Wed Oct 13 13:09:00 UTC 2021 I: starting to build nanosv/bullseye/amd64 on jenkins on '2021-10-13 13:08' Wed Oct 13 13:09:00 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_9/25981/console.log Wed Oct 13 13:09:00 UTC 2021 I: Downloading source for bullseye/nanosv=1.2.4+git20190409.c1ae30c-3 --2021-10-13 13:09:00-- http://cdn-fastly.deb.debian.org/debian/pool/main/n/nanosv/nanosv_1.2.4%2bgit20190409.c1ae30c-3.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2144 (2.1K) Saving to: ‘nanosv_1.2.4+git20190409.c1ae30c-3.dsc’ 0K .. 100% 220M=0s 2021-10-13 13:09:00 (220 MB/s) - ‘nanosv_1.2.4+git20190409.c1ae30c-3.dsc’ saved [2144/2144] Wed Oct 13 13:09:01 UTC 2021 I: nanosv_1.2.4+git20190409.c1ae30c-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: nanosv Binary: nanosv Architecture: all Version: 1.2.4+git20190409.c1ae30c-3 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller Homepage: https://github.com/mroosmalen/nanosv Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/nanosv Vcs-Git: https://salsa.debian.org/med-team/nanosv.git Build-Depends: debhelper-compat (= 13), dh-python, python3-setuptools, python3-all, help2man, python3-vcf, python3-nose Package-List: nanosv deb science optional arch=all Checksums-Sha1: f333586be6145b26fd2394061b081a9b11e2feba 2895140 nanosv_1.2.4+git20190409.c1ae30c.orig.tar.xz 0d5e02d8d56ea60c823f118fe1a7d2daae4b62ff 3748 nanosv_1.2.4+git20190409.c1ae30c-3.debian.tar.xz Checksums-Sha256: e79073d4a3d6f6f1d1c87f462b2289cb7b19b3affd1c3eedcdc443658e76adbe 2895140 nanosv_1.2.4+git20190409.c1ae30c.orig.tar.xz dffa31f923520b715918c6c5cd9cbeb199980be40fa1162222636200fa82a92d 3748 nanosv_1.2.4+git20190409.c1ae30c-3.debian.tar.xz Files: 977ab7bb8626de0f467c564b4e4e4d4a 2895140 nanosv_1.2.4+git20190409.c1ae30c.orig.tar.xz a9a58f10bdbeab3d7ce561905faf293f 3748 nanosv_1.2.4+git20190409.c1ae30c-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl/zDDcRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFE/Q/+KTNe7Roi2BLTR07MeI8s7l+WBkj2sH5m Z9xOoi7TyX1PQBo4LKmNjmMCaL+rZp2xqXLzWRxK9R/cdwzlk75YWF+XmdTrnbl0 RNHgaEfTMmgMJKQbSYuGNEU5qPxpo8ja2HE3PwScqaoMbk4lL9acYRcPsAfBmF2T zij/2qiaMJRwAacciNAxv7VhC64ZszvrNFYzQr6/Gm+zgc4OySPCTPjEuWVMEGcg ToDp5rYeCCFkNGSl4haDhFqhZZad+N+b/pcoc1SenMKEQV9TrTi7cjDFNVX5Q0T/ 2D4P+qwvBIV6LT0TsMv8ly/Nwxxpmr7QMZ0soDxwq9sv9fsYiXEzTfbcsgOUynIt /1fbB+xuW2My4vuAhd6XZ0p3VjKROLugXz84PfHZe+SoK6k7Iw9X4/TlVla9W+h+ jIA5723q/UalVu921Wq7bJVzkPYE41G4xbixCcNjnTiHgImn1Daj2PPvyqoO6N6W eR7t4bon7EY/AkU904L6Ncr3gidqPtlFbhDLAAkeLAgiRkRNu5MMpqP1JJ1tg18Z uFJSX9yfkCoPeavyhm1k3x2XKKya4FlP+r6LoBoQ6CsG6/v4qnE7pQB5o1hjKlnh +ViE8nkNQpbTIcl6w+sqJnSl4+tQpRsZQs/XfzsJhDYvjOiP3eMfnGbvpy0M57wB f5qoDPyVSe4= =Z/12 -----END PGP SIGNATURE----- Wed Oct 13 13:09:01 UTC 2021 I: Checking whether the package is not for us Wed Oct 13 13:09:01 UTC 2021 I: Starting 1st build on remote node ionos1-amd64.debian.net. Wed Oct 13 13:09:01 UTC 2021 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Wed Oct 13 13:11:26 UTC 2021 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Oct 13 01:09:03 -12 2021 I: pbuilder-time-stamp: 1634130543 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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-3.dsc] I: copying [./nanosv_1.2.4+git20190409.c1ae30c.orig.tar.xz] I: copying [./nanosv_1.2.4+git20190409.c1ae30c-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.pYftENdz/trustedkeys.kbx': General error gpgv: Signature made Mon Jan 4 00:38:15 2021 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./nanosv_1.2.4+git20190409.c1ae30c-3.dsc 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-3.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3364210/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' 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,-fixfilepath parallel=15' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='70a047ef36134ba28ca8cd1c8ff0c732' 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='3364210' 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/tmp.zjldWvk4Hi/pbuilderrc_bmBJ --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.zjldWvk4Hi/b1 --logfile b1/build.log nanosv_1.2.4+git20190409.c1ae30c-3.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos1-amd64 5.10.0-9-amd64 #1 SMP Debian 5.10.70-1 (2021-09-30) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Aug 4 08:25 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 23 2020 date -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd -rwxr-xr-x 1 root root 93936 Sep 23 2020 df -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir -rwxr-xr-x 1 root root 84440 Jul 28 07:09 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 39680 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 69032 Jul 28 07:09 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 98048 Mar 2 2021 gzip -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls -rwxr-xr-x 1 root root 149736 Jul 28 07:09 lsblk -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 59632 Jul 28 07:09 more -rwsr-xr-x 1 root root 55528 Jul 28 07:09 mount -rwxr-xr-x 1 root root 18664 Jul 28 07:09 mountpoint -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Oct 6 21:24 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty -rwsr-xr-x 1 root root 71912 Jul 28 07:09 su -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch -rwxr-xr-x 1 root root 39680 Sep 23 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jul 28 07:09 umount -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63744 Jul 28 07:09 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/3364210/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, python3-setuptools, python3-all, help2man, python3-vcf, python3-nose dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19655 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on python3-vcf; however: Package python3-vcf is not installed. pbuilder-satisfydepends-dummy depends on python3-nose; however: Package python3-nose 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} libcurl3-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libhts3{a} libicu67{a} libldap-2.4-2{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libmpdec3{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-all{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-nose{a} python3-pkg-resources{a} python3-pysam{a} python3-setuptools{a} python3-vcf{a} python3.9{a} python3.9-minimal{a} readline-common{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 65 newly installed, 0 to remove and 0 not upgraded. Need to get 28.4 MB of archives. After unpacking 103 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 liblocale-gettext-perl amd64 1.07-4+b1 [19.0 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2 [96.9 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7 [693 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 python3-distutils all 3.9.2-1 [143 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 help2man amd64 1.48.1 [190 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1 [69.1 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1 [106 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3 [232 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+b1 [338 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 libhts3 amd64 1.11-4 [378 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 python3-all amd64 3.9.2-3 [1056 B] Get: 61 http://deb.debian.org/debian bullseye/main amd64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 python3-nose all 1.3.7-7 [133 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 python3-pysam amd64 0.15.4+ds-3+b2 [1536 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 python3-setuptools all 52.0.0-4 [366 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 python3-vcf amd64 0.6.8+git20170215.476169c-7+b3 [42.5 kB] Fetched 28.4 MB in 1s (29.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19655 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8_amd64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../1-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_amd64.deb ... 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Setting up bsdextrautils (2.36.1-8) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:amd64 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b2) ... Setting up libnghttp2-14:amd64 (1.43.0-1) ... Setting up libmagic1:amd64 (1:5.39-3) ... Setting up libdeflate0:amd64 (1.7-1) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2.1) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libmpdec3:amd64 (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:amd64 (1.9.0-2) ... Setting up libelf1:amd64 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7) ... Setting up liblocale-gettext-perl (1.07-4+b1) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:amd64 (7.74.0-1.3+b1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up help2man (1.48.1) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libhts3:amd64 (1.11-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up python3.9 (3.9.2-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up python3-distutils (3.9.2-1) ... Setting up dh-python (4.20201102+nmu1) ... Setting up python3-pysam (0.15.4+ds-3+b2) ... Setting up python3-setuptools (52.0.0-4) ... Setting up python3-all (3.9.2-3) ... Setting up python3-nose (1.3.7-7) ... Setting up python3-vcf (0.6.8+git20170215.476169c-7+b3) ... Processing triggers for libc-bin (2.31-13+deb11u2) ... 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/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-3_source.changes dpkg-buildpackage: info: source package nanosv dpkg-buildpackage: info: source version 1.2.4+git20190409.c1ae30c-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille 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 --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/nanosv-1.2.4+git20190409.c1ae30c' dh_auto_clean install -d /build/nanosv-1.2.4\+git20190409.c1ae30c/debian/.debhelper/generated/_source/home pybuild --clean --test-nose -i python{version} -p 3.9 I: pybuild base:232: python3.9 setup.py clean /usr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'including_package_data' warnings.warn(msg) running clean removing '/build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.9' does not exist -- can't clean it rm -rf .pybuild/ find . -name \*.pyc -exec rm {} \; rm -rf /build/nanosv-1.2.4+git20190409.c1ae30c/debian/python3-nanosv* rm -f /build/nanosv-1.2.4+git20190409.c1ae30c/debian/NanoSV.1 make[1]: Leaving directory '/build/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 \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) 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 install -d /build/nanosv-1.2.4\+git20190409.c1ae30c/debian/.debhelper/generated/_source/home pybuild --configure --test-nose -i python{version} -p 3.9 I: pybuild base:232: python3.9 setup.py config /usr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'including_package_data' warnings.warn(msg) running config dh_auto_build -O--buildsystem=pybuild pybuild --build --test-nose -i python{version} -p 3.9 I: pybuild base:232: /usr/bin/python3 setup.py build /usr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'including_package_data' warnings.warn(msg) running build running build_py creating /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv copying nanosv/version.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv copying nanosv/__init__.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv copying nanosv/NanoSV.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv creating /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/utils copying nanosv/utils/phasing.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/utils copying nanosv/utils/parse_svs.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/utils copying nanosv/utils/parse_reads.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/utils copying nanosv/utils/parse_breakpoints.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/utils copying nanosv/utils/parse_bam.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/utils copying nanosv/utils/create_vcf.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/utils copying nanosv/utils/coverage.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/utils copying nanosv/utils/__init__.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/utils creating /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/classes copying nanosv/classes/variant.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/classes copying nanosv/classes/sv.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/classes copying nanosv/classes/segment.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/classes copying nanosv/classes/read.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/classes copying nanosv/classes/breakpoint.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/classes copying nanosv/classes/__init__.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/classes copying nanosv/config.ini -> /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv creating /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/bedfiles copying nanosv/bedfiles/human_hg19.bed -> /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/bedfiles debian/rules override_dh_auto_test make[1]: Entering directory '/build/nanosv-1.2.4+git20190409.c1ae30c' dh_auto_test -- --system=custom --test-args="PYTHONPATH={build_dir} {interpreter} -m nose -v" pybuild --test --test-nose -i python{version} -p 3.9 --system=custom "--test-args=PYTHONPATH={build_dir} {interpreter} -m nose -v" I: pybuild base:232: PYTHONPATH=/build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build python3.9 -m nose -v rm -fr -- /tmp/dh-xdg-rundir-mJ272uUI make[1]: Leaving directory '/build/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/ rm -f debian/nanosv.debhelper.log debian/rules override_dh_auto_install make[1]: Entering directory '/build/nanosv-1.2.4+git20190409.c1ae30c' dh_auto_install install -d /build/nanosv-1.2.4\+git20190409.c1ae30c/debian/nanosv pybuild --install --test-nose -i python{version} -p 3.9 --dest-dir /build/nanosv-1.2.4\+git20190409.c1ae30c/debian/nanosv I: pybuild base:232: /usr/bin/python3 setup.py install --root /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv /usr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'including_package_data' warnings.warn(msg) running install running build running build_py running install_lib creating /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr creating /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib creating /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9 creating /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages creating /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv creating /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/bedfiles copying /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/bedfiles/human_hg19.bed -> /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/bedfiles copying /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/config.ini -> /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv creating /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/classes copying /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/classes/__init__.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/classes copying /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/classes/breakpoint.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/classes copying /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/classes/read.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/classes copying /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/classes/segment.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/classes copying /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/classes/sv.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/classes copying /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/classes/variant.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/classes creating /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils copying /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/utils/__init__.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils copying /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/utils/coverage.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils copying /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/utils/create_vcf.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils copying /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/utils/parse_bam.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils copying /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/utils/parse_breakpoints.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils copying /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/utils/parse_reads.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils copying /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/utils/parse_svs.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils copying /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/utils/phasing.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils copying /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/NanoSV.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv copying /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/__init__.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv copying /build/nanosv-1.2.4+git20190409.c1ae30c/.pybuild/cpython3_3.9_nanosv/build/nanosv/version.py -> /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv byte-compiling /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/classes/__init__.py to __init__.cpython-39.pyc byte-compiling /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/classes/breakpoint.py to breakpoint.cpython-39.pyc byte-compiling /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/classes/read.py to read.cpython-39.pyc byte-compiling /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/classes/segment.py to segment.cpython-39.pyc byte-compiling /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/classes/sv.py to sv.cpython-39.pyc byte-compiling /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/classes/variant.py to variant.cpython-39.pyc byte-compiling /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils/__init__.py to __init__.cpython-39.pyc byte-compiling /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils/coverage.py to coverage.cpython-39.pyc byte-compiling /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils/create_vcf.py to create_vcf.cpython-39.pyc byte-compiling /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils/parse_bam.py to parse_bam.cpython-39.pyc byte-compiling /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils/parse_breakpoints.py to parse_breakpoints.cpython-39.pyc byte-compiling /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils/parse_reads.py to parse_reads.cpython-39.pyc byte-compiling /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils/parse_svs.py to parse_svs.cpython-39.pyc byte-compiling /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/utils/phasing.py to phasing.cpython-39.pyc byte-compiling /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/NanoSV.py to NanoSV.cpython-39.pyc byte-compiling /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/__init__.py to __init__.cpython-39.pyc byte-compiling /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/nanosv/version.py to version.cpython-39.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' writing manifest file 'NanoSV.egg-info/SOURCES.txt' Copying NanoSV.egg-info to /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/lib/python3.9/dist-packages/NanoSV-1.2.4.egg-info Skipping SOURCES.txt running install_scripts Installing NanoSV script to /build/nanosv-1.2.4+git20190409.c1ae30c/debian/nanosv/usr/bin find /build/nanosv-1.2.4+git20190409.c1ae30c/debian -name "*.bed" -o -name "*.ini" | xargs -r chmod -x PYTHONPATH=./debian/nanosv/usr/lib/python3.9/dist-packages/ help2man --include=debian/NanoSV.h2m ./debian/nanosv/usr/bin/NanoSV > /build/nanosv-1.2.4+git20190409.c1ae30c/debian/NanoSV.1 make[1]: Leaving directory '/build/nanosv-1.2.4+git20190409.c1ae30c' dh_installdocs -O--buildsystem=pybuild install -d debian/nanosv/usr/share/doc/nanosv install -d debian/.debhelper/generated/nanosv install -p -m0644 debian/copyright debian/nanosv/usr/share/doc/nanosv/copyright dh_installchangelogs -O--buildsystem=pybuild install -p -m0644 debian/changelog debian/nanosv/usr/share/doc/nanosv/changelog.Debian dh_installman -O--buildsystem=pybuild install -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_python3:161: version: 4.20201102+nmu1 D: dh_python3 dh_python3:162: argv: ['/usr/bin/dh_python3', '-O--buildsystem=pybuild'] D: dh_python3 dh_python3:163: options: {'guess_deps': True, 'skip_private': False, 'verbose': False, 'arch': None, 'package': None, 'no_package': None, '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, 'O': '--buildsystem=pybuild'} D: dh_python3 dh_python3:164: args: [] D: dh_python3 dh_python3:165: supported Python versions: 3.9 (default=3.9) D: dh_python3 debhelper:152: source=nanosv, binary packages=['nanosv'] D: dh_python3 dh_python3:183: processing package nanosv... D: dh_python3 fs:49: moving files from debian/nanosv/usr/lib/python3.9/dist-packages to debian/nanosv/usr/lib/python3/dist-packages/ D: dh_python3 fs:260: package nanosv details = {'requires.txt': {'debian/nanosv/usr/lib/python3/dist-packages/NanoSV-1.2.4.egg-info/requires.txt'}, 'egg-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:117: generating dependencies for package nanosv D: dh_python3 pydist:142: trying to find dependency for pysam>=0.11 (python=None) D: dh_python3 pydist:142: trying to find dependency for pyvcf (python=None) D: dh_python3 depends:275: D={'python3-pysam', 'python3:any', 'python3-vcf'}; 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/changelog.Debian usr/share/man/man1/NanoSV.1 gzip -9nf usr/share/doc/nanosv/changelog.Debian usr/share/man/man1/NanoSV.1 cd '/build/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 -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 echo misc:Depends= >> debian/nanosv.substvars echo misc:Pre-Depends= >> debian/nanosv.substvars dpkg-gencontrol -pnanosv -ldebian/changelog -Tdebian/nanosv.substvars -Pdebian/nanosv chmod 0644 -- debian/nanosv/DEBIAN/control dh_md5sums -O--buildsystem=pybuild 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-3_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../nanosv_1.2.4+git20190409.c1ae30c-3_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/3364210 and its subdirectories I: Current time: Wed Oct 13 01:11:25 -12 2021 I: pbuilder-time-stamp: 1634130685 Wed Oct 13 13:11:26 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Wed Oct 13 13:11:26 UTC 2021 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Wed Oct 13 13:12:26 UTC 2021 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Wed Oct 13 13:12:27 UTC 2021 I: nanosv_1.2.4+git20190409.c1ae30c-3_amd64.changes: Format: 1.8 Date: Mon, 04 Jan 2021 13:26:30 +0100 Source: nanosv Binary: nanosv Architecture: all Version: 1.2.4+git20190409.c1ae30c-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: nanosv - structural variant caller for nanopore data Closes: 978338 Changes: nanosv (1.2.4+git20190409.c1ae30c-3) unstable; urgency=medium . * Team upload. * Enable building with Python3.9 Closes: #978338 * Standards-Version: 4.5.1 (routine-update) Checksums-Sha1: a2b454f4a08665bea033d128af9ccb95d655d61f 2888968 nanosv_1.2.4+git20190409.c1ae30c-3_all.deb 8c7e7483adad67abf2a1309d07a04d6da66a6d25 6105 nanosv_1.2.4+git20190409.c1ae30c-3_amd64.buildinfo Checksums-Sha256: 42684bf02723244cf3b47f189131ffdfbf47ac799c619204499611276108e82a 2888968 nanosv_1.2.4+git20190409.c1ae30c-3_all.deb 99e2b3fe9c4a08387b4fc0f18b4fbdcb6fc15d8720a6a852a34e732093fed6a2 6105 nanosv_1.2.4+git20190409.c1ae30c-3_amd64.buildinfo Files: 3cadcec5925baff2839bf312f9f4028b 2888968 science optional nanosv_1.2.4+git20190409.c1ae30c-3_all.deb 4901886cdd25e0e806421d0d1f119ace 6105 science optional nanosv_1.2.4+git20190409.c1ae30c-3_amd64.buildinfo Wed Oct 13 13:12:28 UTC 2021 I: will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.zjldWvk4Hi/nanosv_1.2.4+git20190409.c1ae30c-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.zjldWvk4Hi/nanosv_1.2.4+git20190409.c1ae30c-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.zjldWvk4Hi/nanosv_1.2.4+git20190409.c1ae30c-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.zjldWvk4Hi/b1/nanosv_1.2.4+git20190409.c1ae30c-3_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.zjldWvk4Hi/b2/nanosv_1.2.4+git20190409.c1ae30c-3_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: 0.322s) 0.322s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.054s) 0.054s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Wed Oct 13 13:12:29 UTC 2021 I: found no differences in the changes files, and a .buildinfo file also exists. Wed Oct 13 13:12:29 UTC 2021 I: nanosv from bullseye built successfully and reproducibly on amd64. Wed Oct 13 13:12:30 UTC 2021 I: Submitting .buildinfo files to external archives: Wed Oct 13 13:12:30 UTC 2021 I: Submitting 8.0K b1/nanosv_1.2.4+git20190409.c1ae30c-3_amd64.buildinfo.asc Wed Oct 13 13:12:31 UTC 2021 I: Submitting 8.0K b2/nanosv_1.2.4+git20190409.c1ae30c-3_amd64.buildinfo.asc Wed Oct 13 13:12:32 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Oct 13 13:12:32 UTC 2021 I: Done submitting .buildinfo files. Wed Oct 13 13:12:32 UTC 2021 I: Removing signed nanosv_1.2.4+git20190409.c1ae30c-3_amd64.buildinfo.asc files: removed './b1/nanosv_1.2.4+git20190409.c1ae30c-3_amd64.buildinfo.asc' removed './b2/nanosv_1.2.4+git20190409.c1ae30c-3_amd64.buildinfo.asc'