp.o -c /build/kallisto-0.46.2+dfsg/src/main.cpp [ 85%] Building CXX object src/CMakeFiles/kallisto_core.dir/weights.cpp.o cd /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/weights.cpp.o -c /build/kallisto-0.46.2+dfsg/src/weights.cpp In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /build/kallisto-0.46.2+dfsg/src/weights.h:4, from /build/kallisto-0.46.2+dfsg/src/weights.cpp:1: /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable::rndup(size_t)': /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]': /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:125:13: required from 'void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]' /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:92:5: required from 'KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]' /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:96:106: required from here /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /build/kallisto-0.46.2+dfsg/src/MinCollector.h:11, from /build/kallisto-0.46.2+dfsg/src/ProcessReads.h:18, from /build/kallisto-0.46.2+dfsg/src/main.cpp:17: /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable::rndup(size_t)': /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ In file included from /build/kallisto-0.46.2+dfsg/src/PseudoBam.h:13, from /build/kallisto-0.46.2+dfsg/src/ProcessReads.h:21, from /build/kallisto-0.46.2+dfsg/src/main.cpp:17: /build/kallisto-0.46.2+dfsg/src/GeneModel.h: In member function 'std::size_t std::hash >::operator()(const std::pair&) const': /build/kallisto-0.46.2+dfsg/src/GeneModel.h:66:105: warning: left shift count >= width of type [-Wshift-count-overflow] 66 | return std::hash()(x.first) ^ (std::hash()(x.second)<<32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /build/kallisto-0.46.2+dfsg/src/MinCollector.h:11, from /build/kallisto-0.46.2+dfsg/src/ProcessReads.h:18, from /build/kallisto-0.46.2+dfsg/src/main.cpp:17: /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]': /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:125:13: required from 'void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]' /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:92:5: required from 'KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]' /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:96:106: required from here /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ [ 90%] Linking CXX static library libkallisto_core.a cd /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/kallisto_core.dir/cmake_clean_target.cmake cd /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kallisto_core.dir/link.txt --verbose=1 /usr/bin/ar qc libkallisto_core.a CMakeFiles/kallisto_core.dir/BUSData.cpp.o CMakeFiles/kallisto_core.dir/BUSTools.cpp.o CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o CMakeFiles/kallisto_core.dir/GeneModel.cpp.o CMakeFiles/kallisto_core.dir/H5Writer.cpp.o CMakeFiles/kallisto_core.dir/Kmer.cpp.o CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o CMakeFiles/kallisto_core.dir/Merge.cpp.o CMakeFiles/kallisto_core.dir/MinCollector.cpp.o CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o CMakeFiles/kallisto_core.dir/common.cpp.o CMakeFiles/kallisto_core.dir/h5utils.cpp.o CMakeFiles/kallisto_core.dir/hash.cpp.o CMakeFiles/kallisto_core.dir/main.cpp.o CMakeFiles/kallisto_core.dir/weights.cpp.o /usr/bin/ranlib libkallisto_core.a make[3]: Leaving directory '/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu' [ 90%] Built target kallisto_core make -f src/CMakeFiles/kallisto.dir/build.make src/CMakeFiles/kallisto.dir/depend make[3]: Entering directory '/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu' cd /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kallisto-0.46.2+dfsg /build/kallisto-0.46.2+dfsg/src /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src/CMakeFiles/kallisto.dir/DependInfo.cmake --color= Dependee "/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src/CMakeFiles/kallisto.dir/DependInfo.cmake" is newer than depender "/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src/CMakeFiles/kallisto.dir/depend.internal". Dependee "/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src/CMakeFiles/kallisto.dir/depend.internal". Scanning dependencies of target kallisto make[3]: Leaving directory '/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu' make -f src/CMakeFiles/kallisto.dir/build.make src/CMakeFiles/kallisto.dir/build make[3]: Entering directory '/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu' [ 95%] Building CXX object src/CMakeFiles/kallisto.dir/main.cpp.o cd /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/build/kallisto-0.46.2+dfsg/src -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto.dir/main.cpp.o -c /build/kallisto-0.46.2+dfsg/src/main.cpp In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /build/kallisto-0.46.2+dfsg/src/MinCollector.h:11, from /build/kallisto-0.46.2+dfsg/src/ProcessReads.h:18, from /build/kallisto-0.46.2+dfsg/src/main.cpp:17: /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In member function 'size_t KmerHashTable::rndup(size_t)': /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ In file included from /build/kallisto-0.46.2+dfsg/src/PseudoBam.h:13, from /build/kallisto-0.46.2+dfsg/src/ProcessReads.h:21, from /build/kallisto-0.46.2+dfsg/src/main.cpp:17: /build/kallisto-0.46.2+dfsg/src/GeneModel.h: In member function 'std::size_t std::hash >::operator()(const std::pair&) const': /build/kallisto-0.46.2+dfsg/src/GeneModel.h:66:105: warning: left shift count >= width of type [-Wshift-count-overflow] 66 | return std::hash()(x.first) ^ (std::hash()(x.second)<<32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:18, from /build/kallisto-0.46.2+dfsg/src/MinCollector.h:11, from /build/kallisto-0.46.2+dfsg/src/ProcessReads.h:18, from /build/kallisto-0.46.2+dfsg/src/main.cpp:17: /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h: In instantiation of 'size_t KmerHashTable::rndup(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]': /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:125:13: required from 'void KmerHashTable::init_table(size_t) [with T = KmerEntry; Hash = KmerHash; size_t = unsigned int]' /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:92:5: required from 'KmerHashTable::KmerHashTable(const Hash&) [with T = KmerEntry; Hash = KmerHash]' /build/kallisto-0.46.2+dfsg/src/KmerIndex.h:96:106: required from here /build/kallisto-0.46.2+dfsg/src/KmerHashTable.h:240:12: warning: right shift count >= width of type [-Wshift-count-overflow] 240 | v |= v >> 32; | ~~^~~~~ [100%] Linking CXX executable kallisto cd /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kallisto.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/kallisto-0.46.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/kallisto.dir/main.cpp.o -o kallisto libkallisto_core.a -lpthread -lhts libkallisto_core.a -lz -lrt make[3]: Leaving directory '/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu' [100%] Built target kallisto make[2]: Leaving directory '/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-i686-linux-gnu && make -j8 install DESTDIR=/build/kallisto-0.46.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/kallisto-0.46.2+dfsg -B/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/CMakeFiles /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu' make -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/depend make[3]: Entering directory '/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu' cd /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kallisto-0.46.2+dfsg /build/kallisto-0.46.2+dfsg/src /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src/CMakeFiles/kallisto_core.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu' make -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/build make[3]: Entering directory '/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'src/CMakeFiles/kallisto_core.dir/build'. make[3]: Leaving directory '/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu' [ 90%] Built target kallisto_core make -f src/CMakeFiles/kallisto.dir/build.make src/CMakeFiles/kallisto.dir/depend make[3]: Entering directory '/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu' cd /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kallisto-0.46.2+dfsg /build/kallisto-0.46.2+dfsg/src /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/src/CMakeFiles/kallisto.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu' make -f src/CMakeFiles/kallisto.dir/build.make src/CMakeFiles/kallisto.dir/build make[3]: Entering directory '/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'src/CMakeFiles/kallisto.dir/build'. make[3]: Leaving directory '/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu' [100%] Built target kallisto make[2]: Leaving directory '/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/kallisto-0.46.2+dfsg/debian/tmp/usr/bin/kallisto make[1]: Leaving directory '/build/kallisto-0.46.2+dfsg/obj-i686-linux-gnu' dh_install dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'kallisto-dbgsym' in '../kallisto-dbgsym_0.46.2+dfsg-2_i386.deb'. dpkg-deb: building package 'kallisto' in '../kallisto_0.46.2+dfsg-2_i386.deb'. dpkg-deb: building package 'kallisto-examples' in '../kallisto-examples_0.46.2+dfsg-2_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../kallisto_0.46.2+dfsg-2_i386.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/27037 and its subdirectories I: Current time: Mon Aug 16 21:21:11 -12 2021 I: pbuilder-time-stamp: 1629192071 Tue Aug 17 09:21:12 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos6-i386.debian.net. Tue Aug 17 09:21:12 UTC 2021 I: Preparing to do remote build '2' on ionos6-i386.debian.net. Tue Aug 17 09:22:01 UTC 2021 I: Deleting $TMPDIR on ionos6-i386.debian.net. Tue Aug 17 09:22:01 UTC 2021 I: kallisto_0.46.2+dfsg-2_i386.changes: Format: 1.8 Date: Sat, 16 May 2020 04:47:12 +0530 Source: kallisto Binary: kallisto kallisto-dbgsym kallisto-examples Architecture: i386 all Version: 0.46.2+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Pranav Ballaney Description: kallisto - near-optimal RNA-Seq quantification kallisto-examples - near-optimal RNA-Seq quantification (example data) Closes: 960368 Changes: kallisto (0.46.2+dfsg-2) unstable; urgency=medium . * Team upload * Patch to avoid segfault (Closes: #960368) Checksums-Sha1: 0830280439fe8810f5543c2623bddada24a98dab 3711380 kallisto-dbgsym_0.46.2+dfsg-2_i386.deb 95603ca37771044a9f6a8b406ae9a1350eb134e6 666976 kallisto-examples_0.46.2+dfsg-2_all.deb 2ab0c20025e6a6194fd2b02f77c19ce2dd03c629 6684 kallisto_0.46.2+dfsg-2_i386.buildinfo 9c5949ab37349391a2697d37202e19f459c2b2ff 259636 kallisto_0.46.2+dfsg-2_i386.deb Checksums-Sha256: c2c7e9b23edc7ebfb407ab6066efc54eea4ef3bd16bc95c6fd24ba85f1e21896 3711380 kallisto-dbgsym_0.46.2+dfsg-2_i386.deb cff0f65416301402af29e81c35bdd32f2bd4503def36d44695cd024be133c99f 666976 kallisto-examples_0.46.2+dfsg-2_all.deb 6393ad0670411bb8612cd16a20cae1dec522c5c8443d3a12d3f34aab28db21ee 6684 kallisto_0.46.2+dfsg-2_i386.buildinfo f5c520d76dcd5c308c5bded30f7ab50fa2d887892843ea55d46fdc552c4d3e12 259636 kallisto_0.46.2+dfsg-2_i386.deb Files: f350fbd9af70d930a8d26524887644da 3711380 debug optional kallisto-dbgsym_0.46.2+dfsg-2_i386.deb 9e6038f61b14bd329ba2dc829243d511 666976 science optional kallisto-examples_0.46.2+dfsg-2_all.deb 17fa52f7b1263f04e0627ae2b0106540 6684 science optional kallisto_0.46.2+dfsg-2_i386.buildinfo 39cd1f0ca51784f0358180e1c16c0d6a 259636 science optional kallisto_0.46.2+dfsg-2_i386.deb Tue Aug 17 09:22:03 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.TlK0Y14zgc/kallisto_0.46.2+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.TlK0Y14zgc/kallisto_0.46.2+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.TlK0Y14zgc/kallisto_0.46.2+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.TlK0Y14zgc/b1/kallisto_0.46.2+dfsg-2_i386.changes /srv/reproducible-results/rbuild-debian/tmp.TlK0Y14zgc/b2/kallisto_0.46.2+dfsg-2_i386.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: 0.310s) 0.310s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.087s) 0.087s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Tue Aug 17 09:22:05 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Tue Aug 17 09:22:05 UTC 2021 I: kallisto from bullseye built successfully and reproducibly on i386. Tue Aug 17 09:22:06 UTC 2021 I: Submitting .buildinfo files to external archives: Tue Aug 17 09:22:06 UTC 2021 I: Submitting 8.0K b1/kallisto_0.46.2+dfsg-2_i386.buildinfo.asc Tue Aug 17 09:22:07 UTC 2021 I: Submitting 8.0K b2/kallisto_0.46.2+dfsg-2_i386.buildinfo.asc Tue Aug 17 09:22:08 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Aug 17 09:22:08 UTC 2021 I: Done submitting .buildinfo files. Tue Aug 17 09:22:08 UTC 2021 I: Removing signed kallisto_0.46.2+dfsg-2_i386.buildinfo.asc files: removed './b1/kallisto_0.46.2+dfsg-2_i386.buildinfo.asc' removed './b2/kallisto_0.46.2+dfsg-2_i386.buildinfo.asc'