Sat Jun 19 17:04:32 UTC 2021 I: starting to build seer/bullseye/i386 on jenkins on '2021-06-19 17:04' Sat Jun 19 17:04:32 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_13/14608/console.log Sat Jun 19 17:04:32 UTC 2021 I: Downloading source for bullseye/seer=1.1.4-5 --2021-06-19 17:04:32-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/seer/seer_1.1.4-5.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2045 (2.0K) Saving to: ‘seer_1.1.4-5.dsc’ 0K . 100% 141M=0s 2021-06-19 17:04:32 (141 MB/s) - ‘seer_1.1.4-5.dsc’ saved [2045/2045] Sat Jun 19 17:04:33 UTC 2021 I: seer_1.1.4-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: seer Binary: seer Architecture: any Version: 1.1.4-5 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/johnlees/seer Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/seer Vcs-Git: https://salsa.debian.org/med-team/seer.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libarmadillo-dev (>= 1:6.700.6+dfsg-1~), libdlib-dev, libhdf5-dev, libgzstream-dev, libboost-dev, libboost-program-options-dev Package-List: seer deb science optional arch=any Checksums-Sha1: 01aa93df82b6e563f5e06ae47592ae0d98dce2da 972155 seer_1.1.4.orig.tar.gz afe26bb4075932add3812a648728ff14eea0fe5b 8508 seer_1.1.4-5.debian.tar.xz Checksums-Sha256: 96e55b9fe2cde089ff05bbcd55088832e90f44a968a81a8dca9f9cffa6faa9c1 972155 seer_1.1.4.orig.tar.gz d8224022efe9bdcae52e9e115e6069258d9f96e57c517923c89cc4a99a9c3696 8508 seer_1.1.4-5.debian.tar.xz Files: e4b331eaf17819aabc545b032148d8c2 972155 seer_1.1.4.orig.tar.gz 624efe7b641fcf0d28f7501e8d4a9484 8508 seer_1.1.4-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAmBAMtgUHG5wYXRyYTk3 NEBnbWFpbC5jb20ACgkQALrnSzQzafEaDw//fHGAfl5f1/56YzdOiBZ+WshWu89g oiFGx/rJt32Tc1h8gp5e9OEOKm0sm6bOaCxRxG4xghVKHTLzIs2ZWMjpoFd9i7ix bpbrvV55wYgZPHadlSWJbj+5vgQIkviOsbJrRv4g+dLCWYrVnn6O2k6rPIIAYAnQ 5i2v1lG+qZAcXpNe0ppG8AcomdmqlSq8XvIXkWrqCylOxLYZggE0jrmvBXemeccH kFKK3FKyMsEIFpNCIZceMHH+2glEDseheUcfa+8/eRrHxFaz/yZyqbndU++K0HhI 32jf/AzGtLH6tWI9KeHpd9lecgqxUy4AQH5Rtcm8a7VDxesbtTi/FSx6edKEfAAn cw2QC2VhjkJL9yhlp8GCC/Oksj+w7x4Q1offrn+v6A+W0o+wCVhDrwLvpd3BoCL9 HSFPk5BAG5qoQVLbFjtGNYwHZ0kaDnVmc7Dlcc5Tf1NxjiYmPEOp4TmqkcEGGBTt ooCVnUQA/V828PIhgVN1Q88UdFO6BkFHAFTYrHeGmUeArL+32oX0Xl6EH1QXArdF 4VEPaEowZVc3rUUxXNxUn9xLrlXpVGWi2nopO2Dw2+sTKNISMR6IGGyZtv3naq0m 8tPongpeLjcM+VZzNb+OVwoIwhu273cYk04+puH7W0+bJonXcZSL5rLdD7azS5ir /D7/dGz5vhV9tRM= =UCGl -----END PGP SIGNATURE----- Sat Jun 19 17:04:33 UTC 2021 I: Checking whether the package is not for us Sat Jun 19 17:04:33 UTC 2021 I: Starting 1st build on remote node ionos12-i386.debian.net. Sat Jun 19 17:04:33 UTC 2021 I: Preparing to do remote build '1' on ionos12-i386.debian.net. Sat Jun 19 17:10:48 UTC 2021 I: Deleting $TMPDIR on ionos12-i386.debian.net. unshare: unshare failed: Cannot allocate memory W: pbuilder: unshare CLONE_NEWNET not available I: pbuilder: network access is available during build! I: Current time: Sat Jun 19 05:04:36 -12 2021 I: pbuilder-time-stamp: 1624122276 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 [seer_1.1.4-5.dsc] I: copying [./seer_1.1.4.orig.tar.gz] I: copying [./seer_1.1.4-5.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.RtAvG55G/trustedkeys.kbx': General error gpgv: Signature made Wed Mar 3 13:07:36 2021 -12 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./seer_1.1.4-5.dsc dpkg-source: info: extracting seer in seer-1.1.4 dpkg-source: info: unpacking seer_1.1.4.orig.tar.gz dpkg-source: info: unpacking seer_1.1.4-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_lib_location.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying gcc11.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/25464/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=10' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='5f6040aae9cf411593863a62e0ba9331' 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='25464' 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.JjQuM0Hcua/pbuilderrc_u4Vh --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.JjQuM0Hcua/b1 --logfile b1/build.log seer_1.1.4-5.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 ionos12-i386 4.19.0-16-686-pae #1 SMP Debian 4.19.181-1 (2021-03-19) i686 GNU/Linux I: ls -l /bin total 5780 -rwxr-xr-x 1 root root 1367848 Feb 24 08:57 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 Feb 7 02:38 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 Feb 7 02:38 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 Feb 7 02:38 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 Feb 7 02:38 more -rwsr-xr-x 1 root root 50720 Feb 7 02:38 mount -rwxr-xr-x 1 root root 13856 Feb 7 02:38 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 Feb 24 08:57 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 Jun 17 21:27 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 Feb 7 02:38 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 Feb 7 02:38 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 Feb 7 02:38 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/25464/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 (= 13), libarmadillo-dev (>= 1:6.700.6+dfsg-1~), libdlib-dev, libhdf5-dev, libgzstream-dev, libboost-dev, libboost-program-options-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 (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libarmadillo-dev (>= 1:6.700.6+dfsg-1~); however: Package libarmadillo-dev is not installed. pbuilder-satisfydepends-dummy depends on libdlib-dev; however: Package libdlib-dev is not installed. pbuilder-satisfydepends-dummy depends on libhdf5-dev; however: Package libhdf5-dev is not installed. pbuilder-satisfydepends-dummy depends on libgzstream-dev; however: Package libgzstream-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-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} 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} libarmadillo-dev{a} libarmadillo10{a} libarpack2{a} libarpack2-dev{a} libblas-dev{a} libblas3{a} libboost-dev{a} libboost-program-options-dev{a} libboost-program-options1.74-dev{a} libboost-program-options1.74.0{a} libboost1.74-dev{a} libdebhelper-perl{a} libdlib-data{a} libdlib-dev{a} libdlib19{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgzstream-dev{a} libgzstream0{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} libicu67{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} liblapack-dev{a} liblapack3{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libpng16-16{a} libsigsegv2{a} libsub-override-perl{a} libsuperlu-dev{a} libsuperlu5{a} libsz2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 68 newly installed, 0 to remove and 0 not upgraded. Need to get 111 MB of archives. After unpacking 395 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-7 [148 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 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3 [133 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3 [69.0 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-6 [8776 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7 [728 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 hdf5-helpers i386 1.10.6+repack-2 [40.0 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 libaec0 i386 1.0.4-1 [22.6 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 libsz2 i386 1.0.4-1 [6820 B] Get: 35 http://deb.debian.org/debian bullseye/main i386 libaec-dev i386 1.0.4-1 [21.5 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 libblas3 i386 3.9.0-3 [147 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 libgfortran5 i386 10.2.1-6 [643 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 liblapack3 i386 3.9.0-3 [1960 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 libarpack2 i386 3.8.0-1 [103 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 libsuperlu5 i386 5.2.2+dfsg1-2 [161 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 libarmadillo10 i386 1:10.1.2+dfsg-5 [103 kB] Get: 42 http://deb.debian.org/debian bullseye/main i386 libblas-dev i386 3.9.0-3 [157 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 liblapack-dev i386 3.9.0-3 [3759 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 libarpack2-dev i386 3.8.0-1 [123 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 libhdf5-103-1 i386 1.10.6+repack-2 [1153 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 libhdf5-fortran-102 i386 1.10.6+repack-2 [112 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 libhdf5-hl-100 i386 1.10.6+repack-2 [93.2 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 libhdf5-hl-fortran-100 i386 1.10.6+repack-2 [57.0 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 libhdf5-cpp-103-1 i386 1.10.6+repack-2 [152 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 libhdf5-hl-cpp-100 i386 1.10.6+repack-2 [37.7 kB] Get: 51 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2 [194 kB] Get: 52 http://deb.debian.org/debian bullseye/main i386 libjpeg62-turbo i386 1:2.0.6-4 [160 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 libjpeg62-turbo-dev i386 1:2.0.6-4 [299 kB] Get: 54 http://deb.debian.org/debian bullseye/main i386 libjpeg-dev i386 1:2.0.6-4 [67.8 kB] Get: 55 http://deb.debian.org/debian bullseye/main i386 libhdf5-dev i386 1.10.6+repack-2 [2594 kB] Get: 56 http://deb.debian.org/debian bullseye/main i386 libsuperlu-dev i386 5.2.2+dfsg1-2 [21.4 kB] Get: 57 http://deb.debian.org/debian bullseye/main i386 libarmadillo-dev i386 1:10.1.2+dfsg-5 [386 kB] Get: 58 http://deb.debian.org/debian bullseye/main i386 libboost1.74-dev i386 1.74.0-9 [9534 kB] Get: 59 http://deb.debian.org/debian bullseye/main i386 libboost-dev i386 1.74.0.3 [4548 B] Get: 60 http://deb.debian.org/debian bullseye/main i386 libboost-program-options1.74.0 i386 1.74.0-9 [365 kB] Get: 61 http://deb.debian.org/debian bullseye/main i386 libboost-program-options1.74-dev i386 1.74.0-9 [397 kB] Get: 62 http://deb.debian.org/debian bullseye/main i386 libboost-program-options-dev i386 1.74.0.3 [4344 B] Get: 63 http://deb.debian.org/debian bullseye/main i386 libdlib-data all 19.10-3 [63.4 MB] Get: 64 http://deb.debian.org/debian bullseye/main i386 libpng16-16 i386 1.6.37-3 [303 kB] Get: 65 http://deb.debian.org/debian bullseye/main i386 libdlib19 i386 19.10-3+b1 [3799 kB] Get: 66 http://deb.debian.org/debian bullseye/main i386 libdlib-dev i386 19.10-3+b1 [1760 kB] Get: 67 http://deb.debian.org/debian bullseye/main i386 libgzstream0 i386 1.5+dfsg-5 [6896 B] Get: 68 http://deb.debian.org/debian bullseye/main i386 libgzstream-dev i386 1.5+dfsg-5 [7188 B] Fetched 111 MB in 8s (13.5 MB/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_2.36.1-7_i386.deb ... Unpacking bsdextrautils (2.36.1-7) ... 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 ... 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Preparing to unpack .../67-libgzstream-dev_1.5+dfsg-5_i386.deb ... Unpacking libgzstream-dev (1.5+dfsg-5) ... Setting up libpipeline1:i386 (1.5.3-1) ... Setting up libboost1.74-dev:i386 (1.74.0-9) ... Setting up bsdextrautils (2.36.1-7) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up hdf5-helpers (1.10.6+repack-2) ... Setting up libicu67:i386 (67.1-6) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libboost-program-options1.74.0:i386 (1.74.0-9) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libmagic1:i386 (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libaec0:i386 (1.0.4-1) ... Setting up libboost-program-options1.74-dev:i386 (1.74.0-9) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libblas3:i386 (3.9.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libjpeg62-turbo:i386 (1:2.0.6-4) ... Setting up libboost-program-options-dev:i386 (1.74.0.3) ... Setting up libjpeg62-turbo-dev:i386 (1:2.0.6-4) ... Setting up libsigsegv2:i386 (2.13-1) ... Setting up libpng16-16:i386 (1.6.37-3) ... Setting up autopoint (0.21-4) ... Setting up libgfortran5:i386 (10.2.1-6) ... Setting up libgzstream0 (1.5+dfsg-5) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libboost-dev:i386 (1.74.0.3) ... Setting up libelf1:i386 (0.183-1) ... Setting up libxml2:i386 (2.9.10+dfsg-6.7) ... Setting up libdlib-data (19.10-3) ... Setting up libblas-dev:i386 (3.9.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so to provide /usr/lib/i386-linux-gnu/libblas.so (libblas.so-i386-linux-gnu) in auto mode Setting up libsz2:i386 (1.0.4-1) ... Setting up libfile-stripnondeterminism-perl (1.11.0-1) ... Setting up liblapack3:i386 (3.9.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libaec-dev:i386 (1.0.4-1) ... Setting up libarpack2:i386 (3.8.0-1) ... Setting up libjpeg-dev:i386 (1:2.0.6-4) ... Setting up libsuperlu5:i386 (5.2.2+dfsg1-2) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libgzstream-dev (1.5+dfsg-5) ... Setting up libdlib19:i386 (19.10-3+b1) ... Setting up liblapack-dev:i386 (3.9.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so to provide /usr/lib/i386-linux-gnu/liblapack.so (liblapack.so-i386-linux-gnu) in auto mode Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.11.0-1) ... Setting up libhdf5-103-1:i386 (1.10.6+repack-2) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up libhdf5-cpp-103-1:i386 (1.10.6+repack-2) ... Setting up libsuperlu-dev:i386 (5.2.2+dfsg1-2) ... Setting up libhdf5-hl-100:i386 (1.10.6+repack-2) ... 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 libarmadillo10 (1:10.1.2+dfsg-5) ... Setting up libarpack2-dev:i386 (3.8.0-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libdlib-dev:i386 (19.10-3+b1) ... Setting up dh-autoreconf (20) ... Setting up libhdf5-hl-cpp-100:i386 (1.10.6+repack-2) ... Setting up libhdf5-fortran-102:i386 (1.10.6+repack-2) ... Setting up libhdf5-hl-fortran-100:i386 (1.10.6+repack-2) ... Setting up debhelper (13.3.4) ... Setting up libhdf5-dev (1.10.6+repack-2) ... 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 Setting up libarmadillo-dev (1:10.1.2+dfsg-5) ... Processing triggers for libc-bin (2.31-12) ... 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/seer-1.1.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package seer dpkg-buildpackage: info: source version 1.1.4-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean dh_auto_clean make -j10 clean make[1]: Entering directory '/build/seer-1.1.4' cd src && make clean make[2]: Entering directory '/build/seer-1.1.4/src' rm -f *.o ~* seer kmds map_back combineKmers filter_seer make[2]: Leaving directory '/build/seer-1.1.4/src' cd test && make clean make[2]: Entering directory '/build/seer-1.1.4/test' rm -f *.o ~* tests_passed make[2]: Leaving directory '/build/seer-1.1.4/test' make[1]: Leaving directory '/build/seer-1.1.4' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/seer-1.1.4' dh_auto_build -- LDFLAGS+=-L/usr/lib/i386-linux-gnu/hdf5/serial make -j10 "INSTALL=install --strip-program=true" LDFLAGS\+=-L/usr/lib/i386-linux-gnu/hdf5/serial make[2]: Entering directory '/build/seer-1.1.4' cd src && make all make[3]: Entering directory '/build/seer-1.1.4/src' g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o sample.o sample.cpp g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o significant_kmer.o significant_kmer.cpp g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o kmer.o kmer.cpp g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o covar.o covar.cpp g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerCommon.o seerCommon.cpp g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerErr.o seerErr.cpp g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerIO.o seerIO.cpp g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerBasicFilter.o seerBasicFilter.cpp g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerMain.o seerMain.cpp g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerCmdLine.o seerCmdLine.cpp g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerStats.o seerStats.cpp g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerContinuousAssoc.o seerContinuousAssoc.cpp g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerBinaryAssoc.o seerBinaryAssoc.cpp g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o logitFunction.o logitFunction.cpp seerCommon.cpp: In function 'arma::vec dlib_to_arma(const column_vector&)': seerCommon.cpp:174:31: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'long int' [-Wsign-compare] 174 | for (unsigned int i = 0; i < dlib_vec.nr(); ++i) | ~~^~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o linearFunction.o linearFunction.cpp g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o kmdsMain.o kmdsMain.cpp g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o kmdsStruct.o kmdsStruct.cpp g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o kmdsCmdLine.o kmdsCmdLine.cpp g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o fasta.o fasta.cpp g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o mapMain.o mapMain.cpp g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o mapCmdLine.o mapCmdLine.cpp g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o combineInit.o combineInit.cpp g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o combineCmdLine.o combineCmdLine.cpp g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o combineKmers.o combineKmers.cpp g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o filter_seer.o filter_seer.cpp g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o filterCmdLine.o filterCmdLine.cpp g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -Wl,-z,relro -Wl,-z,now -L/usr/lib/i386-linux-gnu/hdf5/serial significant_kmer.o filter_seer.o filterCmdLine.o -lboost_program_options -Wl,-z,relro -Wl,-z,now -L/usr/lib/i386-linux-gnu/hdf5/serial -Wl,-z,relro -Wl,-z,now -L/usr/lib/i386-linux-gnu/hdf5/serial -o filter_seer g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -Wl,-z,relro -Wl,-z,now -L/usr/lib/i386-linux-gnu/hdf5/serial combineInit.o combineCmdLine.o combineKmers.o -lgzstream -lz -lboost_program_options -Wl,-z,relro -Wl,-z,now -L/usr/lib/i386-linux-gnu/hdf5/serial -Wl,-z,relro -Wl,-z,now -L/usr/lib/i386-linux-gnu/hdf5/serial -o combineKmers g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -Wl,-z,relro -Wl,-z,now -L/usr/lib/i386-linux-gnu/hdf5/serial fasta.o significant_kmer.o mapMain.o mapCmdLine.o -lboost_program_options -lpthread -Wl,-z,relro -Wl,-z,now -L/usr/lib/i386-linux-gnu/hdf5/serial -Wl,-z,relro -Wl,-z,now -L/usr/lib/i386-linux-gnu/hdf5/serial -o map_back g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -Wl,-z,relro -Wl,-z,now -L/usr/lib/i386-linux-gnu/hdf5/serial sample.o significant_kmer.o kmer.o covar.o seerCommon.o seerErr.o seerIO.o seerBasicFilter.o seerMain.o seerCmdLine.o seerStats.o seerContinuousAssoc.o seerBinaryAssoc.o logitFunction.o linearFunction.o -lhdf5 -lgzstream -lz -larmadillo -lboost_program_options -llapack -lblas -lpthread -Wl,-z,relro -Wl,-z,now -L/usr/lib/i386-linux-gnu/hdf5/serial -o seer g++ -g -O2 -fdebug-prefix-map=/build/seer-1.1.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -Wl,-z,relro -Wl,-z,now -L/usr/lib/i386-linux-gnu/hdf5/serial sample.o significant_kmer.o kmer.o covar.o seerCommon.o seerErr.o seerIO.o seerBasicFilter.o kmdsMain.o kmdsStruct.o kmdsCmdLine.o -lhdf5 -lgzstream -lz -larmadillo -lboost_program_options -llapack -lblas -lpthread -Wl,-z,relro -Wl,-z,now -L/usr/lib/i386-linux-gnu/hdf5/serial -o kmds make[3]: Leaving directory '/build/seer-1.1.4/src' make[2]: Leaving directory '/build/seer-1.1.4' make[1]: Leaving directory '/build/seer-1.1.4' debian/rules override_dh_auto_test make[1]: Entering directory '/build/seer-1.1.4' if dh_auto_test ; then echo Test passed ; else echo '****************************** TEST FAILED. Please contact upstream *******************************' ; fi make -j10 test make[2]: Entering directory '/build/seer-1.1.4' cd src && make all make[3]: Entering directory '/build/seer-1.1.4/src' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/seer-1.1.4/src' cd test && make test make[3]: Entering directory '/build/seer-1.1.4/test' ./run_test.pl && touch tests_passed PASSED test 1, basic filters PASSED test 2, binary phenotype assocation PASSED test 3, print output PASSED test 4, continuous phenotype assocation FAILED test 5, assocation with population structure Files /tmp/7X4Mgyzvkk and test5.o.txt differ make[3]: *** [Makefile:2: all] Error 1 make[3]: Leaving directory '/build/seer-1.1.4/test' make[2]: *** [Makefile:15: test] Error 2 make[2]: Leaving directory '/build/seer-1.1.4' dh_auto_test: error: make -j10 test returned exit code 2 ****************************** TEST FAILED. Please contact upstream ******************************* make[1]: Leaving directory '/build/seer-1.1.4' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/seer-1.1.4' dh_auto_install -- PREFIX=/build/seer-1.1.4/debian/seer/usr make -j10 install DESTDIR=/build/seer-1.1.4/debian/seer AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" PREFIX=/build/seer-1.1.4/debian/seer/usr make[2]: Entering directory '/build/seer-1.1.4' cd src && make all make[3]: Entering directory '/build/seer-1.1.4/src' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/seer-1.1.4/src' cd src && make install make[3]: Entering directory '/build/seer-1.1.4/src' install -d /build/seer-1.1.4/debian/seer/usr/bin install seer kmds map_back combineKmers filter_seer /build/seer-1.1.4/debian/seer/usr/bin make[3]: Leaving directory '/build/seer-1.1.4/src' make[2]: Leaving directory '/build/seer-1.1.4' for pl in scripts/*.pl ; do \ plbase=`basename ${pl} .pl` ; \ sed "s+Usage: ./${plbase}.pl+Usage: ${plbase}+" ${pl} > /build/seer-1.1.4/debian/seer/usr/bin/${plbase} ; \ done # Fix broken usage hint: sed -i "s+Usage: ./hits_to_matrix.pl+Usage: reformat_output+" /build/seer-1.1.4/debian/seer/usr/bin/reformat_output make[1]: Leaving directory '/build/seer-1.1.4' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/seer-1.1.4' dh_fixperms find debian -name Makefile -exec chmod -x \{\} \; find debian -name "*.fa" -exec chmod -x \{\} \; make[1]: Leaving directory '/build/seer-1.1.4' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/seer/usr/bin/combineKmers was not linked against libz.so.1 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'seer-dbgsym' in '../seer-dbgsym_1.1.4-5_i386.deb'. dpkg-deb: building package 'seer' in '../seer_1.1.4-5_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../seer_1.1.4-5_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: 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/25464 and its subdirectories I: Current time: Sat Jun 19 05:10:48 -12 2021 I: pbuilder-time-stamp: 1624122648 Sat Jun 19 17:10:49 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos6-i386.debian.net. Sat Jun 19 17:10:49 UTC 2021 I: Preparing to do remote build '2' on ionos6-i386.debian.net. Sat Jun 19 17:14:54 UTC 2021 I: Deleting $TMPDIR on ionos6-i386.debian.net. Sat Jun 19 17:14:54 UTC 2021 I: seer_1.1.4-5_i386.changes: Format: 1.8 Date: Thu, 04 Mar 2021 06:33:51 +0530 Source: seer Binary: seer seer-dbgsym Architecture: i386 Version: 1.1.4-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: seer - genomic sequence element (kmer) enrichment analysis Closes: 984328 Changes: seer (1.1.4-5) unstable; urgency=medium . * Team Upload. * debian/patches/gcc11.patch: Fix gcc-11 FTBFS (Closes: #984328) Checksums-Sha1: b1b75863b9fb3fa1a5e82ce7eb527ed535e5446a 8632508 seer-dbgsym_1.1.4-5_i386.deb 1ef3725a9aca2d7a6b090c619fee5ffec90c868e 6008 seer_1.1.4-5_i386.buildinfo eac06318a6c6ad8bdafe6a88161b8cf7183be1c5 1177788 seer_1.1.4-5_i386.deb Checksums-Sha256: d68ed3f845b3bcbb1c6dd7301f6825621a461a427a580d17c684b1ebf636210a 8632508 seer-dbgsym_1.1.4-5_i386.deb 3df9b4282102bb8cd1d2bef1cf555c322c2a67958bafce0eaff70dcbbdc749a7 6008 seer_1.1.4-5_i386.buildinfo cc2c62bb4c803aa6e25fe0e130f00aa2a262e90c90eb58b8adaf1ceac1dd201c 1177788 seer_1.1.4-5_i386.deb Files: e153b467323c99c327c7ae4ce6d1e932 8632508 debug optional seer-dbgsym_1.1.4-5_i386.deb e32e60d46f567683a495218032aeef55 6008 science optional seer_1.1.4-5_i386.buildinfo 339c5260bd46edb9b8ef389dc0429c66 1177788 science optional seer_1.1.4-5_i386.deb Sat Jun 19 17:14:55 UTC 2021 I: diffoscope 172 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.JjQuM0Hcua/seer_1.1.4-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.JjQuM0Hcua/seer_1.1.4-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.JjQuM0Hcua/seer_1.1.4-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.JjQuM0Hcua/b1/seer_1.1.4-5_i386.changes /srv/reproducible-results/rbuild-debian/tmp.JjQuM0Hcua/b2/seer_1.1.4-5_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: 0.391s) 0.391s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.112s) 0.111s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Sat Jun 19 17:18:40 UTC 2021 I: diffoscope 172 found no differences in the changes files, and a .buildinfo file also exists. Sat Jun 19 17:18:40 UTC 2021 I: seer from bullseye built successfully and reproducibly on i386. Sat Jun 19 17:18:42 UTC 2021 I: Submitting .buildinfo files to external archives: Sat Jun 19 17:18:42 UTC 2021 I: Submitting 8.0K b1/seer_1.1.4-5_i386.buildinfo.asc Sat Jun 19 17:18:43 UTC 2021 I: Submitting 8.0K b2/seer_1.1.4-5_i386.buildinfo.asc Sat Jun 19 17:18:44 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Jun 19 17:18:44 UTC 2021 I: Done submitting .buildinfo files. Sat Jun 19 17:18:44 UTC 2021 I: Removing signed seer_1.1.4-5_i386.buildinfo.asc files: removed './b1/seer_1.1.4-5_i386.buildinfo.asc' removed './b2/seer_1.1.4-5_i386.buildinfo.asc'