Sun Nov 10 15:58:10 UTC 2024 I: starting to build parsnp/trixie/i386 on jenkins on '2024-11-10 15:58' Sun Nov 10 15:58:10 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_19/29348/console.log Sun Nov 10 15:58:10 UTC 2024 I: Downloading source for trixie/parsnp=2.0.6+dfsg-1 --2024-11-10 15:58:11-- http://deb.debian.org/debian/pool/main/p/parsnp/parsnp_2.0.6%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2245 (2.2K) [text/prs.lines.tag] Saving to: ‘parsnp_2.0.6+dfsg-1.dsc’ 0K .. 100% 222M=0s 2024-11-10 15:58:11 (222 MB/s) - ‘parsnp_2.0.6+dfsg-1.dsc’ saved [2245/2245] Sun Nov 10 15:58:11 UTC 2024 I: parsnp_2.0.6+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: parsnp Binary: parsnp Architecture: any Version: 2.0.6+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://harvest.readthedocs.org/en/latest/content/parsnp.html Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/parsnp Vcs-Git: https://salsa.debian.org/med-team/parsnp.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all-dev, python3-setuptools, cython3, libmuscle-dev Package-List: parsnp deb science optional arch=any Checksums-Sha1: b54afea33468fb9e2c64178114ca7f5015e19c61 142280 parsnp_2.0.6+dfsg.orig.tar.xz 4a7749dd98d644ec2ac93f6bb4a5ad482314374b 10256 parsnp_2.0.6+dfsg-1.debian.tar.xz Checksums-Sha256: 796bd591486d2dac236f9e1d5141fdd0b852bfde349c7be5e22a1e187e902f84 142280 parsnp_2.0.6+dfsg.orig.tar.xz 285c1f28e6a05ac8695967768d51dda5bfecfa3aa4f8b442124cc978701aa691 10256 parsnp_2.0.6+dfsg-1.debian.tar.xz Files: c97415d435ae528a5b162dcfef7e2172 142280 parsnp_2.0.6+dfsg.orig.tar.xz de8ad2d7b72e119c314b1d712db05e92 10256 parsnp_2.0.6+dfsg-1.debian.tar.xz Dgit: b1f33fab8a21d578529f45157debacecaf0d9e3c debian archive/debian/2.0.6+dfsg-1 https://git.dgit.debian.org/parsnp -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmcnnIYUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdq3UhAAsCpMmkvXG9So9gTin/UDKTGVBpVo 6WHNWpRabeR+t8j2u/hjxpRExjAwsgUdYUmLuexA9d6UONwUv3VoVPQvIKDR3xsY nCfloL/R4VlsWAQSfgxBF0UH9qnqH61J1cRNpHz91E/CZtC7+b3Kn03bm97nNeDc AshnRJ6dLHFzcJ74UeRm/qzC8TIH91rlspwcGyQm2yFfnx9+sFjjJa9KDTxOg3Qq +p7V3d4ffu7XhVcamBaXbrhVip7+dzDrr9OWlDzM73erV6qh3M+Ljv5dfzuDMJnW tp48uZp6oh1ThNWCZBqoWj0X6/42DFqVAdrRq4SZ/+N1L8budashkiBut6XBrywz DmUsBbngqqB/W3OSmml5hrcfF+F3ZP9aWw4VgCJ8nw+pMR0/lWSPvDGuJVKdxHUO KUoUbktSux+Tk4q9ETKEM/26pHOIAJgwTYjsKjIuqGTq54iU0H6LxWy8Ghg8Zxb4 IKgQy9uFlIhI05cxpxiEu2f3hHx7hTWF9IXqzcqqalmqL4+CEGCPgxKF46T8gUa3 MmaXFVLYF3S/WoJAKNCNcn6pr5VfUziViHX648BM7ka5uHQ3ybig/7eDkIMnFxDq GkjC+DD+i0Cj4GUVvmZf+Sx3kwDpIGdq/zAmz6rN5nernblDKFFkZPY5sD9usZYm 3ZNdD+YHZt8H8zU= =Wy5K -----END PGP SIGNATURE----- Sun Nov 10 15:58:11 UTC 2024 I: Checking whether the package is not for us Sun Nov 10 15:58:11 UTC 2024 I: Starting 1st build on remote node infom07-i386.debian.net. Sun Nov 10 15:58:11 UTC 2024 I: Preparing to do remote build '1' on infom07-i386.debian.net. Sun Nov 10 15:59:07 UTC 2024 I: Deleting $TMPDIR on infom07-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Nov 10 03:58:13 -12 2024 I: pbuilder-time-stamp: 1731254293 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 [parsnp_2.0.6+dfsg-1.dsc] I: copying [./parsnp_2.0.6+dfsg.orig.tar.xz] I: copying [./parsnp_2.0.6+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Nov 3 15:53:42 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./parsnp_2.0.6+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting parsnp in parsnp-2.0.6+dfsg dpkg-source: info: unpacking parsnp_2.0.6+dfsg.orig.tar.xz dpkg-source: info: unpacking parsnp_2.0.6+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying add_missing_interpreter_line.patch dpkg-source: info: applying proper_calls_to_tools.patch dpkg-source: info: applying drop_m64.patch dpkg-source: info: applying fix_build_with_as-needed.patch dpkg-source: info: applying non-versioned-libs.patch dpkg-source: info: applying blhc-fix.patch dpkg-source: info: applying py3-parsnp-libs.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/29292/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=6 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='7f60bffda6dd4dfd99829b2fc3c0f2ba' 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='29292' 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.kQz6T86e/pbuilderrc_hRZN --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.kQz6T86e/b1 --logfile b1/build.log parsnp_2.0.6+dfsg-1.dsc' SUDO_GID='111' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom07-i386 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/29292/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all-dev, python3-setuptools, cython3, libmuscle-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 ... 19955 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-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on libmuscle-dev; however: Package libmuscle-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} cython3{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} libcom-err2{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libmagic-mgc{a} libmagic1t64{a} libmuscle-dev{a} libmuscle1{a} libnsl2{a} libpipeline1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libreadline8t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-all-dev{a} python3-autocommand{a} python3-dev{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common krb5-locales libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 78 newly installed, 0 to remove and 0 not upgraded. Need to get 41.2 MB of archives. After unpacking 159 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 libpython3.12-minimal i386 3.12.7-3 [814 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.3-2 [107 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 python3.12-minimal i386 3.12.7-3 [2236 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 tzdata all 2024b-3 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 libcom-err2 i386 1.47.1-1+b1 [23.4 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 libkeyutils1 i386 1.6.3-4 [9600 B] Get: 12 http://deb.debian.org/debian trixie/main i386 libkrb5-3 i386 1.21.3-3 [350 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 libtirpc3t64 i386 1.3.4+ds-1.3+b1 [90.5 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 libnsl2 i386 1.3.0-3+b3 [42.7 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 libreadline8t64 i386 8.2-5 [173 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libpython3.12-stdlib i386 3.12.7-3 [1964 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 python3.12 i386 3.12.7-3 [671 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian trixie/main i386 python3 i386 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-5 [1196 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.2-9 [102 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 autopoint all 0.22.5-2 [723 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 cython3 i386 3.0.11+dfsg-1 [2429 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-8 [517 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 43 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 45 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-5+b1 [9583 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.1 [733 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 debhelper all 13.20 [915 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 57 http://deb.debian.org/debian trixie/main i386 python3-inflect all 7.3.1-2 [32.4 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 59 http://deb.debian.org/debian trixie/main i386 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 60 http://deb.debian.org/debian trixie/main i386 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 61 http://deb.debian.org/debian trixie/main i386 python3-zipp all 3.20.2-1 [10.3 kB] Get: 62 http://deb.debian.org/debian trixie/main i386 python3-setuptools all 74.1.2-2 [736 kB] Get: 63 http://deb.debian.org/debian trixie/main i386 dh-python all 6.20241024 [109 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 libexpat1-dev i386 2.6.3-2 [165 kB] Get: 65 http://deb.debian.org/debian trixie/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 66 http://deb.debian.org/debian trixie/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 67 http://deb.debian.org/debian trixie/main i386 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 68 http://deb.debian.org/debian trixie/main i386 libmuscle1 i386 3.7+4565-8 [234 kB] Get: 69 http://deb.debian.org/debian trixie/main i386 libmuscle-dev i386 3.7+4565-8 [293 kB] Get: 70 http://deb.debian.org/debian trixie/main i386 libpython3.12t64 i386 3.12.7-3 [2170 kB] Get: 71 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB] Get: 72 http://deb.debian.org/debian trixie/main i386 libpython3.12-dev i386 3.12.7-3 [5282 kB] Get: 73 http://deb.debian.org/debian trixie/main i386 libpython3-dev i386 3.12.6-1 [9956 B] Get: 74 http://deb.debian.org/debian trixie/main i386 libpython3-all-dev i386 3.12.6-1 [1068 B] Get: 75 http://deb.debian.org/debian trixie/main i386 python3-all i386 3.12.6-1 [1040 B] Get: 76 http://deb.debian.org/debian trixie/main i386 python3.12-dev i386 3.12.7-3 [505 kB] Get: 77 http://deb.debian.org/debian trixie/main i386 python3-dev i386 3.12.6-1 [26.1 kB] Get: 78 http://deb.debian.org/debian trixie/main i386 python3-all-dev i386 3.12.6-1 [1068 B] Fetched 41.2 MB in 4s (11.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal: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 ... 19955 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_i386.deb ... Unpacking libpython3.12-minimal:i386 (3.12.7-3) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.6.3-2_i386.deb ... Unpacking libexpat1:i386 (2.6.3-2) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_i386.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:i386 (3.12.7-3) ... Setting up libexpat1:i386 (2.6.3-2) ... Setting up python3.12-minimal (3.12.7-3) ... 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 ... 20275 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_i386.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:i386. Preparing to unpack .../04-libkrb5support0_1.21.3-3_i386.deb ... Unpacking libkrb5support0:i386 (1.21.3-3) ... Selecting previously unselected package libcom-err2:i386. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_i386.deb ... Unpacking libcom-err2:i386 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:i386. Preparing to unpack .../06-libk5crypto3_1.21.3-3_i386.deb ... Unpacking libk5crypto3:i386 (1.21.3-3) ... 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Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3 to /lib/i386-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3.0.0 to /lib/i386-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:i386 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:i386. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_i386.deb ... Unpacking libnsl2:i386 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:i386. Preparing to unpack .../14-libreadline8t64_8.2-5_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:i386. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_i386.deb ... Unpacking libpython3.12-stdlib:i386 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_i386.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... 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 ... 21337 files and directories currently installed.) Preparing to unpack .../00-python3_3.12.6-1_i386.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sensible-utils. 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Selecting previously unselected package libxml2:i386. Preparing to unpack .../26-libxml2_2.12.7+dfsg+really2.9.14-0.1_i386.deb ... Unpacking libxml2:i386 (2.12.7+dfsg+really2.9.14-0.1) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.22.5-2_i386.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package python3-autocommand. Preparing to unpack .../31-python3-autocommand_2.2.2-3_all.deb ... Unpacking python3-autocommand (2.2.2-3) ... 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Unpacking python3.12-dev (3.12.7-3) ... Selecting previously unselected package python3-dev. Preparing to unpack .../55-python3-dev_3.12.6-1_i386.deb ... Unpacking python3-dev (3.12.6-1) ... Selecting previously unselected package python3-all-dev. Preparing to unpack .../56-python3-all-dev_3.12.6-1_i386.deb ... Unpacking python3-all-dev (3.12.6-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:i386 (1.5.8-1) ... Setting up libkeyutils1:i386 (1.6.3-4) ... Setting up libicu72:i386 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-9) ... Setting up libmuscle1 (3.7+4565-8) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:i386 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:i386 (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:i386 (0.192-4) ... Setting up libkrb5support0:i386 (1.21.3-3) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Nov 10 15:58:35 UTC 2024. Universal Time is now: Sun Nov 10 15:58:35 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libexpat1-dev:i386 (2.6.3-2) ... Setting up libmuscle-dev (3.7+4565-8) ... Setting up autopoint (0.22.5-2) ... Setting up libk5crypto3:i386 (1.21.3-3) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:i386 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:i386 (0.0.8-1+b2) ... Setting up netbase (6.4) ... Setting up libkrb5-3:i386 (1.21.3-3) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 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 (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:i386 (1.21.3-3) ... Setting up libjs-sphinxdoc (7.4.7-4) ... Setting up libreadline8t64:i386 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libtirpc3t64:i386 (1.3.4+ds-1.3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libnsl2:i386 (1.3.0-3+b3) ... Setting up libpython3.12-stdlib:i386 (3.12.7-3) ... Setting up python3.12 (3.12.7-3) ... Setting up debhelper (13.20) ... Setting up libpython3.12t64:i386 (3.12.7-3) ... Setting up libpython3-stdlib:i386 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up libpython3.12-dev:i386 (3.12.7-3) ... Setting up python3-zipp (3.20.2-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3.12-dev (3.12.7-3) ... Setting up cython3 (3.0.11+dfsg-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up libpython3-dev:i386 (3.12.6-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-all (3.12.6-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up libpython3-all-dev:i386 (3.12.6-1) ... Setting up python3-dev (3.12.6-1) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-all-dev (3.12.6-1) ... Setting up python3-setuptools (74.1.2-2) ... Setting up dh-python (6.20241024) ... Processing triggers for libc-bin (2.40-3) ... 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/parsnp-2.0.6+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 > ../parsnp_2.0.6+dfsg-1_source.changes dpkg-buildpackage: info: source package parsnp dpkg-buildpackage: info: source version 2.0.6+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf configure.ac:23: warning: AC_OUTPUT should be used without arguments. configure.ac:23: You should run autoupdate. configure.ac:3: installing './compile' configure.ac:2: installing './install-sh' configure.ac:2: installing './missing' src/Makefile.am:4: warning: source file './ext/iniFile.cpp' is in a subdirectory, src/Makefile.am:4: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least one source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, this automake: behavior may change in a future Automake major version, with object automake: files being placed in the same subdirectory as the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibilities. src/Makefile.am: installing './depcomp' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/parsnp-2.0.6+dfsg' dh_auto_configure -- --with-libmuscle=/usr/include/libMUSCLE-3.7 ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-libmuscle=/usr/include/libMUSCLE-3.7 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for libMUSCLE/muscle.h... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: executing depfiles commands make[1]: Leaving directory '/build/reproducible-path/parsnp-2.0.6+dfsg' dh_auto_build make -j6 make[1]: Entering directory '/build/reproducible-path/parsnp-2.0.6+dfsg' Making all in src make[2]: Entering directory '/build/reproducible-path/parsnp-2.0.6+dfsg/src' g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parsnp_core-MuscleInterface.o `test -f 'MuscleInterface.cpp' || echo './'`MuscleInterface.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parsnp_core-parsnp.o `test -f 'parsnp.cpp' || echo './'`parsnp.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parsnp_core-LCB.o `test -f 'LCB.cpp' || echo './'`LCB.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parsnp_core-LCR.o `test -f 'LCR.cpp' || echo './'`LCR.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parsnp_core-TMum.o `test -f 'TMum.cpp' || echo './'`TMum.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parsnp_core-Converter.o `test -f 'Converter.cpp' || echo './'`Converter.cpp g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parsnp_core-iniFile.o `test -f './ext/iniFile.cpp' || echo './'`./ext/iniFile.cpp parsnp.cpp: In member function 'void Aligner::writeOutput(std::string, std::vector&)': parsnp.cpp:955:28: warning: '%d' directive writing between 1 and 11 bytes into a region of size 9 [-Wformat-overflow=] 955 | sprintf(b,"%d",(int)z+1);// C-style string formed without null | ^~ parsnp.cpp:955:27: note: directive argument in the range [-2147483647, 2147483647] 955 | sprintf(b,"%d",(int)z+1);// C-style string formed without null | ^~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from parsnp.hh:14, from parsnp.cpp:54: In function 'int sprintf(char*, const char*, ...)', inlined from 'void Aligner::writeOutput(std::string, std::vector&)' at parsnp.cpp:955:24: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 12 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/parsnp-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o parsnp_core parsnp_core-MuscleInterface.o parsnp_core-parsnp.o parsnp_core-LCB.o parsnp_core-LCR.o parsnp_core-TMum.o parsnp_core-Converter.o parsnp_core-iniFile.o -fopenmp -lstdc++ -lpthread -L/usr/include/libMUSCLE-3.7/lib -lMUSCLE make[2]: Leaving directory '/build/reproducible-path/parsnp-2.0.6+dfsg/src' make[2]: Entering directory '/build/reproducible-path/parsnp-2.0.6+dfsg' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/reproducible-path/parsnp-2.0.6+dfsg' make[1]: Leaving directory '/build/reproducible-path/parsnp-2.0.6+dfsg' dh_auto_test make -j6 check "TESTSUITEFLAGS=-j6 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/parsnp-2.0.6+dfsg' Making check in src make[2]: Entering directory '/build/reproducible-path/parsnp-2.0.6+dfsg/src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/parsnp-2.0.6+dfsg/src' make[2]: Entering directory '/build/reproducible-path/parsnp-2.0.6+dfsg' make[2]: Nothing to be done for 'check-am'. make[2]: Leaving directory '/build/reproducible-path/parsnp-2.0.6+dfsg' make[1]: Leaving directory '/build/reproducible-path/parsnp-2.0.6+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/parsnp/ make -j6 install DESTDIR=/build/reproducible-path/parsnp-2.0.6\+dfsg/debian/parsnp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/parsnp-2.0.6+dfsg' Making install in src make[2]: Entering directory '/build/reproducible-path/parsnp-2.0.6+dfsg/src' make[3]: Entering directory '/build/reproducible-path/parsnp-2.0.6+dfsg/src' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/parsnp-2.0.6+dfsg/debian/parsnp../bin' /usr/bin/install -c parsnp_core '/build/reproducible-path/parsnp-2.0.6+dfsg/debian/parsnp../bin' make[3]: Leaving directory '/build/reproducible-path/parsnp-2.0.6+dfsg/src' make[2]: Leaving directory '/build/reproducible-path/parsnp-2.0.6+dfsg/src' make[2]: Entering directory '/build/reproducible-path/parsnp-2.0.6+dfsg' make[3]: Entering directory '/build/reproducible-path/parsnp-2.0.6+dfsg' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/parsnp-2.0.6+dfsg' make[2]: Leaving directory '/build/reproducible-path/parsnp-2.0.6+dfsg' make[1]: Leaving directory '/build/reproducible-path/parsnp-2.0.6+dfsg' dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_python3 dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/parsnp-2.0.6+dfsg' dh_fixperms chmod -x debian/parsnp/usr/share/parsnp/template.ini make[1]: Leaving directory '/build/reproducible-path/parsnp-2.0.6+dfsg' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'parsnp' in '../parsnp_2.0.6+dfsg-1_i386.deb'. dpkg-deb: building package 'parsnp-dbgsym' in '../parsnp-dbgsym_2.0.6+dfsg-1_i386.deb'. dpkg-genbuildinfo --build=binary -O../parsnp_2.0.6+dfsg-1_i386.buildinfo dpkg-genchanges --build=binary -O../parsnp_2.0.6+dfsg-1_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: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/29292 and its subdirectories I: Current time: Sun Nov 10 03:59:06 -12 2024 I: pbuilder-time-stamp: 1731254346 Sun Nov 10 15:59:08 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom08-i386.debian.net. Sun Nov 10 15:59:08 UTC 2024 I: Preparing to do remote build '2' on infom08-i386.debian.net. Sun Nov 10 16:00:25 UTC 2024 I: Deleting $TMPDIR on infom08-i386.debian.net. Sun Nov 10 16:00:26 UTC 2024 I: parsnp_2.0.6+dfsg-1_i386.changes: Format: 1.8 Date: Sun, 03 Nov 2024 16:39:17 +0100 Source: parsnp Binary: parsnp parsnp-dbgsym Architecture: i386 Version: 2.0.6+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: parsnp - rapid core genome multi-alignment Changes: parsnp (2.0.6+dfsg-1) unstable; urgency=medium . * New upstream version 2.0.6+dfsg * proper_calls_to_tools.patch: unfuzz. * py3-parsnp-libs.patch: adjust to new import of "extend". * d/patches/*.patch: normalize last update dates. Checksums-Sha1: 4b745830c3e5011bb15f0c803f9434e52855d224 1236068 parsnp-dbgsym_2.0.6+dfsg-1_i386.deb 4099cfbf22ef43b27771c887714e226d3ddafeab 6508 parsnp_2.0.6+dfsg-1_i386.buildinfo b845e7c512edf6a4e1503420f21bf426624d998c 210640 parsnp_2.0.6+dfsg-1_i386.deb Checksums-Sha256: 44a8035ea3a8a8f3f749a2b992076660fb9c4faf4102de7bb63db54cf2950ead 1236068 parsnp-dbgsym_2.0.6+dfsg-1_i386.deb 23fb23fa6e2892a91aa84cf409878e5f53f7d7d667061a7ae1ff590eee2d0903 6508 parsnp_2.0.6+dfsg-1_i386.buildinfo 09a433f8e72fd7502d2dd5f0d0ec303b36ff0eb24ae4503a7b74f56aa3e3cc0b 210640 parsnp_2.0.6+dfsg-1_i386.deb Files: ac4f7346589328c84c9bc73c4426a3fd 1236068 debug optional parsnp-dbgsym_2.0.6+dfsg-1_i386.deb b80f709669b40bd2a6d87fda82849895 6508 science optional parsnp_2.0.6+dfsg-1_i386.buildinfo aa2d571f2a158be2f8de17ffd939a444 210640 science optional parsnp_2.0.6+dfsg-1_i386.deb Sun Nov 10 16:00:27 UTC 2024 I: diffoscope 283 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_19-29348.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.kQz6T86e/parsnp_2.0.6+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.kQz6T86e/parsnp_2.0.6+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.kQz6T86e/parsnp_2.0.6+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.kQz6T86e/b1/parsnp_2.0.6+dfsg-1_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.kQz6T86e/b2/parsnp_2.0.6+dfsg-1_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: 0.414s) 0.414s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.033s) 0.033s 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: 770ms CPU time consumed: 766ms Sun Nov 10 16:00:30 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Sun Nov 10 16:00:30 UTC 2024 I: parsnp from trixie built successfully and reproducibly on i386. Sun Nov 10 16:00:31 UTC 2024 I: Submitting .buildinfo files to external archives: Sun Nov 10 16:00:31 UTC 2024 I: Submitting 8.0K b1/parsnp_2.0.6+dfsg-1_i386.buildinfo.asc Sun Nov 10 16:00:32 UTC 2024 I: Submitting 8.0K b2/parsnp_2.0.6+dfsg-1_i386.buildinfo.asc Sun Nov 10 16:00:33 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Nov 10 16:00:33 UTC 2024 I: Done submitting .buildinfo files. Sun Nov 10 16:00:33 UTC 2024 I: Removing signed parsnp_2.0.6+dfsg-1_i386.buildinfo.asc files: removed './b1/parsnp_2.0.6+dfsg-1_i386.buildinfo.asc' removed './b2/parsnp_2.0.6+dfsg-1_i386.buildinfo.asc'