Thu Dec 12 20:20:30 UTC 2024 I: starting to build nanosv/trixie/amd64 on jenkins on '2024-12-12 20:20' Thu Dec 12 20:20:30 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_31/27527/console.log Thu Dec 12 20:20:30 UTC 2024 I: Downloading source for trixie/nanosv=1.2.4+git20190409.c1ae30c-7 --2024-12-12 20:20:30-- http://deb.debian.org/debian/pool/main/n/nanosv/nanosv_1.2.4%2bgit20190409.c1ae30c-7.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2187 (2.1K) [text/prs.lines.tag] Saving to: ‘nanosv_1.2.4+git20190409.c1ae30c-7.dsc’ 0K .. 100% 254M=0s 2024-12-12 20:20:30 (254 MB/s) - ‘nanosv_1.2.4+git20190409.c1ae30c-7.dsc’ saved [2187/2187] Thu Dec 12 20:20:30 UTC 2024 I: nanosv_1.2.4+git20190409.c1ae30c-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: nanosv Binary: nanosv Architecture: all Version: 1.2.4+git20190409.c1ae30c-7 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller Homepage: https://github.com/mroosmalen/nanosv Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/nanosv Vcs-Git: https://salsa.debian.org/med-team/nanosv.git Testsuite: autopkgtest Testsuite-Triggers: bedtools, sambamba, samtools Build-Depends: debhelper-compat (= 13), dh-sequence-python3, help2man, python3-all, python3-setuptools, python3-vcf Package-List: nanosv deb science optional arch=all Checksums-Sha1: f333586be6145b26fd2394061b081a9b11e2feba 2895140 nanosv_1.2.4+git20190409.c1ae30c.orig.tar.xz 4a9dd3827a5d088087e5abcb3096b308f581fd7e 5316 nanosv_1.2.4+git20190409.c1ae30c-7.debian.tar.xz Checksums-Sha256: e79073d4a3d6f6f1d1c87f462b2289cb7b19b3affd1c3eedcdc443658e76adbe 2895140 nanosv_1.2.4+git20190409.c1ae30c.orig.tar.xz 410368505ea75dadc28e52d59da04d7a2d107aeabdd469d6500f3b01c14afbaa 5316 nanosv_1.2.4+git20190409.c1ae30c-7.debian.tar.xz Files: 977ab7bb8626de0f467c564b4e4e4d4a 2895140 nanosv_1.2.4+git20190409.c1ae30c.orig.tar.xz 79b138076b5fd34549b1f0ed754fd023 5316 nanosv_1.2.4+git20190409.c1ae30c-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEUtW9Dn1NsITjS1hl1KQc+t2yDbUFAmdTGsoACgkQ1KQc+t2y DbUyvhAAsycepG2VeJ8PT4rsZk6sCAqozkZOB8/pPK7M4cvHfld/SZMjq2D6iT/X Io+COZhb4C516K5/NLkkLFrNjLbiqEGmgWVHVBwQXLvLC2M9jv7TP48YZq6DN6d1 8tff0kygnErV6RA/rOrqV7kaONi1gpUbkix6K0LWqOINhF50t6pkWcA3l9wlEy41 ZVGbDb/OKj59FrHJdHtQIY3RBk9BBYfprb2Xay41VVQMtpb4staP1t8f8b1oDUsq nZlqBA2b0T6NE1vRMvfF5mko2UkJ538ZvFG8H6oCrM8NpQLERpBDG9RcPXX/VJrV FWCO/WchU5plz8aQH7etncEi/PKdoTTwARqvfkjHiVBPvCsxZWKj762e2a2TGfeD AvI5ndaxEd0+psGPatbvw7AYxBmwAo6nZULW8Wk9V6YXbV/v3t6ywieRFdqnFIrs exIOqEw8Q8jerZUK5RoPGhVSF2gzsqg6hv9e1K36r2t6TrNSb0JA60tJDsGaG+v2 6YUrGEYqhkf2nPyG00YuFDYYyAvUoOG9UMBhAyL/sccL5wIeWTO+G3fzGlEhLE2+ 65F7+2pZEEI5GDJ2h0F3oYpug3zQ/u1+R68qvIb1apXiT+N2ymMZswvQ4znqPX/m L+hDI6Zwa3mxI9/14zc9ZO2aE+Ab4ILVRwg/8gF3wE91L5vDhtQ= =/hs2 -----END PGP SIGNATURE----- Thu Dec 12 20:20:30 UTC 2024 I: Checking whether the package is not for us Thu Dec 12 20:20:30 UTC 2024 I: Starting 1st build on remote node ionos11-amd64.debian.net. Thu Dec 12 20:20:30 UTC 2024 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Thu Dec 12 20:24:48 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Dec 12 08:20:33 -12 2024 I: pbuilder-time-stamp: 1734034833 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [nanosv_1.2.4+git20190409.c1ae30c-7.dsc] I: copying [./nanosv_1.2.4+git20190409.c1ae30c.orig.tar.xz] I: copying [./nanosv_1.2.4+git20190409.c1ae30c-7.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Dec 6 15:39:54 2024 gpgv: using RSA key 52D5BD0E7D4DB084E34B5865D4A41CFADDB20DB5 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./nanosv_1.2.4+git20190409.c1ae30c-7.dsc: no acceptable signature found dpkg-source: info: extracting nanosv in nanosv-1.2.4+git20190409.c1ae30c dpkg-source: info: unpacking nanosv_1.2.4+git20190409.c1ae30c.orig.tar.xz dpkg-source: info: unpacking nanosv_1.2.4+git20190409.c1ae30c-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_setup.patch dpkg-source: info: applying python3_has_buildin_configparser.patch dpkg-source: info: applying use-raw-strings.patch dpkg-source: info: applying fix-invalid-dash-seperation.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1486676/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=20 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='abf6dd21662943bcbfd398d636def266' 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='1486676' 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.dcQFv7cn/pbuilderrc_GQ4Y --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.dcQFv7cn/b1 --logfile b1/build.log nanosv_1.2.4+git20190409.c1ae30c-7.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1486676/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-sequence-python3, help2man, python3-all, python3-setuptools, python3-vcf dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19965 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 help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-vcf; however: Package python3-vcf 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} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnsl2{a} libpipeline1{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{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-autocommand{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-pysam{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-vcf{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 83 newly installed, 0 to remove and 0 not upgraded. Need to get 35.1 MB of archives. After unpacking 159 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.8-1 [815 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.8-1 [2163 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024b-4 [256 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2~rc1-2 [23.8 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 13 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.8-1 [1970 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.8-1 [677 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get: 23 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-6 [1184 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-12 [92.0 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 45 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 59 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 75.2.0-1 [731 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20241024 [109 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 help2man amd64 1.49.3 [198 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.11.0-1 [359 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.20+ds-2 [455 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.12.6-1 [1040 B] Get: 82 http://deb.debian.org/debian trixie/main amd64 python3-pysam amd64 0.22.1+ds-2+b2 [4412 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 python3-vcf amd64 0.6.8+git20170215.476169c-11 [61.2 kB] Fetched 35.1 MB in 2s (21.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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 ... 19965 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-7+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package libpython3.12-minimal:amd64. Preparing to unpack .../libpython3.12-minimal_3.12.8-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.8-1) ... Selecting previously unselected package libexpat1:amd64. 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Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libkeyutils1:amd64 (1.6.3-4) ... Setting up libicu72:amd64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-12) ... 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 libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libdeflate0:amd64 (1.22-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:amd64 (1.47.2~rc1-2) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Dec 12 20:22:15 UTC 2024. Universal Time is now: Thu Dec 12 20:22:15 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up autopoint (0.22.5-2) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:amd64 (1.6.0-2) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:amd64 (1.9.1-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... 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 libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-6) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.11.0-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up libhts3t64:amd64 (1.20+ds-2) ... Setting up libpython3.12-stdlib:amd64 (3.12.8-1) ... Setting up python3.12 (3.12.8-1) ... Setting up debhelper (13.20) ... Setting up libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-pysam (0.22.1+ds-2+b2) ... 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-vcf (0.6.8+git20170215.476169c-11) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up python3-setuptools (75.2.0-1) ... Setting up dh-python (6.20241024) ... Processing triggers for libc-bin (2.40-4) ... 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/nanosv-1.2.4+git20190409.c1ae30c/ && 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 > ../nanosv_1.2.4+git20190409.c1ae30c-7_source.changes dpkg-buildpackage: info: source package nanosv dpkg-buildpackage: info: source version 1.2.4+git20190409.c1ae30c-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Ananthu C V dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from nanosv-1.2.4+git20190409.c1ae30c/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild pybuild --clean -i python{version} -p 3.12 I: pybuild base:311: python3.12 setup.py clean /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'including_package_data' warnings.warn(msg) running clean removing '/build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it rm -rf .pybuild/ find . -name \*.pyc -exec rm {} \; debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c' rm -rf /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/python3-nanosv* rm -f /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/NanoSV.1 make[1]: Leaving directory '/build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/nanosv.substvars debian/files rm -fr -- debian/nanosv/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild pybuild --configure -i python{version} -p 3.12 I: pybuild base:311: python3.12 setup.py config /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'including_package_data' warnings.warn(msg) running config dh_auto_build -O--buildsystem=pybuild pybuild --build -i python{version} -p 3.12 I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'including_package_data' warnings.warn(msg) running build running build_py creating /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv copying nanosv/__init__.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv copying nanosv/version.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv copying nanosv/NanoSV.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv creating /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/utils copying nanosv/utils/create_vcf.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/utils copying nanosv/utils/__init__.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/utils copying nanosv/utils/coverage.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/utils copying nanosv/utils/parse_bam.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/utils copying nanosv/utils/parse_breakpoints.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/utils copying nanosv/utils/phasing.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/utils copying nanosv/utils/parse_reads.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/utils copying nanosv/utils/parse_svs.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/utils creating /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/classes copying nanosv/classes/__init__.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/classes copying nanosv/classes/breakpoint.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/classes copying nanosv/classes/segment.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/classes copying nanosv/classes/read.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/classes copying nanosv/classes/sv.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/classes copying nanosv/classes/variant.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/classes copying nanosv/config.ini -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv creating /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/bedfiles copying nanosv/bedfiles/human_hg19.bed -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/bedfiles debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c' echo "I: Do nothing" I: Do nothing make[1]: Leaving directory '/build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild rm -f -- debian/nanosv.substvars rm -fr -- debian/.debhelper/generated/nanosv/ debian/nanosv/ debian/tmp/ dh_auto_install --destdir=debian/nanosv/ -O--buildsystem=pybuild install -m0755 -d /build/reproducible-path/nanosv-1.2.4\+git20190409.c1ae30c/debian/nanosv pybuild --install -i python{version} -p 3.12 --dest-dir /build/reproducible-path/nanosv-1.2.4\+git20190409.c1ae30c/debian/nanosv I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'including_package_data' warnings.warn(msg) 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 running install_lib creating /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages creating /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv copying /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/__init__.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv creating /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/classes copying /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/classes/__init__.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/classes copying /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/classes/breakpoint.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/classes copying /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/classes/segment.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/classes copying /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/classes/read.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/classes copying /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/classes/sv.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/classes copying /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/classes/variant.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/classes creating /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/bedfiles copying /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/bedfiles/human_hg19.bed -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/bedfiles copying /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/version.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv copying /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/config.ini -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv creating /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/utils copying /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/utils/create_vcf.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/utils copying /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/utils/__init__.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/utils copying /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/utils/coverage.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/utils copying /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/utils/parse_bam.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/utils copying /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/utils/parse_breakpoints.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/utils copying /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/utils/phasing.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/utils copying /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/utils/parse_reads.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/utils copying /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/utils/parse_svs.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/utils copying /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.12_nanosv/build/nanosv/NanoSV.py -> /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv byte-compiling /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/classes/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/classes/breakpoint.py to breakpoint.cpython-312.pyc byte-compiling /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/classes/segment.py to segment.cpython-312.pyc byte-compiling /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/classes/read.py to read.cpython-312.pyc byte-compiling /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/classes/sv.py to sv.cpython-312.pyc byte-compiling /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/classes/variant.py to variant.cpython-312.pyc byte-compiling /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/version.py to version.cpython-312.pyc byte-compiling /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/utils/create_vcf.py to create_vcf.cpython-312.pyc byte-compiling /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/utils/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/utils/coverage.py to coverage.cpython-312.pyc byte-compiling /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/utils/parse_bam.py to parse_bam.cpython-312.pyc byte-compiling /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/utils/parse_breakpoints.py to parse_breakpoints.cpython-312.pyc byte-compiling /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/utils/phasing.py to phasing.cpython-312.pyc byte-compiling /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/utils/parse_reads.py to parse_reads.cpython-312.pyc byte-compiling /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/utils/parse_svs.py to parse_svs.cpython-312.pyc byte-compiling /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/nanosv/NanoSV.py to NanoSV.cpython-312.pyc running install_egg_info running egg_info creating NanoSV.egg-info writing NanoSV.egg-info/PKG-INFO writing dependency_links to NanoSV.egg-info/dependency_links.txt writing entry points to NanoSV.egg-info/entry_points.txt writing requirements to NanoSV.egg-info/requires.txt writing top-level names to NanoSV.egg-info/top_level.txt writing manifest file 'NanoSV.egg-info/SOURCES.txt' reading manifest file 'NanoSV.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'README.rst' adding license file 'LICENSE' writing manifest file 'NanoSV.egg-info/SOURCES.txt' Copying NanoSV.egg-info to /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.12/dist-packages/NanoSV-1.2.4.egg-info Skipping SOURCES.txt running install_scripts Installing NanoSV script to /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/bin debian/rules execute_after_dh_auto_install make[1]: Entering directory '/build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c' find /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian -name "*.bed" -o -name "*.ini" | xargs -r chmod -x PYTHONPATH=./debian/nanosv/usr/lib/python3.12/dist-packages/ help2man --include=debian/NanoSV.h2m ./debian/nanosv/usr/bin/NanoSV > /build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c/debian/NanoSV.1 make[1]: Leaving directory '/build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c' dh_installdocs -O--buildsystem=pybuild install -m0755 -d debian/nanosv/usr/share/doc/nanosv install -m0755 -d debian/nanosv/usr/share/doc/nanosv cp --reflink=auto -a ./README.md debian/nanosv/usr/share/doc/nanosv cp --reflink=auto -a ./debian/README.test debian/nanosv/usr/share/doc/nanosv cp --reflink=auto -a ./debian/tests/run-unit-test debian/nanosv/usr/share/doc/nanosv chmod -R u\+rw,go=rX debian/nanosv/usr/share/doc install -p -m0644 debian/copyright debian/nanosv/usr/share/doc/nanosv/copyright dh_installchangelogs -O--buildsystem=pybuild install -m0755 -d debian/nanosv/usr/share/doc/nanosv install -p -m0644 debian/.debhelper/generated/nanosv/dh_installchangelogs.dch.trimmed debian/nanosv/usr/share/doc/nanosv/changelog.Debian dh_installman -O--buildsystem=pybuild install -m0755 -d debian/nanosv/usr/share/man/man1/ install -p -m0644 ./debian/NanoSV.1 debian/nanosv/usr/share/man/man1/NanoSV.1 man-recode --to-code UTF-8 --suffix .dh-new debian/nanosv/usr/share/man/man1/NanoSV.1 mv debian/nanosv/usr/share/man/man1/NanoSV.1.dh-new debian/nanosv/usr/share/man/man1/NanoSV.1 chmod 0644 -- debian/nanosv/usr/share/man/man1/NanoSV.1 dh_python3 -O--buildsystem=pybuild D: dh_python3 dh_python3:180: version: 6.20241024 D: dh_python3 dh_python3:181: argv: ['/usr/bin/dh_python3', '-O--buildsystem=pybuild'] D: dh_python3 dh_python3:182: options: Namespace(guess_deps=True, skip_private=False, verbose=True, arch=None, package=None, no_package=None, remaining_packages=False, compile_all=False, vrange=None, regexpr=None, accept_upstream_versions=False, depends=None, depends_section=None, recommends=None, recommends_section=None, suggests=None, suggests_section=None, requires=None, shebang=None, ignore_shebangs=False, clean_dbg_pkg=True, no_ext_rename=False, no_shebang_rewrite=False, private_dir=None, O=['--buildsystem=pybuild']) D: dh_python3 dh_python3:183: supported Python versions: 3.12 (default=3.12) D: dh_python3 debhelper:174: source=nanosv, binary packages=['nanosv'] D: dh_python3 dh_python3:205: processing package nanosv... D: dh_python3 fs:50: moving files from debian/nanosv/usr/lib/python3.12/dist-packages to debian/nanosv/usr/lib/python3/dist-packages/ D: dh_python3 fs:338: package nanosv details = {'requires.txt': {'debian/nanosv/usr/lib/python3/dist-packages/NanoSV-1.2.4.egg-info/requires.txt'}, 'egg-info': {'debian/nanosv/usr/lib/python3/dist-packages/NanoSV-1.2.4.egg-info/PKG-INFO'}, 'dist-info': set(), 'nsp.txt': set(), 'shebangs': {/usr/bin/python3}, 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': True, 'ext_vers': set(), 'ext_no_version': set()} D: dh_python3 depends:103: generating dependencies for package nanosv D: dh_python3 pydist:175: trying to find dependency for pysam>=0.11 (python=None) D: dh_python3 pydist:209: dependency: module seems to be installed D: dh_python3 pydist:284: dependency: included in build-deps D: dh_python3 pydist:175: trying to find dependency for pyvcf (python=None) D: dh_python3 pydist:209: dependency: module seems to be installed D: dh_python3 pydist:284: dependency: included in build-deps D: dh_python3 depends:253: D={'python3:any', 'python3-vcf', 'python3-pysam'}; R=[]; S=[]; E=[], B=[]; RT=[] 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 cd debian/nanosv chmod a-x usr/share/doc/nanosv/README.md usr/share/doc/nanosv/changelog.Debian usr/share/man/man1/NanoSV.1 gzip -9nf usr/share/doc/nanosv/README.md usr/share/doc/nanosv/changelog.Debian usr/share/man/man1/NanoSV.1 cd '/build/reproducible-path/nanosv-1.2.4+git20190409.c1ae30c' dh_fixperms -O--buildsystem=pybuild find debian/nanosv ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/nanosv/usr/share/doc -type f -a -true -a ! -regex 'debian/nanosv/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/nanosv/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/nanosv/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/nanosv -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/nanosv/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/nanosv/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w dh_missing -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild install -m0755 -d debian/nanosv/DEBIAN printf '#!/bin/sh\nset -e\n' > debian/nanosv/DEBIAN/postinst cat debian/nanosv.postinst.debhelper >> debian/nanosv/DEBIAN/postinst chmod 0755 -- debian/nanosv/DEBIAN/postinst printf '#!/bin/sh\nset -e\n' > debian/nanosv/DEBIAN/prerm cat debian/nanosv.prerm.debhelper >> debian/nanosv/DEBIAN/prerm chmod 0755 -- debian/nanosv/DEBIAN/prerm dh_gencontrol -O--buildsystem=pybuild install -m0755 -d debian/nanosv/DEBIAN echo misc:Depends= >> debian/nanosv.substvars echo misc:Pre-Depends= >> debian/nanosv.substvars dpkg-gencontrol -pnanosv -ldebian/changelog -Tdebian/nanosv.substvars -cdebian/control -Pdebian/nanosv chmod 0644 -- debian/nanosv/DEBIAN/control dh_md5sums -O--buildsystem=pybuild install -m0755 -d debian/nanosv/DEBIAN cd debian/nanosv >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/nanosv/DEBIAN/md5sums dh_builddeb -O--buildsystem=pybuild dpkg-deb --root-owner-group --build debian/nanosv .. dpkg-deb: building package 'nanosv' in '../nanosv_1.2.4+git20190409.c1ae30c-7_all.deb'. dpkg-genbuildinfo --build=binary -O../nanosv_1.2.4+git20190409.c1ae30c-7_amd64.buildinfo dpkg-genchanges --build=binary -O../nanosv_1.2.4+git20190409.c1ae30c-7_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from nanosv-1.2.4+git20190409.c1ae30c/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ 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/1486676 and its subdirectories I: Current time: Thu Dec 12 08:24:44 -12 2024 I: pbuilder-time-stamp: 1734035084 Thu Dec 12 20:24:49 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Thu Dec 12 20:24:49 UTC 2024 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Thu Dec 12 20:25:58 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Thu Dec 12 20:25:58 UTC 2024 I: nanosv_1.2.4+git20190409.c1ae30c-7_amd64.changes: Format: 1.8 Date: Fri, 06 Dec 2024 20:59:53 +0530 Source: nanosv Binary: nanosv Architecture: all Version: 1.2.4+git20190409.c1ae30c-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Ananthu C V Description: nanosv - structural variant caller for nanopore data Closes: 1085733 Changes: nanosv (1.2.4+git20190409.c1ae30c-7) unstable; urgency=medium . * Team upload. * Bump standards version to 4.7.0 (no changes needed) * Update patch header metadata * Use execute_after_* hooks instead of overrides in d/rules * Use dh-sequence-python3 and run wrap-and-sort * Add repository fields to upstream metadata * Add patch to fix syntaxwarnings (Closes: #1085733) * Fix deprecated dash separated option in setup.cfg Checksums-Sha1: ba16a3907726e7c124ec013183a823b27427cb30 2872372 nanosv_1.2.4+git20190409.c1ae30c-7_all.deb 797bc422e865599a5067b7cec9c00d448ad7f89e 6767 nanosv_1.2.4+git20190409.c1ae30c-7_amd64.buildinfo Checksums-Sha256: 8ead774020939c3aeee36a07c86950a82fa6d970f57641c8a182bd245ca269bd 2872372 nanosv_1.2.4+git20190409.c1ae30c-7_all.deb ec5776d1d123652252c764d2434c1abb2536aaf003cb23aea79b1fd92579417f 6767 nanosv_1.2.4+git20190409.c1ae30c-7_amd64.buildinfo Files: 8e9789f10485ccccbcbb8750c5c6cc86 2872372 science optional nanosv_1.2.4+git20190409.c1ae30c-7_all.deb 684fa052a78133a239b8c6e810771d6b 6767 science optional nanosv_1.2.4+git20190409.c1ae30c-7_amd64.buildinfo Thu Dec 12 20:25:59 UTC 2024 I: diffoscope 284 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_31-27527.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.dcQFv7cn/nanosv_1.2.4+git20190409.c1ae30c-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.dcQFv7cn/nanosv_1.2.4+git20190409.c1ae30c-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.dcQFv7cn/nanosv_1.2.4+git20190409.c1ae30c-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.dcQFv7cn/b1/nanosv_1.2.4+git20190409.c1ae30c-7_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.dcQFv7cn/b2/nanosv_1.2.4+git20190409.c1ae30c-7_amd64.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: 0.390s) 0.390s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.042s) 0.042s 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: 758ms CPU time consumed: 742ms Thu Dec 12 20:26:00 UTC 2024 I: diffoscope 284 found no differences in the changes files, and a .buildinfo file also exists. Thu Dec 12 20:26:00 UTC 2024 I: nanosv from trixie built successfully and reproducibly on amd64. Thu Dec 12 20:26:02 UTC 2024 I: Submitting .buildinfo files to external archives: Thu Dec 12 20:26:02 UTC 2024 I: Submitting 8.0K b1/nanosv_1.2.4+git20190409.c1ae30c-7_amd64.buildinfo.asc Thu Dec 12 20:26:02 UTC 2024 I: Submitting 8.0K b2/nanosv_1.2.4+git20190409.c1ae30c-7_amd64.buildinfo.asc Thu Dec 12 20:26:05 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Dec 12 20:26:05 UTC 2024 I: Done submitting .buildinfo files. Thu Dec 12 20:26:05 UTC 2024 I: Removing signed nanosv_1.2.4+git20190409.c1ae30c-7_amd64.buildinfo.asc files: removed './b1/nanosv_1.2.4+git20190409.c1ae30c-7_amd64.buildinfo.asc' removed './b2/nanosv_1.2.4+git20190409.c1ae30c-7_amd64.buildinfo.asc'