Tue Nov 5 16:56:04 UTC 2024 I: starting to build porechop/unstable/amd64 on jenkins on '2024-11-05 16:56' Tue Nov 5 16:56:04 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_37/36272/console.log Tue Nov 5 16:56:04 UTC 2024 I: Downloading source for unstable/porechop=0.2.4+dfsg-6 --2024-11-05 16:56:05-- http://deb.debian.org/debian/pool/main/p/porechop/porechop_0.2.4%2bdfsg-6.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2215 (2.2K) [text/prs.lines.tag] Saving to: ‘porechop_0.2.4+dfsg-6.dsc’ 0K .. 100% 287M=0s 2024-11-05 16:56:05 (287 MB/s) - ‘porechop_0.2.4+dfsg-6.dsc’ saved [2215/2215] Tue Nov 5 16:56:05 UTC 2024 I: porechop_0.2.4+dfsg-6.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: porechop Binary: porechop Architecture: any Version: 0.2.4+dfsg-6 Maintainer: Debian Med Packaging Team Uploaders: Cédric Lood , Andreas Tille Homepage: https://rrwick.github.io/Porechop Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/porechop Vcs-Git: https://salsa.debian.org/med-team/porechop.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-python, libseqan2-dev, python3-dev, python3-setuptools Package-List: porechop deb science optional arch=any Checksums-Sha1: ca42641ad185404433d21282554185aa184bf437 726312 porechop_0.2.4+dfsg.orig.tar.xz bb290af32705362aa5ff264977de724eab70f86e 6152 porechop_0.2.4+dfsg-6.debian.tar.xz Checksums-Sha256: 6d018c3c39777b36697cb1182ecaac9f981ee78c3660347fb83e52351cd79a2c 726312 porechop_0.2.4+dfsg.orig.tar.xz 4adf0600768b96d2efc1cda4c87031d01b09796b8da7cd09ccde621d3bd34807 6152 porechop_0.2.4+dfsg-6.debian.tar.xz Files: a09d363d707181eb1013200716142ad7 726312 porechop_0.2.4+dfsg.orig.tar.xz 81be161a3f63d898d8cbf0fab2d09398 6152 porechop_0.2.4+dfsg-6.debian.tar.xz Dgit: 34a1fd15de707d4b2e997798036702b1f8a39647 debian archive/debian/0.2.4+dfsg-6 https://git.dgit.debian.org/porechop -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmaRpbwUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdpBGw//TMkPc+2B/Rlat4qylZWpqnOHEl2W vb7frakcZcT6yi72qdId0lm2YiJb4CrsIO7lMDa3YTzq7ARXvFLhEqRtJWlzw2SH XMqpL6wS/Ncll4NccDK0ihMUHOPQpP/SE6rbDKRftC2ck1s10aCVhD9nN3lb8lWQ jl+tQTwXujOypxqzomAPbpue6KOchhhWJb6MRCEkfShFN0r2kzr04hACd2gGfq5X 6XVURcnJAT3CXGmOfCAj191C7XoJwFROM6px2rpepN5riMZvBGWLEqyP8j7k1cvi 9RMR7GFrWQNbaoCOhRRYT6QsXpCXqsU8fL3DT//uwRaKIaEVHTS67mE0BFIzMtWk Hzj5FgNDU0o8e4wRgyycMB1eoNRe+hOZ65hqJt275lx5CtpVh8iBIrQsDBUqYO53 Pi4snT6Eb9mz6E2k0efHQbBp2ECd7OXROwwwCBrson6GtXGTkaz4fju0qtbCpv3h bwcOjD6IIri78KD8zvl3UqMY5lf7NvT/SR0GkKWLEWV4PoBO6zznhOthh54vbfLJ BUmNbCUDpkUCsD3oZHYMHlgzlCNl276fQdvu7tSyYmvQbVDxP8KSDQ3e6xnZUF/l I4K5t7oGzE148v71q/xyN4ABSKCf1eq9uQVboZeoFv2u1sOBl99JTAWYPVJYTbkr 62MEvWGdZ8RD9I4= =AT3M -----END PGP SIGNATURE----- Tue Nov 5 16:56:05 UTC 2024 I: Checking whether the package is not for us Tue Nov 5 16:56:05 UTC 2024 I: Starting 1st build on remote node infom01-amd64.debian.net. Tue Nov 5 16:56:05 UTC 2024 I: Preparing to do remote build '1' on infom01-amd64.debian.net. Tue Nov 5 16:57:22 UTC 2024 I: Deleting $TMPDIR on infom01-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Nov 5 04:56:06 -12 2024 I: pbuilder-time-stamp: 1730825766 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [porechop_0.2.4+dfsg-6.dsc] I: copying [./porechop_0.2.4+dfsg.orig.tar.xz] I: copying [./porechop_0.2.4+dfsg-6.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Jul 12 21:53:00 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 ./porechop_0.2.4+dfsg-6.dsc: no acceptable signature found dpkg-source: info: extracting porechop in porechop-0.2.4+dfsg dpkg-source: info: unpacking porechop_0.2.4+dfsg.orig.tar.xz dpkg-source: info: unpacking porechop_0.2.4+dfsg-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying add_python_interpreter_line.patch dpkg-source: info: applying no_soname.patch dpkg-source: info: applying define-all-attribute-in-clean.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1712969/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='3c72fea398d24b99ba3d2b3c93087cbb' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1712969' 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.BwCxxkDo/pbuilderrc_ThlW --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.BwCxxkDo/b1 --logfile b1/build.log porechop_0.2.4+dfsg-6.dsc' SUDO_GID='109' 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 infom01-amd64 6.1.0-26-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) 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/1712969/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, libseqan2-dev, python3-dev, python3-setuptools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19968 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on libseqan2-dev; however: Package libseqan2-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} 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} libnsl2{a} libpipeline1{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libreadline8t64{a} libseqan2-dev{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-autocommand{a} python3-dev{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{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, 74 newly installed, 0 to remove and 0 not upgraded. Need to get 38.9 MB of archives. After unpacking 167 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.7-2 [815 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.3-2 [105 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.7-2 [2161 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024b-3 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 12 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.7-2 [1967 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.7-2 [671 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-10 [97.2 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 44 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.1 [699 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 58 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.20.2-1 [10.3 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.2.0-1 [731 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20241024 [109 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.3-2 [157 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libpython3.12t64 amd64 3.12.7-2 [2150 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libpython3.12-dev amd64 3.12.7-2 [5125 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.12.6-1 [9952 B] Get: 72 http://deb.debian.org/debian unstable/main amd64 libseqan2-dev all 2.4.0+dfsg-16 [1216 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 python3.12-dev amd64 3.12.7-2 [505 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.12.6-1 [26.1 kB] Fetched 38.9 MB in 4s (10.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. 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Preparing to unpack .../python3.12-minimal_3.12.7-2_amd64.deb ... Unpacking python3.12-minimal (3.12.7-2) ... Setting up libpython3.12-minimal:amd64 (3.12.7-2) ... Setting up libexpat1:amd64 (2.6.3-2) ... Setting up python3.12-minimal (3.12.7-2) ... 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 ... 20288 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... 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Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up netbase (6.4) ... Setting up libkrb5-3:amd64 (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:amd64 (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:amd64 (1.21.3-3) ... Setting up libjs-sphinxdoc (7.4.7-4) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/porechop-0.2.4+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 > ../porechop_0.2.4+dfsg-6_source.changes dpkg-buildpackage: info: source package porechop dpkg-buildpackage: info: source version 0.2.4+dfsg-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 --buildsystem pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py clean running clean Deleting directory: /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build dh_autoreconf_clean -O--buildsystem=pybuild debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/porechop-0.2.4+dfsg' dh_clean # Removing left .so files. find . -name "*.so" -delete make[1]: Leaving directory '/build/reproducible-path/porechop-0.2.4+dfsg' debian/rules binary dh binary --with python3 --buildsystem pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop copying porechop/adapters.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop copying porechop/nanopore_read.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop copying porechop/version.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop copying porechop/misc.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop copying porechop/cpp_function_wrappers.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop copying porechop/__init__.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop copying porechop/porechop.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop Cleaning previous compilation: make clean make[1]: Entering directory '/build/reproducible-path/porechop-0.2.4+dfsg' rm -f porechop/src/alignment.o porechop/src/adapter_align.o make[1]: Leaving directory '/build/reproducible-path/porechop-0.2.4+dfsg' Compiling Porechop: make -j 8 make[1]: Entering directory '/build/reproducible-path/porechop-0.2.4+dfsg' g++ -std=c++14 -Iporechop/include -fPIC -O3 -D NDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/porechop-0.2.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o porechop/src/alignment.o porechop/src/alignment.cpp g++ -std=c++14 -Iporechop/include -fPIC -O3 -D NDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/porechop-0.2.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o porechop/src/adapter_align.o porechop/src/adapter_align.cpp g++ -std=c++14 -Iporechop/include -fPIC -O3 -D NDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/porechop-0.2.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -shared -o porechop/cpp_functions.so porechop/src/alignment.o porechop/src/adapter_align.o make[1]: Leaving directory '/build/reproducible-path/porechop-0.2.4+dfsg' dh_auto_test -O--buildsystem=pybuild create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/porechop/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py Cleaning previous compilation: make clean make[1]: Entering directory '/build/reproducible-path/porechop-0.2.4+dfsg' rm -f porechop/src/alignment.o porechop/src/adapter_align.o make[1]: Leaving directory '/build/reproducible-path/porechop-0.2.4+dfsg' Compiling Porechop: make -j 8 make[1]: Entering directory '/build/reproducible-path/porechop-0.2.4+dfsg' g++ -std=c++14 -Iporechop/include -fPIC -O3 -D NDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/porechop-0.2.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o porechop/src/alignment.o porechop/src/alignment.cpp g++ -std=c++14 -Iporechop/include -fPIC -O3 -D NDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/porechop-0.2.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o porechop/src/adapter_align.o porechop/src/adapter_align.cpp g++ -std=c++14 -Iporechop/include -fPIC -O3 -D NDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/porechop-0.2.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -shared -o porechop/cpp_functions.so porechop/src/alignment.o porechop/src/adapter_align.o make[1]: Leaving directory '/build/reproducible-path/porechop-0.2.4+dfsg' running install_lib creating /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages creating /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop/adapters.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop/nanopore_read.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop/version.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop/misc.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop/cpp_function_wrappers.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop/__init__.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop/porechop.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop/adapters.py to adapters.cpython-312.pyc byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop/nanopore_read.py to nanopore_read.cpython-312.pyc byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop/version.py to version.cpython-312.pyc byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop/misc.py to misc.cpython-312.pyc /usr/lib/python3.12/dist-packages/porechop/misc.py:261: SyntaxWarning: invalid escape sequence '\[' byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop/cpp_function_wrappers.py to cpp_function_wrappers.cpython-312.pyc byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop/porechop.py to porechop.cpython-312.pyc running install_egg_info running egg_info creating porechop.egg-info writing porechop.egg-info/PKG-INFO writing dependency_links to porechop.egg-info/dependency_links.txt writing entry points to porechop.egg-info/entry_points.txt writing top-level names to porechop.egg-info/top_level.txt writing manifest file 'porechop.egg-info/SOURCES.txt' reading manifest file 'porechop.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'porechop.egg-info/SOURCES.txt' Copying porechop.egg-info to /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop-0.2.4.egg-info Skipping SOURCES.txt running install_scripts Installing porechop script to /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/bin debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/porechop-0.2.4+dfsg' dh_install mv -v debian/porechop/usr/bin/porechop-runner.py debian/porechop/usr/bin/porechop renamed 'debian/porechop/usr/bin/porechop-runner.py' -> 'debian/porechop/usr/bin/porechop' make[1]: Leaving directory '/build/reproducible-path/porechop-0.2.4+dfsg' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild debian/rules override_dh_python3 make[1]: Entering directory '/build/reproducible-path/porechop-0.2.4+dfsg' dh_python3 --no-ext-rename I: dh_python3 tools:113: replacing shebang in debian/porechop/usr/bin/porechop make[1]: Leaving directory '/build/reproducible-path/porechop-0.2.4+dfsg' dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'porechop' in '../porechop_0.2.4+dfsg-6_amd64.deb'. dpkg-deb: building package 'porechop-dbgsym' in '../porechop-dbgsym_0.2.4+dfsg-6_amd64.deb'. dpkg-genbuildinfo --build=binary -O../porechop_0.2.4+dfsg-6_amd64.buildinfo dpkg-genchanges --build=binary -O../porechop_0.2.4+dfsg-6_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1712969 and its subdirectories I: Current time: Tue Nov 5 04:57:21 -12 2024 I: pbuilder-time-stamp: 1730825841 Tue Nov 5 16:57:23 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom02-amd64.debian.net. Tue Nov 5 16:57:23 UTC 2024 I: Preparing to do remote build '2' on infom02-amd64.debian.net. Tue Nov 5 16:58:28 UTC 2024 I: Deleting $TMPDIR on infom02-amd64.debian.net. Tue Nov 5 16:58:29 UTC 2024 I: porechop_0.2.4+dfsg-6_amd64.changes: Format: 1.8 Date: Fri, 12 Jul 2024 23:49:53 +0200 Source: porechop Binary: porechop porechop-dbgsym Architecture: amd64 Version: 0.2.4+dfsg-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: porechop - adapter trimmer for Oxford Nanopore reads Closes: 1074677 Changes: porechop (0.2.4+dfsg-6) unstable; urgency=medium . * Team upload. * d/rules: remove the now broken workaround against setuptools 50 bug. (Closes: #1074677) Checksums-Sha1: a6a1c4efa50d686bc7c54bf68bc3f32542801b19 392544 porechop-dbgsym_0.2.4+dfsg-6_amd64.deb 33287b975cc04f1d6a8b851e96ccaa102d361d82 6480 porechop_0.2.4+dfsg-6_amd64.buildinfo 352eeec55b41096c6f9b3af7c9c07a0301a95385 57464 porechop_0.2.4+dfsg-6_amd64.deb Checksums-Sha256: 412084be1ebbc50cf2f672181e36ab5cd56b9e504cb709ed685e69cb4eee78fd 392544 porechop-dbgsym_0.2.4+dfsg-6_amd64.deb 1957fdf64ac53d1a5a6ef2c502bbdd1481ca22b0844ef3c6accaa82ccd0f00ec 6480 porechop_0.2.4+dfsg-6_amd64.buildinfo 078bcf477ce41c360584bb6e881688f5326229c7cfa7056420f5f81e6549078f 57464 porechop_0.2.4+dfsg-6_amd64.deb Files: 31124ea6e541cc2c3c6d45b552e222fd 392544 debug optional porechop-dbgsym_0.2.4+dfsg-6_amd64.deb ec0eb1ed6c80065f37db1ce6ee7f22f7 6480 science optional porechop_0.2.4+dfsg-6_amd64.buildinfo 57ddd2b0f9107a3e02aa7a9d59d89063 57464 science optional porechop_0.2.4+dfsg-6_amd64.deb Tue Nov 5 16:58:35 UTC 2024 I: diffoscope 282 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_37-36272.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.BwCxxkDo/porechop_0.2.4+dfsg-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.BwCxxkDo/porechop_0.2.4+dfsg-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.BwCxxkDo/porechop_0.2.4+dfsg-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.BwCxxkDo/b1/porechop_0.2.4+dfsg-6_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.BwCxxkDo/b2/porechop_0.2.4+dfsg-6_amd64.changes ## close_archive (total time: 0.000s) 0.000s 18 calls diffoscope.comparators.xz.XzContainer 0.000s 12 calls diffoscope.comparators.tar.TarContainer 0.000s 8 calls diffoscope.comparators.deb.DebContainer 0.000s 6 calls diffoscope.comparators.deb.DebTarContainer ## command (total time: 3.357s) 1.368s 56 calls diff 1.198s 77 calls objdump 0.439s 427 calls readelf 0.211s 2 calls objcopy 0.126s 18 calls xz 0.013s 11 calls strings 0.002s 19 calls cmp (internal) ## compare_files (cumulative) (total time: 16.826s) 3.070s 1 call abc.DotChangesFile 3.052s 2 calls abc.DebFile 2.995s 4 calls abc.XzFile 2.823s 2 calls abc.DebDataTarFile 2.666s 1 call abc.ElfFile 1.888s 5 calls diffoscope.comparators.elf.ElfCodeSection 0.199s 13 calls diffoscope.comparators.elf.ElfSection 0.089s 2 calls abc.TarFile 0.017s 1 call abc.TextFile 0.015s 2 calls abc.Md5sumsFile 0.012s 1 call diffoscope.comparators.elf.MonkeyPatchedElfSection ## container_extract (total time: 0.175s) 0.127s 18 calls diffoscope.comparators.xz.XzContainer 0.019s 38 calls diffoscope.comparators.deb.DebTarContainer 0.015s 20 calls diffoscope.comparators.tar.TarContainer 0.015s 22 calls diffoscope.comparators.deb.DebContainer ## diff (total time: 1.316s) 1.316s 354 calls linediff ## has_same_content_as (total time: 0.004s) 0.001s 6 calls abc.TextFile 0.001s 4 calls abc.Md5sumsFile 0.001s 4 calls abc.XzFile 0.000s 2 calls abc.DebDataTarFile 0.000s 2 calls abc.TarFile 0.000s 2 calls abc.DebFile 0.000s 1 call abc.ElfFile 0.000s 1 call abc.DotChangesFile 0.000s 1 call diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.000s 13 calls diffoscope.comparators.elf.ElfSection 0.000s 5 calls diffoscope.comparators.elf.ElfCodeSection 0.000s 1 call diffoscope.comparators.elf.MonkeyPatchedElfSection ## main (total time: 10.262s) 10.262s 2 calls outputs 0.000s 1 call cleanup ## open_archive (total time: 0.001s) 0.000s 18 calls diffoscope.comparators.xz.XzContainer 0.000s 12 calls diffoscope.comparators.tar.TarContainer 0.000s 8 calls diffoscope.comparators.deb.DebContainer 0.000s 6 calls diffoscope.comparators.deb.DebTarContainer ## output (total time: 6.753s) 6.681s 1 call html 0.046s 1 call text 0.025s 1 call json ## recognizes (total time: 0.237s) 0.116s 1674 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.085s 780 calls diffoscope.comparators.utils.archive.ArchiveMember 0.026s 12 calls diffoscope.comparators.binary.FilesystemFile 0.010s 216 calls diffoscope.comparators.debian.DebControlMember ## specialize (total time: 0.086s) 0.086s 42 calls specialize Finished with result: success Main processes terminated with: code=exited/status=1 Service runtime: 16.115s CPU time consumed: 16.693s Tue Nov 5 16:59:00 UTC 2024 W: Diffoscope claims the build is reproducible, but there is a diffoscope file. Please investigate. Tue Nov 5 16:59:00 UTC 2024 E: porechop failed to build reproducibly in unstable on amd64. Tue Nov 5 16:59:02 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Nov 5 16:59:02 UTC 2024 I: Submitting 8.0K b1/porechop_0.2.4+dfsg-6_amd64.buildinfo.asc Tue Nov 5 16:59:03 UTC 2024 I: Submitting 8.0K b2/porechop_0.2.4+dfsg-6_amd64.buildinfo.asc Tue Nov 5 16:59:04 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Nov 5 16:59:04 UTC 2024 I: Done submitting .buildinfo files. Tue Nov 5 16:59:04 UTC 2024 I: Removing signed porechop_0.2.4+dfsg-6_amd64.buildinfo.asc files: removed './b1/porechop_0.2.4+dfsg-6_amd64.buildinfo.asc' removed './b2/porechop_0.2.4+dfsg-6_amd64.buildinfo.asc'