Thu Apr 4 02:02:36 UTC 2024 I: starting to build ngmlr/trixie/i386 on jenkins on '2024-04-04 02:02' Thu Apr 4 02:02:36 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_8/21412/console.log Thu Apr 4 02:02:36 UTC 2024 I: Downloading source for trixie/ngmlr=0.2.7+git20210816.a2a31fb+dfsg-2 --2024-04-04 02:02:36-- http://deb.debian.org/debian/pool/main/n/ngmlr/ngmlr_0.2.7%2bgit20210816.a2a31fb%2bdfsg-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2209 (2.2K) [text/prs.lines.tag] Saving to: ‘ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2.dsc’ 0K .. 100% 212M=0s 2024-04-04 02:02:36 (212 MB/s) - ‘ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2.dsc’ saved [2209/2209] Thu Apr 4 02:02:36 UTC 2024 I: ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: ngmlr Binary: ngmlr Architecture: any Version: 0.2.7+git20210816.a2a31fb+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Nilesh Patra Homepage: https://github.com/philres/ngmlr Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/ngmlr Vcs-Git: https://salsa.debian.org/med-team/ngmlr.git Testsuite: autopkgtest Testsuite-Triggers: bedtools, samtools Build-Depends: debhelper-compat (= 13), cmake, zlib1g-dev, libssw-dev, libtclap-dev, libhts-dev, libsimde-dev Package-List: ngmlr deb science optional arch=any Checksums-Sha1: 162e7971ec0b0a830c2ff517f2fe83ccc36b30fd 667893 ngmlr_0.2.7+git20210816.a2a31fb+dfsg.orig.tar.gz d242cf198d0aa22b3ff3f682707f72a2424b8352 8084 ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2.debian.tar.xz Checksums-Sha256: df7d9a0074b4d5d307258b8f23e1df2960f6af071bac07c41e64d38ef442592d 667893 ngmlr_0.2.7+git20210816.a2a31fb+dfsg.orig.tar.gz e919ef334b228ca2e49701a28f0a5f40939a1fb0d3c5a0fe83032ca14d32cba1 8084 ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2.debian.tar.xz Files: 3f5470714ec6bf26aa5e24df22e66b92 667893 ngmlr_0.2.7+git20210816.a2a31fb+dfsg.orig.tar.gz 2efd9c80430797646299ab17ae555b6c 8084 ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAmFoIRoSHG5pbGVzaEBk ZWJpYW4ub3JnAAoJEAC650s0M2nx4XkP/3Ia0pduXZczXZ4lJp65pwxVe6kj6ENu iTUenTZUJuKigqMmSExqNR+isiCIuc9azXOoSImsEQgV5ioNECb7o7D6n0EfjIpz 4wgqAxzS+PtPbdjd3mYMU6tSUNOdGfU3H3Ruzh83G1X/E3QmpHqiig4A2oQ4775D gp5TzI80ibdd7JGPSvrxQv3dZ7fWkLMoFFSkn2DKES9Nt6X4ohsiAUs0TADkbVu0 1+QCJXqG+BguGEK1XDac9imKJ9NaVA+rTBjRoQaEbAGfwX5HICjhRnayY4d0oDU8 k74DVUFdgRkMd7bzYdBpxVtYwjkLXisXP5lIsrIEwQDBZvL6lxFMHK/UHU946vC7 S+8Fn3c4L8lCpOcuKLv0z48YyvmCUFMy+jgQuw/Nx2obyjAvP7BpKcRg8yQKBqfX 1Bbdu0r3s0Lv8lzYs/8Ui6Ww4g2E9U9YApTnjmkiyGk/rpg9RHbfBSbNwVZBu2zs nKPSVrSAyeKWFuOpZZFNowhuvFkuytVB7l9N68AAa8LkgwPV7sgjXeL+pU4zWqxv iayLUFirV10K5zIBh7+N4eqXg2/yLAs4vYZ51EUrTP3gLYFly85YDx2oIB6Hd3OK yCEoULFyePmcy5cAVn6SPiLii10xwNfmAYvfdoaytaaG1/wPLU8Bb2q7fL4lSe+/ JMcxrCSbuMh6 =kL8F -----END PGP SIGNATURE----- Thu Apr 4 02:02:36 UTC 2024 I: Checking whether the package is not for us Thu Apr 4 02:02:37 UTC 2024 I: Starting 1st build on remote node ionos16-i386.debian.net. Thu Apr 4 02:02:37 UTC 2024 I: Preparing to do remote build '1' on ionos16-i386.debian.net. Thu Apr 4 02:03:14 UTC 2024 I: Deleting $TMPDIR on ionos16-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue May 6 20:25:39 -12 2025 I: pbuilder-time-stamp: 1746606339 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: using eatmydata during job I: Copying source file I: copying [ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2.dsc] I: copying [./ngmlr_0.2.7+git20210816.a2a31fb+dfsg.orig.tar.gz] I: copying [./ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Oct 14 12:22:50 2021 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting ngmlr in ngmlr-0.2.7+git20210816.a2a31fb+dfsg dpkg-source: info: unpacking ngmlr_0.2.7+git20210816.a2a31fb+dfsg.orig.tar.gz dpkg-source: info: unpacking ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use-system-libs.patch dpkg-source: info: applying spellings.patch dpkg-source: info: applying simde.patch dpkg-source: info: applying VarArgsDefines.patch dpkg-source: info: applying AlignmentBuffer_noMatch.patch dpkg-source: info: applying fix-arm64.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/96322/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='849c8522778c42919b5e22a58691045f' 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='96322' 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.VZwyWDlS/pbuilderrc_HEym --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.VZwyWDlS/b1 --logfile b1/build.log ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2.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 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 6 17:46 /bin -> usr/bin I: user script /srv/workspace/pbuilder/96322/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), cmake, zlib1g-dev, libssw-dev, libtclap-dev, libhts-dev, libsimde-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19876 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 cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libssw-dev; however: Package libssw-dev is not installed. pbuilder-satisfydepends-dummy depends on libtclap-dev; however: Package libtclap-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libbrotli1{a} libcurl3-gnutls{a} libcurl4{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libjsoncpp25{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libproc2-0{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsimde-dev{a} libssh2-1{a} libssw-dev{a} libssw0{a} libsub-override-perl{a} libtclap-dev{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} m4{a} man-db{a} po-debconf{a} procps{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget 0 packages upgraded, 61 newly installed, 0 to remove and 0 not upgraded. Need to get 44.9 MB of archives. After unpacking 168 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 libproc2-0 i386 2:4.0.4-4 [65.4 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 procps i386 2:4.0.4-4 [876 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-2+b1 [314 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 libmagic1 i386 1:5.45-2+b1 [114 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-2+b1 [43.0 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-3 [1195 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.39.3-6 [93.3 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.7-1+b2 [39.6 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 man-db i386 2.12.0-3 [1413 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 autoconf all 2.71-3 [332 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 autopoint all 0.21-14 [496 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.9.14+dfsg-1.3+b2 [727 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 libarchive13 i386 3.7.2-1 [386 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b3 [314 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-4+b1 [20.7 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-4+b1 [60.7 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5+b3 [196 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.59.0-1 [82.5 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 libpsl5 i386 0.21.2-1+b1 [59.7 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 libssh2-1 i386 1.11.0-4 [224 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 libcurl4 i386 8.5.0-2 [463 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.5.0-2+b2 [104 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 libjsoncpp25 i386 1.9.5-6+b2 [89.2 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 librhash0 i386 1.4.3-3+b1 [143 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 libuv1 i386 1.48.0-1 [156 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 cmake-data all 3.28.3-1 [2128 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 cmake i386 3.28.3-1 [11.7 MB] Get: 36 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-7 [517 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 43 http://deb.debian.org/debian trixie/main i386 libelf1 i386 0.190-1+b1 [182 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1 [118 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 debhelper all 13.15.3 [901 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 libcurl3-gnutls i386 8.5.0-2 [454 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 libcurl4-gnutls-dev i386 8.5.0-2 [574 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 libdeflate0 i386 1.20-1 [46.9 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 libdeflate-dev i386 1.20-1 [56.0 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 libhtscodecs2 i386 1.6.0-1+b1 [68.5 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 libhts3 i386 1.19+ds-1 [490 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 liblzma-dev i386 5.6.1+really5.4.5-1 [304 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg-3+b1 [915 kB] Get: 57 http://deb.debian.org/debian trixie/main i386 libhts-dev i386 1.19+ds-1 [1660 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 libsimde-dev all 0.8.0-1 [458 kB] Get: 59 http://deb.debian.org/debian trixie/main i386 libssw0 i386 1.1-14 [25.6 kB] Get: 60 http://deb.debian.org/debian trixie/main i386 libssw-dev i386 1.1-14 [28.7 kB] Get: 61 http://deb.debian.org/debian trixie/main i386 libtclap-dev i386 1.2.5-1+b1 [3360 kB] Fetched 44.9 MB in 2s (29.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:i386. (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 ... 19876 files and directories currently installed.) Preparing to unpack .../00-libproc2-0_2%3a4.0.4-4_i386.deb ... Unpacking libproc2-0:i386 (2:4.0.4-4) ... Selecting previously unselected package procps. Preparing to unpack .../01-procps_2%3a4.0.4-4_i386.deb ... Unpacking procps (2:4.0.4-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.45-2+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../04-libmagic1_1%3a5.45-2+b1_i386.deb ... Unpacking libmagic1:i386 (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.45-2+b1_i386.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.21-14+b1_i386.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../07-libuchardet0_0.0.8-1+b1_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.23.0-3_i386.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.39.3-6_i386.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../10-libpipeline1_1.5.7-1+b2_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-1+b2) ... Selecting previously unselected package man-db. Preparing to unpack .../11-man-db_2.12.0-3_i386.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.5-1.3_all.deb ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+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 > ../ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2_source.changes dpkg-buildpackage: info: source package ngmlr dpkg-buildpackage: info: source version 0.2.7+git20210816.a2a31fb+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean --buildsystem cmake debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg' dh_auto_clean rm -rf bin make[1]: Leaving directory '/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg' dh_autoreconf_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake debian/rules binary dh binary --buildsystem cmake dh_update_autotools_config -O--buildsystem=cmake dh_autoreconf -O--buildsystem=cmake dh_auto_configure -O--buildsystem=cmake cd obj-i686-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/i386-linux-gnu .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 13.2.0 -- The CXX compiler identification is GNU 13.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found ZLIB: /usr/lib/i386-linux-gnu/libz.so (found version "1.3") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Performing Test COMPILER_SUPPORTS_CXX11 -- Performing Test COMPILER_SUPPORTS_CXX11 - Success CMake Deprecation Warning at src/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring done (0.8s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu dh_auto_build -O--buildsystem=cmake cd obj-i686-linux-gnu && make -j22 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg -B/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu --check-build-system 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Leaving directory '/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu' make -f src/CMakeFiles/recompile_always.dir/build.make src/CMakeFiles/recompile_always.dir/build make[3]: Entering directory '/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu' cd /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu/src && touch /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/main.cpp make[3]: Leaving directory '/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu' make -f src/CMakeFiles/ngmlr.dir/build.make src/CMakeFiles/ngmlr.dir/build make[3]: Leaving directory '/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu' [ 0%] Built target recompile_always [ 4%] Building CXX object src/CMakeFiles/ngmlr.dir/CS.cpp.o [ 8%] Building 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28%] Building CXX object src/CMakeFiles/ngmlr.dir/Logging.cpp.o cd /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/htslib -I/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/../lib -g -O2 -ffile-prefix-map=/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/ngmlr.dir/AlignmentMatrixFast.cpp.o -MF CMakeFiles/ngmlr.dir/AlignmentMatrixFast.cpp.o.d -o CMakeFiles/ngmlr.dir/AlignmentMatrixFast.cpp.o -c /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/AlignmentMatrixFast.cpp [ 32%] Building CXX object src/CMakeFiles/ngmlr.dir/CSstatic.cpp.o [ 36%] Building CXX object src/CMakeFiles/ngmlr.dir/LinearRegression.cpp.o cd /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/htslib -I/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/../lib -g -O2 -ffile-prefix-map=/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/ngmlr.dir/ArgParser.cpp.o -MF CMakeFiles/ngmlr.dir/ArgParser.cpp.o.d -o CMakeFiles/ngmlr.dir/ArgParser.cpp.o -c /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/ArgParser.cpp [ 40%] Building CXX object src/CMakeFiles/ngmlr.dir/ConvexAlign.cpp.o cd /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/htslib -I/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/../lib -g -O2 -ffile-prefix-map=/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 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/usr/bin/c++ -I/usr/include/htslib -I/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/../lib -g -O2 -ffile-prefix-map=/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/ngmlr.dir/CSstatic.cpp.o -MF CMakeFiles/ngmlr.dir/CSstatic.cpp.o.d -o CMakeFiles/ngmlr.dir/CSstatic.cpp.o -c /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/CSstatic.cpp cd /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/htslib -I/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/../lib -g -O2 -ffile-prefix-map=/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/ngmlr.dir/ConvexAlign.cpp.o -MF CMakeFiles/ngmlr.dir/ConvexAlign.cpp.o.d -o CMakeFiles/ngmlr.dir/ConvexAlign.cpp.o -c /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/ConvexAlign.cpp cd /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/htslib -I/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/../lib -g -O2 -ffile-prefix-map=/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/ngmlr.dir/ConvexAlignFast.cpp.o -MF CMakeFiles/ngmlr.dir/ConvexAlignFast.cpp.o.d -o CMakeFiles/ngmlr.dir/ConvexAlignFast.cpp.o -c /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/ConvexAlignFast.cpp cd /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/htslib -I/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/../lib -g -O2 -ffile-prefix-map=/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/ngmlr.dir/LinearRegression.cpp.o -MF CMakeFiles/ngmlr.dir/LinearRegression.cpp.o.d -o CMakeFiles/ngmlr.dir/LinearRegression.cpp.o -c /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/LinearRegression.cpp [ 44%] Building CXX object src/CMakeFiles/ngmlr.dir/main.cpp.o [ 48%] Building CXX object src/CMakeFiles/ngmlr.dir/PrefixTable.cpp.o cd /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/htslib -I/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/../lib -g -O2 -ffile-prefix-map=/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/ngmlr.dir/Logging.cpp.o -MF CMakeFiles/ngmlr.dir/Logging.cpp.o.d -o CMakeFiles/ngmlr.dir/Logging.cpp.o -c /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/Logging.cpp [ 52%] Building CXX object src/CMakeFiles/ngmlr.dir/NGM.cpp.o [ 56%] Building CXX object src/CMakeFiles/ngmlr.dir/AlignmentBuffer.cpp.o [ 60%] Building CXX object src/CMakeFiles/ngmlr.dir/NGMTask.cpp.o cd /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/htslib -I/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/../lib -g -O2 -ffile-prefix-map=/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/ngmlr.dir/main.cpp.o -MF CMakeFiles/ngmlr.dir/main.cpp.o.d -o CMakeFiles/ngmlr.dir/main.cpp.o -c /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/main.cpp cd /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/htslib -I/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/../lib -g -O2 -ffile-prefix-map=/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/ngmlr.dir/PrefixTable.cpp.o -MF CMakeFiles/ngmlr.dir/PrefixTable.cpp.o.d -o CMakeFiles/ngmlr.dir/PrefixTable.cpp.o -c /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/PrefixTable.cpp [ 64%] Building CXX object src/CMakeFiles/ngmlr.dir/SAMWriter.cpp.o [ 68%] Building CXX object src/CMakeFiles/ngmlr.dir/ReadProvider.cpp.o [ 72%] Building CXX object src/CMakeFiles/ngmlr.dir/SamParser.cpp.o cd /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/htslib -I/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/../lib -g -O2 -ffile-prefix-map=/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/ngmlr.dir/NGM.cpp.o -MF CMakeFiles/ngmlr.dir/NGM.cpp.o.d -o CMakeFiles/ngmlr.dir/NGM.cpp.o -c /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/NGM.cpp cd /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/htslib -I/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/../lib -g -O2 -ffile-prefix-map=/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/ngmlr.dir/NGMTask.cpp.o -MF CMakeFiles/ngmlr.dir/NGMTask.cpp.o.d -o CMakeFiles/ngmlr.dir/NGMTask.cpp.o -c /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/NGMTask.cpp [ 76%] Building CXX object src/CMakeFiles/ngmlr.dir/SequenceProvider.cpp.o cd /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/htslib -I/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/../lib -g -O2 -ffile-prefix-map=/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/ngmlr.dir/AlignmentBuffer.cpp.o -MF CMakeFiles/ngmlr.dir/AlignmentBuffer.cpp.o.d -o CMakeFiles/ngmlr.dir/AlignmentBuffer.cpp.o -c /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/AlignmentBuffer.cpp [ 80%] Building CXX object src/CMakeFiles/ngmlr.dir/OutputReadBuffer.cpp.o cd /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/htslib -I/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/../lib -g -O2 -ffile-prefix-map=/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/ngmlr.dir/ReadProvider.cpp.o -MF CMakeFiles/ngmlr.dir/ReadProvider.cpp.o.d -o CMakeFiles/ngmlr.dir/ReadProvider.cpp.o -c /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/ReadProvider.cpp cd /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/htslib -I/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/../lib -g -O2 -ffile-prefix-map=/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/ngmlr.dir/SamParser.cpp.o -MF CMakeFiles/ngmlr.dir/SamParser.cpp.o.d -o CMakeFiles/ngmlr.dir/SamParser.cpp.o -c /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/SamParser.cpp cd /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/htslib -I/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/../lib -g -O2 -ffile-prefix-map=/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/ngmlr.dir/SAMWriter.cpp.o -MF CMakeFiles/ngmlr.dir/SAMWriter.cpp.o.d -o CMakeFiles/ngmlr.dir/SAMWriter.cpp.o -c /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/SAMWriter.cpp [ 84%] Building CXX object src/CMakeFiles/ngmlr.dir/ScoreBuffer.cpp.o cd /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/htslib -I/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/../lib -g -O2 -ffile-prefix-map=/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/ngmlr.dir/SequenceProvider.cpp.o -MF CMakeFiles/ngmlr.dir/SequenceProvider.cpp.o.d -o CMakeFiles/ngmlr.dir/SequenceProvider.cpp.o -c /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/SequenceProvider.cpp cd /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/htslib -I/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/../lib -g -O2 -ffile-prefix-map=/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/ngmlr.dir/OutputReadBuffer.cpp.o -MF CMakeFiles/ngmlr.dir/OutputReadBuffer.cpp.o.d -o CMakeFiles/ngmlr.dir/OutputReadBuffer.cpp.o -c /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/OutputReadBuffer.cpp cd /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/htslib -I/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/../lib -g -O2 -ffile-prefix-map=/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/ngmlr.dir/ScoreBuffer.cpp.o -MF CMakeFiles/ngmlr.dir/ScoreBuffer.cpp.o.d -o CMakeFiles/ngmlr.dir/ScoreBuffer.cpp.o -c /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/ScoreBuffer.cpp [ 88%] Building CXX object src/CMakeFiles/ngmlr.dir/StrippedSW.cpp.o cd /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/htslib -I/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/../lib -g -O2 -ffile-prefix-map=/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/ngmlr.dir/StrippedSW.cpp.o -MF CMakeFiles/ngmlr.dir/StrippedSW.cpp.o.d -o CMakeFiles/ngmlr.dir/StrippedSW.cpp.o -c /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/StrippedSW.cpp /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/main.cpp:56:153: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 56 | Log.Message("ngmlr %s%s (build: %s %s, start: %s)", version.str().c_str(), cDebug ? " debug" : "", __DATE__, __TIME__, currentDateTime().c_str()); | ^ /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/main.cpp:56:108: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 56 | Log.Message("ngmlr %s%s (build: %s %s, start: %s)", version.str().c_str(), cDebug ? " debug" : "", __DATE__, __TIME__, currentDateTime().c_str()); | ^~~~~~~~ /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/Logging.cpp: In function ‘std::string add_timestamp(std::string)’: /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/Logging.cpp:118:41: warning: ‘%02i’ directive writing between 2 and 11 bytes into a region of size between 8 and 15 [-Wformat-overflow=] 118 | sprintf(timestamp, "%4i-%02i-%02i_%02i-%02i-%02i", tm->tm_year + 1900, tm->tm_mon + 1, tm->tm_mday, tm->tm_hour, tm->tm_min, | ^~~~ /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/Logging.cpp:118:36: note: directive argument in the range [-2147483647, 2147483647] 118 | sprintf(timestamp, "%4i-%02i-%02i_%02i-%02i-%02i", tm->tm_year + 1900, tm->tm_mon + 1, tm->tm_mday, tm->tm_hour, tm->tm_min, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:906, from /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/Logging.cpp:7: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘std::string add_timestamp(std::string)’ at /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/Logging.cpp:118:10: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 20 and 72 bytes into a destination of size 20 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 92%] Building CXX object src/CMakeFiles/ngmlr.dir/unix.cpp.o cd /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/htslib -I/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/../lib -g -O2 -ffile-prefix-map=/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/ngmlr.dir/unix.cpp.o -MF CMakeFiles/ngmlr.dir/unix.cpp.o.d -o CMakeFiles/ngmlr.dir/unix.cpp.o -c /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/unix.cpp [ 96%] Building CXX object src/CMakeFiles/ngmlr.dir/unix_threads.cpp.o cd /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -I/usr/include/htslib -I/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/../lib -g -O2 -ffile-prefix-map=/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/ngmlr.dir/unix_threads.cpp.o -MF CMakeFiles/ngmlr.dir/unix_threads.cpp.o.d -o CMakeFiles/ngmlr.dir/unix_threads.cpp.o -c /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/unix_threads.cpp /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/OutputReadBuffer.cpp: In destructor ‘OutputReadBuffer::~OutputReadBuffer()’: /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/OutputReadBuffer.cpp:17:17: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 17 | throw "Elements left in buffer!"; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/OutputReadBuffer.cpp:17:17: note: in C++11 destructors default to ‘noexcept’ /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/ConvexAlignFast.cpp: In member function ‘Convex::AlignmentMatrixFast::Score Convex::ConvexAlignFast::fwdFillMatrixSSESimple(const char*, const char*, FwdResults&, int)’: /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/ConvexAlignFast.cpp:974:48: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] 974 | diag_score_sse = _mm_setr_ps(matrix->getElementUp(x - 1, y - 1)->score,up0.score,up1.score,up2.score); | ^ /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/ConvexAlignFast.cpp: In function ‘float Convex::ssat(__m128, int)’: /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/ConvexAlignFast.cpp:908:7: note: the ABI for passing parameters with 16-byte alignment has changed in GCC 4.6 908 | float ssat(__m128 d, int i) | ^~~~ /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/src/ConvexAlignFast.cpp:908:7: warning: SSE vector argument without SSE enabled changes the ABI [-Wpsabi] [100%] Linking CXX executable /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/bin/ngmlr-0.2.8/ngmlr cd /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngmlr.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ngmlr.dir/AlignmentMatrix.cpp.o CMakeFiles/ngmlr.dir/AlignmentMatrixFast.cpp.o CMakeFiles/ngmlr.dir/ArgParser.cpp.o CMakeFiles/ngmlr.dir/CS.cpp.o CMakeFiles/ngmlr.dir/CSstatic.cpp.o CMakeFiles/ngmlr.dir/ConvexAlign.cpp.o CMakeFiles/ngmlr.dir/ConvexAlignFast.cpp.o CMakeFiles/ngmlr.dir/LinearRegression.cpp.o CMakeFiles/ngmlr.dir/Logging.cpp.o CMakeFiles/ngmlr.dir/MappedRead.cpp.o CMakeFiles/ngmlr.dir/main.cpp.o CMakeFiles/ngmlr.dir/NGM.cpp.o CMakeFiles/ngmlr.dir/NGMTask.cpp.o CMakeFiles/ngmlr.dir/AlignmentBuffer.cpp.o CMakeFiles/ngmlr.dir/PrefixTable.cpp.o CMakeFiles/ngmlr.dir/ReadProvider.cpp.o CMakeFiles/ngmlr.dir/SamParser.cpp.o CMakeFiles/ngmlr.dir/SAMWriter.cpp.o CMakeFiles/ngmlr.dir/SequenceProvider.cpp.o CMakeFiles/ngmlr.dir/OutputReadBuffer.cpp.o CMakeFiles/ngmlr.dir/ScoreBuffer.cpp.o CMakeFiles/ngmlr.dir/StrippedSW.cpp.o CMakeFiles/ngmlr.dir/unix.cpp.o CMakeFiles/ngmlr.dir/unix_threads.cpp.o -o /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/bin/ngmlr-0.2.8/ngmlr -lz -lssw make[3]: Leaving directory '/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu' [100%] Built target ngmlr make[2]: Leaving directory '/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu' dh_auto_test -O--buildsystem=cmake create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_auto_install --destdir=debian/ngmlr/ -O--buildsystem=cmake cd obj-i686-linux-gnu && make -j22 install DESTDIR=/build/reproducible-path/ngmlr-0.2.7\+git20210816.a2a31fb\+dfsg/debian/ngmlr AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg -B/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/debian/ngmlr/usr/bin/ngmlr make[1]: Leaving directory '/build/reproducible-path/ngmlr-0.2.7+git20210816.a2a31fb+dfsg/obj-i686-linux-gnu' dh_installdocs -O--buildsystem=cmake dh_installchangelogs -O--buildsystem=cmake dh_installexamples -O--buildsystem=cmake dh_installman -O--buildsystem=cmake dh_installsystemduser -O--buildsystem=cmake dh_perl -O--buildsystem=cmake dh_link -O--buildsystem=cmake dh_strip_nondeterminism -O--buildsystem=cmake dh_compress -O--buildsystem=cmake dh_fixperms -O--buildsystem=cmake dh_missing -O--buildsystem=cmake dh_dwz -a -O--buildsystem=cmake dh_strip -a -O--buildsystem=cmake dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'ngmlr' in '../ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2_i386.deb'. dpkg-deb: building package 'ngmlr-dbgsym' in '../ngmlr-dbgsym_0.2.7+git20210816.a2a31fb+dfsg-2_i386.deb'. dpkg-genbuildinfo --build=binary -O../ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2_i386.buildinfo dpkg-genchanges --build=binary -O../ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2_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) 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/96322 and its subdirectories I: Current time: Tue May 6 20:26:13 -12 2025 I: pbuilder-time-stamp: 1746606373 Thu Apr 4 02:03:15 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos12-i386.debian.net. Thu Apr 4 02:03:15 UTC 2024 I: Preparing to do remote build '2' on ionos12-i386.debian.net. Thu Apr 4 02:05:14 UTC 2024 I: Deleting $TMPDIR on ionos12-i386.debian.net. Thu Apr 4 02:05:15 UTC 2024 I: ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2_i386.changes: Format: 1.8 Date: Thu, 14 Oct 2021 17:34:16 +0530 Source: ngmlr Binary: ngmlr ngmlr-dbgsym Architecture: i386 Version: 0.2.7+git20210816.a2a31fb+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: ngmlr - CoNvex Gap-cost alignMents for Long Reads Changes: ngmlr (0.2.7+git20210816.a2a31fb+dfsg-2) unstable; urgency=medium . * Add patch to fix arm build * d/control: Remove Pranav from uploaders (not active) * d/t/run-unit-test: diff with -u flag Checksums-Sha1: 81b1ea048d74b9413087e195d4097295b7431a00 1104936 ngmlr-dbgsym_0.2.7+git20210816.a2a31fb+dfsg-2_i386.deb 6cd64842d8d376c90d49ab18ee8354441bf0b14e 6677 ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2_i386.buildinfo cd7ad350fae3d9bdd1b647e77cf031106aee0d85 696480 ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2_i386.deb Checksums-Sha256: cd82aea1261cad18635812c382b5610a2c27ec71c30cffd2bf15cfb695e74cb4 1104936 ngmlr-dbgsym_0.2.7+git20210816.a2a31fb+dfsg-2_i386.deb c380b18c1deed642df0e20ae29fa9386d348a201aa6825bc45cee943f4b6d182 6677 ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2_i386.buildinfo 7d8693f30831b5dd5719b724bb3d3076fc672ff99403a2f7726a5c6041459ec7 696480 ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2_i386.deb Files: b86c435f0b0d84f42f24d907b2afbde1 1104936 debug optional ngmlr-dbgsym_0.2.7+git20210816.a2a31fb+dfsg-2_i386.deb 69aa6d41cffd1c5a84b11b1a47e79543 6677 science optional ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2_i386.buildinfo aaf9bdb7107c4183edc71b4a1881ca44 696480 science optional ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2_i386.deb Thu Apr 4 02:05:16 UTC 2024 I: diffoscope 262 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_8-21412.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.VZwyWDlS/ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.VZwyWDlS/ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.VZwyWDlS/ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.VZwyWDlS/b1/ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.VZwyWDlS/b2/ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2_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: 0.357s) 0.357s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.034s) 0.034s 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: 694ms CPU time consumed: 689ms Thu Apr 4 02:05:17 UTC 2024 I: diffoscope 262 found no differences in the changes files, and a .buildinfo file also exists. Thu Apr 4 02:05:17 UTC 2024 I: ngmlr from trixie built successfully and reproducibly on i386. Thu Apr 4 02:05:19 UTC 2024 I: Submitting .buildinfo files to external archives: Thu Apr 4 02:05:19 UTC 2024 I: Submitting 8.0K b1/ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2_i386.buildinfo.asc Thu Apr 4 02:05:20 UTC 2024 I: Submitting 8.0K b2/ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2_i386.buildinfo.asc Thu Apr 4 02:05:20 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Apr 4 02:05:20 UTC 2024 I: Done submitting .buildinfo files. Thu Apr 4 02:05:20 UTC 2024 I: Removing signed ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2_i386.buildinfo.asc files: removed './b1/ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2_i386.buildinfo.asc' removed './b2/ngmlr_0.2.7+git20210816.a2a31fb+dfsg-2_i386.buildinfo.asc'