Tue Jul 20 09:29:39 UTC 2021 I: starting to build lumpy-sv/bullseye/i386 on jenkins on '2021-07-20 09:29' Tue Jul 20 09:29:39 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_8/18910/console.log Tue Jul 20 09:29:39 UTC 2021 I: Downloading source for bullseye/lumpy-sv=0.3.1+dfsg-5 --2021-07-20 09:29:39-- http://cdn-fastly.deb.debian.org/debian/pool/main/l/lumpy-sv/lumpy-sv_0.3.1+dfsg-5.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2271 (2.2K) Saving to: ‘lumpy-sv_0.3.1+dfsg-5.dsc’ 0K .. 100% 16.5M=0s 2021-07-20 09:29:39 (16.5 MB/s) - ‘lumpy-sv_0.3.1+dfsg-5.dsc’ saved [2271/2271] Tue Jul 20 09:29:39 UTC 2021 I: lumpy-sv_0.3.1+dfsg-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: lumpy-sv Binary: lumpy-sv, lumpy-sv-examples Architecture: any all Version: 0.3.1+dfsg-5 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Nilesh Patra Homepage: https://github.com/arq5x/lumpy-sv Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/lumpy-sv Vcs-Git: https://salsa.debian.org/med-team/lumpy-sv.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-python, python3, libbamtools-dev, libfastahack-dev, libgzstream-dev, libsqlite3-dev, libhts-dev, libssl-dev, libcurl4-gnutls-dev, samtools, python3-pysam Package-List: lumpy-sv deb science optional arch=any lumpy-sv-examples deb science optional arch=all Checksums-Sha1: b75a3ba46fb5197a96d8d5dccda356384c06bb77 111836 lumpy-sv_0.3.1+dfsg.orig.tar.xz 2791b73da1ab2560390660bfd1434c858fdabb21 39161696 lumpy-sv_0.3.1+dfsg-5.debian.tar.xz Checksums-Sha256: 78a6fe414739286d1f799bbdf3e34b9a1d6ed03b4c6dd17bfef1fcbba84bd35a 111836 lumpy-sv_0.3.1+dfsg.orig.tar.xz 5c5a9ed0379342d9b36f437d876592e3f4fb77971b3c7123c64222881d66e206 39161696 lumpy-sv_0.3.1+dfsg-5.debian.tar.xz Files: 1167e4a94bceb29ac5b83cb170058e25 111836 lumpy-sv_0.3.1+dfsg.orig.tar.xz 6b08225b536cdefcdc19e45f4b348242 39161696 lumpy-sv_0.3.1+dfsg-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl/+w2IRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFd8A//STpTexkAELyEIFUP7Ny5A8zrvAhNmb9r qOBbprPX5VJdR3+1yMHmDvLmHabMHu/GMyWncF6CjHn1oNXRaAmNPjQRCC4ENBTO ZNcYsLdpKv8ZdYloKiuXEX8FPc7vBfTTG+d0yvTjPN23w3AJBKeNrIVfeCvTxvgp sYYZ5Vkkso3wyOAlrvqMvUU0q5h8JU3u3e/OK2Bwpbzpb7yNQvqARkqv5EkoDkav NSkZ2K/sn7ZLL0pHMG19Bi0fwwSSO5jZar9dHZx9xvhYvm0sBeaP+16tXwkiMOUa 3wYy4832hA94+Ina8zM5jSLfmcXI8mWUSq/5PBnlZZ8JEDOxHCy4ybNGkFhfETVy x2iBeXeWNV887YWIFD+UsSrhQ8N4FUeenNBvhqy8X/an5ewz5PGEONKf/bCXp1OV XviIn8uW5dcLt37e4THjyO1XVGMSLbOf2VAaGEEIN+WjVesSEwBZKPQ1qXvZB7BO jlsNN3iBgN8joCVs+aESNeheYUVSZchWluSgwgr0r/EIUcl6wA5b3PgIQHETrrHr 1d9EWUprmWGMMlEDvQC8yoQATg7W7+clId/k3EE4Ix2BaM3ZhppTPPwMnF3I3TdJ 641EGXztM3BKEhI9/ZYI9aQYtqE/z4v2HucshMLzGzZn9AKmyXbYDve9I6cW7hYx GbWkBL8DR58= =YX3G -----END PGP SIGNATURE----- Tue Jul 20 09:29:39 UTC 2021 I: Checking whether the package is not for us Tue Jul 20 09:29:39 UTC 2021 I: Starting 1st build on remote node ionos16-i386.debian.net. Tue Jul 20 09:29:39 UTC 2021 I: Preparing to do remote build '1' on ionos16-i386.debian.net. Tue Jul 20 09:30:50 UTC 2021 I: Deleting $TMPDIR on ionos16-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Aug 22 03:52:41 -12 2022 I: pbuilder-time-stamp: 1661183561 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 [lumpy-sv_0.3.1+dfsg-5.dsc] I: copying [./lumpy-sv_0.3.1+dfsg.orig.tar.xz] I: copying [./lumpy-sv_0.3.1+dfsg-5.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.eEO2JjZ2/trustedkeys.kbx': General error gpgv: Signature made Tue Jan 12 21:54:42 2021 -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 ./lumpy-sv_0.3.1+dfsg-5.dsc dpkg-source: info: extracting lumpy-sv in lumpy-sv-0.3.1+dfsg dpkg-source: info: unpacking lumpy-sv_0.3.1+dfsg.orig.tar.xz dpkg-source: info: unpacking lumpy-sv_0.3.1+dfsg-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libs.patch dpkg-source: info: applying lumpyexpress.config.patch dpkg-source: info: applying fix_shebang.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/15669/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=18' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='24eeeac35250492a8b50c1acd4a9735a' 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='15669' 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.q9jnf9NIjC/pbuilderrc_xpQp --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.q9jnf9NIjC/b1 --logfile b1/build.log lumpy-sv_0.3.1+dfsg-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://85.184.249.68:3128' I: uname -a Linux ionos16-i386 4.19.0-17-amd64 #1 SMP Debian 4.19.194-2 (2021-06-21) x86_64 GNU/Linux I: ls -l /bin total 5776 -rwxr-xr-x 1 root root 1367848 Jun 21 2021 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 2021 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 2021 findmnt -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 210488 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 100952 Mar 2 2021 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 2021 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 2021 more -rwsr-xr-x 1 root root 50720 Feb 7 2021 mount -rwxr-xr-x 1 root root 13856 Feb 7 2021 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 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Jun 21 2021 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 22 03:46 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 2021 su -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync -rwxr-xr-x 1 root root 602584 Feb 16 2021 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 2021 ulockmgr_server -rwsr-xr-x 1 root root 30236 Feb 7 2021 umount -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir -rwxr-xr-x 1 root root 63024 Feb 7 2021 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/15669/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), dh-python, python3, libbamtools-dev, libfastahack-dev, libgzstream-dev, libsqlite3-dev, libhts-dev, libssl-dev, libcurl4-gnutls-dev, samtools, python3-pysam 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 dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on libbamtools-dev; however: Package libbamtools-dev is not installed. pbuilder-satisfydepends-dummy depends on libfastahack-dev; however: Package libfastahack-dev is not installed. pbuilder-satisfydepends-dummy depends on libgzstream-dev; however: Package libgzstream-dev is not installed. pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however: Package libsqlite3-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libssl-dev; however: Package libssl-dev is not installed. pbuilder-satisfydepends-dummy depends on libcurl4-gnutls-dev; however: Package libcurl4-gnutls-dev is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam; however: Package python3-pysam 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-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbamtools-dev{a} libbamtools2.5.1{a} libbrotli1{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libexpat1{a} libfastahack-dev{a} libfastahack0{a} libfile-stripnondeterminism-perl{a} libgzstream-dev{a} libgzstream0{a} libhts-dev{a} libhts3{a} libicu67{a} libldap-2.4-2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libmpdec3{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsqlite3-dev{a} libssh2-1{a} libssl-dev{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pysam{a} python3.9{a} python3.9-minimal{a} readline-common{a} samtools{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 73 newly installed, 0 to remove and 0 not upgraded. Need to get 36.6 MB of archives. After unpacking 122 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 libpython3.9-minimal i386 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libexpat1 i386 2.2.10-2 [98.8 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 python3.9-minimal i386 3.9.2-1 [1956 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 python3-minimal i386 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 libmpdec3 i386 2.5.1-1 [91.9 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 libreadline8 i386 8.1-1 [173 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 libpython3.9-stdlib i386 3.9.2-1 [1703 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 python3.9 i386 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 libpython3-stdlib i386 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 python3 i386 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3 [273 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3 [133 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3 [69.0 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-7 [8775 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7 [728 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 42 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 python3-distutils all 3.9.2-1 [143 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 libbamtools2.5.1 i386 2.5.1+dfsg-9 [176 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 libbamtools-dev i386 2.5.1+dfsg-9 [230 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 libbrotli1 i386 1.0.9-2+b2 [286 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 libsasl2-modules-db i386 2.1.27+dfsg-2.1 [70.0 kB] Get: 51 http://deb.debian.org/debian bullseye/main i386 libsasl2-2 i386 2.1.27+dfsg-2.1 [110 kB] Get: 52 http://deb.debian.org/debian bullseye/main i386 libldap-2.4-2 i386 2.4.57+dfsg-3 [244 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 libnghttp2-14 i386 1.43.0-1 [85.7 kB] Get: 54 http://deb.debian.org/debian bullseye/main i386 libpsl5 i386 0.21.0-1.2 [57.9 kB] Get: 55 http://deb.debian.org/debian bullseye/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 56 http://deb.debian.org/debian bullseye/main i386 libssh2-1 i386 1.9.0-2 [164 kB] Get: 57 http://deb.debian.org/debian bullseye/main i386 libcurl3-gnutls i386 7.74.0-1.3+b1 [368 kB] Get: 58 http://deb.debian.org/debian bullseye/main i386 libcurl4-gnutls-dev i386 7.74.0-1.3+b1 [471 kB] Get: 59 http://deb.debian.org/debian bullseye/main i386 libdeflate0 i386 1.7-1 [48.4 kB] Get: 60 http://deb.debian.org/debian bullseye/main i386 libdeflate-dev i386 1.7-1 [44.4 kB] Get: 61 http://deb.debian.org/debian bullseye/main i386 libfastahack0 i386 1.0.0+dfsg-7 [28.1 kB] Get: 62 http://deb.debian.org/debian bullseye/main i386 libfastahack-dev i386 1.0.0+dfsg-7 [29.9 kB] Get: 63 http://deb.debian.org/debian bullseye/main i386 libgzstream0 i386 1.5+dfsg-5 [6896 B] Get: 64 http://deb.debian.org/debian bullseye/main i386 libgzstream-dev i386 1.5+dfsg-5 [7188 B] Get: 65 http://deb.debian.org/debian bullseye/main i386 libhts3 i386 1.11-4 [408 kB] Get: 66 http://deb.debian.org/debian bullseye/main i386 liblzma-dev i386 5.2.5-2 [240 kB] Get: 67 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2 [194 kB] Get: 68 http://deb.debian.org/debian bullseye/main i386 libhts-dev i386 1.11-4 [3817 kB] Get: 69 http://deb.debian.org/debian bullseye/main i386 libncurses6 i386 6.2+20201114-2 [110 kB] Get: 70 http://deb.debian.org/debian bullseye/main i386 libsqlite3-dev i386 3.34.1-3 [1001 kB] Get: 71 http://deb.debian.org/debian bullseye/main i386 libssl-dev i386 1.1.1k-1 [1841 kB] Get: 72 http://deb.debian.org/debian bullseye/main i386 python3-pysam i386 0.15.4+ds-3+b2 [1571 kB] Get: 73 http://deb.debian.org/debian bullseye/main i386 samtools i386 1.11-1 [576 kB] Fetched 36.6 MB in 0s (87.6 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 ... 19675 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-7_i386.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../1-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_i386.deb ... 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Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20542 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_i386.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:i386. 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(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 ... 20963 files and directories currently installed.) Preparing to unpack .../00-python3_3.9.2-3_i386.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.39-3_i386.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../03-libmagic1_1%3a5.39-3_i386.deb ... Unpacking libmagic1:i386 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.39-3_i386.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-4_i386.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../06-libsigsegv2_2.13-1_i386.deb ... Unpacking libsigsegv2:i386 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../07-m4_1.4.18-5_i386.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../08-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. 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Preparing to unpack .../33-libsasl2-modules-db_2.1.27+dfsg-2.1_i386.deb ... Unpacking libsasl2-modules-db:i386 (2.1.27+dfsg-2.1) ... Selecting previously unselected package libsasl2-2:i386. Preparing to unpack .../34-libsasl2-2_2.1.27+dfsg-2.1_i386.deb ... Unpacking libsasl2-2:i386 (2.1.27+dfsg-2.1) ... Selecting previously unselected package libldap-2.4-2:i386. Preparing to unpack .../35-libldap-2.4-2_2.4.57+dfsg-3_i386.deb ... Unpacking libldap-2.4-2:i386 (2.4.57+dfsg-3) ... Selecting previously unselected package libnghttp2-14:i386. Preparing to unpack .../36-libnghttp2-14_1.43.0-1_i386.deb ... Unpacking libnghttp2-14:i386 (1.43.0-1) ... Selecting previously unselected package libpsl5:i386. Preparing to unpack .../37-libpsl5_0.21.0-1.2_i386.deb ... Unpacking libpsl5:i386 (0.21.0-1.2) ... Selecting previously unselected package librtmp1:i386. Preparing to unpack .../38-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_i386.deb ... Unpacking librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:i386. Preparing to unpack .../39-libssh2-1_1.9.0-2_i386.deb ... Unpacking libssh2-1:i386 (1.9.0-2) ... Selecting previously unselected package libcurl3-gnutls:i386. Preparing to unpack .../40-libcurl3-gnutls_7.74.0-1.3+b1_i386.deb ... Unpacking libcurl3-gnutls:i386 (7.74.0-1.3+b1) ... Selecting previously unselected package libcurl4-gnutls-dev:i386. Preparing to unpack .../41-libcurl4-gnutls-dev_7.74.0-1.3+b1_i386.deb ... Unpacking libcurl4-gnutls-dev:i386 (7.74.0-1.3+b1) ... Selecting previously unselected package libdeflate0:i386. Preparing to unpack .../42-libdeflate0_1.7-1_i386.deb ... Unpacking libdeflate0:i386 (1.7-1) ... Selecting previously unselected package libdeflate-dev:i386. Preparing to unpack .../43-libdeflate-dev_1.7-1_i386.deb ... Unpacking libdeflate-dev:i386 (1.7-1) ... Selecting previously unselected package libfastahack0. Preparing to unpack .../44-libfastahack0_1.0.0+dfsg-7_i386.deb ... Unpacking libfastahack0 (1.0.0+dfsg-7) ... Selecting previously unselected package libfastahack-dev. Preparing to unpack .../45-libfastahack-dev_1.0.0+dfsg-7_i386.deb ... Unpacking libfastahack-dev (1.0.0+dfsg-7) ... Selecting previously unselected package libgzstream0. Preparing to unpack .../46-libgzstream0_1.5+dfsg-5_i386.deb ... Unpacking libgzstream0 (1.5+dfsg-5) ... Selecting previously unselected package libgzstream-dev. Preparing to unpack .../47-libgzstream-dev_1.5+dfsg-5_i386.deb ... Unpacking libgzstream-dev (1.5+dfsg-5) ... Selecting previously unselected package libhts3:i386. Preparing to unpack .../48-libhts3_1.11-4_i386.deb ... Unpacking libhts3:i386 (1.11-4) ... Selecting previously unselected package liblzma-dev:i386. Preparing to unpack .../49-liblzma-dev_5.2.5-2_i386.deb ... Unpacking liblzma-dev:i386 (5.2.5-2) ... Selecting previously unselected package zlib1g-dev:i386. Preparing to unpack .../50-zlib1g-dev_1%3a1.2.11.dfsg-2_i386.deb ... Unpacking zlib1g-dev:i386 (1:1.2.11.dfsg-2) ... Selecting previously unselected package libhts-dev:i386. Preparing to unpack .../51-libhts-dev_1.11-4_i386.deb ... Unpacking libhts-dev:i386 (1.11-4) ... Selecting previously unselected package libncurses6:i386. Preparing to unpack .../52-libncurses6_6.2+20201114-2_i386.deb ... Unpacking libncurses6:i386 (6.2+20201114-2) ... Selecting previously unselected package libsqlite3-dev:i386. Preparing to unpack .../53-libsqlite3-dev_3.34.1-3_i386.deb ... Unpacking libsqlite3-dev:i386 (3.34.1-3) ... Selecting previously unselected package libssl-dev:i386. Preparing to unpack .../54-libssl-dev_1.1.1k-1_i386.deb ... Unpacking libssl-dev:i386 (1.1.1k-1) ... Selecting previously unselected package python3-pysam. Preparing to unpack .../55-python3-pysam_0.15.4+ds-3+b2_i386.deb ... Unpacking python3-pysam (0.15.4+ds-3+b2) ... Selecting previously unselected package samtools. Preparing to unpack .../56-samtools_1.11-1_i386.deb ... Unpacking samtools (1.11-1) ... Setting up media-types (4.0.0) ... Setting up libpipeline1:i386 (1.5.3-1) ... Setting up libpsl5:i386 (0.21.0-1.2) ... 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 libicu67:i386 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:i386 (1.0.9-2+b2) ... Setting up libnghttp2-14:i386 (1.43.0-1) ... Setting up libmagic1:i386 (1:5.39-3) ... Setting up libdeflate0:i386 (1.7-1) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libfastahack0 (1.0.0+dfsg-7) ... Setting up libsasl2-modules-db:i386 (2.1.27+dfsg-2.1) ... Setting up libfastahack-dev (1.0.0+dfsg-7) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libsqlite3-dev:i386 (3.34.1-3) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:i386 (6.2+20201114-2) ... Setting up libsigsegv2:i386 (2.13-1) ... Setting up libbamtools2.5.1:i386 (2.5.1+dfsg-9) ... Setting up libssl-dev:i386 (1.1.1k-1) ... Setting up autopoint (0.21-4) ... Setting up libsasl2-2:i386 (2.1.27+dfsg-2.1) ... Setting up libgzstream0 (1.5+dfsg-5) ... Setting up liblzma-dev:i386 (5.2.5-2) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up libmpdec3:i386 (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:i386 (1.9.0-2) ... Setting up libdeflate-dev:i386 (1.7-1) ... Setting up libelf1:i386 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:i386 (2.9.10+dfsg-6.7) ... Setting up libfile-stripnondeterminism-perl (1.11.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libreadline8:i386 (8.1-1) ... Setting up libldap-2.4-2:i386 (2.4.57+dfsg-3) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:i386 (7.74.0-1.3+b1) ... Setting up libcurl4-gnutls-dev:i386 (7.74.0-1.3+b1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libgzstream-dev (1.5+dfsg-5) ... Setting up libbamtools-dev:i386 (2.5.1+dfsg-9) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.11.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up libpython3.9-stdlib:i386 (3.9.2-1) ... Setting up libpython3-stdlib:i386 (3.9.2-3) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libhts3:i386 (1.11-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhts-dev:i386 (1.11-4) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up samtools (1.11-1) ... Setting up dh-autoreconf (20) ... Setting up python3.9 (3.9.2-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up python3-distutils (3.9.2-1) ... Setting up dh-python (4.20201102+nmu1) ... Setting up python3-pysam (0.15.4+ds-3+b2) ... 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/lumpy-sv-0.3.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package lumpy-sv dpkg-buildpackage: info: source version 0.3.1+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean --with python3 dh_auto_clean make -j18 clean make[1]: Entering directory '/build/lumpy-sv-0.3.1+dfsg' Cleaning up. #rm -Rf /lib #rm -f /src/api/*.o #rm -f /src/api/internal/*.o #rm -Rf /include make[1]: Leaving directory '/build/lumpy-sv-0.3.1+dfsg' dh_clean debian/rules binary dh binary --with python3 dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j18 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/lumpy-sv-0.3.1+dfsg' [ -d bin ] || mkdir -p bin [ -d bin ] || mkdir -p bin [ -d obj ] || mkdir -p obj make --no-print-directory -C src/filter/ cp scripts/lumpyexpress bin/lumpyexpress [ -d bin ] || mkdir -p bin cc -g -I/usr/include/htslib -o lumpy_filter filter.c -lhts -lcrypto -lcurl -lpthread -lz > bin/lumpyexpress.config Building lumpy: ========================================================= #make --no-print-directory --directory= api for dir in src/utils/bedFile src/utils/version src/utils/fileType src/utils/bedFilePE src/utils/genomeFile src/utils/BamTools-Ancillary src/utils/sequenceUtilities ; do \ echo "- Building in $dir"; \ make --no-print-directory -C $dir; \ echo ""; \ done - Building in src/utils/bedFile * compiling bedFile.cpp cp src/filter/lumpy_filter bin - Building in src/utils/version * compiling version.cpp - Building in src/utils/fileType * compiling fileType.cpp - Building in src/utils/bedFilePE * compiling bedFilePE.cpp - Building in src/utils/genomeFile * compiling genomeFile.cpp genomeFile.cpp: In member function ‘void GenomeFile::loadGenomeFileIntoMap()’: genomeFile.cpp:61:26: warning: variable ‘c2’ set but not used [-Wunused-but-set-variable] 61 | long c2; | ^~ - Building in src/utils/BamTools-Ancillary * compiling BamAncillary.cpp * compiling BamAncillary.cpp - Building in src/utils/sequenceUtilities * compiling sequenceUtils.cpp - Building in src/lumpy * compiling lumpy.cpp g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack lumpy.cpp -o ../../obj//lumpy.o * compiling SV_Pair.cpp g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Pair.cpp -o ../../obj//SV_Pair.o * compiling SV_Evidence.cpp g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Evidence.cpp -o ../../obj//SV_Evidence.o * compiling SV_BreakPoint.cpp g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BreakPoint.cpp -o ../../obj//SV_BreakPoint.o * compiling SV_Bedpe.cpp g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Bedpe.cpp -o ../../obj//SV_Bedpe.o * compiling SV_SplitRead.cpp g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_SplitRead.cpp -o ../../obj//SV_SplitRead.o * compiling SV_SplitReadReader.cpp g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_SplitReadReader.cpp -o ../../obj//SV_SplitReadReader.o * compiling SV_PairReader.cpp g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_PairReader.cpp -o ../../obj//SV_PairReader.o * compiling SV_BedpeReader.cpp g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BedpeReader.cpp -o ../../obj//SV_BedpeReader.o * compiling SV_BamReader.cpp g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BamReader.cpp -o ../../obj//SV_BamReader.o * compiling SV_InterChromBamReader.cpp g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_InterChromBamReader.cpp -o ../../obj//SV_InterChromBamReader.o * compiling SV_EvidenceReader.cpp g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_EvidenceReader.cpp -o ../../obj//SV_EvidenceReader.o * compiling SV_Tools.cpp g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Tools.cpp -o ../../obj//SV_Tools.o * compiling SV_VcfVariant.cpp g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_VcfVariant.cpp -o ../../obj//SV_VcfVariant.o * compiling log_space.cpp g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack log_space.cpp -o ../../obj//log_space.o SV_SplitRead.cpp: In member function ‘bool SV_SplitRead::is_sane()’: SV_SplitRead.cpp:538:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 538 | if ( min_mapping_quality < reader->min_mapping_threshold ) | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SV_Evidence.cpp: In member function ‘virtual void SV_Evidence::set_bp_interval_probability(breakpoint_interval*)’: SV_Evidence.cpp:81:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 81 | for (j = 0; j < size; ++j) { | ~~^~~~~~ SV_BreakPoint.cpp: In member function ‘bool SV_BreakPoint::merge(SV_BreakPoint*)’: SV_BreakPoint.cpp:266:33: warning: variable ‘a_overlap_intr’ set but not used [-Wunused-but-set-variable] 266 | struct breakpoint_interval *a_overlap_intr, *b_overlap_intr; | ^~~~~~~~~~~~~~ SV_BreakPoint.cpp:266:50: warning: variable ‘b_overlap_intr’ set but not used [-Wunused-but-set-variable] 266 | struct breakpoint_interval *a_overlap_intr, *b_overlap_intr; | ^~~~~~~~~~~~~~ SV_BamReader.cpp: In member function ‘virtual void SV_BamReader::process_input_chr_pos(std::string, CHR_POS, UCSCBins&)’: SV_BamReader.cpp:208:28: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘CHR_POS’ {aka ‘long long unsigned int’} [-Wsign-compare] 208 | ( bam.Position < pos ) ) { | ~~~~~~~~~~~~~^~~~~ SV_Tools.cpp: In function ‘int read_distro_file(std::string, double**, int*, int*)’: SV_Tools.cpp:156:7: warning: ‘last’ may be used uninitialized in this function [-Wmaybe-uninitialized] 156 | *end = last; | ~~~~~^~~~~~ SV_BreakPoint.cpp: In static member function ‘static void SV_BreakPoint::trim_interval(log_space*, unsigned int, int*, int*)’: SV_BreakPoint.cpp:708:17: warning: ‘max_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 708 | *trim_end = r; | ^ SV_BreakPoint.cpp: In static member function ‘static int SV_BreakPoint::get_product(std::vector&, CHR_POS*, CHR_POS*, CHR_POS*, CHR_POS*, log_space**, log_space**)’: SV_BreakPoint.cpp:1662:41: warning: ‘r_max_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1662 | CHR_POS abs_max_r = m_start_r + r_max_i; | ^~~~~~~ SV_BreakPoint.cpp:1650:41: warning: ‘l_max_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1650 | CHR_POS abs_max_l = m_start_l + l_max_i; | ^~~~~~~ * linking lumpy g++ -Wl,-z,relro -Wl,-z,now -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -o ../../bin//lumpy ../../obj//lumpy.o ../../obj//SV_Pair.o ../../obj//SV_Evidence.o ../../obj//SV_BreakPoint.o ../../obj//SV_Bedpe.o ../../obj//SV_SplitRead.o ../../obj//SV_SplitReadReader.o ../../obj//SV_PairReader.o ../../obj//SV_BedpeReader.o ../../obj//SV_BamReader.o ../../obj//SV_InterChromBamReader.o ../../obj//SV_EvidenceReader.o ../../obj//SV_Tools.o ../../obj//SV_VcfVariant.o ../../obj//log_space.o ../../obj//BamAncillary.o ../../obj//sequenceUtils.o ../../obj//bedFilePE.o ../../obj//bedFile.o ../../obj//genomeFile.o ../../obj//fileType.o \ -L../utils//BamTools/lib/ -lbamtools \ -lz -L /build/lumpy-sv-0.3.1+dfsg/debian/.debhelper/generated/_source/home/src/zlib-1.2.8 \ -lgzstream -lz -lm -ldl -lpthread make[1]: Leaving directory '/build/lumpy-sv-0.3.1+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install debian/rules override_dh_install make[1]: Entering directory '/build/lumpy-sv-0.3.1+dfsg' cat debian/missing-sources/pe.pos_sorted.sam |samtools view -Sb - > data/pe.pos_sorted.bam cat debian/missing-sources/sr.pos_sorted.sam |samtools view -Sb - > data/sr.pos_sorted.bam dh_install rm -f debian/lumpy-sv*/usr/share/lumpy-sv/scripts/lumpyexpress.config make[1]: Leaving directory '/build/lumpy-sv-0.3.1+dfsg' dh_installdocs dh_installchangelogs dh_installman debian/rules override_dh_python3 make[1]: Entering directory '/build/lumpy-sv-0.3.1+dfsg' dh_python3 --shebang=/usr/bin/python3 I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/bedpe_sort.py I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/check_sorting.py I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/cnvanator_to_bedpes.py I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/extractSplitReads_BwaMem I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/get_coverages.py I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/get_exclude_regions.py I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/l_merge.py I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/l_sort.py I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/pairend_distro.py I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/prob_bedpe_to_bedgraph.py I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/vcfToBedpe make[1]: Leaving directory '/build/lumpy-sv-0.3.1+dfsg' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dwz: debian/lumpy-sv/usr/bin/lumpy: DWARF compression not beneficial - old size 3779664 new size 3789346 dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package lumpy-sv: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package lumpy-sv: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'lumpy-sv' in '../lumpy-sv_0.3.1+dfsg-5_i386.deb'. dpkg-deb: building package 'lumpy-sv-dbgsym' in '../lumpy-sv-dbgsym_0.3.1+dfsg-5_i386.deb'. dpkg-deb: building package 'lumpy-sv-examples' in '../lumpy-sv-examples_0.3.1+dfsg-5_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../lumpy-sv_0.3.1+dfsg-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: 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/15669 and its subdirectories I: Current time: Mon Aug 22 03:53:49 -12 2022 I: pbuilder-time-stamp: 1661183629 Tue Jul 20 09:30:50 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos12-i386.debian.net. Tue Jul 20 09:30:50 UTC 2021 I: Preparing to do remote build '2' on ionos12-i386.debian.net. Tue Jul 20 09:47:11 UTC 2021 I: Deleting $TMPDIR on ionos12-i386.debian.net. Tue Jul 20 09:47:36 UTC 2021 I: lumpy-sv_0.3.1+dfsg-5_i386.changes: Format: 1.8 Date: Wed, 13 Jan 2021 10:34:36 +0100 Source: lumpy-sv Binary: lumpy-sv lumpy-sv-dbgsym lumpy-sv-examples Architecture: i386 all Version: 0.3.1+dfsg-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: lumpy-sv - general probabilistic framework for structural variant discovery lumpy-sv-examples - general probabilistic framework for structural variant discovery Closes: 980005 Changes: lumpy-sv (0.3.1+dfsg-5) unstable; urgency=medium . * Fix configure patch according to a hint of Ken Yamaguchi Closes: #980005 * Standards-Version: 4.5.1 (routine-update) Checksums-Sha1: 7121c5670cbe659b7f57fcb6e987f8c842f90519 1969048 lumpy-sv-dbgsym_0.3.1+dfsg-5_i386.deb bdad678f7f544f6eee0b00516a1e59ce4e2a61ed 55664728 lumpy-sv-examples_0.3.1+dfsg-5_all.deb ee51075186aafffba5e5bc24a8dcca654d4bcb60 6714 lumpy-sv_0.3.1+dfsg-5_i386.buildinfo e59413542f3e63a5328141341032d0614015c3e6 203068 lumpy-sv_0.3.1+dfsg-5_i386.deb Checksums-Sha256: 0fd0407dfc737de2f6a673720f75f8b95e20a9133353852603f1ab151d5907a7 1969048 lumpy-sv-dbgsym_0.3.1+dfsg-5_i386.deb ceaebaf115ca52dcb1a7e90ae34fff181db2869ec4186d777f98061627a64a2a 55664728 lumpy-sv-examples_0.3.1+dfsg-5_all.deb 0a2d55da4b2ce04d8c72f271f309fcb4ffec10805a5b4db64ca43cecff5b145c 6714 lumpy-sv_0.3.1+dfsg-5_i386.buildinfo cc298822643db27065f1c66e67d0155747f46120f4aca50d37ef5e044f74f233 203068 lumpy-sv_0.3.1+dfsg-5_i386.deb Files: 6f7260850dd0464948578c6af8284aec 1969048 debug optional lumpy-sv-dbgsym_0.3.1+dfsg-5_i386.deb 09bd3a608c94af347620d979cf537a62 55664728 science optional lumpy-sv-examples_0.3.1+dfsg-5_all.deb a834edab8cdb2e2726118a72ddc5825a 6714 science optional lumpy-sv_0.3.1+dfsg-5_i386.buildinfo 28745cedd933a7c252220f3a036d18fd 203068 science optional lumpy-sv_0.3.1+dfsg-5_i386.deb Tue Jul 20 09:47:37 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.q9jnf9NIjC/lumpy-sv_0.3.1+dfsg-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.q9jnf9NIjC/lumpy-sv_0.3.1+dfsg-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.q9jnf9NIjC/lumpy-sv_0.3.1+dfsg-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.q9jnf9NIjC/b1/lumpy-sv_0.3.1+dfsg-5_i386.changes /srv/reproducible-results/rbuild-debian/tmp.q9jnf9NIjC/b2/lumpy-sv_0.3.1+dfsg-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: 0.950s) 0.950s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.677s) 0.676s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Tue Jul 20 09:47:40 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Tue Jul 20 09:47:40 UTC 2021 I: lumpy-sv from bullseye built successfully and reproducibly on i386. Tue Jul 20 09:47:41 UTC 2021 I: Submitting .buildinfo files to external archives: Tue Jul 20 09:47:41 UTC 2021 I: Submitting 8.0K b1/lumpy-sv_0.3.1+dfsg-5_i386.buildinfo.asc Tue Jul 20 09:47:41 UTC 2021 I: Submitting 8.0K b2/lumpy-sv_0.3.1+dfsg-5_i386.buildinfo.asc Tue Jul 20 09:47:42 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Jul 20 09:47:42 UTC 2021 I: Done submitting .buildinfo files. Tue Jul 20 09:47:42 UTC 2021 I: Removing signed lumpy-sv_0.3.1+dfsg-5_i386.buildinfo.asc files: removed './b1/lumpy-sv_0.3.1+dfsg-5_i386.buildinfo.asc' removed './b2/lumpy-sv_0.3.1+dfsg-5_i386.buildinfo.asc'