I: pbuilder: network access will be disabled during build I: Current time: Thu Dec 4 06:25:41 +14 2025 I: pbuilder-time-stamp: 1764779141 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 [uncalled_2.3+ds-2.dsc] I: copying [./uncalled_2.3+ds.orig.tar.xz] I: copying [./uncalled_2.3+ds-2.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Aug 21 15:42:41 2024 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./uncalled_2.3+ds-2.dsc: no acceptable signature found dpkg-source: info: extracting uncalled in uncalled-2.3+ds dpkg-source: info: unpacking uncalled_2.3+ds.orig.tar.xz dpkg-source: info: unpacking uncalled_2.3+ds-2.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 skip_read_until dpkg-source: info: applying debian_pdqsort 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/644592/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-amd64. 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 Dec 3 16:25 /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/644592/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/644592/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]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=521e5c5c327d45f5a1f4fdd30eada731 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-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=644592 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.bUwIElSI/pbuilderrc_CJPT --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bUwIElSI/b2 --logfile b2/build.log uncalled_2.3+ds-2.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.10.11+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.11-1~bpo12+1 (2024-10-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/644592/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), python3-all, python3-all-dev, python3-setuptools, python3-pybind11, python3-numpy, pdqsort-dev, dh-python, libbwa-dev, libhdf5-dev, pkgconf, 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 ... 19969 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 pkgconf; however: Package pkgconf 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} libbrotli-dev{a} libbrotli1{a} libbwa-dev{a} libcom-err2{a} libcurl4-openssl-dev{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libexpat1-dev{a} libfast5-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgssapi-krb5-2{a} libhdf5-103-1t64{a} libhdf5-cpp-103-1t64{a} libhdf5-dev{a} libhdf5-fortran-102t64{a} libhdf5-hl-100t64{a} libhdf5-hl-cpp-100t64{a} libhdf5-hl-fortran-100t64{a} libicu72{a} libidn2-dev{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnsl2{a} libp11-kit-dev{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libreadline8t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libsz2{a} libtasn1-6-dev{a} libtirpc-common{a} libtirpc3t64{a} libtoml11-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} netbase{a} nettle-dev{a} pdqsort-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} pybind11-dev{a} python3{a} python3-all{a} python3-all-dev{a} python3-autocommand{a} python3-dev{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-pkg-resources{a} python3-pybind11{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common krb5-locales libarchive-cpio-perl libeigen3-dev libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget 0 packages upgraded, 130 newly installed, 0 to remove and 0 not upgraded. Need to get 62.7 MB of archives. After unpacking 255 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.6-1 [814 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.3-2 [105 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.6-1 [2168 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 12 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.6-1 [1963 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.6-1 [669 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-9 [97.2 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 44 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.1 [699 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.3.0-1 [36.5 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 58 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.20.2-1 [10.3 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 74.1.2-2 [736 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20241024 [109 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 hdf5-helpers amd64 1.10.10+repack-4 [23.5 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libaec0 amd64 1.1.3-1+b1 [23.8 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libsz2 amd64 1.1.3-1+b1 [8080 B] Get: 66 http://deb.debian.org/debian trixie/main amd64 libaec-dev amd64 1.1.3-1+b1 [21.5 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3+b1 [152 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b5 [307 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libbrotli-dev amd64 1.1.0-2+b5 [316 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libbwa-dev amd64 0.7.18-1 [156 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.63.0-1 [74.8 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.10.1-2 [352 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libnghttp2-dev amd64 1.63.0-1 [115 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-2+b2 [329 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-2+b2 [642 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libunbound8 amd64 1.22.0-1 [598 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libgnutls-dane0t64 amd64 3.8.6-2+b1 [439 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libgnutls-openssl27t64 amd64 3.8.6-2+b1 [439 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libp11-kit-dev amd64 0.25.5-2+b1 [208 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libtasn1-6-dev amd64 4.19.0-3+b3 [98.9 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 nettle-dev amd64 3.10-1+b1 [1317 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libgnutls28-dev amd64 3.8.6-2+b1 [1385 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libssl-dev amd64 3.3.2-1 [2742 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libzstd-dev amd64 1.5.6+dfsg-1+b1 [365 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libcurl4-openssl-dev amd64 8.10.1-2 [462 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.6.3-2 [157 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libhdf5-103-1t64 amd64 1.10.10+repack-4 [1253 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-6 [836 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libhdf5-fortran-102t64 amd64 1.10.10+repack-4 [89.5 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-4 [63.9 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-fortran-100t64 amd64 1.10.10+repack-4 [40.5 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libhdf5-cpp-103-1t64 amd64 1.10.10+repack-4 [130 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-cpp-100t64 amd64 1.10.10+repack-4 [21.4 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-3+b1 [292 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libjpeg-dev amd64 1:2.1.5-3+b1 [72.2 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libhdf5-dev amd64 1.10.10+repack-4 [2652 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libfast5-dev all 0.6.5-8 [49.0 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 7.4.7-3 [158 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3+b1 [2450 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libpython3.12t64 amd64 3.12.6-1 [2147 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libpython3.12-dev amd64 3.12.6-1 [5127 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libpython3-dev amd64 3.12.6-1 [9952 B] Get: 121 http://deb.debian.org/debian trixie/main amd64 libpython3-all-dev amd64 3.12.6-1 [1064 B] Get: 122 http://deb.debian.org/debian trixie/main amd64 libtoml11-dev all 4.2.0-1 [74.7 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 pdqsort-dev all 0.0.0+git20180419-2.1 [9988 B] Get: 124 http://deb.debian.org/debian trixie/main amd64 pybind11-dev all 2.13.6-1 [204 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.12.6-1 [1040 B] Get: 126 http://deb.debian.org/debian trixie/main amd64 python3.12-dev amd64 3.12.6-1 [506 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 python3-dev amd64 3.12.6-1 [26.1 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 python3-all-dev amd64 3.12.6-1 [1068 B] Get: 129 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-11 [4236 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 python3-pybind11 all 2.13.6-1 [215 kB] Fetched 62.7 MB in 3s (19.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (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 ... 19969 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.6-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.6-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.3-2_amd64.deb ... Unpacking libexpat1:amd64 (2.6.3-2) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.6-1_amd64.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:amd64 (3.12.6-1) ... Setting up libexpat1:amd64 (2.6.3-2) ... Setting up python3.12-minimal (3.12.6-1) ... 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 ... 20289 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../07-libkeyutils1_1.6.3-4_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.6-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.6-1_amd64.deb ... Unpacking python3.12 (3.12.6-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... 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 ... 21363 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_amd64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../002-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../003-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../005-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../006-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../007-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../008-bsdextrautils_2.40.2-9_amd64.deb ... Unpacking bsdextrautils (2.40.2-9) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../009-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../010-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../011-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../012-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../013-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../014-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 .../015-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../016-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../017-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../018-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../019-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../020-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../021-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../022-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../023-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../024-libicu72_72.1-5+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-5+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../025-libxml2_2.12.7+dfsg+really2.9.14-0.1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... Selecting previously unselected package gettext. Preparing to unpack .../026-gettext_0.22.5-2_amd64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../027-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 .../028-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../029-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package python3-autocommand. Preparing to unpack .../030-python3-autocommand_2.2.2-3_all.deb ... Unpacking python3-autocommand (2.2.2-3) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../031-python3-more-itertools_10.5.0-1_all.deb ... Unpacking python3-more-itertools (10.5.0-1) ... Selecting previously unselected package python3-typing-extensions. Preparing to unpack .../032-python3-typing-extensions_4.12.2-2_all.deb ... Unpacking python3-typing-extensions (4.12.2-2) ... Selecting previously unselected package python3-typeguard. Preparing to unpack .../033-python3-typeguard_4.3.0-1_all.deb ... Unpacking python3-typeguard (4.3.0-1) ... Selecting previously unselected package python3-inflect. Preparing to unpack .../034-python3-inflect_7.3.1-2_all.deb ... Unpacking python3-inflect (7.3.1-2) ... Selecting previously unselected package python3-jaraco.context. Preparing to unpack .../035-python3-jaraco.context_6.0.0-1_all.deb ... Unpacking python3-jaraco.context (6.0.0-1) ... Selecting previously unselected package python3-jaraco.functools. Preparing to unpack .../036-python3-jaraco.functools_4.1.0-1_all.deb ... Unpacking python3-jaraco.functools (4.1.0-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../037-python3-pkg-resources_74.1.2-2_all.deb ... Unpacking python3-pkg-resources (74.1.2-2) ... Selecting previously unselected package python3-zipp. Preparing to unpack .../038-python3-zipp_3.20.2-1_all.deb ... Unpacking python3-zipp (3.20.2-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../039-python3-setuptools_74.1.2-2_all.deb ... Unpacking python3-setuptools (74.1.2-2) ... Selecting previously unselected package dh-python. Preparing to unpack .../040-dh-python_6.20241024_all.deb ... Unpacking dh-python (6.20241024) ... Selecting previously unselected package hdf5-helpers. Preparing to unpack .../041-hdf5-helpers_1.10.10+repack-4_amd64.deb ... Unpacking hdf5-helpers (1.10.10+repack-4) ... Selecting previously unselected package libaec0:amd64. Preparing to unpack .../042-libaec0_1.1.3-1+b1_amd64.deb ... Unpacking libaec0:amd64 (1.1.3-1+b1) ... Selecting previously unselected package libsz2:amd64. 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Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Dec 3 16:26:41 UTC 2025. Universal Time is now: Wed Dec 3 16:26:41 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libunbound8:amd64 (1.22.0-1) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-2+b2) ... Setting up libexpat1-dev:amd64 (2.6.3-2) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Setting up libgnutls-dane0t64:amd64 (3.8.6-2+b1) ... Setting up libjpeg62-turbo-dev:amd64 (1:2.1.5-3+b1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up pdqsort-dev (0.0.0+git20180419-2.1) ... Setting up libssl-dev:amd64 (3.3.2-1) ... Setting up autopoint (0.22.5-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libidn2-dev:amd64 (2.3.7-2+b1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:amd64 (14.2.0-6) ... Setting up autoconf (2.72-3) ... Setting up libbwa-dev (0.7.18-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up netbase (6.4) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libtasn1-6-dev:amd64 (4.19.0-3+b3) ... Setting up readline-common (8.2-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b5) ... Setting up libp11-kit-dev:amd64 (0.25.5-2+b1) ... Setting up libsz2:amd64 (1.1.3-1+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 (1.14.0-1) ... Setting up liblapack3:amd64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-2+b2) ... Setting up nettle-dev:amd64 (3.10-1+b1) ... Setting up libtool (2.4.7-7) ... Setting up libaec-dev:amd64 (1.1.3-1+b1) ... Setting up libjpeg-dev:amd64 (1:2.1.5-3+b1) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up libjs-sphinxdoc (7.4.7-3) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libgnutls28-dev:amd64 (3.8.6-2+b1) ... Setting up libnghttp2-dev:amd64 (1.63.0-1) ... Setting up libcurl4t64:amd64 (8.10.1-2) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-4) ... Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-4) ... Setting up libpython3.12-stdlib:amd64 (3.12.6-1) ... Setting up python3.12 (3.12.6-1) ... Setting up libhdf5-cpp-103-1t64:amd64 (1.10.10+repack-4) ... Setting up libhdf5-fortran-102t64:amd64 (1.10.10+repack-4) ... Setting up debhelper (13.20) ... Setting up libpython3.12t64:amd64 (3.12.6-1) ... Setting up libcurl4-openssl-dev:amd64 (8.10.1-2) ... Setting up libhdf5-hl-cpp-100t64:amd64 (1.10.10+repack-4) ... Setting up libpython3-stdlib:amd64 (3.12.6-1) ... Setting up libhdf5-hl-fortran-100t64:amd64 (1.10.10+repack-4) ... Setting up python3 (3.12.6-1) ... Setting up libpython3.12-dev:amd64 (3.12.6-1) ... Setting up python3-zipp (3.20.2-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up libhdf5-dev (1.10.10+repack-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up python3.12-dev (3.12.6-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up libpython3-dev:amd64 (3.12.6-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-typeguard (4.3.0-1) ... Setting up python3-all (3.12.6-1) ... Setting up pybind11-dev (2.13.6-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up libfast5-dev (0.6.5-8) ... Setting up libpython3-all-dev:amd64 (3.12.6-1) ... Setting up python3-dev (3.12.6-1) ... Setting up python3-pybind11 (2.13.6-1) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-all-dev (3.12.6-1) ... Setting up python3-setuptools (74.1.2-2) ... Setting up python3-numpy (1:1.26.4+ds-11) ... Setting up dh-python (6.20241024) ... Processing triggers for libc-bin (2.40-3) ... 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: user script /srv/workspace/pbuilder/644592/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/644592/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/uncalled-2.3+ds/ && 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_2.3+ds-2_source.changes dpkg-buildpackage: info: source package uncalled dpkg-buildpackage: info: source version 2.3+ds-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pierre Gruet dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/uncalled-2.3+ds' 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:311: python3.12 setup.py clean /usr/lib/python3/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) running clean removing '/build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it make[1]: Leaving directory '/build/reproducible-path/uncalled-2.3+ds' 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:311: python3.12 setup.py config /usr/lib/python3/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) running build running build_py creating /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled copying uncalled/debug.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled copying uncalled/args.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled copying uncalled/__init__.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled copying uncalled/index.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled copying uncalled/sim_utils.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled copying uncalled/minknow_client.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled copying uncalled/pafstats.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_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 requirements to uncalled.egg-info/requires.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:218: _Warning: Package 'uncalled.conf' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'uncalled.conf' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'uncalled.conf' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'uncalled.conf' to be distributed and are already explicitly excluding 'uncalled.conf' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) creating /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/conf copying uncalled/conf/defaults.toml -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/conf copying uncalled/conf/r94_5mers.txt -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/conf copying uncalled/conf/r94_5mers_threshs.txt -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_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-x86_64-cpython-312 creating build/temp.linux-x86_64-cpython-312/src x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DH5_USE_110_API -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/python3.12 -c src/chunk.cpp -o build/temp.linux-x86_64-cpython-312/src/chunk.o -std=c++11 -O3 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DH5_USE_110_API -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/python3.12 -c src/client_sim.cpp -o build/temp.linux-x86_64-cpython-312/src/client_sim.o -std=c++11 -O3 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DH5_USE_110_API -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/python3.12 -c src/event_detector.cpp -o build/temp.linux-x86_64-cpython-312/src/event_detector.o -std=c++11 -O3 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DH5_USE_110_API -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/python3.12 -c src/event_profiler.cpp -o build/temp.linux-x86_64-cpython-312/src/event_profiler.o -std=c++11 -O3 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DH5_USE_110_API -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/python3.12 -c src/fast5_reader.cpp -o build/temp.linux-x86_64-cpython-312/src/fast5_reader.o -std=c++11 -O3 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DH5_USE_110_API -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/python3.12 -c src/map_pool.cpp -o build/temp.linux-x86_64-cpython-312/src/map_pool.o -std=c++11 -O3 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DH5_USE_110_API -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/python3.12 -c src/mapper.cpp -o build/temp.linux-x86_64-cpython-312/src/mapper.o -std=c++11 -O3 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DH5_USE_110_API -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/python3.12 -c src/normalizer.cpp -o build/temp.linux-x86_64-cpython-312/src/normalizer.o -std=c++11 -O3 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DH5_USE_110_API -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/python3.12 -c src/pybinder.cpp -o build/temp.linux-x86_64-cpython-312/src/pybinder.o -std=c++11 -O3 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DH5_USE_110_API -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/python3.12 -c src/range.cpp -o build/temp.linux-x86_64-cpython-312/src/range.o -std=c++11 -O3 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DH5_USE_110_API -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/python3.12 -c src/read_buffer.cpp -o build/temp.linux-x86_64-cpython-312/src/read_buffer.o -std=c++11 -O3 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DH5_USE_110_API -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/python3.12 -c src/realtime_pool.cpp -o build/temp.linux-x86_64-cpython-312/src/realtime_pool.o -std=c++11 -O3 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DH5_USE_110_API -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/python3.12 -c src/seed_tracker.cpp -o build/temp.linux-x86_64-cpython-312/src/seed_tracker.o -std=c++11 -O3 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DH5_USE_110_API -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/python3.12 -c src/self_align_ref.cpp -o build/temp.linux-x86_64-cpython-312/src/self_align_ref.o -std=c++11 -O3 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DH5_USE_110_API -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/uncalled-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DH5_USE_110_API build/temp.linux-x86_64-cpython-312/src/chunk.o build/temp.linux-x86_64-cpython-312/src/client_sim.o build/temp.linux-x86_64-cpython-312/src/event_detector.o build/temp.linux-x86_64-cpython-312/src/event_profiler.o build/temp.linux-x86_64-cpython-312/src/fast5_reader.o build/temp.linux-x86_64-cpython-312/src/map_pool.o build/temp.linux-x86_64-cpython-312/src/mapper.o build/temp.linux-x86_64-cpython-312/src/normalizer.o build/temp.linux-x86_64-cpython-312/src/pybinder.o build/temp.linux-x86_64-cpython-312/src/range.o build/temp.linux-x86_64-cpython-312/src/read_buffer.o build/temp.linux-x86_64-cpython-312/src/realtime_pool.o build/temp.linux-x86_64-cpython-312/src/seed_tracker.o build/temp.linux-x86_64-cpython-312/src/self_align_ref.o -L/usr/lib/x86_64-linux-gnu/hdf5/serial -L/usr/lib/x86_64-linux-gnu -lbwa -lhdf5 -lz -ldl -lm -o /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/_uncalled.cpython-312-x86_64-linux-gnu.so running build_scripts creating build/scripts-3.12 copying and adjusting scripts/uncalled -> build/scripts-3.12 changing mode of build/scripts-3.12/uncalled from 644 to 755 dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build; python3.12 -m unittest discover -v /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/debug.py:23: SyntaxWarning: invalid escape sequence '\d' CIG_RE = re.compile("(\d+)(["+CIG_OPS_STR+"])") ---------------------------------------------------------------------- Ran 0 tests in 0.000s NO TESTS RAN 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:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/uncalled-2.3+ds/debian/uncalled /usr/lib/python3/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running egg_info writing uncalled.egg-info/PKG-INFO writing dependency_links to uncalled.egg-info/dependency_links.txt writing requirements to uncalled.egg-info/requires.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:218: _Warning: Package 'uncalled.conf' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'uncalled.conf' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'uncalled.conf' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'uncalled.conf' to be distributed and are already explicitly excluding 'uncalled.conf' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) running build_ext All submodules present Found libbwa.a Found libhdf5.a running build_scripts running install_lib creating /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr creating /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib creating /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12 creating /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/_uncalled.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages creating /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/debug.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled creating /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/conf copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/conf/r94_5mers_threshs.txt -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/conf copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/conf/defaults.toml -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/conf copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/conf/r94_5mers.txt -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/conf copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/args.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/__init__.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/index.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/sim_utils.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/minknow_client.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled creating /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/__pycache__/args.cpython-312.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/__pycache__/sim_utils.cpython-312.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/__pycache__/debug.cpython-312.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/__pycache__/pafstats.cpython-312.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/__pycache__/minknow_client.cpython-312.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/__pycache__/index.cpython-312.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.12_uncalled/build/uncalled/pafstats.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/debug.py to debug.cpython-312.pyc /usr/lib/python3.12/dist-packages/uncalled/debug.py:23: SyntaxWarning: invalid escape sequence '\d' byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/args.py to args.cpython-312.pyc byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/index.py to index.cpython-312.pyc byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/sim_utils.py to sim_utils.cpython-312.pyc byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/minknow_client.py to minknow_client.cpython-312.pyc byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled/pafstats.py to pafstats.cpython-312.pyc running install_egg_info Copying uncalled.egg-info to /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.12/dist-packages/uncalled-2.3.0.egg-info Skipping SOURCES.txt running install_scripts creating /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/bin copying build/scripts-3.12/uncalled -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/bin changing mode of /build/reproducible-path/uncalled-2.3+ds/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 I: dh_python3 pydist:316: Cannot find package that provides minknow_api. Please add package that provides it to Build-Depends or add "minknow_api python3-minknow-api" line to debian/py3dist-overrides or add proper dependency to Depends by hand and ignore this info. 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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'uncalled' in '../uncalled_2.3+ds-2_amd64.deb'. dpkg-deb: building package 'uncalled-dbgsym' in '../uncalled-dbgsym_2.3+ds-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../uncalled_2.3+ds-2_amd64.buildinfo dpkg-genchanges --build=binary -O../uncalled_2.3+ds-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/644592/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/644592/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/644592 and its subdirectories I: Current time: Thu Dec 4 06:30:46 +14 2025 I: pbuilder-time-stamp: 1764779446