Sun Apr 23 05:17:40 UTC 2023 I: starting to build bolt-lmm/bookworm/amd64 on jenkins on '2023-04-23 05:17' Sun Apr 23 05:17:40 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_19/10368/console.log Sun Apr 23 05:17:40 UTC 2023 I: Downloading source for bookworm/bolt-lmm=2.4.0+dfsg-1 --2023-04-23 05:17:40-- http://cdn-fastly.deb.debian.org/debian/pool/main/b/bolt-lmm/bolt-lmm_2.4.0%2bdfsg-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2254 (2.2K) [text/prs.lines.tag] Saving to: ‘bolt-lmm_2.4.0+dfsg-1.dsc’ 0K .. 100% 162M=0s 2023-04-23 05:17:41 (162 MB/s) - ‘bolt-lmm_2.4.0+dfsg-1.dsc’ saved [2254/2254] Sun Apr 23 05:17:41 UTC 2023 I: bolt-lmm_2.4.0+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: bolt-lmm Binary: bolt-lmm, bolt-lmm-example Architecture: amd64 i386 ppc64el all Version: 2.4.0+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Dylan Aïssi Homepage: https://data.broadinstitute.org/alkesgroup/BOLT-LMM/ Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/bolt-lmm Vcs-Git: https://salsa.debian.org/med-team/bolt-lmm.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), gfortran, libboost-dev, libboost-iostreams-dev, libboost-program-options-dev, libnlopt-dev, libnlopt-cxx-dev, libopenblas-dev, zlib1g-dev Package-List: bolt-lmm deb science optional arch=amd64,i386,ppc64el bolt-lmm-example deb science optional arch=all Checksums-Sha1: 843abfefecae3e3596c5c01eb906c6b80ce0e08e 2805624 bolt-lmm_2.4.0+dfsg.orig.tar.xz 90c5167195864dfe66e461e19c6c9a197a271076 9384 bolt-lmm_2.4.0+dfsg-1.debian.tar.xz Checksums-Sha256: 6e284c81fd1ab57c233ae930c042405fd44480fe3d99b761a82589c9e0e4b91b 2805624 bolt-lmm_2.4.0+dfsg.orig.tar.xz 8c0e0d71696b5accb01cbaac33cf45ef161c588090d17d8b9a720af85169f16e 9384 bolt-lmm_2.4.0+dfsg-1.debian.tar.xz Files: b06c59dd4f1ecf2878a64176d0e4fd72 2805624 bolt-lmm_2.4.0+dfsg.orig.tar.xz 599a22554fb58a3c3b11c69a5f560620 9384 bolt-lmm_2.4.0+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmNFxWgRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHFuA//QuD6qnldLg1KBBKtEEqd93lWu/5PlK7+ /cuJvHSS9+zlnr9d8U7rEN+yOk6ZDieiNJLLj5s9EL0BYvVLhb60CPuGcsPRRjiR HahUe/YCvTbX61OlBgxPM5LIsX4BZxJ/F7WJlnn5UCLc7h8YQ1jdIWS84HaB2cHe vDniaXJri8XH6yOT4m/wx+PvApm5NNS6opqXOwxv7CWKnQ6194+j0Z9YOrOMwVYV tGqy+q3D2Ne/mH4pcksYijR4+QAYwArTKZIH76rrnnRbp2yF3uNxKDuIm5qo7NFR 8Pw2+z4wHcS6S6SveaVlZ1IxdP/7TdYwey6OL22IAty32r5md8DvKjZTqeFemmqi 94v5BvIP2pgTwxnt8wpMBNwnt9xYi16YFShOzNMiOe4yv3CvMi+MY0uRmMKc2ETI aFqRZKACepAMtLnE/ghKEld7ipiayzpsyfIbtKzVSRcnFT3u8kBKfCnrBqv89hro y8iMl0q+YDy6mTHcIm9pHliTtQO4jq+a8GKx/8lQLvHMtoJrfh9zgRp+CKXOuw3A P90amj36sGAyPT6ipNIIXeYn5L9ICyq+fALGsEf6kx+TChi2uY5cegJGpwdrENer KUTqwbOSR4J8szagGVx5sJjc32nCWd7em7ZxXdBFnDB+jY5v16X0ufj3gDsmoESd F4caTS/O+i0= =6aBn -----END PGP SIGNATURE----- Sun Apr 23 05:17:41 UTC 2023 I: Checking whether the package is not for us Sun Apr 23 05:17:41 UTC 2023 I: Starting 1st build on remote node ionos1-amd64.debian.net. Sun Apr 23 05:17:41 UTC 2023 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Sun Apr 23 05:21:32 UTC 2023 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Apr 22 17:17:43 -12 2023 I: pbuilder-time-stamp: 1682227063 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [bolt-lmm_2.4.0+dfsg-1.dsc] I: copying [./bolt-lmm_2.4.0+dfsg.orig.tar.xz] I: copying [./bolt-lmm_2.4.0+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Oct 11 07:35:04 2022 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./bolt-lmm_2.4.0+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting bolt-lmm in bolt-lmm-2.4.0+dfsg dpkg-source: info: unpacking bolt-lmm_2.4.0+dfsg.orig.tar.xz dpkg-source: info: unpacking bolt-lmm_2.4.0+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Fix_makefile.patch dpkg-source: info: applying timer-for-other-arches.patch dpkg-source: info: applying dont-hardcode-glibc-version.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/877276/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='2e07e6be4b5a4a5a99f404a2326cf39c' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='877276' 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/r-b-build.5tIv1kRO/pbuilderrc_0oL6 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.5tIv1kRO/b1 --logfile b1/build.log bolt-lmm_2.4.0+dfsg-1.dsc' SUDO_GID='110' SUDO_UID='105' 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 ionos1-amd64 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Feb 12 08:05 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Feb 12 08:05 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 04:31 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar -rwxr-xr-x 1 root root 14520 Nov 2 04:31 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/877276/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), gfortran, libboost-dev, libboost-iostreams-dev, libboost-program-options-dev, libnlopt-dev, libnlopt-cxx-dev, libopenblas-dev, zlib1g-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 ... 19596 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 gfortran; however: Package gfortran is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-dev is not installed. pbuilder-satisfydepends-dummy depends on libnlopt-dev; however: Package libnlopt-dev is not installed. pbuilder-satisfydepends-dummy depends on libnlopt-cxx-dev; however: Package libnlopt-cxx-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenblas-dev; however: Package libopenblas-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-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} gfortran{a} gfortran-12{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libboost-dev{a} libboost-iostreams-dev{a} libboost-iostreams1.74-dev{a} libboost-program-options-dev{a} libboost-program-options1.74-dev{a} libboost-program-options1.74.0{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost1.74-dev{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgfortran-12-dev{a} libgfortran5{a} libicu-dev{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libnlopt-cxx-dev{a} libnlopt-cxx0{a} libnlopt-dev{a} libnlopt0{a} libopenblas-dev{a} libopenblas-pthread-dev{a} libopenblas0{a} libopenblas0-pthread{a} libpipeline1{a} libsub-override-perl{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, 54 newly installed, 0 to remove and 0 not upgraded. Need to get 65.7 MB of archives. After unpacking 429 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libgfortran-12-dev amd64 12.2.0-14 [834 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 gfortran-12 amd64 12.2.0-14 [10.2 MB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 gfortran amd64 4:12.2.0-3 [1428 B] Get: 35 http://deb.debian.org/debian bookworm/main amd64 icu-devtools amd64 72.1-3 [206 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-20 [9510 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libboost-regex1.74.0 amd64 1.74.0+ds1-20 [487 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libicu-dev amd64 72.1-3 [10.3 MB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libboost-regex1.74-dev amd64 1.74.0+ds1-20 [558 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libboost-iostreams1.74-dev amd64 1.74.0+ds1-20 [248 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libboost-iostreams-dev amd64 1.74.0.3 [4316 B] Get: 43 http://deb.debian.org/debian bookworm/main amd64 libboost-program-options1.74.0 amd64 1.74.0+ds1-20 [328 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 libboost-program-options1.74-dev amd64 1.74.0+ds1-20 [358 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 libboost-program-options-dev amd64 1.74.0.3 [4340 B] Get: 46 http://deb.debian.org/debian bookworm/main amd64 libnlopt0 amd64 2.7.1-4+b4 [174 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libnlopt-dev amd64 2.7.1-4+b4 [46.5 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libnlopt-cxx0 amd64 2.7.1-4+b4 [201 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 libnlopt-cxx-dev amd64 2.7.1-4+b4 [13.3 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libopenblas0-pthread amd64 0.3.21+ds-4 [6709 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libopenblas0 amd64 0.3.21+ds-4 [32.6 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libopenblas-pthread-dev amd64 0.3.21+ds-4 [4971 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libopenblas-dev amd64 0.3.21+ds-4 [44.9 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Fetched 65.7 MB in 2s (28.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. 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Setting up libopenblas0-pthread:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-x86_64-linux-gnu) in auto mode Setting up libtool (2.4.7-5) ... Setting up libgfortran-12-dev:amd64 (12.2.0-14) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up gfortran-12 (12.2.0-14) ... Setting up libnlopt-cxx-dev:amd64 (2.7.1-4+b4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up libboost-regex1.74-dev:amd64 (1.74.0+ds1-20) ... Setting up libopenblas0:amd64 (0.3.21+ds-4) ... Setting up groff-base (1.22.4-10) ... Setting up libopenblas-pthread-dev:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/x86_64-linux-gnu/libopenblas.so (libopenblas.so-x86_64-linux-gnu) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up gfortran (4:12.2.0-3) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libboost-iostreams1.74-dev:amd64 (1.74.0+ds1-20) ... Setting up libopenblas-dev:amd64 (0.3.21+ds-4) ... Setting up debhelper (13.11.4) ... Setting up libboost-iostreams-dev:amd64 (1.74.0.3) ... Processing triggers for libc-bin (2.36-9) ... 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/bolt-lmm-2.4.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../bolt-lmm_2.4.0+dfsg-1_source.changes dpkg-buildpackage: info: source package bolt-lmm dpkg-buildpackage: info: source version 2.4.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src cd src && make -j15 clean make[1]: Entering directory '/build/bolt-lmm-2.4.0+dfsg/src' rm -f *.o rm -f bolt make[1]: Leaving directory '/build/bolt-lmm-2.4.0+dfsg/src' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/bolt-lmm-2.4.0+dfsg' cd /build/bolt-lmm-2.4.0+dfsg/example/ && \ tar Jcvf examples.tar.xz * --sort=name --mode=go=rX,u+rw,a-s --owner=root --group=root --numeric-owner EUR_subset.bed EUR_subset.bim EUR_subset.dosage.chr17first100 EUR_subset.dosage.chr22last100.gz EUR_subset.dosage.indivs EUR_subset.dosage2.chr17first100.gz EUR_subset.dosage2.chr17first100.map EUR_subset.dosage2.chr17second100 EUR_subset.dosage2.chr17second100.map EUR_subset.dosage2.chr22last100.gz EUR_subset.dosage2.chr22last100.map EUR_subset.dosage2FileList.txt EUR_subset.exclude EUR_subset.exclude2 EUR_subset.fam EUR_subset.impute2.chr17first100.gz EUR_subset.impute2.chr17second100 EUR_subset.impute2.chr22last100.gz EUR_subset.impute2.indivs EUR_subset.impute2FileList.txt EUR_subset.modelSnps EUR_subset.modelSnps2 EUR_subset.pheno.covars EUR_subset.pheno2.covars EUR_subset.remove example.dosage2Snps.stats example.dosageSnps.stats example.impute2Snps.stats example.log example.stats example_reml2.log run_example.sh run_example_reml2.sh make[1]: Leaving directory '/build/bolt-lmm-2.4.0+dfsg' dh_auto_build -O--sourcedirectory=src -Nbolt-lmm-example cd src && make -j15 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bolt-lmm-2.4.0+dfsg/src' g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o BoltMain.o -c BoltMain.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o Bolt.o -c Bolt.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o BoltParams.o -c BoltParams.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o BoltParEstCV.o -c BoltParEstCV.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o BoltReml.o -c BoltReml.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o CovariateBasis.o -c CovariateBasis.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o DataMatrix.o -c DataMatrix.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o FileUtils.o -c FileUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o Jackknife.o -c Jackknife.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o LDscoreCalibration.o -c LDscoreCalibration.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o MapInterpolater.o -c MapInterpolater.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o MatrixUtils.o -c MatrixUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o MemoryUtils.o -c MemoryUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o NonlinearOptMulti.o -c NonlinearOptMulti.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o NumericUtils.o -c NumericUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o PhenoBuilder.o -c PhenoBuilder.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o RestrictSnpSet.o -c RestrictSnpSet.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o SnpData.o -c SnpData.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o SnpInfo.o -c SnpInfo.cpp NonlinearOptMulti.cpp: In function 'std::vector > NonlinearOptMulti::constrainedNR(double&, boost::numeric::ublas::vector&, const std::vector >&, const boost::numeric::ublas::vector&, const boost::numeric::ublas::matrix&, double)': NonlinearOptMulti.cpp:230:21: warning: catching polymorphic type 'class nlopt::roundoff_limited' by value [-Wcatch-value=] 230 | catch (nlopt::roundoff_limited) { | ^~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o SpectrumTools.o -c SpectrumTools.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o StatsUtils.o -c StatsUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o StringUtils.o -c StringUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o Timer.o -c Timer.cpp g++ -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/bolt-lmm-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o memcpy.o -c memcpy.cpp In file included from Bolt.cpp:55: In member function 'LMM::Bolt::VarCompData& LMM::Bolt::VarCompData::operator=(const LMM::Bolt::VarCompData&)', inlined from 'double LMM::Bolt::estLogDelta(double*, double*, const std::vector&, int, double, int, double, int, bool) const' at Bolt.cpp:2218:16: Bolt.hpp:54:12: warning: 'nextVCs.LMM::Bolt::VarCompData::sigma2K' may be used uninitialized [-Wmaybe-uninitialized] 54 | struct VarCompData { | ^~~~~~~~~~~ Bolt.cpp: In member function 'double LMM::Bolt::estLogDelta(double*, double*, const std::vector&, int, double, int, double, int, bool) const': Bolt.cpp:2187:19: note: 'nextVCs' declared here 2187 | VarCompData nextVCs; | ^~~~~~~ Bolt.cpp: In member function 'std::string LMM::Bolt::getSnpStats(const std::string&, int, int, double, const std::string&, const std::string&, double, double, double*, bool, const std::vector&, double) const': Bolt.cpp:2357:56: warning: 'dotProd' may be used uninitialized [-Wmaybe-uninitialized] 2357 | double beta = (stat==BAD_SNP_STAT) ? 0 : invNorm2*dotProd / retroData[0].VinvScaleFactors[0]; | ~~~~~~~~^~~~~~~~ Bolt.cpp:2314:12: note: 'dotProd' was declared here 2314 | double dotProd, stat; | ^~~~~~~ g++ -fopenmp -Wl,-z,relro -Wl,-z,now -o bolt BoltMain.o Bolt.o BoltParams.o BoltParEstCV.o BoltReml.o CovariateBasis.o DataMatrix.o FileUtils.o Jackknife.o LDscoreCalibration.o MapInterpolater.o MatrixUtils.o MemoryUtils.o NonlinearOptMulti.o NumericUtils.o PhenoBuilder.o RestrictSnpSet.o SnpData.o SnpInfo.o SpectrumTools.o StatsUtils.o StringUtils.o Timer.o memcpy.o -lboost_program_options -lboost_iostreams -lz -lnlopt -lopenblas -llapack -lgfortran -lpthread -lm make[1]: Leaving directory '/build/bolt-lmm-2.4.0+dfsg/src' dh_auto_test -O--sourcedirectory=src create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src dh_auto_install -O--sourcedirectory=src dh_install -O--sourcedirectory=src dh_installdocs -O--sourcedirectory=src debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/bolt-lmm-2.4.0+dfsg' dh_installchangelogs debian/upstream.changelog make[1]: Leaving directory '/build/bolt-lmm-2.4.0+dfsg' dh_installman -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src dh_compress -O--sourcedirectory=src dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'bolt-lmm' in '../bolt-lmm_2.4.0+dfsg-1_amd64.deb'. dpkg-deb: building package 'bolt-lmm-example' in '../bolt-lmm-example_2.4.0+dfsg-1_all.deb'. dpkg-deb: building package 'bolt-lmm-dbgsym' in '../bolt-lmm-dbgsym_2.4.0+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../bolt-lmm_2.4.0+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../bolt-lmm_2.4.0+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload 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/877276 and its subdirectories I: Current time: Sat Apr 22 17:21:32 -12 2023 I: pbuilder-time-stamp: 1682227292 Sun Apr 23 05:21:32 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Sun Apr 23 05:21:33 UTC 2023 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Sun Apr 23 05:23:20 UTC 2023 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Sun Apr 23 05:23:21 UTC 2023 I: bolt-lmm_2.4.0+dfsg-1_amd64.changes: Format: 1.8 Date: Tue, 11 Oct 2022 21:26:11 +0200 Source: bolt-lmm Binary: bolt-lmm bolt-lmm-dbgsym bolt-lmm-example Architecture: amd64 all Version: 2.4.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: bolt-lmm - Efficient large cohorts genome-wide Bayesian mixed-model associat bolt-lmm-example - Examples for bolt-lmm Changes: bolt-lmm (2.4.0+dfsg-1) unstable; urgency=medium . * Team upload. * New upstream version Checksums-Sha1: 4a92b3c632f2bc21013f60f2d5d904194893d691 4802820 bolt-lmm-dbgsym_2.4.0+dfsg-1_amd64.deb 56aa23bf00937c615061f694eeb3078105ad46fc 2707136 bolt-lmm-example_2.4.0+dfsg-1_all.deb 676518e6aad8a4ddd2a6c64c9547bb1a87e92e63 6339 bolt-lmm_2.4.0+dfsg-1_amd64.buildinfo 4810fe1a3d2c9e71d2f972fa14a305bd29e13148 337704 bolt-lmm_2.4.0+dfsg-1_amd64.deb Checksums-Sha256: 8994aff5ca9397e45b29ff44be8a03794c4223c59d7c6ca603318ee7761387be 4802820 bolt-lmm-dbgsym_2.4.0+dfsg-1_amd64.deb c9b6275830a8a729a4ce991855a3876ad154454cc6da58df9c92d155fd9d1cd9 2707136 bolt-lmm-example_2.4.0+dfsg-1_all.deb 5a22765deeea337574fb3194768064487b0759ba5688786050da31d5cff9e92a 6339 bolt-lmm_2.4.0+dfsg-1_amd64.buildinfo 7e29e224d224b2f6c77d51ecdbcb3b157260a328ff53d0ec6bc07ae9a7242284 337704 bolt-lmm_2.4.0+dfsg-1_amd64.deb Files: 0eb1e6df5a012b8418eeb7d03a160764 4802820 debug optional bolt-lmm-dbgsym_2.4.0+dfsg-1_amd64.deb 1e75fb96b877fe20a22acb5d1e9fdc4e 2707136 science optional bolt-lmm-example_2.4.0+dfsg-1_all.deb 3c83f3e7d60fdd82444659d8e04f44a7 6339 science optional bolt-lmm_2.4.0+dfsg-1_amd64.buildinfo c6f2ed2fadb54356d9f39a6f2439584a 337704 science optional bolt-lmm_2.4.0+dfsg-1_amd64.deb Sun Apr 23 05:23:22 UTC 2023 I: diffoscope 241 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.5tIv1kRO/bolt-lmm_2.4.0+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.5tIv1kRO/bolt-lmm_2.4.0+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.5tIv1kRO/bolt-lmm_2.4.0+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.5tIv1kRO/b1/bolt-lmm_2.4.0+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.5tIv1kRO/b2/bolt-lmm_2.4.0+dfsg-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.645s) 0.645s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.135s) 0.135s 12 calls diffoscope.comparators.binary.FilesystemFile 0.001s 10 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Sun Apr 23 05:23:24 UTC 2023 I: diffoscope 241 found no differences in the changes files, and a .buildinfo file also exists. Sun Apr 23 05:23:24 UTC 2023 I: bolt-lmm from bookworm built successfully and reproducibly on amd64. Sun Apr 23 05:23:26 UTC 2023 I: Submitting .buildinfo files to external archives: Sun Apr 23 05:23:26 UTC 2023 I: Submitting 8.0K b1/bolt-lmm_2.4.0+dfsg-1_amd64.buildinfo.asc Sun Apr 23 05:23:28 UTC 2023 I: Submitting 8.0K b2/bolt-lmm_2.4.0+dfsg-1_amd64.buildinfo.asc Sun Apr 23 05:23:29 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Apr 23 05:23:29 UTC 2023 I: Done submitting .buildinfo files. Sun Apr 23 05:23:29 UTC 2023 I: Removing signed bolt-lmm_2.4.0+dfsg-1_amd64.buildinfo.asc files: removed './b1/bolt-lmm_2.4.0+dfsg-1_amd64.buildinfo.asc' removed './b2/bolt-lmm_2.4.0+dfsg-1_amd64.buildinfo.asc'