I: pbuilder: network access will be disabled during build I: Current time: Sat May 25 18:13:31 +14 2024 I: pbuilder-time-stamp: 1716610411 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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 [uncalled_2.2+ds1-1.dsc] I: copying [./uncalled_2.2+ds1.orig.tar.xz] I: copying [./uncalled_2.2+ds1-1.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Feb 17 04:54:22 2022 +14 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 ./uncalled_2.2+ds1-1.dsc: no acceptable signature found dpkg-source: info: extracting uncalled in uncalled-2.2+ds1 dpkg-source: info: unpacking uncalled_2.2+ds1.orig.tar.xz dpkg-source: info: unpacking uncalled_2.2+ds1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying debian_hdf5 dpkg-source: info: applying debian_bwa dpkg-source: info: applying debian_fast5 dpkg-source: info: applying debian_pybind11 dpkg-source: info: applying fix_debug dpkg-source: info: applying skip_read_until dpkg-source: info: applying debian_pdqsort dpkg-source: info: applying 32bit dpkg-source: info: applying debian_toml11.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/28274/tmp/hooks/D01_modify_environment starting debug: Running on codethink9-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 25 18:13 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/28274/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/28274/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/var/lib/jenkins HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=28274 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.WnsTZgyk/pbuilderrc_O4BM --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.WnsTZgyk/b2 --logfile b2/build.log --extrapackages usrmerge uncalled_2.2+ds1-1.dsc' SUDO_GID=117 SUDO_UID=110 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root USERNAME=root _='I: set' http_proxy=http://192.168.101.16:3128 I: uname -a Linux i-capture-the-hostname 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 24 06:48 /bin -> usr/bin I: user script /srv/workspace/pbuilder/28274/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: arm64 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), python3-all, python3-all-dev, python3-setuptools, python3-pybind11, python3-numpy, pdqsort-dev, dh-python, libbwa-dev, libhdf5-dev, pkg-config, libfast5-dev, libtoml11-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 ... 19616 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 python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-pybind11; however: Package python3-pybind11 is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on pdqsort-dev; however: Package pdqsort-dev is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on libbwa-dev; however: Package libbwa-dev is not installed. pbuilder-satisfydepends-dummy depends on libhdf5-dev; however: Package libhdf5-dev is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on libfast5-dev; however: Package libfast5-dev is not installed. pbuilder-satisfydepends-dummy depends on libtoml11-dev; however: Package libtoml11-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} hdf5-helpers{a} intltool-debian{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libbwa-dev{a} libcurl4{a} libcurl4-openssl-dev{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfast5-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libhdf5-103-1{a} libhdf5-cpp-103-1{a} libhdf5-dev{a} libhdf5-fortran-102{a} libhdf5-hl-100{a} libhdf5-hl-cpp-100{a} libhdf5-hl-fortran-100{a} libicu72{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack3{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libpsl5{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libssl-dev{a} libsub-override-perl{a} libsz2{a} libtoml11-dev{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} pdqsort-dev{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} pybind11-dev{a} python3{a} python3-all{a} python3-all-dev{a} python3-dev{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-numpy{a} python3-pkg-resources{a} python3-pybind11{a} python3-setuptools{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common libarchive-cpio-perl libeigen3-dev libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 98 newly installed, 0 to remove and 0 not upgraded. Need to get 49.6 MB of archives. After unpacking 220 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-minimal arm64 3.11.2-6 [806 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 python3.11-minimal arm64 3.11.2-6 [1858 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 python3-minimal arm64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 libreadline8 arm64 8.2-1.3 [155 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-stdlib arm64 3.11.2-6 [1747 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 python3.11 arm64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 libpython3-stdlib arm64 3.11.2-1+b1 [9296 B] Get: 11 http://deb.debian.org/debian bookworm/main arm64 python3 arm64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 21 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 23 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 32 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 34 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 35 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 36 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.1+b3 [619 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 40 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 41 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 python3-lib2to3 all 3.11.2-2 [76.2 kB] Get: 43 http://deb.debian.org/debian bookworm/main arm64 python3-distutils all 3.11.2-2 [131 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 dh-python all 5.20230130 [104 kB] Get: 45 http://deb.debian.org/debian bookworm/main arm64 hdf5-helpers arm64 1.10.8+repack1-1 [27.9 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 libaec0 arm64 1.0.6-1+b1 [19.9 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 libsz2 arm64 1.0.6-1+b1 [7740 B] Get: 48 http://deb.debian.org/debian bookworm/main arm64 libaec-dev arm64 1.0.6-1+b1 [18.7 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 libblas3 arm64 3.11.0-2 [91.4 kB] Get: 50 http://deb.debian.org/debian bookworm/main arm64 libbrotli1 arm64 1.0.9-2+b6 [269 kB] Get: 51 http://deb.debian.org/debian bookworm/main arm64 libbwa-dev arm64 0.7.17-7+b2 [147 kB] Get: 52 http://deb.debian.org/debian bookworm/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-10 [20.8 kB] Get: 53 http://deb.debian.org/debian bookworm/main arm64 libsasl2-2 arm64 2.1.28+dfsg-10 [58.0 kB] Get: 54 http://deb.debian.org/debian bookworm/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5 [171 kB] Get: 55 http://deb.debian.org/debian bookworm/main arm64 libnghttp2-14 arm64 1.52.0-1 [67.9 kB] Get: 56 http://deb.debian.org/debian bookworm/main arm64 libpsl5 arm64 0.21.2-1 [58.6 kB] Get: 57 http://deb.debian.org/debian bookworm/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 58 http://deb.debian.org/debian bookworm/main arm64 libssh2-1 arm64 1.10.0-3+b1 [172 kB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 libcurl4 arm64 7.88.1-8 [361 kB] Get: 60 http://deb.debian.org/debian bookworm/main arm64 libcurl4-openssl-dev arm64 7.88.1-8 [471 kB] Get: 61 http://deb.debian.org/debian bookworm/main arm64 libexpat1-dev arm64 2.5.0-1 [135 kB] Get: 62 http://deb.debian.org/debian bookworm/main arm64 libhdf5-103-1 arm64 1.10.8+repack1-1 [1037 kB] Get: 63 http://deb.debian.org/debian bookworm/main arm64 libgfortran5 arm64 12.2.0-14 [340 kB] Get: 64 http://deb.debian.org/debian bookworm/main arm64 libhdf5-fortran-102 arm64 1.10.8+repack1-1 [91.1 kB] Get: 65 http://deb.debian.org/debian bookworm/main arm64 libhdf5-hl-100 arm64 1.10.8+repack1-1 [64.0 kB] Get: 66 http://deb.debian.org/debian bookworm/main arm64 libhdf5-hl-fortran-100 arm64 1.10.8+repack1-1 [42.7 kB] Get: 67 http://deb.debian.org/debian bookworm/main arm64 libhdf5-cpp-103-1 arm64 1.10.8+repack1-1 [119 kB] Get: 68 http://deb.debian.org/debian bookworm/main arm64 libhdf5-hl-cpp-100 arm64 1.10.8+repack1-1 [25.4 kB] Get: 69 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] Get: 70 http://deb.debian.org/debian bookworm/main arm64 libjpeg62-turbo arm64 1:2.1.5-2 [171 kB] Get: 71 http://deb.debian.org/debian bookworm/main arm64 libjpeg62-turbo-dev arm64 1:2.1.5-2 [292 kB] Get: 72 http://deb.debian.org/debian bookworm/main arm64 libjpeg-dev arm64 1:2.1.5-2 [71.8 kB] Get: 73 http://deb.debian.org/debian bookworm/main arm64 libssl-dev arm64 3.0.8-1 [2296 kB] Get: 74 http://deb.debian.org/debian bookworm/main arm64 libhdf5-dev arm64 1.10.8+repack1-1 [2654 kB] Get: 75 http://deb.debian.org/debian bookworm/main arm64 libfast5-dev all 0.6.5-7 [50.2 kB] Get: 76 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 77 http://deb.debian.org/debian bookworm/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 78 http://deb.debian.org/debian bookworm/main arm64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 79 http://deb.debian.org/debian bookworm/main arm64 liblapack3 arm64 3.11.0-2 [1664 kB] Get: 80 http://deb.debian.org/debian bookworm/main arm64 libpkgconf3 arm64 1.8.1-1 [35.3 kB] Get: 81 http://deb.debian.org/debian bookworm/main arm64 libpython3.11 arm64 3.11.2-6 [1841 kB] Get: 82 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-dev arm64 3.11.2-6 [4395 kB] Get: 83 http://deb.debian.org/debian bookworm/main arm64 libpython3-dev arm64 3.11.2-1+b1 [9564 B] Get: 84 http://deb.debian.org/debian bookworm/main arm64 libpython3-all-dev arm64 3.11.2-1+b1 [1068 B] Get: 85 http://deb.debian.org/debian bookworm/main arm64 libtoml11-dev all 3.7.1-3 [58.7 kB] Get: 86 http://deb.debian.org/debian bookworm/main arm64 pdqsort-dev all 0.0.0+git20180419-2.1 [9988 B] Get: 87 http://deb.debian.org/debian bookworm/main arm64 pkgconf-bin arm64 1.8.1-1 [28.9 kB] Get: 88 http://deb.debian.org/debian bookworm/main arm64 pkgconf arm64 1.8.1-1 [25.9 kB] Get: 89 http://deb.debian.org/debian bookworm/main arm64 pkg-config arm64 1.8.1-1 [13.7 kB] Get: 90 http://deb.debian.org/debian bookworm/main arm64 pybind11-dev all 2.10.3-1 [186 kB] Get: 91 http://deb.debian.org/debian bookworm/main arm64 python3-all arm64 3.11.2-1+b1 [1064 B] Get: 92 http://deb.debian.org/debian bookworm/main arm64 python3.11-dev arm64 3.11.2-6 [617 kB] Get: 93 http://deb.debian.org/debian bookworm/main arm64 python3-dev arm64 3.11.2-1+b1 [26.2 kB] Get: 94 http://deb.debian.org/debian bookworm/main arm64 python3-all-dev arm64 3.11.2-1+b1 [1076 B] Get: 95 http://deb.debian.org/debian bookworm/main arm64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 96 http://deb.debian.org/debian bookworm/main arm64 python3-numpy arm64 1:1.24.2-1 [4751 kB] Get: 97 http://deb.debian.org/debian bookworm/main arm64 python3-pybind11 all 2.10.3-1 [199 kB] Get: 98 http://deb.debian.org/debian bookworm/main arm64 python3-setuptools all 66.1.1-1 [521 kB] Fetched 49.6 MB in 1s (48.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. 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Setting up libjpeg62-turbo-dev:arm64 (1:2.1.5-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up pdqsort-dev (0.0.0+git20180419-2.1) ... Setting up libssl-dev:arm64 (3.0.8-1) ... Setting up autopoint (0.21-12) ... Setting up pkgconf-bin (1.8.1-1) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg-10) ... Setting up libgfortran5:arm64 (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up libbwa-dev (0.7.17-7+b2) ... Setting up zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:arm64 (1.10.0-3+b1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libelf1:arm64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.1+b3) ... Setting up libsz2:arm64 (1.0.6-1+b1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up liblapack3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libreadline8:arm64 (8.2-1.3) ... Setting up libaec-dev:arm64 (1.0.6-1+b1) ... Setting up libjpeg-dev:arm64 (1:2.1.5-2) ... Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-5) ... Setting up pkgconf:arm64 (1.8.1-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up pkg-config:arm64 (1.8.1-1) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up libcurl4:arm64 (7.88.1-8) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.2-6) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libcurl4-openssl-dev:arm64 (7.88.1-8) ... Setting up libhdf5-103-1:arm64 (1.10.8+repack1-1) ... Setting up libhdf5-cpp-103-1:arm64 (1.10.8+repack1-1) ... Setting up libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up libhdf5-hl-100:arm64 (1.10.8+repack1-1) ... Setting up python3.11 (3.11.2-6) ... Setting up libpython3.11:arm64 (3.11.2-6) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up libhdf5-hl-cpp-100:arm64 (1.10.8+repack1-1) ... Setting up libpython3.11-dev:arm64 (3.11.2-6) ... Setting up libhdf5-fortran-102:arm64 (1.10.8+repack1-1) ... Setting up libhdf5-hl-fortran-100:arm64 (1.10.8+repack1-1) ... Setting up python3-lib2to3 (3.11.2-2) ... Setting up python3-pybind11 (2.10.3-1) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-2) ... Setting up dh-python (5.20230130) ... Setting up libpython3-dev:arm64 (3.11.2-1+b1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3.11-dev (3.11.2-6) ... Setting up python3-all (3.11.2-1+b1) ... Setting up libpython3-all-dev:arm64 (3.11.2-1+b1) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up libhdf5-dev (1.10.8+repack1-1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up python3-numpy (1:1.24.2-1) ... Setting up python3-all-dev (3.11.2-1+b1) ... Setting up libfast5-dev (0.6.5-7) ... Processing triggers for libc-bin (2.36-9) ... 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 Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/28274/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... I: user script /srv/workspace/pbuilder/28274/tmp/hooks/A99_set_merged_usr finished hostname: Temporary failure in name resolution I: Running cd /build/uncalled-2.2+ds1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../uncalled_2.2+ds1-1_source.changes dpkg-buildpackage: info: source package uncalled dpkg-buildpackage: info: source version 2.2+ds1-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Map '/build/uncalled-2.2+ds1' wordt binnengegaan if dpkg -s python3-pybind11 >/dev/null 2>/dev/null ; then \ dh_auto_clean ; \ else \ echo "skip dh_auto_clean since python3-pybind11 is not installed on your local machine" ; \ fi I: pybuild base:240: python3.11 setup.py clean running clean removing '/build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build' (and everything under it) 'build/bdist.linux-arm64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it make[1]: Map '/build/uncalled-2.2+ds1' wordt verlaten dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:240: python3.11 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py build running build running build_py creating /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled copying uncalled/debug.py -> /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled copying uncalled/sim_utils.py -> /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled copying uncalled/pafstats.py -> /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled copying uncalled/minknow_client.py -> /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled copying uncalled/index.py -> /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled copying uncalled/args.py -> /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled copying uncalled/__init__.py -> /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled running egg_info creating uncalled.egg-info writing uncalled.egg-info/PKG-INFO writing dependency_links to uncalled.egg-info/dependency_links.txt writing top-level names to uncalled.egg-info/top_level.txt writing manifest file 'uncalled.egg-info/SOURCES.txt' reading manifest file 'uncalled.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENCE' writing manifest file 'uncalled.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'uncalled.conf' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'uncalled.conf' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'uncalled.conf' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'uncalled.conf' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) creating /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/conf copying uncalled/conf/defaults.toml -> /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/conf copying uncalled/conf/r94_5mers.txt -> /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/conf copying uncalled/conf/r94_5mers_threshs.txt -> /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/conf running build_ext All submodules present Found libbwa.a Found libhdf5.a building '_uncalled' extension creating build creating build/temp.linux-arm64-cpython-311 creating build/temp.linux-arm64-cpython-311/src aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/chunk.cpp -o build/temp.linux-arm64-cpython-311/src/chunk.o -std=c++11 -O3 aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/client_sim.cpp -o build/temp.linux-arm64-cpython-311/src/client_sim.o -std=c++11 -O3 aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/event_detector.cpp -o build/temp.linux-arm64-cpython-311/src/event_detector.o -std=c++11 -O3 aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/event_profiler.cpp -o build/temp.linux-arm64-cpython-311/src/event_profiler.o -std=c++11 -O3 aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/fast5_reader.cpp -o build/temp.linux-arm64-cpython-311/src/fast5_reader.o -std=c++11 -O3 aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/map_pool.cpp -o build/temp.linux-arm64-cpython-311/src/map_pool.o -std=c++11 -O3 aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/mapper.cpp -o build/temp.linux-arm64-cpython-311/src/mapper.o -std=c++11 -O3 src/mapper.cpp: In member function ‘void Mapper::update_seeds(PathBuffer&, bool)’: src/mapper.cpp:673:13: warning: unused variable ‘sa_start’ [-Wunused-variable] 673 | u64 sa_start = sa_end - ref_len + 1; | ^~~~~~~~ src/mapper.cpp:676:14: warning: variable ‘clust’ set but not used [-Wunused-but-set-variable] 676 | auto clust = seed_tracker_.add_seed( | ^~~~~ src/mapper.cpp: In copy constructor ‘Mapper::PathBuffer::PathBuffer(const Mapper::PathBuffer&)’: src/mapper.cpp:736:16: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class Mapper::PathBuffer’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 736 | std::memcpy(this, &p, sizeof(PathBuffer)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from src/mapper.cpp:26: src/mapper.hpp:139:11: note: ‘class Mapper::PathBuffer’ declared here 139 | class PathBuffer { | ^~~~~~~~~~ aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/normalizer.cpp -o build/temp.linux-arm64-cpython-311/src/normalizer.o -std=c++11 -O3 aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/pybinder.cpp -o build/temp.linux-arm64-cpython-311/src/pybinder.o -std=c++11 -O3 aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/range.cpp -o build/temp.linux-arm64-cpython-311/src/range.o -std=c++11 -O3 aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/read_buffer.cpp -o build/temp.linux-arm64-cpython-311/src/read_buffer.o -std=c++11 -O3 aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/realtime_pool.cpp -o build/temp.linux-arm64-cpython-311/src/realtime_pool.o -std=c++11 -O3 aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/seed_tracker.cpp -o build/temp.linux-arm64-cpython-311/src/seed_tracker.o -std=c++11 -O3 aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/self_align_ref.cpp -o build/temp.linux-arm64-cpython-311/src/self_align_ref.o -std=c++11 -O3 aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/uncalled-2.2+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/src/chunk.o build/temp.linux-arm64-cpython-311/src/client_sim.o build/temp.linux-arm64-cpython-311/src/event_detector.o build/temp.linux-arm64-cpython-311/src/event_profiler.o build/temp.linux-arm64-cpython-311/src/fast5_reader.o build/temp.linux-arm64-cpython-311/src/map_pool.o build/temp.linux-arm64-cpython-311/src/mapper.o build/temp.linux-arm64-cpython-311/src/normalizer.o build/temp.linux-arm64-cpython-311/src/pybinder.o build/temp.linux-arm64-cpython-311/src/range.o build/temp.linux-arm64-cpython-311/src/read_buffer.o build/temp.linux-arm64-cpython-311/src/realtime_pool.o build/temp.linux-arm64-cpython-311/src/seed_tracker.o build/temp.linux-arm64-cpython-311/src/self_align_ref.o -L./submods/bwa -L/usr/lib/aarch64-linux-gnu/hdf5/serial -L/usr/lib/aarch64-linux-gnu -lbwa -lhdf5 -lz -ldl -lm -o /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/_uncalled.cpython-311-aarch64-linux-gnu.so running build_scripts creating build/scripts-3.11 copying and adjusting scripts/uncalled -> build/scripts-3.11 changing mode of build/scripts-3.11/uncalled from 644 to 755 dh_auto_test -O--buildsystem=pybuild I: pybuild base:240: cd /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build; python3.11 -m unittest discover -v ---------------------------------------------------------------------- Ran 0 tests in 0.000s OK create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/uncalled/ -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py install --root /build/uncalled-2.2+ds1/debian/uncalled running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py running egg_info writing uncalled.egg-info/PKG-INFO writing dependency_links to uncalled.egg-info/dependency_links.txt writing top-level names to uncalled.egg-info/top_level.txt reading manifest file 'uncalled.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENCE' writing manifest file 'uncalled.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'uncalled.conf' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'uncalled.conf' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'uncalled.conf' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'uncalled.conf' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) running build_ext All submodules present Found libbwa.a Found libhdf5.a running build_scripts running install_lib creating /build/uncalled-2.2+ds1/debian/uncalled/usr creating /build/uncalled-2.2+ds1/debian/uncalled/usr/lib creating /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11 creating /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/_uncalled.cpython-311-aarch64-linux-gnu.so -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages creating /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled creating /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/__pycache__ copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/__pycache__/debug.cpython-311.pyc -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/__pycache__ copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/__pycache__/args.cpython-311.pyc -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/__pycache__ copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/__pycache__/sim_utils.cpython-311.pyc -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/__pycache__ copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/__pycache__/pafstats.cpython-311.pyc -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/__pycache__ copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/__pycache__/index.cpython-311.pyc -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/__pycache__ copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/__pycache__/__init__.cpython-311.pyc -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/__pycache__ creating /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/conf copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/conf/r94_5mers_threshs.txt -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/conf copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/conf/r94_5mers.txt -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/conf copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/conf/defaults.toml -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/conf copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/__init__.py -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/args.py -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/index.py -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/minknow_client.py -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/pafstats.py -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/sim_utils.py -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled copying /build/uncalled-2.2+ds1/.pybuild/cpython3_3.11_uncalled/build/uncalled/debug.py -> /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled byte-compiling /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/__init__.py to __init__.cpython-311.pyc byte-compiling /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/args.py to args.cpython-311.pyc byte-compiling /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/index.py to index.cpython-311.pyc byte-compiling /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/minknow_client.py to minknow_client.cpython-311.pyc byte-compiling /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/pafstats.py to pafstats.cpython-311.pyc byte-compiling /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/sim_utils.py to sim_utils.cpython-311.pyc byte-compiling /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled/debug.py to debug.cpython-311.pyc running install_egg_info Copying uncalled.egg-info to /build/uncalled-2.2+ds1/debian/uncalled/usr/lib/python3.11/dist-packages/uncalled-2.2.egg-info Skipping SOURCES.txt running install_scripts creating /build/uncalled-2.2+ds1/debian/uncalled/usr/bin copying build/scripts-3.11/uncalled -> /build/uncalled-2.2+ds1/debian/uncalled/usr/bin changing mode of /build/uncalled-2.2+ds1/debian/uncalled/usr/bin/uncalled to 755 dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: pakket 'uncalled-dbgsym' wordt gebouwd in '../uncalled-dbgsym_2.2+ds1-1_arm64.deb'. dpkg-deb: pakket 'uncalled' wordt gebouwd in '../uncalled_2.2+ds1-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../uncalled_2.2+ds1-1_arm64.buildinfo dpkg-genchanges --build=binary -O../uncalled_2.2+ds1-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/28274/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/28274/tmp/hooks/B01_cleanup finished 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/28274 and its subdirectories I: Current time: Sat May 25 18:26:09 +14 2024 I: pbuilder-time-stamp: 1716611169