Thu May 30 08:20:26 UTC 2024 I: starting to build lumpy-sv/trixie/armhf on jenkins on '2024-05-30 08:19' Thu May 30 08:20:26 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_31/6021/console.log Thu May 30 08:20:26 UTC 2024 I: Downloading source for trixie/lumpy-sv=0.3.1+dfsg-7 --2024-05-30 08:20:26-- http://deb.debian.org/debian/pool/main/l/lumpy-sv/lumpy-sv_0.3.1%2bdfsg-7.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2269 (2.2K) [text/prs.lines.tag] Saving to: ‘lumpy-sv_0.3.1+dfsg-7.dsc’ 0K .. 100% 311M=0s 2024-05-30 08:20:26 (311 MB/s) - ‘lumpy-sv_0.3.1+dfsg-7.dsc’ saved [2269/2269] Thu May 30 08:20:26 UTC 2024 I: lumpy-sv_0.3.1+dfsg-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: lumpy-sv Binary: lumpy-sv, lumpy-sv-examples Architecture: any all Version: 0.3.1+dfsg-7 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Nilesh Patra Homepage: https://github.com/arq5x/lumpy-sv Standards-Version: 4.6.1 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 114493ca4517a5d0b6cb2271454957b84585fa18 39162060 lumpy-sv_0.3.1+dfsg-7.debian.tar.xz Checksums-Sha256: 78a6fe414739286d1f799bbdf3e34b9a1d6ed03b4c6dd17bfef1fcbba84bd35a 111836 lumpy-sv_0.3.1+dfsg.orig.tar.xz 5fee7d3bc51b58d2ecbb5cabb8c276e637a322db4c71eb64cb85d33381ba6452 39162060 lumpy-sv_0.3.1+dfsg-7.debian.tar.xz Files: 1167e4a94bceb29ac5b83cb170058e25 111836 lumpy-sv_0.3.1+dfsg.orig.tar.xz 004edde98e33fa584084b44f65dd3a66 39162060 lumpy-sv_0.3.1+dfsg-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmM+owQRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtE5ThAAjgRi9csoDFOz7iTgGBz8JIvmtpcqTt6o EfdUr4Eb/Jt0gfCbil4KEmlWTEc5gEw2LMZA6KSlzEA/i79Kb7D7A6oP9B1Ve92K 4GXMRmSU0NaogM++pHISOh9AIAgQF7aP/wmGNrW4epWAhWtRsefa8Mx1QXrg5BEv RRWFhcIvJa+7f+ir2fky+lcTQs3500AjZEG+bVZeQnDHVQF6hW/9U/FUaZrP0Qli nN/0exhzMJlBz5V2n++XAncZlH2AmIW9Z4/+ehMkZN9hfTP8NIdHS6rCQ5qNvDK7 VUAJ00Pzco2/Y6248QJJ/TaUqhg/CSQm27lka/W9cbCVQA4fYq7SmIVRm+U1C3jP eCvcXxxDRxpwA2SWUZB1y7rzDvN8Ty+1ZzHg4RnlUk7tPNwBuQCtdiHUnng7ehO+ 7/gfpNdaa1ljmcX6PL86FrWh5YNuYcslLJFkCw9t11zhDQBOdtabPnQ5OZ+aS2zI S/G6NZxivCDV3HSOWtIBBskurkPiHMO7B11v9k6rTTjII1e4dqCpKCjiUviXHGUe EDBLPgHjxI7kfNNy+Y/Tetc7Pj7OpkWdFmE7Ofh8QwkolystJC220mK00Z5idvmB 7HtYemoohCajY2R4K48iqiXCE1ClRCvLbiYbjl9sa7rCy4dg7UmZWdRKH3tCxAsx S9BTtvy9UIM= =0GoI -----END PGP SIGNATURE----- Thu May 30 08:20:26 UTC 2024 I: Checking whether the package is not for us Thu May 30 08:20:26 UTC 2024 I: Starting 1st build on remote node virt64c-armhf-rb.debian.net. Thu May 30 08:20:26 UTC 2024 I: Preparing to do remote build '1' on virt64c-armhf-rb.debian.net. Thu May 30 08:33:32 UTC 2024 I: Deleting $TMPDIR on virt64c-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed May 29 20:20:45 -12 2024 I: pbuilder-time-stamp: 1717057245 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [lumpy-sv_0.3.1+dfsg-7.dsc] I: copying [./lumpy-sv_0.3.1+dfsg.orig.tar.xz] I: copying [./lumpy-sv_0.3.1+dfsg-7.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Oct 6 09:42:28 2022 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./lumpy-sv_0.3.1+dfsg-7.dsc: no acceptable signature found 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-7.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/9701/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='26479e6592604f19b0f8f5956f1745d8' 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='9701' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.bqLug0aJ/pbuilderrc_tL3o --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bqLug0aJ/b1 --logfile b1/build.log lumpy-sv_0.3.1+dfsg-7.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt64c 6.1.0-21-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 28 11:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/9701/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: armhf 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 ... 19444 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} libbamtools2.5.2{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfastahack-dev{a} libfastahack0{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libgzstream-dev{a} libgzstream0{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsqlite3-dev{a} libssh2-1t64{a} libssl-dev{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-pysam{a} python3-setuptools{a} python3.11{a} python3.11-minimal{a} readline-common{a} samtools{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 81 newly installed, 0 to remove and 0 not upgraded. Need to get 39.2 MB of archives. After unpacking 160 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf libpython3.11-minimal armhf 3.11.9-1 [805 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libexpat1 armhf 2.6.2-1 [83.5 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf python3.11-minimal armhf 3.11.9-1 [1600 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf python3-minimal armhf 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libreadline8t64 armhf 8.2-4 [145 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf libpython3.11-stdlib armhf 3.11.9-1 [1704 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf python3.11 armhf 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf libpython3-stdlib armhf 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian trixie/main armhf python3 armhf 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3 [314 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3 [98.1 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3 [42.0 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-4 [1090 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40.1-2 [85.7 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.12.1-1 [1375 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf autoconf all 2.71-3 [332 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf autopoint all 0.21-14 [496 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 35 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.191-1+b1 [183 kB] Get: 36 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b3 [598 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf python3-pkg-resources all 68.1.2-2 [241 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf python3-distutils all 3.12.3-1 [131 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf python3-setuptools all 68.1.2-2 [468 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf dh-python all 6.20240422 [107 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf libbamtools2.5.2 armhf 2.5.2+dfsg-5 [139 kB] Get: 49 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1 [904 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf libbamtools-dev armhf 2.5.2+dfsg-5 [206 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b3 [284 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf libcom-err2 armhf 1.47.1-1 [22.1 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf libkrb5support0 armhf 1.20.1-6+b1 [30.6 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf libk5crypto3 armhf 1.20.1-6+b1 [75.5 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf libkeyutils1 armhf 1.6.3-3 [7908 B] Get: 56 http://deb.debian.org/debian trixie/main armhf libkrb5-3 armhf 1.20.1-6+b1 [290 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf libgssapi-krb5-2 armhf 1.20.1-6+b1 [112 kB] Get: 58 http://deb.debian.org/debian trixie/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-6 [18.0 kB] Get: 59 http://deb.debian.org/debian trixie/main armhf libsasl2-2 armhf 2.1.28+dfsg1-6 [50.1 kB] Get: 60 http://deb.debian.org/debian trixie/main armhf libldap-2.5-0 armhf 2.5.17+dfsg-1 [161 kB] Get: 61 http://deb.debian.org/debian trixie/main armhf libnghttp2-14 armhf 1.61.0-1+b1 [64.1 kB] Get: 62 http://deb.debian.org/debian trixie/main armhf libpsl5t64 armhf 0.21.2-1.1 [55.6 kB] Get: 63 http://deb.debian.org/debian trixie/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b4 [53.2 kB] Get: 64 http://deb.debian.org/debian trixie/main armhf libssh2-1t64 armhf 1.11.0-5 [199 kB] Get: 65 http://deb.debian.org/debian trixie/main armhf libcurl3t64-gnutls armhf 8.8.0-1 [389 kB] Get: 66 http://deb.debian.org/debian trixie/main armhf libcurl4-gnutls-dev armhf 8.8.0-1 [505 kB] Get: 67 http://deb.debian.org/debian trixie/main armhf libdeflate0 armhf 1.20-1 [35.9 kB] Get: 68 http://deb.debian.org/debian trixie/main armhf libdeflate-dev armhf 1.20-1 [44.0 kB] Get: 69 http://deb.debian.org/debian trixie/main armhf libfastahack0 armhf 1.0.0+dfsg-11+b1 [24.0 kB] Get: 70 http://deb.debian.org/debian trixie/main armhf libfastahack-dev armhf 1.0.0+dfsg-11+b1 [310 kB] Get: 71 http://deb.debian.org/debian trixie/main armhf libgzstream0 armhf 1.5+git20171107.9a20658-2 [6572 B] Get: 72 http://deb.debian.org/debian trixie/main armhf libgzstream-dev armhf 1.5+git20171107.9a20658-2 [6928 B] Get: 73 http://deb.debian.org/debian trixie/main armhf libhtscodecs2 armhf 1.6.0-1+b1 [61.3 kB] Get: 74 http://deb.debian.org/debian trixie/main armhf libhts3t64 armhf 1.19+ds-1.1+b1 [395 kB] Get: 75 http://deb.debian.org/debian trixie/main armhf liblzma-dev armhf 5.6.1+really5.4.5-1 [281 kB] Get: 76 http://deb.debian.org/debian trixie/main armhf libhts-dev armhf 1.19+ds-1.1+b1 [1598 kB] Get: 77 http://deb.debian.org/debian trixie/main armhf libncurses6 armhf 6.5-2 [81.8 kB] Get: 78 http://deb.debian.org/debian trixie/main armhf libsqlite3-dev armhf 3.45.3-1 [988 kB] Get: 79 http://deb.debian.org/debian trixie/main armhf libssl-dev armhf 3.2.1-3 [2348 kB] Get: 80 http://deb.debian.org/debian trixie/main armhf python3-pysam armhf 0.22.1+ds-1 [4118 kB] Get: 81 http://deb.debian.org/debian trixie/main armhf samtools armhf 1.19.2-1+b1 [614 kB] Fetched 39.2 MB in 1s (46.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:armhf. (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 ... 19444 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_armhf.deb ... Unpacking libpython3.11-minimal:armhf (3.11.9-1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.6.2-1_armhf.deb ... Unpacking libexpat1:armhf (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_armhf.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:armhf (3.11.9-1) ... Setting up libexpat1:armhf (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... 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 ... 19760 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_armhf.deb ... 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Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:armhf (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:armhf. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_armhf.deb ... Unpacking libpython3.11-stdlib:armhf (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_armhf.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (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 ... 20752 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.8-1_armhf.deb ... Unpacking python3 (3.11.8-1) ... 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Setting up libbrotli1:armhf (1.1.0-2+b3) ... Setting up libmagic1t64:armhf (1:5.45-3) ... Setting up libpsl5t64:armhf (0.21.2-1.1) ... Setting up libnghttp2-14:armhf (1.61.0-1+b1) ... Setting up libdeflate0:armhf (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:armhf (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libfastahack0:armhf (1.0.0+dfsg-11+b1) ... Setting up libelf1t64:armhf (0.191-1+b1) ... Setting up libkrb5support0:armhf (1.20.1-6+b1) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-6) ... Setting up libfastahack-dev:armhf (1.0.0+dfsg-11+b1) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Thu May 30 08:21:42 UTC 2024. Universal Time is now: Thu May 30 08:21:42 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libsqlite3-dev:armhf (3.45.3-1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libncurses6:armhf (6.5-2) ... Setting up libssl-dev:armhf (3.2.1-3) ... Setting up autopoint (0.21-14) ... Setting up libk5crypto3:armhf (1.20.1-6+b1) ... Setting up libbamtools2.5.2:armhf (2.5.2+dfsg-5) ... Setting up libsasl2-2:armhf (2.1.28+dfsg1-6) ... Setting up autoconf (2.71-3) ... Setting up libgzstream0:armhf (1.5+git20171107.9a20658-2) ... Setting up liblzma-dev:armhf (5.6.1+really5.4.5-1) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:armhf (0.0.8-1+b1) ... Setting up netbase (6.4) ... Setting up libkrb5-3:armhf (1.20.1-6+b1) ... Setting up libssh2-1t64:armhf (1.11.0-5) ... Setting up libdeflate-dev:armhf (1.20-1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3+b3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libldap-2.5-0:armhf (2.5.17+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libgzstream-dev:armhf (1.5+git20171107.9a20658-2) ... Setting up dh-autoreconf (20) ... Setting up libbamtools-dev:armhf (2.5.2+dfsg-5) ... Setting up libgssapi-krb5-2:armhf (1.20.1-6+b1) ... Setting up libreadline8t64:armhf (8.2-4) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:armhf (3.11.9-1) ... Setting up libcurl3t64-gnutls:armhf (8.8.0-1) ... Setting up libcurl4-gnutls-dev:armhf (8.8.0-1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libhts3t64:armhf (1.19+ds-1.1+b1) ... Setting up libpython3-stdlib:armhf (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up libhts-dev:armhf (1.19+ds-1.1+b1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up samtools (1.19.2-1+b1) ... Setting up python3-lib2to3 (3.12.3-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... Setting up python3-pysam (0.22.1+ds-1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up dh-python (6.20240422) ... Processing triggers for libc-bin (2.38-11) ... 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/reproducible-path/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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../lumpy-sv_0.3.1+dfsg-7_source.changes dpkg-buildpackage: info: source package lumpy-sv dpkg-buildpackage: info: source version 0.3.1+dfsg-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --with python3 dh_auto_clean make -j3 clean make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/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 -j3 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' [ -d bin ] || mkdir -p bin [ -d bin ] || mkdir -p bin make --no-print-directory -C src/filter/ cp scripts/lumpyexpress bin/lumpyexpress cc -g -I/usr/include/htslib -o lumpy_filter filter.c -lhts -lcrypto -lcurl -lpthread -lz [ -d obj ] || mkdir -p obj > bin/lumpyexpress.config [ -d bin ] || mkdir -p bin 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 In file included from bedFile.cpp:12: bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ - Building in src/utils/version * compiling version.cpp - Building in src/utils/fileType * compiling fileType.cpp - Building in src/utils/bedFilePE * compiling bedFilePE.cpp In file included from bedFilePE.h:12, from bedFilePE.cpp:15: ../../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ - 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 In file included from BamAncillary.h:12, from BamAncillary.cpp:12: ..//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ..//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from BamAncillary.h:12, from BamAncillary.cpp:12: ..//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ..//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ - Building in src/utils/sequenceUtilities * compiling sequenceUtils.cpp - Building in src/lumpy * compiling lumpy.cpp * compiling SV_Pair.cpp * 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 lumpy.cpp -o ../../obj//lumpy.o 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 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 In file included from SV_BreakPoint.h:19, from SV_Evidence.h:22, from SV_Evidence.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, from SV_Pair.cpp:15: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, from lumpy.cpp:20: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ 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) { | ~~^~~~~~ In file included from SV_BreakPoint.h:19, from SV_PairReader.h:22, from SV_Pair.cpp:19: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_Evidence.h:22, from lumpy.cpp:24: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ * 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 In file included from SV_BreakPoint.h:19, from SV_BreakPoint.cpp:16: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ 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; | ^~~~~~~~~~~~~~ ../utils//UCSCBins/ucsc_bins.hpp: In instantiation of ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS) [with T = SV_BreakPoint*; BIN = unsigned int; CHR_POS = long long unsigned int]’: ../utils//UCSCBins/ucsc_bins.hpp:238:18: required from ‘void UCSCBins::add(std::string, CHR_POS, CHR_POS, char, T) [with T = SV_BreakPoint*; std::string = std::__cxx11::basic_string; CHR_POS = long long unsigned int]’ SV_BreakPoint.cpp:1286:14: required from here ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ * 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 SV_BreakPoint.cpp: In static member function ‘static void SV_BreakPoint::trim_interval(log_space*, unsigned int, int*, int*)’: SV_BreakPoint.cpp:704:24: warning: ‘max_i’ may be used uninitialized [-Wmaybe-uninitialized] 704 | if ((l == r) && (l == max_i)) | ~~~^~~~~~~~~ SV_BreakPoint.cpp:667:21: note: ‘max_i’ was declared here 667 | unsigned int i, max_i; | ^~~~~ 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:1650:41: warning: ‘l_max_i’ may be used uninitialized [-Wmaybe-uninitialized] 1650 | CHR_POS abs_max_l = m_start_l + l_max_i; | ^~~~~~~ SV_BreakPoint.cpp:1643:25: note: ‘l_max_i’ was declared here 1643 | unsigned int i, l_max_i, r_max_i; | ^~~~~~~ SV_BreakPoint.cpp:1662:41: warning: ‘r_max_i’ may be used uninitialized [-Wmaybe-uninitialized] 1662 | CHR_POS abs_max_r = m_start_r + r_max_i; | ^~~~~~~ SV_BreakPoint.cpp:1643:34: note: ‘r_max_i’ was declared here 1643 | unsigned int i, l_max_i, r_max_i; | ^~~~~~~ In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, from SV_Bedpe.cpp:14: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from SV_BedpeReader.h:21, from SV_Bedpe.cpp:17: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ * 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 In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, from SV_SplitRead.cpp:15: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_SplitReadReader.h:22, from SV_SplitRead.cpp:19: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ 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 ) | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * 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 In file included from SV_BreakPoint.h:19, from SV_SplitReadReader.h:22, from SV_SplitReadReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from ../utils//bedFilePE/bedFilePE.h:12, from SV_SplitRead.h:27, from SV_SplitReadReader.cpp:16: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ * 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 In file included from SV_BreakPoint.h:19, from SV_PairReader.h:22, from SV_PairReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ SV_SplitRead.cpp: In static member function ‘static void SV_SplitRead::process_split(const BamTools::BamAlignment&, BamTools::RefVector, std::map, BamTools::BamAlignment>&, UCSCBins&, int, int, SV_SplitReadReader*)’: SV_SplitRead.cpp:653:25: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 653 | free(new_split_read); | ~~~~^~~~~~~~~~~~~~~~ SV_SplitRead.cpp:641:41: note: returned from ‘void* operator new(std::size_t)’ 641 | _reader); | ^ * 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 In file included from SV_BreakPoint.h:19, from SV_Evidence.h:22, from SV_Bedpe.h:18, from SV_BedpeReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ * 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 In file included from ../utils//bedFilePE/bedFilePE.h:12, from SV_BedpeReader.h:23, from SV_Bedpe.h:19: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ * 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 In file included from SV_BreakPoint.h:19, from SV_PairReader.h:22, from SV_BamReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_PairReader.h:22, from SV_InterChromBamReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from ../utils//bedFilePE/bedFilePE.h:12, from SV_SplitRead.h:27, from SV_BamReader.cpp:19: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ 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 ) ) { | ~~~~~~~~~~~~~^~~~~ In file included from ../utils//bedFilePE/bedFilePE.h:12, from SV_SplitRead.h:27, from SV_InterChromBamReader.cpp:19: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ * 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 In file included from SV_EvidenceReader.h:20, from SV_EvidenceReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ * 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 In file included from SV_Tools.h:19, from SV_Tools.cpp:24: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_VcfVariant.h:18, from SV_VcfVariant.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_Tools.cpp:27: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ ../utils//UCSCBins/ucsc_bins.hpp: In instantiation of ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS) [with T = int; BIN = unsigned int; CHR_POS = long long unsigned int]’: ../utils//UCSCBins/ucsc_bins.hpp:238:18: required from ‘void UCSCBins::add(std::string, CHR_POS, CHR_POS, char, T) [with T = int; std::string = std::__cxx11::basic_string; CHR_POS = long long unsigned int]’ SV_Tools.cpp:541:32: required from here ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ SV_Tools.cpp: In function ‘int read_distro_file(std::string, double**, int*, int*)’: SV_Tools.cpp:156:14: warning: ‘last’ may be used uninitialized [-Wmaybe-uninitialized] 156 | *end = last; | ~~~~~^~~~~~ SV_Tools.cpp:143:13: note: ‘last’ was declared here 143 | int last; | ^~~~ In file included from /usr/include/c++/13/vector:72, from /usr/include/bamtools/api/BamAlignment.h:17, from /usr/include/bamtools/api/BamReader.h:14, from /usr/include/bamtools/api/BamMultiReader.h:17, from SV_Tools.cpp:16: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const UCSCElement&}; _Tp = UCSCElement; _Alloc = std::allocator >]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector, std::allocator > >::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = UCSCElement; _Alloc = std::allocator >]’, inlined from ‘void UCSCBins::add(std::string, CHR_POS, CHR_POS, char, T) [with T = int]’ at ../utils//UCSCBins/ucsc_bins.hpp:239:32: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ * 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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/lumpy-sv-0.3.1+dfsg' dh_installdocs dh_installchangelogs dh_installman debian/rules override_dh_python3 make[1]: Entering directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' dh_python3 --shebang=/usr/bin/python3 I: dh_python3 tools:113: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/bedpe_sort.py I: dh_python3 tools:113: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/check_sorting.py I: dh_python3 tools:113: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/cnvanator_to_bedpes.py I: dh_python3 tools:113: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/extractSplitReads_BwaMem I: dh_python3 tools:113: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/get_coverages.py I: dh_python3 tools:113: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/get_exclude_regions.py I: dh_python3 tools:113: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/l_merge.py I: dh_python3 tools:113: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/l_sort.py I: dh_python3 tools:113: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/pairend_distro.py I: dh_python3 tools:113: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/prob_bedpe_to_bedgraph.py I: dh_python3 tools:113: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/vcfToBedpe make[1]: Leaving directory '/build/reproducible-path/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 4478207 new size 4491425 dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/lumpy-sv/usr/bin/lumpy contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin 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-7_armhf.deb'. dpkg-deb: building package 'lumpy-sv-dbgsym' in '../lumpy-sv-dbgsym_0.3.1+dfsg-7_armhf.deb'. dpkg-deb: building package 'lumpy-sv-examples' in '../lumpy-sv-examples_0.3.1+dfsg-7_all.deb'. dpkg-genbuildinfo --build=binary -O../lumpy-sv_0.3.1+dfsg-7_armhf.buildinfo dpkg-genchanges --build=binary -O../lumpy-sv_0.3.1+dfsg-7_armhf.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/9701 and its subdirectories I: Current time: Wed May 29 20:24:27 -12 2024 I: pbuilder-time-stamp: 1717057467 Thu May 30 08:33:36 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ff4a-armhf-rb.debian.net. Thu May 30 08:33:36 UTC 2024 I: Preparing to do remote build '2' on ff4a-armhf-rb.debian.net. Thu May 30 08:46:06 UTC 2024 I: Deleting $TMPDIR on ff4a-armhf-rb.debian.net. Thu May 30 08:46:09 UTC 2024 I: lumpy-sv_0.3.1+dfsg-7_armhf.changes: Format: 1.8 Date: Thu, 06 Oct 2022 11:30:25 +0200 Source: lumpy-sv Binary: lumpy-sv lumpy-sv-dbgsym lumpy-sv-examples Architecture: armhf all Version: 0.3.1+dfsg-7 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 Changes: lumpy-sv (0.3.1+dfsg-7) unstable; urgency=medium . * Fix watch file * Standards-Version: 4.6.1 (routine-update) Checksums-Sha1: 6192b0b557bd98901192f6299cad86710956a21b 2365596 lumpy-sv-dbgsym_0.3.1+dfsg-7_armhf.deb 7d202a49a2474875a2c2aa3dc0b3b941630ba417 54564012 lumpy-sv-examples_0.3.1+dfsg-7_all.deb 1378e86c8c48c41ba8471bc9f85bdac6c1948186 7092 lumpy-sv_0.3.1+dfsg-7_armhf.buildinfo d24f7a54370d75da325f9abe7d5bea5e62960225 172928 lumpy-sv_0.3.1+dfsg-7_armhf.deb Checksums-Sha256: 4eb81f12d6f90f705005a1bff3a8f2ef0efb69a1a91ddfa6544e3947d4c339d8 2365596 lumpy-sv-dbgsym_0.3.1+dfsg-7_armhf.deb f06b7de49d5a5a220eff14572875a56b503e9e7827b88234d9dc9db77c719225 54564012 lumpy-sv-examples_0.3.1+dfsg-7_all.deb f2bf5deb2f48841e1dceef724b4805e8d9132cbea00dda5fced0210d15cf38b0 7092 lumpy-sv_0.3.1+dfsg-7_armhf.buildinfo 26488af249649d2f7d0f2d73677fff62d6f525ec1a964ef7440e1348199508ee 172928 lumpy-sv_0.3.1+dfsg-7_armhf.deb Files: 183ca3418eca988fa9d2eaeb9b0250fa 2365596 debug optional lumpy-sv-dbgsym_0.3.1+dfsg-7_armhf.deb 38e94aa4085abf723e6e812ed9375490 54564012 science optional lumpy-sv-examples_0.3.1+dfsg-7_all.deb 57eb8f859034c2db0d2dcbc70c5f6267 7092 science optional lumpy-sv_0.3.1+dfsg-7_armhf.buildinfo 66a290e2fab1c410ae93d8bddfcdbc3c 172928 science optional lumpy-sv_0.3.1+dfsg-7_armhf.deb Thu May 30 08:46:11 UTC 2024 I: diffoscope 268 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_31-6021.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.bqLug0aJ/lumpy-sv_0.3.1+dfsg-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.bqLug0aJ/lumpy-sv_0.3.1+dfsg-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.bqLug0aJ/lumpy-sv_0.3.1+dfsg-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.bqLug0aJ/b1/lumpy-sv_0.3.1+dfsg-7_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.bqLug0aJ/b2/lumpy-sv_0.3.1+dfsg-7_armhf.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: 0.992s) 0.992s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.638s) 0.638s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 1.351s CPU time consumed: 1.345s Thu May 30 08:46:13 UTC 2024 I: diffoscope 268 found no differences in the changes files, and a .buildinfo file also exists. Thu May 30 08:46:13 UTC 2024 I: lumpy-sv from trixie built successfully and reproducibly on armhf. Thu May 30 08:46:14 UTC 2024 I: Submitting .buildinfo files to external archives: Thu May 30 08:46:14 UTC 2024 I: Submitting 8.0K b1/lumpy-sv_0.3.1+dfsg-7_armhf.buildinfo.asc Thu May 30 08:46:16 UTC 2024 I: Submitting 8.0K b2/lumpy-sv_0.3.1+dfsg-7_armhf.buildinfo.asc Thu May 30 08:46:18 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu May 30 08:46:18 UTC 2024 I: Done submitting .buildinfo files. Thu May 30 08:46:18 UTC 2024 I: Removing signed lumpy-sv_0.3.1+dfsg-7_armhf.buildinfo.asc files: removed './b1/lumpy-sv_0.3.1+dfsg-7_armhf.buildinfo.asc' removed './b2/lumpy-sv_0.3.1+dfsg-7_armhf.buildinfo.asc'