Wed Apr 24 08:11:52 UTC 2024 I: starting to build flye/trixie/armhf on jenkins on '2024-04-24 08:11' Wed Apr 24 08:11:52 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_8/6579/console.log Wed Apr 24 08:11:52 UTC 2024 I: Downloading source for trixie/flye=2.9.3+dfsg2-1 --2024-04-24 08:11:52-- http://deb.debian.org/debian/pool/main/f/flye/flye_2.9.3%2bdfsg2-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2110 (2.1K) [text/prs.lines.tag] Saving to: ‘flye_2.9.3+dfsg2-1.dsc’ 0K .. 100% 327M=0s 2024-04-24 08:11:52 (327 MB/s) - ‘flye_2.9.3+dfsg2-1.dsc’ saved [2110/2110] Wed Apr 24 08:11:52 UTC 2024 I: flye_2.9.3+dfsg2-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: flye Binary: flye Architecture: any Version: 2.9.3+dfsg2-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://github.com/fenderglass/Flye Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/flye Vcs-Git: https://salsa.debian.org/med-team/flye.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3, python3-setuptools, liblemon-dev, libminimap2-dev, samtools, zlib1g-dev Package-List: flye deb science optional arch=any Checksums-Sha1: a47bc0582541c9e1c44fa1b9629deb2187499706 22760396 flye_2.9.3+dfsg2.orig.tar.xz 154699215b08f3f3346750d16f62d5cbc52ac4c7 14404 flye_2.9.3+dfsg2-1.debian.tar.xz Checksums-Sha256: 2a71e7420055bffa95fb1200209cf180ed741137b4e60587ecec9cf962326f73 22760396 flye_2.9.3+dfsg2.orig.tar.xz 02d11ec9c4a9458263c20bbac1a83749374332bd42ede9c58983fe4eef435640 14404 flye_2.9.3+dfsg2-1.debian.tar.xz Files: 2dc92944cd1831fc7989d3ae54722478 22760396 flye_2.9.3+dfsg2.orig.tar.xz 45bf933f804f08c453fd1b7e5317ad88 14404 flye_2.9.3+dfsg2-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmW88+URHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHhNA/6A9j1ah0xxK0/4zPFV7itmcLeK7TW3wdn cHHISplmIh/OwoJP/bRVRKqtdWsY6djk0DzMPqQMD4BBJQuTsLiCzT0qklqgCVI4 F7QaX1+k5sY4m1gXUg5Cy4XJTfUfRMVyCgO1iS8tOudJAkh52wL1pWbDtQGAkBRu oJUm9mXiAfcSYiJ01JX8fjSTqqdJG8JY6I8UcusHUbEc11wiug/TPa+6++pZf6ib unRtjyAr8ZT4RrDqFiLoXtIvqJSfG2SF4XojGO5lc9oS+rixRQjs4JpHpq9jIq8X p6m3aK9jmPe3aSHJsBFPTt5UBcv+0MsiqpsZtbP/74+PDUIdy9TfSX+a2fQ0OBpx zy+/FoNmbVNtzC5szMOCzmo2pAYJ6EIAh58fL2BvrWzWPuRaAAIm+IwVNtRW/8Bt c8wokWgf1nfJpCifNGT+KEe11+50ZthQ62qUWYwDTFVrPZqLvVE+E0xADdMx7hYO d0l67E81a0p8cbb6+Y5ik3XHtl5J5fn9dQS0Aq4yy88OX5i8eOwPop9dAM9eqCKr jQGJ7H0biBf3NIet1W0Qy/G8iitrQOev4+/P7Abtme4dPtTHNq8bbeNcLD/I5lrb qS6iS7XQjC9pWbwZXqZqaGSTAt161khvyOAc95ltvK19LjfaR20MgdzUlgR7WoHX 6AWW+CUMsh0= =vXxr -----END PGP SIGNATURE----- Wed Apr 24 08:11:52 UTC 2024 I: Checking whether the package is not for us Wed Apr 24 08:11:52 UTC 2024 I: Starting 1st build on remote node virt64a-armhf-rb.debian.net. Wed Apr 24 08:11:52 UTC 2024 I: Preparing to do remote build '1' on virt64a-armhf-rb.debian.net. Wed Apr 24 08:17:11 UTC 2024 I: Deleting $TMPDIR on virt64a-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Apr 23 20:12:03 -12 2024 I: pbuilder-time-stamp: 1713946323 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 [flye_2.9.3+dfsg2-1.dsc] I: copying [./flye_2.9.3+dfsg2.orig.tar.xz] I: copying [./flye_2.9.3+dfsg2-1.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Feb 2 13:53:41 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./flye_2.9.3+dfsg2-1.dsc: no acceptable signature found dpkg-source: info: extracting flye in flye-2.9.3+dfsg2 dpkg-source: info: unpacking flye_2.9.3+dfsg2.orig.tar.xz dpkg-source: info: unpacking flye_2.9.3+dfsg2-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libs.patch dpkg-source: info: applying cppflags.patch dpkg-source: info: applying python3.12.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/26723/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='915ccd9bb061447fa60e321223afed73' 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='26723' 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.KeZEBgnp/pbuilderrc_Rptv --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.KeZEBgnp/b1 --logfile b1/build.log flye_2.9.3+dfsg2-1.dsc' SUDO_GID='114' SUDO_UID='108' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt64a 6.1.0-20-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 23 11:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/26723/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: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, python3, python3-setuptools, liblemon-dev, libminimap2-dev, samtools, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19637 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on liblemon-dev; however: Package liblemon-dev is not installed. pbuilder-satisfydepends-dummy depends on libminimap2-dev; however: Package libminimap2-dev is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libamd3{a} libarchive-zip-perl{a} libbrotli1{a} libcolamd3{a} libcurl3-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libglpk40{a} libhts3{a} libhtscodecs2{a} libicu72{a} libldap-2.5-0{a} liblemon-dev{a} liblemon1.3.1{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libminimap2-dev{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libsuitesparseconfig7{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-setuptools{a} python3.11{a} python3.11-minimal{a} readline-common{a} samtools{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 71 newly installed, 0 to remove and 0 not upgraded. Need to get 29.5 MB of archives. After unpacking 105 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf libpython3.11-minimal armhf 3.11.8-1 [802 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libexpat1 armhf 2.6.2-1 [83.5 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf python3.11-minimal armhf 3.11.8-1 [1707 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf python3-minimal armhf 3.11.6-1 [26.2 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf tzdata all 2024a-1 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf readline-common all 8.2-3 [69.1 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libreadline8 armhf 8.2-3+b1 [144 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf libpython3.11-stdlib armhf 3.11.8-1 [1709 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf python3.11 armhf 3.11.8-1 [597 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf libpython3-stdlib armhf 3.11.6-1 [9224 B] Get: 13 http://deb.debian.org/debian trixie/main armhf python3 armhf 3.11.6-1 [26.2 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-2+b1 [314 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libmagic1 armhf 1:5.45-2+b1 [97.9 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-2+b1 [42.2 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-3 [1088 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.39.3-6 [81.2 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.12.0-3 [1367 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf autoconf all 2.71-3 [332 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf autopoint all 0.21-14 [496 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 36 http://deb.debian.org/debian trixie/main armhf libelf1 armhf 0.190-1+b1 [171 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1 [101 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b2 [599 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf python3-pkg-resources all 68.1.2-2 [241 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf python3-lib2to3 all 3.11.5-1 [77.5 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf python3-distutils all 3.11.5-1 [131 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf python3-setuptools all 68.1.2-2 [468 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf dh-python all 6.20240401 [107 kB] Get: 49 http://deb.debian.org/debian trixie/main armhf libsuitesparseconfig7 armhf 1:7.7.0+dfsg-2 [21.8 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf libamd3 armhf 1:7.7.0+dfsg-2 [39.4 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b3 [284 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf libcolamd3 armhf 1:7.7.0+dfsg-2 [32.1 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-4+b1 [18.2 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf libsasl2-2 armhf 2.1.28+dfsg1-4+b1 [50.1 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5+b3 [158 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf libnghttp2-14 armhf 1.59.0-1 [62.0 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB] Get: 58 http://deb.debian.org/debian trixie/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 59 http://deb.debian.org/debian trixie/main armhf libssh2-1 armhf 1.11.0-4 [197 kB] Get: 60 http://deb.debian.org/debian trixie/main armhf libcurl3-gnutls armhf 8.5.0-2 [378 kB] Get: 61 http://deb.debian.org/debian trixie/main armhf libdeflate0 armhf 1.20-1 [35.9 kB] Get: 62 http://deb.debian.org/debian trixie/main armhf libltdl7 armhf 2.4.7-7 [390 kB] Get: 63 http://deb.debian.org/debian trixie/main armhf libglpk40 armhf 5.0-1+b1 [330 kB] Get: 64 http://deb.debian.org/debian trixie/main armhf libhtscodecs2 armhf 1.6.0-1+b1 [61.3 kB] Get: 65 http://deb.debian.org/debian trixie/main armhf libhts3 armhf 1.19+ds-1 [394 kB] Get: 66 http://deb.debian.org/debian trixie/main armhf liblemon1.3.1 armhf 1.3.1+dfsg-6 [47.2 kB] Get: 67 http://deb.debian.org/debian trixie/main armhf liblemon-dev armhf 1.3.1+dfsg-6 [322 kB] Get: 68 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg-3+b1 [904 kB] Get: 69 http://deb.debian.org/debian trixie/main armhf libminimap2-dev armhf 2.27+dfsg-1 [131 kB] Get: 70 http://deb.debian.org/debian trixie/main armhf libncurses6 armhf 6.4+20240414-1 [81.8 kB] Get: 71 http://deb.debian.org/debian trixie/main armhf samtools armhf 1.19.2-1 [614 kB] Fetched 29.5 MB in 2s (15.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:armhf. (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 ... 19637 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.8-1_armhf.deb ... Unpacking libpython3.11-minimal:armhf (3.11.8-1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.6.2-1_armhf.deb ... Unpacking libexpat1:armhf (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.8-1_armhf.deb ... Unpacking python3.11-minimal (3.11.8-1) ... Setting up libpython3.11-minimal:armhf (3.11.8-1) ... Setting up libexpat1:armhf (2.6.2-1) ... Setting up python3.11-minimal (3.11.8-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19953 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.6-1_armhf.deb ... Unpacking python3-minimal (3.11.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-1_all.deb ... Unpacking tzdata (2024a-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-3_all.deb ... Unpacking readline-common (8.2-3) ... Selecting previously unselected package libreadline8:armhf. Preparing to unpack .../5-libreadline8_8.2-3+b1_armhf.deb ... Unpacking libreadline8:armhf (8.2-3+b1) ... Selecting previously unselected package libpython3.11-stdlib:armhf. Preparing to unpack .../6-libpython3.11-stdlib_3.11.8-1_armhf.deb ... Unpacking libpython3.11-stdlib:armhf (3.11.8-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.8-1_armhf.deb ... Unpacking python3.11 (3.11.8-1) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../8-libpython3-stdlib_3.11.6-1_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.11.6-1) ... Setting up python3-minimal (3.11.6-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20941 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.6-1_armhf.deb ... Unpacking python3 (3.11.6-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-2+b1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../03-libmagic1_1%3a5.45-2+b1_armhf.deb ... Unpacking libmagic1:armhf (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-2+b1_armhf.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-14+b1_armhf.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../06-libuchardet0_0.0.8-1+b1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-3_armhf.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.39.3-6_armhf.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../09-libpipeline1_1.5.7-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.12.0-3_armhf.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../20-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../23-libelf1_0.190-1+b1_armhf.deb ... Unpacking libelf1:armhf (0.190-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.15-1_armhf.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../25-libicu72_72.1-4+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-4+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../26-libxml2_2.9.14+dfsg-1.3+b2_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.3+b2) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.21-14+b1_armhf.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../31-python3-pkg-resources_68.1.2-2_all.deb ... Unpacking python3-pkg-resources (68.1.2-2) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../32-python3-lib2to3_3.11.5-1_all.deb ... Unpacking python3-lib2to3 (3.11.5-1) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../33-python3-distutils_3.11.5-1_all.deb ... Unpacking python3-distutils (3.11.5-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../34-python3-setuptools_68.1.2-2_all.deb ... Unpacking python3-setuptools (68.1.2-2) ... Selecting previously unselected package dh-python. Preparing to unpack .../35-dh-python_6.20240401_all.deb ... Unpacking dh-python (6.20240401) ... Selecting previously unselected package libsuitesparseconfig7:armhf. Preparing to unpack .../36-libsuitesparseconfig7_1%3a7.7.0+dfsg-2_armhf.deb ... Unpacking libsuitesparseconfig7:armhf (1:7.7.0+dfsg-2) ... Selecting previously unselected package libamd3:armhf. Preparing to unpack .../37-libamd3_1%3a7.7.0+dfsg-2_armhf.deb ... Unpacking libamd3:armhf (1:7.7.0+dfsg-2) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../38-libbrotli1_1.1.0-2+b3_armhf.deb ... Unpacking libbrotli1:armhf (1.1.0-2+b3) ... Selecting previously unselected package libcolamd3:armhf. Preparing to unpack .../39-libcolamd3_1%3a7.7.0+dfsg-2_armhf.deb ... Unpacking libcolamd3:armhf (1:7.7.0+dfsg-2) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../40-libsasl2-modules-db_2.1.28+dfsg1-4+b1_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg1-4+b1) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../41-libsasl2-2_2.1.28+dfsg1-4+b1_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.28+dfsg1-4+b1) ... Selecting previously unselected package libldap-2.5-0:armhf. Preparing to unpack .../42-libldap-2.5-0_2.5.13+dfsg-5+b3_armhf.deb ... Unpacking libldap-2.5-0:armhf (2.5.13+dfsg-5+b3) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../43-libnghttp2-14_1.59.0-1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.59.0-1) ... Selecting previously unselected package libpsl5:armhf. Preparing to unpack .../44-libpsl5_0.21.2-1+b1_armhf.deb ... Unpacking libpsl5:armhf (0.21.2-1+b1) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../45-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:armhf. Preparing to unpack .../46-libssh2-1_1.11.0-4_armhf.deb ... Unpacking libssh2-1:armhf (1.11.0-4) ... Selecting previously unselected package libcurl3-gnutls:armhf. Preparing to unpack .../47-libcurl3-gnutls_8.5.0-2_armhf.deb ... Unpacking libcurl3-gnutls:armhf (8.5.0-2) ... Selecting previously unselected package libdeflate0:armhf. Preparing to unpack .../48-libdeflate0_1.20-1_armhf.deb ... Unpacking libdeflate0:armhf (1.20-1) ... Selecting previously unselected package libltdl7:armhf. Preparing to unpack .../49-libltdl7_2.4.7-7_armhf.deb ... Unpacking libltdl7:armhf (2.4.7-7) ... Selecting previously unselected package libglpk40:armhf. Preparing to unpack .../50-libglpk40_5.0-1+b1_armhf.deb ... Unpacking libglpk40:armhf (5.0-1+b1) ... Selecting previously unselected package libhtscodecs2:armhf. Preparing to unpack .../51-libhtscodecs2_1.6.0-1+b1_armhf.deb ... Unpacking libhtscodecs2:armhf (1.6.0-1+b1) ... Selecting previously unselected package libhts3:armhf. Preparing to unpack .../52-libhts3_1.19+ds-1_armhf.deb ... Unpacking libhts3:armhf (1.19+ds-1) ... Selecting previously unselected package liblemon1.3.1:armhf. Preparing to unpack .../53-liblemon1.3.1_1.3.1+dfsg-6_armhf.deb ... Unpacking liblemon1.3.1:armhf (1.3.1+dfsg-6) ... Selecting previously unselected package liblemon-dev. Preparing to unpack .../54-liblemon-dev_1.3.1+dfsg-6_armhf.deb ... Unpacking liblemon-dev (1.3.1+dfsg-6) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../55-zlib1g-dev_1%3a1.3.dfsg-3+b1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.3.dfsg-3+b1) ... Selecting previously unselected package libminimap2-dev. Preparing to unpack .../56-libminimap2-dev_2.27+dfsg-1_armhf.deb ... Unpacking libminimap2-dev (2.27+dfsg-1) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../57-libncurses6_6.4+20240414-1_armhf.deb ... Unpacking libncurses6:armhf (6.4+20240414-1) ... Selecting previously unselected package samtools. Preparing to unpack .../58-samtools_1.19.2-1_armhf.deb ... Unpacking samtools (1.19.2-1) ... Setting up libhtscodecs2:armhf (1.6.0-1+b1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:armhf (1.5.7-2) ... Setting up libpsl5:armhf (0.21.2-1+b1) ... Setting up libicu72:armhf (72.1-4+b1) ... Setting up bsdextrautils (2.39.3-6) ... Setting up libmagic-mgc (1:5.45-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:armhf (1.1.0-2+b3) ... Setting up libnghttp2-14:armhf (1.59.0-1) ... Setting up libmagic1:armhf (1:5.45-2+b1) ... Setting up libdeflate0:armhf (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-2+b1) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-4+b1) ... Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Apr 24 08:15:40 UTC 2024. Universal Time is now: Wed Apr 24 08:15:40 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:armhf (6.4+20240414-1) ... Setting up autopoint (0.21-14) ... Setting up libltdl7:armhf (2.4.7-7) ... Setting up libsasl2-2:armhf (2.1.28+dfsg1-4+b1) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg-3+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:armhf (0.0.8-1+b1) ... Setting up libsuitesparseconfig7:armhf (1:7.7.0+dfsg-2) ... Setting up libsub-override-perl (0.10-1) ... Setting up libssh2-1:armhf (1.11.0-4) ... Setting up netbase (6.4) ... Setting up libelf1:armhf (0.190-1+b1) ... Setting up readline-common (8.2-3) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3+b2) ... 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 (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libamd3:armhf (1:7.7.0+dfsg-2) ... Setting up libtool (2.4.7-7) ... Setting up libcolamd3:armhf (1:7.7.0+dfsg-2) ... Setting up libreadline8:armhf (8.2-3+b1) ... Setting up libldap-2.5-0:armhf (2.5.13+dfsg-5+b3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libglpk40:armhf (5.0-1+b1) ... Setting up libminimap2-dev (2.27+dfsg-1) ... Setting up liblemon1.3.1:armhf (1.3.1+dfsg-6) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:armhf (3.11.8-1) ... Setting up liblemon-dev (1.3.1+dfsg-6) ... Setting up libcurl3-gnutls:armhf (8.5.0-2) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3-stdlib:armhf (3.11.6-1) ... Setting up python3.11 (3.11.8-1) ... Setting up libhts3:armhf (1.19+ds-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.6-1) ... Setting up samtools (1.19.2-1) ... Setting up python3-lib2to3 (3.11.5-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.11.5-1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up dh-python (6.20240401) ... Processing triggers for libc-bin (2.37-18) ... 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/flye-2.9.3+dfsg2/ && 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 > ../flye_2.9.3+dfsg2-1_source.changes dpkg-buildpackage: info: source package flye dpkg-buildpackage: info: source version 2.9.3+dfsg2-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/flye-2.9.3+dfsg2' dh_auto_clean I: pybuild base:311: python3.11 setup.py clean running clean removing '/build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build' (and everything under it) 'build/bdist.linux-armv7l' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it find src -name "*.o" -delete rm -f bin/flye-modules rm -rf flye.egg-info/ make[1]: Leaving directory '/build/reproducible-path/flye-2.9.3+dfsg2' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild 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 I: pybuild base:311: python3.11 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye copying flye/main.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye copying flye/__build__.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye copying flye/__version__.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye copying flye/__init__.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye creating /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/assembly copying flye/assembly/assemble.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/assembly copying flye/assembly/scaffolder.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/assembly copying flye/assembly/__init__.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/assembly copying flye/assembly/repeat_graph.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/assembly creating /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/config copying flye/config/configurator.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/config copying flye/config/__init__.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/config copying flye/config/py_cfg.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/config creating /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/polishing copying flye/polishing/consensus.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/polishing copying flye/polishing/alignment.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/polishing copying flye/polishing/__init__.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/polishing copying flye/polishing/polish.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/polishing copying flye/polishing/bubbles.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/polishing creating /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/utils copying flye/utils/utils.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/utils copying flye/utils/fasta_parser.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/utils copying flye/utils/__init__.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/utils copying flye/utils/sam_parser.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/utils copying flye/utils/bytes2human.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/utils creating /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/repeat_graph copying flye/repeat_graph/__init__.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/repeat_graph copying flye/repeat_graph/repeat_graph.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/repeat_graph copying flye/repeat_graph/graph_alignment.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/repeat_graph creating /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/short_plasmids copying flye/short_plasmids/utils.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/short_plasmids copying flye/short_plasmids/unmapped_reads.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/short_plasmids copying flye/short_plasmids/plasmids.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/short_plasmids copying flye/short_plasmids/__init__.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/short_plasmids copying flye/short_plasmids/circular_sequences.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/short_plasmids creating /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/trestle copying flye/trestle/trestle_config.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/trestle copying flye/trestle/divergence.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/trestle copying flye/trestle/graph_resolver.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/trestle copying flye/trestle/__init__.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/trestle copying flye/trestle/trestle.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/trestle creating /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/tests copying flye/tests/test_toy.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/tests copying flye/tests/__init__.py -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/tests creating /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/pacbio_chm13_substitutions.mat -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_raw_reads.cfg -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/pacbio_homopolymers.mat -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/nano_r94_g36_substitutions.mat -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_defaults.cfg -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/pacbio_chm13_homopolymers.mat -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/nano_r94_g36_homopolymers.mat -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_subasm.cfg -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_corrected_reads.cfg -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/nano_r94_substitutions.mat -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_nano_hq.cfg -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/asm_hifi.cfg -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/nano_r94_homopolymers.mat -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/config/bin_cfg copying flye/config/bin_cfg/pacbio_substitutions.mat -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/config/bin_cfg creating /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/tests/data copying flye/tests/data/ecoli_500kb_reads.fastq.gz -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/tests/data copying flye/tests/data/ecoli_500kb_reads_hifi.fastq.gz -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/tests/data copying flye/tests/data/ecoli_500kb.fasta -> /build/reproducible-path/flye-2.9.3+dfsg2/.pybuild/cpython3_3.11/build/flye/tests/data make[1]: Entering directory '/build/reproducible-path/flye-2.9.3+dfsg2' make release -C src -j 4 make[2]: Entering directory '/build/reproducible-path/flye-2.9.3+dfsg2/src' g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.3+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/libcuckoo -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/interval_tree -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG assemble/chimera.cpp -o assemble/chimera.o g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.3+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/libcuckoo -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/interval_tree -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG assemble/extender.cpp -o assemble/extender.o g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.3+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/libcuckoo -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/interval_tree -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG assemble/main_assemble.cpp -o assemble/main_assemble.o g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/flye-2.9.3+dfsg2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/libcuckoo -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/interval_tree -I/build/reproducible-path/flye-2.9.3+dfsg2/lib/lemon -Wall -Wextra -pthread -std=c++11 -g -Wno-missing-field-initializers -O3 -DNDEBUG assemble/parameters_estimator.cpp -o assemble/parameters_estimator.o assemble/main_assemble.cpp:214:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 214 | Logger::get().debug() << "Build date: " << __DATE__ << " " << __TIME__; | ^~~~~~~~ assemble/main_assemble.cpp:214:71: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 214 | Logger::get().debug() << "Build date: " << __DATE__ << " " << __TIME__; | ^~~~~~~~ In file included from assemble/../sequence/kmer.h:11, from assemble/../sequence/vertex_index.h:17, from assemble/parameters_estimator.h:5, from assemble/parameters_estimator.cpp:5: assemble/../sequence/sequence_container.h:271:42: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘1099511627776’ to ‘0’ [-Woverflow] 271 | const size_t MAX_SEQUENCE = 1ULL << (8 * 5); | ~~~~~^~~~~~~~~~ assemble/../sequence/kmer.h:14:30: error: static assertion failed: 32-bit architectures are not supported 14 | static_assert(sizeof(size_t) == 8, "32-bit architectures are not supported"); | ~~~~~~~~~~~~~~~^~~~ assemble/../sequence/kmer.h:14:30: note: the comparison reduces to ‘(4 == 8)’ assemble/../sequence/vertex_index.h: In member function ‘size_t VertexIndex::IndexChunk::get() const’: assemble/../sequence/vertex_index.h:102:44: warning: left shift count >= width of type [-Wshift-count-overflow] 102 | return ((size_t)hi << 32) + (size_t)low; | ~~~~~~~~~~~^~~~~ assemble/../sequence/vertex_index.h: In member function ‘void VertexIndex::IndexChunk::set(size_t)’: assemble/../sequence/vertex_index.h:107:34: warning: right shift count >= width of type [-Wshift-count-overflow] 107 | hi = val >> 32; | ~~~~^~~~~ In file included from assemble/extender.h:9, from assemble/extender.cpp:14: assemble/../sequence/sequence_container.h:271:42: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘1099511627776’ to ‘0’ [-Woverflow] 271 | const size_t MAX_SEQUENCE = 1ULL << (8 * 5); | ~~~~~^~~~~~~~~~ In file included from assemble/../sequence/kmer.h:11, from assemble/../sequence/vertex_index.h:17, from assemble/main_assemble.cpp:12: assemble/../sequence/sequence_container.h:271:42: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘1099511627776’ to ‘0’ [-Woverflow] 271 | const size_t MAX_SEQUENCE = 1ULL << (8 * 5); | ~~~~~^~~~~~~~~~ assemble/../sequence/kmer.h:14:30: error: static assertion failed: 32-bit architectures are not supported 14 | static_assert(sizeof(size_t) == 8, "32-bit architectures are not supported"); | ~~~~~~~~~~~~~~~^~~~ assemble/../sequence/kmer.h:14:30: note: the comparison reduces to ‘(4 == 8)’ assemble/../sequence/vertex_index.h: In member function ‘size_t VertexIndex::IndexChunk::get() const’: assemble/../sequence/vertex_index.h:102:44: warning: left shift count >= width of type [-Wshift-count-overflow] 102 | return ((size_t)hi << 32) + (size_t)low; | ~~~~~~~~~~~^~~~~ assemble/../sequence/vertex_index.h: In member function ‘void VertexIndex::IndexChunk::set(size_t)’: assemble/../sequence/vertex_index.h:107:34: warning: right shift count >= width of type [-Wshift-count-overflow] 107 | hi = val >> 32; | ~~~~^~~~~ In file included from assemble/../sequence/kmer.h:11, from assemble/../sequence/vertex_index.h:17, from assemble/../sequence/overlap.h:14, from assemble/chimera.h:7, from assemble/chimera.cpp:14: assemble/../sequence/sequence_container.h:271:42: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘1099511627776’ to ‘0’ [-Woverflow] 271 | const size_t MAX_SEQUENCE = 1ULL << (8 * 5); | ~~~~~^~~~~~~~~~ assemble/../sequence/kmer.h:14:30: error: static assertion failed: 32-bit architectures are not supported 14 | static_assert(sizeof(size_t) == 8, "32-bit architectures are not supported"); | ~~~~~~~~~~~~~~~^~~~ assemble/../sequence/kmer.h:14:30: note: the comparison reduces to ‘(4 == 8)’ make[2]: *** [Makefile:34: assemble/parameters_estimator.o] Error 1 make[2]: *** Waiting for unfinished jobs.... In file included from assemble/../sequence/vertex_index.h:17, from assemble/../sequence/overlap.h:14, from assemble/extender.h:10: assemble/../sequence/kmer.h:14:30: error: static assertion failed: 32-bit architectures are not supported 14 | static_assert(sizeof(size_t) == 8, "32-bit architectures are not supported"); | ~~~~~~~~~~~~~~~^~~~ assemble/../sequence/kmer.h:14:30: note: the comparison reduces to ‘(4 == 8)’ assemble/../sequence/vertex_index.h: In member function ‘size_t VertexIndex::IndexChunk::get() const’: assemble/../sequence/vertex_index.h:102:44: warning: left shift count >= width of type [-Wshift-count-overflow] 102 | return ((size_t)hi << 32) + (size_t)low; | ~~~~~~~~~~~^~~~~ assemble/../sequence/vertex_index.h: In member function ‘void VertexIndex::IndexChunk::set(size_t)’: assemble/../sequence/vertex_index.h:107:34: warning: right shift count >= width of type [-Wshift-count-overflow] 107 | hi = val >> 32; | ~~~~^~~~~ assemble/../sequence/vertex_index.h: In member function ‘size_t VertexIndex::IndexChunk::get() const’: assemble/../sequence/vertex_index.h:102:44: warning: left shift count >= width of type [-Wshift-count-overflow] 102 | return ((size_t)hi << 32) + (size_t)low; | ~~~~~~~~~~~^~~~~ assemble/../sequence/vertex_index.h: In member function ‘void VertexIndex::IndexChunk::set(size_t)’: assemble/../sequence/vertex_index.h:107:34: warning: right shift count >= width of type [-Wshift-count-overflow] 107 | hi = val >> 32; | ~~~~^~~~~ make[2]: *** [Makefile:34: assemble/main_assemble.o] Error 1 make[2]: *** [Makefile:34: assemble/chimera.o] Error 1 make[2]: *** [Makefile:34: assemble/extender.o] Error 1 make[2]: Leaving directory '/build/reproducible-path/flye-2.9.3+dfsg2/src' make[1]: *** [Makefile:38: all] Error 2 make[1]: Leaving directory '/build/reproducible-path/flye-2.9.3+dfsg2' Traceback (most recent call last): File "/build/reproducible-path/flye-2.9.3+dfsg2/setup.py", line 38, in run subprocess.check_call(["make"]) File "/usr/lib/python3.11/subprocess.py", line 413, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['make']' returned non-zero exit status 2. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/build/reproducible-path/flye-2.9.3+dfsg2/setup.py", line 69, in setup(name='flye', File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 107, in setup return distutils.core.setup(**attrs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/setuptools/_distutils/core.py", line 185, in setup return run_commands(dist) ^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/setuptools/_distutils/core.py", line 201, in run_commands dist.run_commands() File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line 969, in run_commands self.run_command(cmd) File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 1233, in run_command super().run_command(command) File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line 988, in run_command cmd_obj.run() File "/build/reproducible-path/flye-2.9.3+dfsg2/setup.py", line 40, in run sys.exit("Compilation error: ", e) TypeError: exit expected at most 1 argument, got 2 E: pybuild pybuild:389: build: plugin distutils failed with: exit code=1: /usr/bin/python3 setup.py build dh_auto_build: error: pybuild --build -i python{version} -p 3.11 returned exit code 13 make: *** [debian/rules:11: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package 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/26723 and its subdirectories Wed Apr 24 08:17:14 UTC 2024 W: No second build log, what happened?