Thu Jan 13 21:38:31 UTC 2022 I: starting to build bio-eagle/bullseye/amd64 on jenkins on '2022-01-13 21:38' Thu Jan 13 21:38:31 UTC 2022 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_7/90967/console.log Thu Jan 13 21:38:31 UTC 2022 I: Downloading source for bullseye/bio-eagle=2.4.1-3 --2022-01-13 21:38:31-- http://cdn-fastly.deb.debian.org/debian/pool/main/b/bio-eagle/bio-eagle_2.4.1-3.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2210 (2.2K) Saving to: ‘bio-eagle_2.4.1-3.dsc’ 0K .. 100% 101M=0s 2022-01-13 21:38:31 (101 MB/s) - ‘bio-eagle_2.4.1-3.dsc’ saved [2210/2210] Thu Jan 13 21:38:31 UTC 2022 I: bio-eagle_2.4.1-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: bio-eagle Binary: bio-eagle, bio-eagle-examples Architecture: any-amd64 any-i386 all Version: 2.4.1-3 Maintainer: Debian Med Packaging Team Uploaders: Dylan Aïssi Homepage: https://data.broadinstitute.org/alkesgroup/Eagle/ Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/bio-eagle Vcs-Git: https://salsa.debian.org/med-team/bio-eagle.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libopenblas-dev, libboost-dev, libboost-iostreams-dev, libboost-program-options-dev, libhts-dev (>= 1.4), zlib1g-dev Package-List: bio-eagle deb science optional arch=any-amd64,any-i386 bio-eagle-examples deb science optional arch=all Checksums-Sha1: f0520ee1ae5f8d637c671bae1b56c088a50ae8ef 1627875 bio-eagle_2.4.1.orig.tar.gz 849030216b9ff34c5daaca7f1eac3f614713adfe 8668 bio-eagle_2.4.1-3.debian.tar.xz Checksums-Sha256: 85804bfe972186ccb66e602856d6e04044302e5c0dbf9309849b0cde981e3432 1627875 bio-eagle_2.4.1.orig.tar.gz 4880ebbb101fb04990943765e74e4bf5dfc5e4fc1daddee790b528005020fcd1 8668 bio-eagle_2.4.1-3.debian.tar.xz Files: c14a9611f226b7267e7ead92e95a7309 1627875 bio-eagle_2.4.1.orig.tar.gz b2c13234aabf3d5f492f890b1f7026e4 8668 bio-eagle_2.4.1-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl/L/jwRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFNIg//bxYi9oJ25Ykb3fP3SBWjU3n4jcBWc4FG McD46vz3VIn8Lx+QeHEL2fp7Tr8/NdA4J1Yg/jj0lrW82ZXBDvSYnCgJQGxO9Jsy MizB5SY6eo3AtOQ6tHSgfHCEkGPiVSJfZdpNJTgj7MdtmMoqZ09H+30fohqFGdB3 oHAajOs/QqbtFjYRN7TUm5ZznZzX20gJTuCGoJFrW3OvkLFHgcoOLTtgYITlMHos 0vKb+FUoJPvNnF83LAJKzr9Zd7cgVi/roZJ2wNGw8cVhsqKTR/+MECrIJM+RGFU5 iUgx2IGOLaFw48auiI4Bo1EQwLzYr8+6hTj3xvbcHbTnzJCZEOYzaDk0fCeEuEL5 MHspP8BU2CFHl+G4Q8YihOu4BBJv3bh2ZWH/rgNd+Bdb0+n4VJgdLTKTVi13e1z4 TmSDaEb+GhsDDfuelAh+DCpWyoqiaRm/VJ1SfuE2sSoR9r9TVIjJ6q8Ob4eSzKzk /eIM3g5GbIA28EIKLoY9TjU5NwXpmFxDRjCwrOXfhuHOQNj9ICH/USpqIGDKU1BC x0+1nZr0Fz4pFTa6K30TI3MjV6AV8AH4RhotKeYRA+rSuLAXHVQq9/ipYvn7ZQXI 9szfTgTm93agK4cuPef64PiKkyIK0ZVyPMtfyFajgqoNnzIPyrJxayymU7gVz5l9 IKWFpTqt2OA= =imJG -----END PGP SIGNATURE----- Thu Jan 13 21:38:31 UTC 2022 I: Checking whether the package is not for us Thu Jan 13 21:38:31 UTC 2022 I: Starting 1st build on remote node ionos11-amd64.debian.net. Thu Jan 13 21:38:31 UTC 2022 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Thu Jan 13 21:39:25 UTC 2022 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jan 13 09:38:33 -12 2022 I: pbuilder-time-stamp: 1642109913 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: Copying source file I: copying [bio-eagle_2.4.1-3.dsc] I: copying [./bio-eagle_2.4.1.orig.tar.gz] I: copying [./bio-eagle_2.4.1-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.UfWV0LOR/trustedkeys.kbx': General error gpgv: Signature made Sat Dec 5 09:40:12 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 ./bio-eagle_2.4.1-3.dsc dpkg-source: info: extracting bio-eagle in bio-eagle-2.4.1 dpkg-source: info: unpacking bio-eagle_2.4.1.orig.tar.gz dpkg-source: info: unpacking bio-eagle_2.4.1-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Makefile_config.patch dpkg-source: info: applying non_x86_malloc I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3608672/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,-fixfilepath parallel=15' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='070a9c070fb947c0b3464a1bab531fb9' 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='3608672' 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.CyzEmzOfa9/pbuilderrc_cI1I --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.CyzEmzOfa9/b1 --logfile b1/build.log bio-eagle_2.4.1-3.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos11-amd64 5.10.0-10-amd64 #1 SMP Debian 5.10.84-1 (2021-12-08) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Aug 4 08:25 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 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 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 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 43936 Sep 23 2020 cat -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 23 2020 date -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd -rwxr-xr-x 1 root root 93936 Sep 23 2020 df -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir -rwxr-xr-x 1 root root 84440 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 39712 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 39680 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 69032 Jul 28 07:09 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 98048 Mar 2 2021 gzip -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls -rwxr-xr-x 1 root root 149736 Jul 28 07:09 lsblk -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 59632 Jul 28 07:09 more -rwsr-xr-x 1 root root 55528 Jul 28 07:09 mount -rwxr-xr-x 1 root root 18664 Jul 28 07:09 mountpoint -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jan 6 21:24 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty -rwsr-xr-x 1 root root 71912 Jul 28 07:09 su -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch -rwxr-xr-x 1 root root 39680 Sep 23 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jul 28 07:09 umount -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63744 Jul 28 07:09 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/3608672/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), libopenblas-dev, libboost-dev, libboost-iostreams-dev, libboost-program-options-dev, libhts-dev (>= 1.4), 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 ... 19655 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 libopenblas-dev; however: Package libopenblas-dev 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 libhts-dev (>= 1.4); however: Package libhts-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} 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} libbrotli1{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libhts-dev{a} libhts3{a} libicu-dev{a} libicu67{a} libldap-2.4-2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libopenblas-dev{a} libopenblas-pthread-dev{a} libopenblas0{a} libopenblas0-pthread{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{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: ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 63 newly installed, 0 to remove and 0 not upgraded. Need to get 57.6 MB of archives. After unpacking 389 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7 [693 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 icu-devtools amd64 67.1-7 [201 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libboost1.74-dev amd64 1.74.0-9 [9534 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libboost-regex1.74.0 amd64 1.74.0-9 [516 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libicu-dev amd64 67.1-7 [9597 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libboost-regex1.74-dev amd64 1.74.0-9 [588 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libboost-iostreams1.74-dev amd64 1.74.0-9 [273 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libboost-iostreams-dev amd64 1.74.0.3 [4316 B] Get: 40 http://deb.debian.org/debian bullseye/main amd64 libboost-program-options1.74.0 amd64 1.74.0-9 [356 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libboost-program-options1.74-dev amd64 1.74.0-9 [386 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 libboost-program-options-dev amd64 1.74.0.3 [4340 B] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1 [69.1 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1 [106 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3 [232 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+deb11u1 [338 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 libcurl4-gnutls-dev amd64 7.74.0-1.3+deb11u1 [429 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 libdeflate-dev amd64 1.7-1 [46.9 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 libhts3 amd64 1.11-4 [378 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 liblzma-dev amd64 5.2.5-2 [229 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 libhts-dev amd64 1.11-4 [3858 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 libopenblas0-pthread amd64 0.3.13+ds-3 [6034 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 libopenblas0 amd64 0.3.13+ds-3 [32.8 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 libopenblas-pthread-dev amd64 0.3.13+ds-3 [4477 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 libopenblas-dev amd64 0.3.13+ds-3 [44.1 kB] Fetched 57.6 MB in 1s (38.6 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 ... 19655 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8_amd64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_amd64.deb ... 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Setting up libssh2-1:amd64 (1.9.0-2) ... Setting up libboost-dev:amd64 (1.74.0.3) ... Setting up libdeflate-dev:amd64 (1.7-1) ... Setting up libelf1:amd64 (0.183-1) ... Setting up libicu-dev:amd64 (67.1-7) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libopenblas0-pthread:amd64 (0.3.13+ds-3) ... 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 (2.4.6-15) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u1) ... Setting up libcurl4-gnutls-dev:amd64 (7.74.0-1.3+deb11u1) ... 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 dwz (0.13+20210201-1) ... Setting up libboost-regex1.74-dev:amd64 (1.74.0-9) ... Setting up libopenblas0:amd64 (0.3.13+ds-3) ... Setting up groff-base (1.22.4-6) ... 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 libopenblas-pthread-dev:amd64 (0.3.13+ds-3) ... 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 libhts3:amd64 (1.11-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhts-dev:amd64 (1.11-4) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libboost-iostreams1.74-dev:amd64 (1.74.0-9) ... Setting up dh-autoreconf (20) ... Setting up libopenblas-dev:amd64 (0.3.13+ds-3) ... Setting up debhelper (13.3.4) ... Setting up libboost-iostreams-dev:amd64 (1.74.0.3) ... Processing triggers for libc-bin (2.31-13+deb11u2) ... 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/bio-eagle-2.4.1/ && 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 > ../bio-eagle_2.4.1-3_source.changes dpkg-buildpackage: info: source package bio-eagle dpkg-buildpackage: info: source version 2.4.1-3 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/bio-eagle-2.4.1/src' rm -f *.o rm -f eagle make[1]: Leaving directory '/build/bio-eagle-2.4.1/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 -Nbio-eagle-examples dh_auto_build -O--sourcedirectory=src -Nbio-eagle-examples cd src && make -j15 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bio-eagle-2.4.1/src' g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o EagleMain.o -c EagleMain.cpp g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o DipTreePBWT.o -c DipTreePBWT.cpp g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o Eagle.o -c Eagle.cpp g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o EagleImpMiss.o -c EagleImpMiss.cpp g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o EagleParams.o -c EagleParams.cpp g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o EaglePBWT.o -c EaglePBWT.cpp g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o FileUtils.o -c FileUtils.cpp g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o GenoData.o -c GenoData.cpp g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o HapHedge.o -c HapHedge.cpp g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o MapInterpolater.o -c MapInterpolater.cpp g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o MemoryUtils.o -c MemoryUtils.cpp g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o NumericUtils.o -c NumericUtils.cpp g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o StaticMultimap.o -c StaticMultimap.cpp g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o StringUtils.o -c StringUtils.cpp g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o SyncedVcfData.o -c SyncedVcfData.cpp g++ -g -O2 -fdebug-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o Timer.o -c Timer.cpp SyncedVcfData.cpp: In member function 'std::vector > EAGLE::SyncedVcfData::processVcfs(const string&, const string&, const string&, bool, int&, int, double, double, std::vector&, std::vector&, const string&, const string&, int, std::vector > >&, bool, std::vector&)': SyncedVcfData.cpp:228:18: warning: ignoring return value of 'int bcf_hdr_write(htsFile*, bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 228 | bcf_hdr_write(out, tgt_hdr); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ SyncedVcfData.cpp:262:42: warning: ignoring return value of 'int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 262 | if (outputUnphased && tgt) { bcf_write(out, tgt_hdr, tgt); isTmpPhased.push_back(false); } | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ SyncedVcfData.cpp:270:35: warning: ignoring return value of 'int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 270 | if (outputUnphased) { bcf_write(out, tgt_hdr, tgt); isTmpPhased.push_back(false); } | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ SyncedVcfData.cpp:287:35: warning: ignoring return value of 'int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 287 | if (outputUnphased) { bcf_write(out, tgt_hdr, tgt); isTmpPhased.push_back(false); } | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ SyncedVcfData.cpp:293:35: warning: ignoring return value of 'int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 293 | if (outputUnphased) { bcf_write(out, tgt_hdr, tgt); isTmpPhased.push_back(false); } | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ SyncedVcfData.cpp:303:35: warning: ignoring return value of 'int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 303 | if (outputUnphased) { bcf_write(out, tgt_hdr, tgt); isTmpPhased.push_back(false); } | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ SyncedVcfData.cpp:321:35: warning: ignoring return value of 'int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 321 | if (outputUnphased) { bcf_write(out, tgt_hdr, tgt); isTmpPhased.push_back(false); } | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ SyncedVcfData.cpp:377:11: warning: ignoring return value of 'int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 377 | bcf_write(out, tgt_hdr, tgt); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ SyncedVcfData.cpp: In function 'void EAGLE::process_ref_genotypes(int, int, int32_t*, bool, bool, std::vector&, int&, int&, uint&)': SyncedVcfData.cpp:97:14: warning: 'haps[0]' may be used uninitialized in this function [-Wmaybe-uninitialized] 97 | if (haps[0] != haps[1] && ((w=18000*(w&65535)+(w>>16))&1)) | ~~~~~~^ SyncedVcfData.cpp:97:25: warning: 'haps[1]' may be used uninitialized in this function [-Wmaybe-uninitialized] 97 | if (haps[0] != haps[1] && ((w=18000*(w&65535)+(w>>16))&1)) | ~~~~~~^ EagleMain.cpp: In function 'void phaseWithRef(EAGLE::EagleParams&, Timer&, double, int, char**)': EagleMain.cpp:109:17: warning: unused variable 'hapBitsTptr' [-Wunused-variable] 109 | HapBitsT *hapBitsTptr = NULL; | ^~~~~~~~~~~ EagleMain.cpp:110:17: warning: unused variable 'hapHedgePtr' [-Wunused-variable] 110 | HapHedge *hapHedgePtr = NULL; | ^~~~~~~~~~~ EagleMain.cpp:104:25: warning: unused variable 'timeImpMissing' [-Wunused-variable] 104 | double timeMN2 = 0, timeImpMissing = 0; | ^~~~~~~~~~~~~~ EagleMain.cpp: In function 'int main(int, char**)': EagleMain.cpp:448:61: warning: unused variable 'timeImpMissing' [-Wunused-variable] 448 | double t23 = timer.get_time(); timer.update_time(); double timeImpMissing = 0; | ^~~~~~~~~~~~~~ Eagle.cpp: In member function 'void EAGLE::Eagle::readPhaseConfs(const string&)': Eagle.cpp:3108:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3108 | fread(phaseConfs, 1, 2*N*Mseg64*64, fout); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Eagle.cpp: In function 'void EAGLE::bcf_hdr_append_eagle_version(bcf_hdr_t*, int, char**)': Eagle.cpp:3221:17: warning: ignoring return value of 'int bcf_hdr_sync(bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3221 | bcf_hdr_sync(hdr); | ~~~~~~~~~~~~^~~~~ Eagle.cpp: In member function 'void EAGLE::Eagle::writeVcf(const string&, const std::vector&, const string&, int, double, double, const string&, bool, bool, int, char**) const': Eagle.cpp:3248:18: warning: ignoring return value of 'int bcf_hdr_write(htsFile*, bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3248 | bcf_hdr_write(out, hdr); | ~~~~~~~~~~~~~^~~~~~~~~~ Eagle.cpp:3270:13: warning: ignoring return value of 'int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3270 | bcf_write(out, hdr, rec); | ~~~~~~~~~^~~~~~~~~~~~~~~ Eagle.cpp:3282:13: warning: ignoring return value of 'int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3282 | bcf_write(out, hdr, rec); | ~~~~~~~~~^~~~~~~~~~~~~~~ Eagle.cpp:3347:13: warning: ignoring return value of 'int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3347 | bcf_write(out, hdr, rec); | ~~~~~~~~~^~~~~~~~~~~~~~~ Eagle.cpp: In member function 'void EAGLE::Eagle::writeVcfNonRef(const string&, const string&, int, int, double, double, const string&, bool, bool, int, char**) const': Eagle.cpp:3388:18: warning: ignoring return value of 'int bcf_hdr_write(htsFile*, bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3388 | bcf_hdr_write(out, hdr); | ~~~~~~~~~~~~~^~~~~~~~~~ Eagle.cpp:3467:11: warning: ignoring return value of 'int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3467 | bcf_write(out, hdr, rec); | ~~~~~~~~~^~~~~~~~~~~~~~~ Eagle.cpp: In member function 'std::string EAGLE::Eagle::computePhaseString(uint64, uint64, uint64, const std::vector&, const std::vector&, uint64, double, bool) const': Eagle.cpp:1124:43: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 0 and 11 [-Wformat-overflow=] 1124 | char buf[20]; sprintf(buf, "[%.1fcM:%d/%d]", cM-lastPhased, hetCount, snpCount); | ^~ Eagle.cpp:1124:31: note: directive argument in the range [1, 2147483647] 1124 | char buf[20]; sprintf(buf, "[%.1fcM:%d/%d]", cM-lastPhased, hetCount, snpCount); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6545, from /usr/include/c++/10/string:55, from Eagle.cpp:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 12 and 339 bytes into a destination of size 20 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Eagle.cpp:1156:41: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 0 and 11 [-Wformat-overflow=] 1156 | char buf[20]; sprintf(buf, "[%.1fcM:%d/%d]", cM-lastPhased, hetCount, snpCount); | ^~ Eagle.cpp:1156:29: note: directive argument in the range [0, 2147483647] 1156 | char buf[20]; sprintf(buf, "[%.1fcM:%d/%d]", cM-lastPhased, hetCount, snpCount); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6545, from /usr/include/c++/10/string:55, from Eagle.cpp:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 12 and 339 bytes into a destination of size 20 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Eagle.cpp: In member function 'void EAGLE::Eagle::printMatch(uint64, uint64, uint64, const EAGLE::Match&, double (*)[4]) const': Eagle.cpp:1197:43: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 0 and 11 [-Wformat-overflow=] 1197 | char buf[20]; sprintf(buf, "[%.1fcM:%d/%d]", cM-lastPhased, hetCount, snpCount); | ^~ Eagle.cpp:1197:31: note: directive argument in the range [0, 2147483647] 1197 | char buf[20]; sprintf(buf, "[%.1fcM:%d/%d]", cM-lastPhased, hetCount, snpCount); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6545, from /usr/include/c++/10/string:55, from Eagle.cpp:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 12 and 339 bytes into a destination of size 20 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -fopenmp -Wl,-z,relro -Wl,-z,now -o eagle EagleMain.o DipTreePBWT.o Eagle.o EagleImpMiss.o EagleParams.o EaglePBWT.o FileUtils.o GenoData.o HapHedge.o MapInterpolater.o MemoryUtils.o NumericUtils.o StaticMultimap.o StringUtils.o SyncedVcfData.o Timer.o -lhts -lboost_program_options -lboost_iostreams -lz -lopenblas -lpthread -lm make[1]: Leaving directory '/build/bio-eagle-2.4.1/src' dh_auto_test -O--sourcedirectory=src create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src debian/rules override_dh_auto_install-indep make[1]: Entering directory '/build/bio-eagle-2.4.1' echo "I: Nothing to do for arch:indep binary" I: Nothing to do for arch:indep binary make[1]: Leaving directory '/build/bio-eagle-2.4.1' dh_auto_install -O--sourcedirectory=src -Nbio-eagle-examples dh_install -O--sourcedirectory=src dh_installdocs -O--sourcedirectory=src debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/bio-eagle-2.4.1' dh_installchangelogs debian/upstream.changelog make[1]: Leaving directory '/build/bio-eagle-2.4.1' 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 'bio-eagle' in '../bio-eagle_2.4.1-3_amd64.deb'. dpkg-deb: building package 'bio-eagle-dbgsym' in '../bio-eagle-dbgsym_2.4.1-3_amd64.deb'. dpkg-deb: building package 'bio-eagle-examples' in '../bio-eagle-examples_2.4.1-3_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../bio-eagle_2.4.1-3_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: not including original 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/3608672 and its subdirectories I: Current time: Thu Jan 13 09:39:25 -12 2022 I: pbuilder-time-stamp: 1642109965 Thu Jan 13 21:39:25 UTC 2022 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Thu Jan 13 21:39:25 UTC 2022 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Thu Jan 13 21:40:12 UTC 2022 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Thu Jan 13 21:40:12 UTC 2022 I: bio-eagle_2.4.1-3_amd64.changes: Format: 1.8 Date: Sat, 05 Dec 2020 22:31:32 +0100 Source: bio-eagle Binary: bio-eagle bio-eagle-dbgsym bio-eagle-examples Architecture: amd64 all Version: 2.4.1-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: bio-eagle - Haplotype phasing within a genotyped cohort or using a phased ref bio-eagle-examples - Examples for bio-eagle Closes: 976572 Changes: bio-eagle (2.4.1-3) unstable; urgency=medium . [ Andreas Tille ] * Team upload. * Standards-Version: 4.5.1 (routine-update) * Do nothing in dh_auto_configure and dh_auto_build for indep binaries Closes: #976572 . [ Michael R. Crusoe ] * Add patch for compilation on systems without SSE. Use of "rdtsc" assembly still makes it x86 specific. Checksums-Sha1: e60227eac29ff7162b3e46ea45b700457cf8d0c1 3168576 bio-eagle-dbgsym_2.4.1-3_amd64.deb 3f1d282cfed4a63617f8574b94f8c4091264708d 1525704 bio-eagle-examples_2.4.1-3_all.deb 35ebc5d97c7d7228cafe2aebd7399e84767601d8 6614 bio-eagle_2.4.1-3_amd64.buildinfo 458a8f4eb2475de6af66571205bdf71a9e24fa6d 223692 bio-eagle_2.4.1-3_amd64.deb Checksums-Sha256: ef5466fb5bbf1b9023ee6796e64891e613ee2094c69ccb975a1b09880279f1d8 3168576 bio-eagle-dbgsym_2.4.1-3_amd64.deb 1c7eee0c242366251e275dd8043a158f54a46cc261c991e2415a1e4dcb36ad44 1525704 bio-eagle-examples_2.4.1-3_all.deb 1c629ef0dc815c8184eb89705f1d40c9e2dcad0ab2f8ec5a08035e1ad119da69 6614 bio-eagle_2.4.1-3_amd64.buildinfo 4239b49e3def1ca7787038fd6f7893d17ad9c2c2927d1a574f661578c7eda398 223692 bio-eagle_2.4.1-3_amd64.deb Files: 27837a1f9d74832857edb5c142bcbde3 3168576 debug optional bio-eagle-dbgsym_2.4.1-3_amd64.deb 8fd94a776fcf06a6d8ce74b72c51d3f0 1525704 science optional bio-eagle-examples_2.4.1-3_all.deb 1ca15ecdd42c367a0510a444c11718c9 6614 science optional bio-eagle_2.4.1-3_amd64.buildinfo 6bec9b416ed803c54db87c75db5619b4 223692 science optional bio-eagle_2.4.1-3_amd64.deb Thu Jan 13 21:40:13 UTC 2022 I: will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.CyzEmzOfa9/bio-eagle_2.4.1-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.CyzEmzOfa9/bio-eagle_2.4.1-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.CyzEmzOfa9/bio-eagle_2.4.1-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.CyzEmzOfa9/b1/bio-eagle_2.4.1-3_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.CyzEmzOfa9/b2/bio-eagle_2.4.1-3_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: 0.438s) 0.438s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.092s) 0.092s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Thu Jan 13 21:40:16 UTC 2022 I: found no differences in the changes files, and a .buildinfo file also exists. Thu Jan 13 21:40:16 UTC 2022 I: bio-eagle from bullseye built successfully and reproducibly on amd64. Thu Jan 13 21:40:18 UTC 2022 I: Submitting .buildinfo files to external archives: Thu Jan 13 21:40:18 UTC 2022 I: Submitting 8.0K b1/bio-eagle_2.4.1-3_amd64.buildinfo.asc Thu Jan 13 21:40:19 UTC 2022 I: Submitting 8.0K b2/bio-eagle_2.4.1-3_amd64.buildinfo.asc Thu Jan 13 21:40:21 UTC 2022 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Jan 13 21:40:21 UTC 2022 I: Done submitting .buildinfo files. Thu Jan 13 21:40:21 UTC 2022 I: Removing signed bio-eagle_2.4.1-3_amd64.buildinfo.asc files: removed './b1/bio-eagle_2.4.1-3_amd64.buildinfo.asc' removed './b2/bio-eagle_2.4.1-3_amd64.buildinfo.asc'