Fri Feb 21 11:21:38 UTC 2025 I: starting to build uncalled/unstable/amd64 on jenkins on '2025-02-21 11:21' Fri Feb 21 11:21:38 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_21/31823/console.log Fri Feb 21 11:21:38 UTC 2025 I: Downloading source for unstable/uncalled=2.3+ds-3 --2025-02-21 11:21:38-- http://deb.debian.org/debian/pool/main/u/uncalled/uncalled_2.3%2bds-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2261 (2.2K) [text/prs.lines.tag] Saving to: ‘uncalled_2.3+ds-3.dsc’ 0K .. 100% 310M=0s 2025-02-21 11:21:38 (310 MB/s) - ‘uncalled_2.3+ds-3.dsc’ saved [2261/2261] Fri Feb 21 11:21:38 UTC 2025 I: uncalled_2.3+ds-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: uncalled Binary: uncalled Architecture: any Version: 2.3+ds-3 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe Homepage: https://github.com/skovaka/UNCALLED Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/uncalled Vcs-Git: https://salsa.debian.org/med-team/uncalled.git Testsuite: autopkgtest Build-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 Package-List: uncalled deb science optional arch=any Checksums-Sha1: 1f70131d17758676a4dff853f0e0e3aab41a8f33 155052 uncalled_2.3+ds.orig.tar.xz a188b907ef8bb2d9f2f654df08baca49b31de83d 5924 uncalled_2.3+ds-3.debian.tar.xz Checksums-Sha256: b7ccb020555b2f547faba7a2c4e925ac28f7883c5fa3752179c59c3ab7d7b450 155052 uncalled_2.3+ds.orig.tar.xz 776bc7ff9d31934c01fefce48c8badff8ae7cfb4fa0b085e388acc31470c4b6c 5924 uncalled_2.3+ds-3.debian.tar.xz Files: e822e23ebeadea6b48257c626285603f 155052 uncalled_2.3+ds.orig.tar.xz b6085eb0aa9225d438338048e4c33b11 5924 uncalled_2.3+ds-3.debian.tar.xz Dgit: eba6ee765f0ecee0e3196313180b26fb4bd97bc2 debian archive/debian/2.3+ds-3 https://git.dgit.debian.org/uncalled -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmdPcOsUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdpDpBAAv3XdKUPUIg5N34p6UGD2RakMi/O7 KhpiB4U6uNpaSKbivkLeNMvmqTHYdNPjLdN0cexKtN0XxFDfgVF9njZBRCO+fHXi gLuNgGH4R1vSMjZLnZuxa6/tjUBhW0m6AU7GggolSFQVdVX4TMXjhvkrGd0IwEPe WA9fT8KC1V3CeuOFFJPxt8eH9m+MlLEm52WExm2zFpmMAhGCDR+LFwlRIgMjXZGH A35FJMZIlDWYf1FmbfCHiEVmH+/8ugGz2gX0EykKIUCEOilkThYy2eo6ykormrmt 9iMAVY4Kx829OirMUMKu6aT4QSY2CgikhTs3A5VBIOQa2yBvXXNkgXcdcT5tlJPO ZtJf1fe7bC2DH5ms+9NJLUTu1laFA5ellDq9Kppk4Fe8zSPNhNwIKiAGSGk82kP/ nglRZl3yL9R7fFucs0z6nZsgE2Bdr2mHHLvgz5FhG3Qn+nBUnKSuxeBd9Lq2yN4S p7qFb/+aanT7zua3HSIdeTXlbxkSx8SM+vsmQ1/rslxBSOtGExb8QV9bX/Kmt7VE kxoy0gZjh2ZO261g6euTxkUXbtGvKbFbGw9pnnuCc841gyHJSOWfFg7Aznk3E5b+ lOMGfejv2wpnOEtkrXPiVaDXnfU/4TAx6Ny+Q0rEWDI0O++vHO9xFDnnNqn5CmZi cgJ1XTXbzQoCBjw= =eM5a -----END PGP SIGNATURE----- Fri Feb 21 11:21:38 UTC 2025 I: Checking whether the package is not for us Fri Feb 21 11:21:38 UTC 2025 I: Starting 1st build on remote node ionos11-amd64.debian.net. Fri Feb 21 11:21:38 UTC 2025 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Fri Feb 21 11:38:20 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Feb 20 23:21:40 -12 2025 I: pbuilder-time-stamp: 1740136900 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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-3.dsc] I: copying [./uncalled_2.3+ds.orig.tar.xz] I: copying [./uncalled_2.3+ds-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./uncalled_2.3+ds-3.dsc: unsupported subcommand 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-3.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 dpkg-source: info: applying syntax-warning.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1255531/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='80f724efd9004e9289222dd40993f8af' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1255531' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.EOCD11kg/pbuilderrc_TUD2 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.EOCD11kg/b1 --logfile b1/build.log uncalled_2.3+ds-3.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1255531/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 ... 19798 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} comerr-dev{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} krb5-multidev{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} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhdf5-310{a} libhdf5-cpp-310{a} libhdf5-dev{a} libhdf5-fortran-310{a} libhdf5-hl-310{a} libhdf5-hl-cpp-310{a} libhdf5-hl-fortran-310{a} libicu72{a} libidn2-0{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} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} liblapack3{a} libldap-dev{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libnsl2{a} libp11-kit-dev{a} libp11-kit0{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} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{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{a} libtasn1-6-dev{a} libtirpc-common{a} libtirpc3t64{a} libtoml11-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{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-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-numpy-dev{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} python3.13{a} python3.13-dev{a} python3.13-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, 155 newly installed, 0 to remove and 0 not upgraded. Need to get 83.9 MB of archives. After unpacking 349 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 11.0.0 [27.6 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025a-2 [259 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.2-1 [745 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.1-2 [28.0 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-2 [138 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-17 [836 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:2.2.3+ds-2 [7517 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.9-1 [817 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.9-1 [2163 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-4 [92.4 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-1 [55.7 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-3 [539 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 45 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 60 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.8.0-1 [222 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.8.0-1 [724 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250108 [113 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 hdf5-helpers amd64 1.14.5+repack-3 [26.6 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 70 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-4 [60.0 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-4 [42.2 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-4 [42.4 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-4 [54.2 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-4 [126 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.1.3-1+b1 [23.8 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.1.3-1+b1 [8080 B] Get: 79 http://deb.debian.org/debian unstable/main amd64 libaec-dev amd64 1.1.3-1+b1 [21.5 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b6 [316 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libbwa-dev amd64 0.7.18-1 [156 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8+b1 [19.9 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8+b1 [57.6 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.12.1-2 [369 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-4 [15.9 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.6.9+dfsg-1 [307 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.6.0-2 [88.5 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.9-2 [455 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.9-2 [455 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.9-2 [1401 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.4.1-1 [2787 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-2 [365 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libcurl4-openssl-dev amd64 8.12.1-2 [483 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libhdf5-310 amd64 1.14.5+repack-3 [1344 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libhdf5-fortran-310 amd64 1.14.5+repack-3 [111 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [69.3 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-fortran-310 amd64 1.14.5+repack-3 [43.9 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libhdf5-cpp-310 amd64 1.14.5+repack-3 [133 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-cpp-310 amd64 1.14.5+repack-3 [24.4 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-3+b1 [292 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libjpeg-dev amd64 1:2.1.5-3+b1 [72.2 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libhdf5-dev amd64 1.14.5+repack-3 [3165 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libfast5-dev all 0.6.5-9 [49.1 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.2-1 [2151 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.2-1 [5005 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.1-2 [10.2 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.9-1 [1974 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libpython3.12t64 amd64 3.12.9-1 [2151 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libpython3.12-dev amd64 3.12.9-1 [5125 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.13.1-2 [1072 B] Get: 146 http://deb.debian.org/debian unstable/main amd64 libtoml11-dev all 4.4.0-1 [77.1 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 pdqsort-dev all 0.0.0+git20180419-2.1 [9988 B] Get: 148 http://deb.debian.org/debian unstable/main amd64 pybind11-dev all 2.13.6-2 [205 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.9-1 [681 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.13.1-2 [1056 B] Get: 151 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.2-1 [507 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.1-2 [26.1 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 python3.12-dev amd64 3.12.9-1 [505 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.13.1-2 [1076 B] Get: 155 http://deb.debian.org/debian unstable/main amd64 python3-pybind11 all 2.13.6-2 [215 kB] Fetched 83.9 MB in 4s (20.0 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-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 ... 19798 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.2-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.2-1_amd64.deb ... Unpacking python3.13-minimal (3.13.2-1) ... Setting up libpython3.13-minimal:amd64 (3.13.2-1) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.2-1) ... 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 ... 20132 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.1-2_amd64.deb ... Unpacking python3-minimal (3.13.1-2) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_11.0.0_all.deb ... Unpacking media-types (11.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025a-2_all.deb ... Unpacking tzdata (2025a-2) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../4-libffi8_3.4.7-1_amd64.deb ... Unpacking libffi8:amd64 (3.4.7-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../6-libreadline8t64_8.2-6_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 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_amd64.deb ... Unpacking python3.13 (3.13.2-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.1-2_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.1-2) ... Setting up python3-minimal (3.13.1-2) ... 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 ... 21142 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.1-2_amd64.deb ... Unpacking python3 (3.13.1-2) ... Selecting previously unselected package python3-numpy-dev:amd64. Preparing to unpack .../001-python3-numpy-dev_1%3a2.2.3+ds-2_amd64.deb ... Unpacking python3-numpy-dev:amd64 (1:2.2.3+ds-2) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../002-libblas3_3.12.1-2_amd64.deb ... Unpacking libblas3:amd64 (3.12.1-2) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../003-libgfortran5_14.2.0-17_amd64.deb ... Unpacking libgfortran5:amd64 (14.2.0-17) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../004-liblapack3_3.12.1-2_amd64.deb ... Unpacking liblapack3:amd64 (3.12.1-2) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../005-python3-numpy_1%3a2.2.3+ds-2_amd64.deb ... Unpacking python3-numpy (1:2.2.3+ds-2) ... Selecting previously unselected package libpython3.12-minimal:amd64. Preparing to unpack .../006-libpython3.12-minimal_3.12.9-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.9-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../007-python3.12-minimal_3.12.9-1_amd64.deb ... Unpacking python3.12-minimal (3.12.9-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../008-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../009-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 .../010-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../011-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../012-gettext-base_0.23.1-1_amd64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../013-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 .../014-groff-base_1.23.0-7_amd64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../015-bsdextrautils_2.40.4-4_amd64.deb ... Unpacking bsdextrautils (2.40.4-4) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../016-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../017-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../018-m4_1.4.19-5_amd64.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. 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Unpacking libpython3.12t64:amd64 (3.12.9-1) ... Selecting previously unselected package libpython3.12-dev:amd64. Preparing to unpack .../130-libpython3.12-dev_3.12.9-1_amd64.deb ... Unpacking libpython3.12-dev:amd64 (3.12.9-1) ... Selecting previously unselected package libpython3-all-dev:amd64. Preparing to unpack .../131-libpython3-all-dev_3.13.1-2_amd64.deb ... Unpacking libpython3-all-dev:amd64 (3.13.1-2) ... Selecting previously unselected package libtoml11-dev. Preparing to unpack .../132-libtoml11-dev_4.4.0-1_all.deb ... Unpacking libtoml11-dev (4.4.0-1) ... Selecting previously unselected package pdqsort-dev. Preparing to unpack .../133-pdqsort-dev_0.0.0+git20180419-2.1_all.deb ... Unpacking pdqsort-dev (0.0.0+git20180419-2.1) ... Selecting previously unselected package pybind11-dev. Preparing to unpack .../134-pybind11-dev_2.13.6-2_all.deb ... Unpacking pybind11-dev (2.13.6-2) ... Selecting previously unselected package python3.12. 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Preparing to unpack .../141-python3-pybind11_2.13.6-2_all.deb ... Unpacking python3-pybind11 (2.13.6-2) ... Setting up media-types (11.0.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libkeyutils1:amd64 (1.6.3-4) ... Setting up libicu72:amd64 (72.1-6) ... Setting up libzstd-dev:amd64 (1.5.6+dfsg-2) ... Setting up bsdextrautils (2.40.4-4) ... Setting up hdf5-helpers (1.14.5+repack-3) ... Setting up libtoml11-dev (4.4.0-1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up libpython3.12-minimal:amd64 (3.12.9-1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libcom-err2:amd64 (1.47.2-1) ... Setting up file (1:5.45-3+b1) ... Setting up libaec0:amd64 (1.1.3-1+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libkrb5support0:amd64 (1.21.3-4) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8+b1) ... Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Feb 21 11:23:17 UTC 2025. Universal Time is now: Fri Feb 21 11:23:17 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.12.1-2) ... 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+b1) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-3) ... Setting up libexpat1-dev:amd64 (2.6.4-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Setting up libjpeg62-turbo-dev:amd64 (1:2.1.5-3+b1) ... Setting up pdqsort-dev (0.0.0+git20180419-2.1) ... Setting up comerr-dev:amd64 (2.1-1.47.2-1) ... Setting up libunistring5:amd64 (1.3-1) ... Setting up libssl-dev:amd64 (3.4.1-1) ... Setting up python3-numpy-dev:amd64 (1:2.2.3+ds-2) ... Setting up autopoint (0.23.1-1) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-4) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8+b1) ... Setting up libgfortran5:amd64 (14.2.0-17) ... Setting up autoconf (2.72-3) ... Setting up libbwa-dev (0.7.18-1) ... Setting up libnghttp3-9:amd64 (1.6.0-2) ... Setting up libnghttp3-dev:amd64 (1.6.0-2) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.4.7-1) ... 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 libtasn1-6:amd64 (4.20.0-2) ... Setting up netbase (6.4) ... Setting up libkrb5-3:amd64 (1.21.3-4) ... 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 (4.20.0-2) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libldap2:amd64 (2.6.9+dfsg-1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b6) ... Setting up libsz2:amd64 (1.1.3-1+b1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up python3.12-minimal (3.12.9-1) ... Setting up liblapack3:amd64 (3.12.1-2) ... 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 (0.23.1-1) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-3) ... Setting up nettle-dev:amd64 (3.10.1-1) ... Setting up libtool (2.5.4-3) ... Setting up libaec-dev:amd64 (1.1.3-1+b1) ... Setting up libjpeg-dev:amd64 (1:2.1.5-3+b1) ... Setting up libidn2-0:amd64 (2.3.7-2+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 libldap-dev:amd64 (2.6.9+dfsg-1) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up libidn2-dev:amd64 (2.3.7-2+b1) ... Setting up libjs-sphinxdoc (8.1.3-5) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up libpython3.13-stdlib:amd64 (3.13.2-1) ... Setting up libp11-kit-dev:amd64 (0.25.5-3) ... Setting up libpython3-stdlib:amd64 (3.13.1-2) ... Setting up libpython3.13:amd64 (3.13.2-1) ... Setting up libgnutls30t64:amd64 (3.8.9-2) ... Setting up libgnutls-openssl27t64:amd64 (3.8.9-2) ... Setting up libnghttp2-dev:amd64 (1.64.0-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up python3.13 (3.13.2-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.1-2) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libgnutls-dane0t64:amd64 (3.8.9-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libgssrpc4t64:amd64 (1.21.3-4) ... Setting up libpython3.13-dev:amd64 (3.13.2-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-numpy (1:2.2.3+ds-2) ... Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-4) ... Setting up libgnutls28-dev:amd64 (3.8.9-2) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up libpython3-dev:amd64 (3.13.1-2) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up libpython3.12-stdlib:amd64 (3.12.9-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up libcurl4t64:amd64 (8.12.1-2) ... Setting up libkdb5-10t64:amd64 (1.21.3-4) ... Setting up python3.13-dev (3.13.2-1) ... Setting up python3.12 (3.12.9-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-all (3.13.1-2) ... Setting up debhelper (13.24.1) ... Setting up pybind11-dev (2.13.6-2) ... Setting up libpython3.12t64:amd64 (3.12.9-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.13.1-2) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libhdf5-310:amd64 (1.14.5+repack-3) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-4) ... Setting up libhdf5-fortran-310:amd64 (1.14.5+repack-3) ... Setting up python3-pybind11 (2.13.6-2) ... Setting up krb5-multidev:amd64 (1.21.3-4) ... Setting up libhdf5-cpp-310:amd64 (1.14.5+repack-3) ... Setting up python3-pkg-resources (75.8.0-1) ... Setting up libhdf5-hl-310:amd64 (1.14.5+repack-3) ... Setting up python3-setuptools (75.8.0-1) ... Setting up libpython3.12-dev:amd64 (3.12.9-1) ... Setting up libkrb5-dev:amd64 (1.21.3-4) ... Setting up libcurl4-openssl-dev:amd64 (8.12.1-2) ... Setting up libpython3-all-dev:amd64 (3.13.1-2) ... Setting up python3.12-dev (3.12.9-1) ... Setting up dh-python (6.20250108) ... Setting up python3-all-dev (3.13.1-2) ... Setting up libhdf5-hl-cpp-310:amd64 (1.14.5+repack-3) ... Setting up libhdf5-hl-fortran-310:amd64 (1.14.5+repack-3) ... Setting up libhdf5-dev (1.14.5+repack-3) ... 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 libfast5-dev (0.6.5-9) ... Processing triggers for libc-bin (2.40-7) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/uncalled-2.3+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../uncalled_2.3+ds-3_source.changes dpkg-buildpackage: info: source package uncalled dpkg-buildpackage: info: source version 2.3+ds-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier 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 I: pybuild base:311: python3.13 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_3.13_uncalled/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.13' 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 I: pybuild base:311: python3.13 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/python3.12 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/__init__.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 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/args.py -> /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 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:212: _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/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 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_3.13_uncalled/build/uncalled copying uncalled/__init__.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/uncalled copying uncalled/pafstats.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/uncalled copying uncalled/index.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/uncalled copying uncalled/sim_utils.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/uncalled copying uncalled/minknow_client.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/uncalled copying uncalled/args.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/uncalled copying uncalled/debug.py -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/uncalled 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:212: _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_3.13_uncalled/build/uncalled/conf copying uncalled/conf/defaults.toml -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/uncalled/conf copying uncalled/conf/r94_5mers.txt -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/uncalled/conf copying uncalled/conf/r94_5mers_threshs.txt -> /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/uncalled/conf running build_ext All submodules present Found libbwa.a Found libhdf5.a building '_uncalled' extension creating build/temp.linux-x86_64-cpython-313/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/python3.13 -c src/chunk.cpp -o build/temp.linux-x86_64-cpython-313/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/python3.13 -c src/client_sim.cpp -o build/temp.linux-x86_64-cpython-313/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/python3.13 -c src/event_detector.cpp -o build/temp.linux-x86_64-cpython-313/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/python3.13 -c src/event_profiler.cpp -o build/temp.linux-x86_64-cpython-313/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/python3.13 -c src/fast5_reader.cpp -o build/temp.linux-x86_64-cpython-313/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/python3.13 -c src/map_pool.cpp -o build/temp.linux-x86_64-cpython-313/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/python3.13 -c src/mapper.cpp -o build/temp.linux-x86_64-cpython-313/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/python3.13 -c src/normalizer.cpp -o build/temp.linux-x86_64-cpython-313/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/python3.13 -c src/pybinder.cpp -o build/temp.linux-x86_64-cpython-313/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/python3.13 -c src/range.cpp -o build/temp.linux-x86_64-cpython-313/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/python3.13 -c src/read_buffer.cpp -o build/temp.linux-x86_64-cpython-313/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/python3.13 -c src/realtime_pool.cpp -o build/temp.linux-x86_64-cpython-313/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/python3.13 -c src/seed_tracker.cpp -o build/temp.linux-x86_64-cpython-313/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/python3.13 -c src/self_align_ref.cpp -o build/temp.linux-x86_64-cpython-313/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-313/src/chunk.o build/temp.linux-x86_64-cpython-313/src/client_sim.o build/temp.linux-x86_64-cpython-313/src/event_detector.o build/temp.linux-x86_64-cpython-313/src/event_profiler.o build/temp.linux-x86_64-cpython-313/src/fast5_reader.o build/temp.linux-x86_64-cpython-313/src/map_pool.o build/temp.linux-x86_64-cpython-313/src/mapper.o build/temp.linux-x86_64-cpython-313/src/normalizer.o build/temp.linux-x86_64-cpython-313/src/pybinder.o build/temp.linux-x86_64-cpython-313/src/range.o build/temp.linux-x86_64-cpython-313/src/read_buffer.o build/temp.linux-x86_64-cpython-313/src/realtime_pool.o build/temp.linux-x86_64-cpython-313/src/seed_tracker.o build/temp.linux-x86_64-cpython-313/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_3.13_uncalled/build/_uncalled.cpython-313-x86_64-linux-gnu.so running build_scripts creating build/scripts-3.13 copying and adjusting scripts/uncalled -> build/scripts-3.13 changing mode of build/scripts-3.13/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 ---------------------------------------------------------------------- Ran 0 tests in 0.000s NO TESTS RAN I: pybuild base:311: cd /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build; python3.13 -m unittest discover -v ---------------------------------------------------------------------- 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/python3.12 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:79: 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:212: _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/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/__init__.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/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/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/pafstats.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__/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__/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__/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/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 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/debug.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/__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/pafstats.py to pafstats.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/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/debug.py to debug.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 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:79: 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:212: _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/lib/python3.13/dist-packages creating /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/uncalled/__init__.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled creating /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled/conf copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/uncalled/conf/defaults.toml -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled/conf copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/uncalled/conf/r94_5mers.txt -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled/conf copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/uncalled/conf/r94_5mers_threshs.txt -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled/conf copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/uncalled/pafstats.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled creating /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/uncalled/__pycache__/pafstats.cpython-313.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/uncalled/__pycache__/minknow_client.cpython-313.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/uncalled/__pycache__/debug.cpython-313.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/uncalled/__pycache__/sim_utils.cpython-313.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/uncalled/__pycache__/index.cpython-313.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/uncalled/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/uncalled/__pycache__/args.cpython-313.pyc -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled/__pycache__ copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/uncalled/index.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/uncalled/sim_utils.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/uncalled/minknow_client.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/uncalled/args.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/uncalled/debug.py -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled copying /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpython3_3.13_uncalled/build/_uncalled.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled/pafstats.py to pafstats.cpython-313.pyc byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled/index.py to index.cpython-313.pyc byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled/sim_utils.py to sim_utils.cpython-313.pyc byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled/minknow_client.py to minknow_client.cpython-313.pyc byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled/args.py to args.cpython-313.pyc byte-compiling /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled/debug.py to debug.cpython-313.pyc running install_egg_info Copying uncalled.egg-info to /build/reproducible-path/uncalled-2.3+ds/debian/uncalled/usr/lib/python3.13/dist-packages/uncalled-2.3.0.egg-info Skipping SOURCES.txt running install_scripts copying build/scripts-3.13/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-3_amd64.deb'. dpkg-deb: building package 'uncalled-dbgsym' in '../uncalled-dbgsym_2.3+ds-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../uncalled_2.3+ds-3_amd64.buildinfo dpkg-genchanges --build=binary -O../uncalled_2.3+ds-3_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: 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/1255531 and its subdirectories I: Current time: Thu Feb 20 23:38:19 -12 2025 I: pbuilder-time-stamp: 1740137899 Fri Feb 21 11:38:21 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Fri Feb 21 11:38:21 UTC 2025 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Fri Feb 21 11:47:13 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Fri Feb 21 11:47:14 UTC 2025 I: uncalled_2.3+ds-3_amd64.changes: Format: 1.8 Date: Tue, 03 Dec 2024 20:44:38 +0100 Source: uncalled Binary: uncalled uncalled-dbgsym Architecture: amd64 Version: 2.3+ds-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: uncalled - Utility for Nanopore Current Alignment to Large Expanses of DNA Closes: 1087156 Changes: uncalled (2.3+ds-3) unstable; urgency=medium . * Team upload * debian_toml11.patch: normalize last-update timestamp. * skip_read_until: unfuzz patch. * syntax-warning.patch: new: fix SyntaxWarnings. (Closes: #1087156) Checksums-Sha1: 3eafd6df0a09379d9335bf039da1141cd8b30e41 25891436 uncalled-dbgsym_2.3+ds-3_amd64.deb 4c1f1400bb50c07d60803e8abc080f10a120cb2a 8933 uncalled_2.3+ds-3_amd64.buildinfo 07dace736e986f854345867d20f92ad65f97ce45 824568 uncalled_2.3+ds-3_amd64.deb Checksums-Sha256: a71cd7f1f52011fd95e5d08db2c5593042ea425188776ee029ef86dd77cf887b 25891436 uncalled-dbgsym_2.3+ds-3_amd64.deb f09967375b3105978e1851776d312dba2971681dbc0e2b45e3d8a55d1b0fb498 8933 uncalled_2.3+ds-3_amd64.buildinfo 59fb4d2a111fdfb783f4ac53ba52b2cc6c6d75852d6f551d7e9da0cc511b3596 824568 uncalled_2.3+ds-3_amd64.deb Files: 8804dae1f5686150f4569d35674d99ae 25891436 debug optional uncalled-dbgsym_2.3+ds-3_amd64.deb 4d819c6f131374c37afb2c0d70510318 8933 science optional uncalled_2.3+ds-3_amd64.buildinfo 487caf6325d6cceed3c61f9a531e7105 824568 science optional uncalled_2.3+ds-3_amd64.deb Fri Feb 21 11:47:15 UTC 2025 I: diffoscope 288 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_21-31823.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.EOCD11kg/uncalled_2.3+ds-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.EOCD11kg/uncalled_2.3+ds-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.EOCD11kg/uncalled_2.3+ds-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.EOCD11kg/b1/uncalled_2.3+ds-3_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.EOCD11kg/b2/uncalled_2.3+ds-3_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 222ms CPU time consumed: 223ms Fri Feb 21 11:47:16 UTC 2025 I: diffoscope 288 found no differences in the changes files, and a .buildinfo file also exists. Fri Feb 21 11:47:16 UTC 2025 I: uncalled from unstable built successfully and reproducibly on amd64. Fri Feb 21 11:47:17 UTC 2025 I: Submitting .buildinfo files to external archives: Fri Feb 21 11:47:17 UTC 2025 I: Submitting 12K b1/uncalled_2.3+ds-3_amd64.buildinfo.asc Fri Feb 21 11:47:18 UTC 2025 I: Submitting 12K b2/uncalled_2.3+ds-3_amd64.buildinfo.asc Fri Feb 21 11:47:18 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Feb 21 11:47:18 UTC 2025 I: Done submitting .buildinfo files. Fri Feb 21 11:47:18 UTC 2025 I: Removing signed uncalled_2.3+ds-3_amd64.buildinfo.asc files: removed './b1/uncalled_2.3+ds-3_amd64.buildinfo.asc' removed './b2/uncalled_2.3+ds-3_amd64.buildinfo.asc'