Tue May 7 23:06:14 UTC 2024 I: starting to build tombo/unstable/amd64 on jenkins on '2024-05-07 23:06' Tue May 7 23:06:14 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_33/11284/console.log Tue May 7 23:06:14 UTC 2024 I: Downloading source for unstable/tombo=1.5.1-6 --2024-05-07 23:06:14-- http://deb.debian.org/debian/pool/main/t/tombo/tombo_1.5.1-6.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2292 (2.2K) [text/prs.lines.tag] Saving to: ‘tombo_1.5.1-6.dsc’ 0K .. 100% 345M=0s 2024-05-07 23:06:14 (345 MB/s) - ‘tombo_1.5.1-6.dsc’ saved [2292/2292] Tue May 7 23:06:14 UTC 2024 I: tombo_1.5.1-6.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: tombo Binary: tombo, tombo-doc Architecture: any all Version: 1.5.1-6 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/nanoporetech/tombo Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/tombo Vcs-Git: https://salsa.debian.org/med-team/tombo.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-python, python3-all-dev, python3-setuptools, cython3, sphinx-doc, python3-sphinx, python3-sphinx-rtd-theme, python3-sphinx-argparse, libjs-mathjax, python3-h5py , python3-mappy , python3-numpy , python3-scipy , python3-tqdm , python3-nose2 Package-List: tombo deb science optional arch=any tombo-doc deb doc optional arch=all Checksums-Sha1: 94f33539552d8c2f7e6c06987fd264400fc17f84 22294835 tombo_1.5.1.orig.tar.gz 698e4cfe6b42253c1bb5e7fa5e8a36c6cd6e07f6 7024 tombo_1.5.1-6.debian.tar.xz Checksums-Sha256: f5f7ce37baee40b851ea867c2b835e6eae324ef90bdeb23fb931fde3272769a0 22294835 tombo_1.5.1.orig.tar.gz d3fb4aa21c5f0076c85497035a5ddca3d9226c7586b00265b53d491d45cdd2c7 7024 tombo_1.5.1-6.debian.tar.xz Files: 3709e4f4d6f4c58ec2d6ae216059929c 22294835 tombo_1.5.1.orig.tar.gz 2a6ce15a7eb1ba753b79b4644dbd8ac2 7024 tombo_1.5.1-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmV/SsIRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtF7Dw/7B/FranIpCYEXfTgZbtqWl8ZQxcImQelh xtZj0bZwT/NQZEed4+mKaaq77ohRcAFw/q0SAOtHj6JX+hNfwj6eoj6UIc1DIGHD Adr19kdNSM78Qr4ESgue8qCS1rQO1PRa+2OcCZN1i32KY3jJJt+9HfZGoTMcbyIB +KMg+UgaZ4mIm/ap540wiyD/Kps9kzA39ykdbTCmrwDEhyQu88fd+9bW9kOTKVIu G9PWnABJX8kDGeOaYXvnFW8bDhJov/VIIlTSOeVfX29ACpYFZ/8Tblexz7Hv/mmp boVAyRxR7AoDUxFeKBMHeF0IaNfz75pOyGjK0Wq8uyZ2SUu6/88zDETEekmn6Bhp nBLiKeZSG0RjjhiEQbFnqXDOz6t5WDV4gD4VKnVG/g8yS19Rd8cfhN544j9l/W0X HRWfe6dyj8s/HU3ecjgxVgNq1c+mIk5Bnaucs2iIUPgNKQT6didShNS71EuMuUXs vFKViRB/oF1voOsJIbJLRrRzSjozAXMulA26dN1gCr0Xjz9I4O0uZ4GafmA620Fj r2M0+Uou4yYcFpAwG1+0mDQiKH2UI/3wKcAWt9PKagDl1QZGSn0qr4O6qYs8RDHf WYacuV4Rj8EHSMQYvAZ+20P0XlltunEUPjVA4KORF8r53zLLfOaU6mNVHsAmwvHy Y6b2L3a3jCE= =Byih -----END PGP SIGNATURE----- Tue May 7 23:06:14 UTC 2024 I: Checking whether the package is not for us Tue May 7 23:06:14 UTC 2024 I: Starting 1st build on remote node infom01-amd64.debian.net. Tue May 7 23:06:14 UTC 2024 I: Preparing to do remote build '1' on infom01-amd64.debian.net. Tue May 7 23:09:07 UTC 2024 I: Deleting $TMPDIR on infom01-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue May 7 11:06:16 -12 2024 I: pbuilder-time-stamp: 1715123176 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 [tombo_1.5.1-6.dsc] I: copying [./tombo_1.5.1.orig.tar.gz] I: copying [./tombo_1.5.1-6.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Dec 17 19:23:46 2023 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-6.dsc: no acceptable signature found dpkg-source: info: extracting tombo in tombo-1.5.1 dpkg-source: info: unpacking tombo_1.5.1.orig.tar.gz dpkg-source: info: unpacking tombo_1.5.1-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_future.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying mathjax.patch dpkg-source: info: applying cython3-fix.patch dpkg-source: info: applying no_install_depends_cython.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4189424/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=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='89d69388b58f4a50a82182ea0a9e5f1d' 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='4189424' 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.qcLXvUPe/pbuilderrc_gNJP --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.qcLXvUPe/b1 --logfile b1/build.log tombo_1.5.1-6.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom01-amd64 6.1.0-21-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 6 07:42 /bin -> usr/bin I: user script /srv/workspace/pbuilder/4189424/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, python3-all-dev, python3-setuptools, cython3, sphinx-doc, python3-sphinx, python3-sphinx-rtd-theme, python3-sphinx-argparse, libjs-mathjax, python3-h5py, python3-mappy, python3-numpy, python3-scipy, python3-tqdm, python3-nose2 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19699 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-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 cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on sphinx-doc; however: Package sphinx-doc is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-rtd-theme; however: Package python3-sphinx-rtd-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-argparse; however: Package python3-sphinx-argparse is not installed. pbuilder-satisfydepends-dummy depends on libjs-mathjax; however: Package libjs-mathjax is not installed. pbuilder-satisfydepends-dummy depends on python3-h5py; however: Package python3-h5py is not installed. pbuilder-satisfydepends-dummy depends on python3-mappy; however: Package python3-mappy is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-tqdm; however: Package python3-tqdm is not installed. pbuilder-satisfydepends-dummy depends on python3-nose2; however: Package python3-nose2 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} ca-certificates{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} docutils-doc{a} dwz{a} file{a} fonts-font-awesome{a} fonts-lato{a} fonts-mathjax{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libaec0{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgssapi-krb5-2{a} libhdf5-103-1t64{a} libhdf5-hl-100t64{a} libicu72{a} libjs-jquery{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} libldap-2.5-0{a} liblzf1{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libpipeline1{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.11t64{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libsub-override-perl{a} libsz2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} python-babel-localedata{a} python-requests-doc{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-decorator{a} python3-dev{a} python3-distutils{a} python3-doc{a} python3-docutils{a} python3-h5py{a} python3-h5py-serial{a} python3-idna{a} python3-imagesize{a} python3-jinja2{a} python3-lib2to3{a} python3-mappy{a} python3-markupsafe{a} python3-minimal{a} python3-nose2{a} python3-numpy{a} python3-packaging{a} python3-pkg-resources{a} python3-pygments{a} python3-requests{a} python3-roman{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sphinx-argparse{a} python3-sphinx-rtd-theme{a} python3-sphinxcontrib.jquery{a} python3-tqdm{a} python3-urllib3{a} python3.11{a} python3.11-dev{a} python3.11-doc{a} python3.11-minimal{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-doc{a} sphinx-rtd-theme-common{a} tzdata{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common krb5-locales libarchive-cpio-perl libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules lynx publicsuffix python3-coverage python3-pil wget 0 packages upgraded, 140 newly installed, 0 to remove and 0 not upgraded. Need to get 124 MB of archives. After unpacking 586 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.3-1 [809 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.3-1 [2139 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 cython3 amd64 3.0.10+dfsg-5 [3571 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 43 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 python3-distutils all 3.12.3-1 [131 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20240422 [107 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 docutils-common all 0.20.1+dfsg-3 [128 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 docutils-doc all 0.20.1+dfsg-3 [1114 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.1.3-1 [23.4 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1~rc2-1 [22.6 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 68 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.7.1-5 [441 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.2-1 [155 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14-20240429-1 [836 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.1.3-1 [7740 B] Get: 81 http://deb.debian.org/debian unstable/main amd64 libhdf5-103-1t64 amd64 1.10.10+repack-3.3 [1241 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-3.3 [63.3 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 7.2.6-6 [150 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b1 [29.1 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 liblzf1 amd64 3.6-4+b1 [10.4 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libpython3.11t64 amd64 3.11.9-1 [1960 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libpython3.11-dev amd64 3.11.9-1 [4513 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.11.8-1 [9560 B] Get: 95 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.3-1 [1951 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libpython3.12t64 amd64 3.12.3-1 [2107 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libpython3.12-dev amd64 3.12.3-1 [5069 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.11.8-1 [1072 B] Get: 99 http://deb.debian.org/debian unstable/main amd64 python-babel-localedata all 2.14.0-1 [5701 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 python-requests-doc all 2.31.0+dfsg-1 [190 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 0.7.12-1 [20.8 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.3-1 [659 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.11.8-1 [1056 B] Get: 104 http://deb.debian.org/debian unstable/main amd64 python3.11-dev amd64 3.11.9-1 [501 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.11.8-1 [26.1 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 python3.12-dev amd64 3.12.3-1 [499 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.11.8-1 [1072 B] Get: 108 http://deb.debian.org/debian unstable/main amd64 python3-babel all 2.14.0-1 [111 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2023.11.17-1 [155 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer all 3.3.2-1 [51.6 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 python3.11-doc all 3.11.9-1 [12.6 MB] Get: 114 http://deb.debian.org/debian unstable/main amd64 python3-doc all 3.11.8-1 [9528 B] Get: 115 http://deb.debian.org/debian unstable/main amd64 python3-roman all 3.3-3 [9880 B] Get: 116 http://deb.debian.org/debian unstable/main amd64 python3-docutils all 0.20.1+dfsg-3 [389 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:1.26.4+ds-8 [5466 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 python3-h5py-serial amd64 3.10.0-1+b3 [1400 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 python3-h5py all 3.10.0-1 [14.4 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.6-2 [37.0 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 122 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 2.1.5-1 [14.5 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 python3-mappy amd64 2.27+dfsg-1 [180 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 python3-nose2 all 0.14.0-2 [115 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.0-1 [45.5 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.17.2+dfsg-1 [818 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 python3-six all 1.16.0-6 [16.3 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 1.26.18-2 [116 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.31.0+dfsg-1 [68.6 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.11.4-6 [19.5 MB] Get: 132 http://deb.debian.org/debian unstable/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 7.2.6-6 [702 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 7.2.6-6 [552 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1021 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-argparse all 0.4.0-1 [37.7 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 138 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-rtd-theme all 2.0.0+dfsg-1 [28.3 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 python3-tqdm all 4.66.4-1 [90.8 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 sphinx-doc all 7.2.6-6 [2375 kB] Fetched 124 MB in 1s (99.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package fonts-lato. (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 ... 19699 files and directories currently installed.) Preparing to unpack .../fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. 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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 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21033 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libpython3.12-minimal:amd64. 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Selecting previously unselected package libxml2:amd64. Preparing to unpack .../032-libxml2_2.9.14+dfsg-1.3+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../033-gettext_0.21-14+b1_amd64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../034-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../035-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../036-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../037-python3-pkg-resources_68.1.2-2_all.deb ... Unpacking python3-pkg-resources (68.1.2-2) ... 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Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libpython3.12-minimal:amd64 (3.12.3-1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.61.0-1+b1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:amd64 (1.47.1~rc2-1) ... Setting up file (1:5.45-3) ... Setting up libaec0:amd64 (1.1.3-1) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up python-babel-localedata (2.14.0-1) ... Setting up libkrb5support0:amd64 (1.20.1-6+b1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Tue May 7 23:07:25 UTC 2024. Universal Time is now: Tue May 7 23:07:25 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.12.0-3) ... 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 libexpat1-dev:amd64 (2.6.2-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up liblzf1:amd64 (3.6-4+b1) ... Setting up autopoint (0.21-14) ... Setting up libk5crypto3:amd64 (1.20.1-6+b1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up libgfortran5:amd64 (14-20240429-1) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libjson-perl (4.10000-1) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:amd64 (1.20.1-6+b1) ... Setting up libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up openssl (3.2.1-3) ... Setting up readline-common (8.2-4) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (2.0.0+dfsg-1) ... Setting up libsz2:amd64 (1.1.3-1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.12-minimal (3.12.3-1) ... Setting up liblapack3:amd64 (3.12.0-3) ... 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 (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up python3.11-doc (3.11.9-1) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up libjs-sphinxdoc (7.2.6-6) ... Setting up python-requests-doc (2.31.0+dfsg-1) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up xml-core (0.19) ... Setting up python3-doc (3.11.8-1) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b1) ... Setting up sphinx-doc (7.2.6-6) ... Setting up libpython3.12-stdlib:amd64 (3.12.3-1) ... Setting up libcurl4t64:amd64 (8.7.1-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up python3.12 (3.12.3-1) ... Setting up libpython3.11t64:amd64 (3.11.9-1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3.12t64:amd64 (3.12.3-1) ... Setting up libpython3.11-dev:amd64 (3.11.9-1) ... Setting up sphinx-common (7.2.6-6) ... Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-3.3) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-3.3) ... Setting up python3.11 (3.11.9-1) ... Setting up libpython3-dev:amd64 (3.11.8-1) ... Setting up python3.11-dev (3.11.9-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up libpython3.12-dev:amd64 (3.12.3-1) ... Setting up python3-markupsafe (2.1.5-1) ... Setting up python3-six (1.16.0-6) ... Setting up python3-roman (3.3-3) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up python3-packaging (24.0-1) ... Setting up python3-certifi (2023.11.17-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up libpython3-all-dev:amd64 (3.11.8-1) ... Setting up python3-idna (3.6-2) ... Setting up python3.12-dev (3.12.3-1) ... Setting up cython3 (3.0.10+dfsg-5) ... Setting up python3-urllib3 (1.26.18-2) ... Setting up python3-lib2to3 (3.12.3-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... python3.12: can't get files for byte-compilation Setting up python3-setuptools (68.1.2-2) ... Setting up python3-babel (2.14.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-charset-normalizer (3.3.2-1) ... Setting up python3-alabaster (0.7.12-1) ... Setting up python3-tqdm (4.66.4-1) ... Setting up python3-all (3.11.8-1) ... Setting up python3-mappy (2.27+dfsg-1) ... Setting up python3-nose2 (0.14.0-2) ... Setting up python3-pygments (2.17.2+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-dev (3.11.8-1) ... Setting up python3-requests (2.31.0+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-8) ... Setting up dh-python (6.20240422) ... Setting up python3-all-dev (3.11.8-1) ... Setting up python3-scipy (1.11.4-6) ... Setting up python3-h5py-serial (3.10.0-1+b3) ... Setting up python3-h5py (3.10.0-1) ... Processing triggers for libc-bin (2.38-8) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.20.1+dfsg-3) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.20.1+dfsg-3) ... Setting up python3-sphinx (7.2.6-6) ... Setting up python3-sphinxcontrib.jquery (4.1-5) ... Setting up python3-sphinx-argparse (0.4.0-1) ... Setting up python3-sphinx-rtd-theme (2.0.0+dfsg-1) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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/tombo-1.5.1/ && 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 > ../tombo_1.5.1-6_source.changes dpkg-buildpackage: info: source package tombo dpkg-buildpackage: info: source version 1.5.1-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py clean running clean removing '/build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/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: python3.11 setup.py clean running clean removing '/build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3,sphinxdoc --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 running config I: pybuild base:311: python3.11 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/tombo-1.5.1' dh_auto_build I: pybuild base:311: /usr/bin/python3.12 setup.py build running build running build_py creating /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo copying tombo/_default_parameters.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo copying tombo/_filter_reads.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo copying tombo/_plot_commands.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo copying tombo/resquiggle.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo copying tombo/__main__.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo copying tombo/_option_parsers.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo copying tombo/_version.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo copying tombo/tombo_helper.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo copying tombo/_event_resquiggle.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo copying tombo/_text_output_commands.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo copying tombo/__init__.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo copying tombo/_preprocess.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo copying tombo/tombo_stats.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo running egg_info creating ont_tombo.egg-info writing ont_tombo.egg-info/PKG-INFO writing dependency_links to ont_tombo.egg-info/dependency_links.txt writing entry points to ont_tombo.egg-info/entry_points.txt writing requirements to ont_tombo.egg-info/requires.txt writing top-level names to ont_tombo.egg-info/top_level.txt writing manifest file 'ont_tombo.egg-info/SOURCES.txt' reading manifest file 'ont_tombo.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*' under directory 'cython' adding license file 'LICENSE.md' writing manifest file 'ont_tombo.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'tombo.R_scripts' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'tombo.R_scripts' 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 'tombo.R_scripts' 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 'tombo.R_scripts' to be distributed and are already explicitly excluding 'tombo.R_scripts' 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) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'tombo.tombo_models' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'tombo.tombo_models' 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 'tombo.tombo_models' 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 'tombo.tombo_models' to be distributed and are already explicitly excluding 'tombo.tombo_models' 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) copying tombo/_c_dynamic_programming.pyx -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo copying tombo/_c_helper.pyx -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo creating /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/debugDP.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/debugFit.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/debugRawDP.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/plotGroupComp.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/plotKmerDist.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/plotModelComp.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/plotMotifStats.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/plotMultiReadCorr.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/plotPerReadStats.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/plotROC.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/plotROCPerRead.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/plotReadCorr.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/plotSigMDS.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/plotSingleRead.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/plotSingleRun.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts creating /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.5mC.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.6mA.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.CpG.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.dam.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.dcm.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models copying tombo/tombo_models/tombo.RNA.180mV.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models copying tombo/tombo_models/tombo.RNA.200mV.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models copying tombo/tombo_models/tombo.RNA.5mC.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models running build_ext /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tombo-1.5.1/tombo/_c_dynamic_programming.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling tombo/_c_dynamic_programming.pyx because it changed. [1/1] Cythonizing tombo/_c_dynamic_programming.pyx building 'tombo._c_dynamic_programming' extension creating build creating build/temp.linux-x86_64-cpython-312 creating build/temp.linux-x86_64-cpython-312/tombo x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c tombo/_c_dynamic_programming.cpp -o build/temp.linux-x86_64-cpython-312/tombo/_c_dynamic_programming.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from tombo/_c_dynamic_programming.cpp:1262: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function 'PyObject* __pyx_pf_5tombo_22_c_dynamic_programming_2c_reg_z_scores(PyObject*, PyArrayObject*, PyArrayObject*, PyArrayObject*, PyArrayObject*, __pyx_t_5tombo_22_c_dynamic_programming_DTYPE_INT_t, __pyx_t_5tombo_22_c_dynamic_programming_DTYPE_INT_t, __pyx_t_5tombo_22_c_dynamic_programming_DTYPE_INT_t, __pyx_t_5tombo_22_c_dynamic_programming_DTYPE_INT_t, PyObject*)', inlined from 'PyObject* __pyx_pw_5tombo_22_c_dynamic_programming_3c_reg_z_scores(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)' at tombo/_c_dynamic_programming.cpp:5869:69: tombo/_c_dynamic_programming.cpp:6684:36: warning: '__pyx_v_np_max_half_z_score' may be used uninitialized [-Wmaybe-uninitialized] 6684 | __pyx_t_20 = PyFloat_FromDouble(__pyx_v_np_max_half_z_score); if (unlikely(!__pyx_t_20)) __PYX_ERR(0, 93, __pyx_L1_error) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tombo/_c_dynamic_programming.cpp: In function 'PyObject* __pyx_pw_5tombo_22_c_dynamic_programming_3c_reg_z_scores(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)': tombo/_c_dynamic_programming.cpp:5895:51: note: '__pyx_v_np_max_half_z_score' was declared here 5895 | __pyx_t_5tombo_22_c_dynamic_programming_DTYPE_t __pyx_v_np_max_half_z_score; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/tombo/_c_dynamic_programming.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_c_dynamic_programming.cpython-312-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tombo-1.5.1/tombo/_c_helper.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling tombo/_c_helper.pyx because it changed. [1/1] Cythonizing tombo/_c_helper.pyx building 'tombo._c_helper' extension x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c tombo/_c_helper.cpp -o build/temp.linux-x86_64-cpython-312/tombo/_c_helper.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from tombo/_c_helper.cpp:1262: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/tombo/_c_helper.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_c_helper.cpython-312-x86_64-linux-gnu.so I: pybuild base:311: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/_default_parameters.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/_filter_reads.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/_plot_commands.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/resquiggle.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/__main__.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/_option_parsers.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/_version.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/tombo_helper.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/_event_resquiggle.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/_text_output_commands.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/__init__.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/_preprocess.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/tombo_stats.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo running egg_info writing ont_tombo.egg-info/PKG-INFO writing dependency_links to ont_tombo.egg-info/dependency_links.txt writing entry points to ont_tombo.egg-info/entry_points.txt writing requirements to ont_tombo.egg-info/requires.txt writing top-level names to ont_tombo.egg-info/top_level.txt reading manifest file 'ont_tombo.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*' under directory 'cython' adding license file 'LICENSE.md' writing manifest file 'ont_tombo.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'tombo.R_scripts' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'tombo.R_scripts' 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 'tombo.R_scripts' 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 'tombo.R_scripts' to be distributed and are already explicitly excluding 'tombo.R_scripts' 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) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'tombo.tombo_models' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'tombo.tombo_models' 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 'tombo.tombo_models' 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 'tombo.tombo_models' to be distributed and are already explicitly excluding 'tombo.tombo_models' 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) copying tombo/_c_dynamic_programming.pyx -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/_c_helper.pyx -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo creating /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/debugDP.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/debugFit.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/debugRawDP.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/plotGroupComp.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/plotKmerDist.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/plotModelComp.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/plotMotifStats.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/plotMultiReadCorr.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/plotPerReadStats.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/plotROC.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/plotROCPerRead.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/plotReadCorr.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/plotSigMDS.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/plotSingleRead.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/plotSingleRun.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts creating /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.5mC.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.6mA.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.CpG.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.dam.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.dcm.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models copying tombo/tombo_models/tombo.RNA.180mV.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models copying tombo/tombo_models/tombo.RNA.200mV.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models copying tombo/tombo_models/tombo.RNA.5mC.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models running build_ext building 'tombo._c_dynamic_programming' extension creating build/temp.linux-x86_64-cpython-311 creating build/temp.linux-x86_64-cpython-311/tombo x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c tombo/_c_dynamic_programming.cpp -o build/temp.linux-x86_64-cpython-311/tombo/_c_dynamic_programming.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from tombo/_c_dynamic_programming.cpp:1262: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function 'PyObject* __pyx_pf_5tombo_22_c_dynamic_programming_2c_reg_z_scores(PyObject*, PyArrayObject*, PyArrayObject*, PyArrayObject*, PyArrayObject*, __pyx_t_5tombo_22_c_dynamic_programming_DTYPE_INT_t, __pyx_t_5tombo_22_c_dynamic_programming_DTYPE_INT_t, __pyx_t_5tombo_22_c_dynamic_programming_DTYPE_INT_t, __pyx_t_5tombo_22_c_dynamic_programming_DTYPE_INT_t, PyObject*)', inlined from 'PyObject* __pyx_pw_5tombo_22_c_dynamic_programming_3c_reg_z_scores(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)' at tombo/_c_dynamic_programming.cpp:5869:69: tombo/_c_dynamic_programming.cpp:6684:36: warning: '__pyx_v_np_max_half_z_score' may be used uninitialized [-Wmaybe-uninitialized] 6684 | __pyx_t_20 = PyFloat_FromDouble(__pyx_v_np_max_half_z_score); if (unlikely(!__pyx_t_20)) __PYX_ERR(0, 93, __pyx_L1_error) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tombo/_c_dynamic_programming.cpp: In function 'PyObject* __pyx_pw_5tombo_22_c_dynamic_programming_3c_reg_z_scores(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)': tombo/_c_dynamic_programming.cpp:5895:51: note: '__pyx_v_np_max_half_z_score' was declared here 5895 | __pyx_t_5tombo_22_c_dynamic_programming_DTYPE_t __pyx_v_np_max_half_z_score; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/tombo/_c_dynamic_programming.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_c_dynamic_programming.cpython-311-x86_64-linux-gnu.so building 'tombo._c_helper' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c tombo/_c_helper.cpp -o build/temp.linux-x86_64-cpython-311/tombo/_c_helper.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from tombo/_c_helper.cpp:1262: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/tombo/_c_helper.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_c_helper.cpython-311-x86_64-linux-gnu.so sphinx-build -N -bhtml docs docs/build Running Sphinx v7.2.6 making output directory... done building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 11 source files that are out of date updating environment: [new config] 11 added, 0 changed, 0 removed reading sources... [ 9%] examples reading sources... [ 18%] filtering reading sources... [ 27%] index reading sources... [ 36%] model_training reading sources... [ 45%] modified_base_detection reading sources... [ 55%] plotting reading sources... [ 64%] resquiggle reading sources... [ 73%] rna reading sources... [ 82%] text_output reading sources... [ 91%] tombo reading sources... [100%] tutorials WARNING: autodoc: failed to import module 'tombo'; the following exception was raised: No module named 'tombo' WARNING: autodoc: failed to import module 'resquiggle' from module 'tombo'; the following exception was raised: No module named 'tombo' WARNING: autodoc: failed to import module 'tombo_helper' from module 'tombo'; the following exception was raised: No module named 'tombo' WARNING: autodoc: failed to import module 'tombo_stats' from module 'tombo'; the following exception was raised: No module named 'tombo' looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done copying assets... copying static files... done copying extra files... done done writing output... [ 9%] examples writing output... [ 18%] filtering writing output... [ 27%] index writing output... [ 36%] model_training writing output... [ 45%] modified_base_detection writing output... [ 55%] plotting writing output... [ 64%] resquiggle writing output... [ 73%] rna writing output... [ 82%] text_output writing output... [ 91%] tombo writing output... [100%] tutorials generating indices... genindex done highlighting module code... writing additional pages... search done copying images... [ 4%] _images/testing_method_comparison.png copying images... [ 9%] _images/alt_density_est.png copying images... [ 13%] _images/old_correction_plot.png copying images... [ 17%] _images/outlier_robust_llr.gif copying images... [ 22%] _images/dampened_fraction.png copying images... [ 26%] _images/single_samp.png copying images... [ 30%] _images/sample_comp.png copying images... [ 35%] _images/model_comp.png copying images... [ 39%] _images/alt_model_comp.png copying images... [ 43%] _images/boxplot.png copying images... [ 48%] _images/quantile.png copying images... [ 52%] _images/density.png copying images... [ 57%] _images/pre_read_5mC.png copying images... [ 61%] _images/per_read_do_novo.png copying images... [ 65%] _images/stat_dist.png copying images... [ 70%] _images/kmer_levels.png copying images... [ 74%] _images/roc.png copying images... [ 78%] _images/per_read_stat_dist.png copying images... [ 83%] _images/begin_half_z_scores.png copying images... [ 87%] _images/begin_forward_pass.png copying images... [ 91%] _images/adaptive_half_z_scores.png copying images... [ 96%] _images/adaptive_forward_pass.png copying images... [100%] _images/stat_dist_null.png dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 4 warnings. The HTML pages are in docs/build. make[1]: Leaving directory '/build/reproducible-path/tombo-1.5.1' dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build; python3.12 -m nose2 -v ---------------------------------------------------------------------- Ran 0 tests in 0.000s OK I: pybuild base:311: cd /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build; python3.11 -m nose2 -v ---------------------------------------------------------------------- Ran 0 tests in 0.000s OK create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.12 setup.py install --root /build/reproducible-path/tombo-1.5.1/debian/tmp running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running egg_info writing ont_tombo.egg-info/PKG-INFO writing dependency_links to ont_tombo.egg-info/dependency_links.txt writing entry points to ont_tombo.egg-info/entry_points.txt writing requirements to ont_tombo.egg-info/requires.txt writing top-level names to ont_tombo.egg-info/top_level.txt reading manifest file 'ont_tombo.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*' under directory 'cython' adding license file 'LICENSE.md' writing manifest file 'ont_tombo.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'tombo.R_scripts' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'tombo.R_scripts' 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 'tombo.R_scripts' 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 'tombo.R_scripts' to be distributed and are already explicitly excluding 'tombo.R_scripts' 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) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'tombo.tombo_models' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'tombo.tombo_models' 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 'tombo.tombo_models' 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 'tombo.tombo_models' to be distributed and are already explicitly excluding 'tombo.tombo_models' 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 running install_lib creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12 creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models/tombo.DNA.dam.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models/tombo.RNA.200mV.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models/tombo.DNA.5mC.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models/tombo.RNA.180mV.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models/tombo.DNA.6mA.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models/tombo.DNA.dcm.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models/tombo.DNA.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models/tombo.RNA.5mC.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models/tombo.DNA.CpG.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_default_parameters.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_filter_reads.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_plot_commands.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/resquiggle.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/__main__.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_option_parsers.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/plotMultiReadCorr.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/plotSingleRun.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/plotROCPerRead.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/plotGroupComp.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/debugRawDP.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/plotROC.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/debugFit.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/plotSigMDS.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/plotModelComp.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/plotSingleRead.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/plotReadCorr.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/plotMotifStats.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/debugDP.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/plotPerReadStats.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/plotKmerDist.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_c_dynamic_programming.pyx -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_c_dynamic_programming.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_version.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_helper.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_event_resquiggle.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_c_helper.pyx -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_text_output_commands.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/__init__.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_c_helper.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_preprocess.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_stats.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/_default_parameters.py to _default_parameters.cpython-312.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/_filter_reads.py to _filter_reads.cpython-312.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/_plot_commands.py to _plot_commands.cpython-312.pyc /usr/lib/python3.12/dist-packages/tombo/_plot_commands.py:2253: SyntaxWarning: invalid escape sequence '\|' byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/resquiggle.py to resquiggle.cpython-312.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/__main__.py to __main__.cpython-312.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/_option_parsers.py to _option_parsers.cpython-312.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/_version.py to _version.cpython-312.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/tombo_helper.py to tombo_helper.cpython-312.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/_event_resquiggle.py to _event_resquiggle.cpython-312.pyc /usr/lib/python3.12/dist-packages/tombo/_event_resquiggle.py:68: SyntaxWarning: invalid escape sequence '\d' byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/_text_output_commands.py to _text_output_commands.cpython-312.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/_preprocess.py to _preprocess.cpython-312.pyc /usr/lib/python3.12/dist-packages/tombo/_preprocess.py:156: SyntaxWarning: invalid escape sequence '\+' byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/tombo_stats.py to tombo_stats.cpython-312.pyc running install_egg_info Copying ont_tombo.egg-info to /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/ont_tombo-1.5.1.egg-info Skipping SOURCES.txt running install_scripts Installing tombo script to /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/bin I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/tombo-1.5.1/debian/tmp running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running egg_info writing ont_tombo.egg-info/PKG-INFO writing dependency_links to ont_tombo.egg-info/dependency_links.txt writing entry points to ont_tombo.egg-info/entry_points.txt writing requirements to ont_tombo.egg-info/requires.txt writing top-level names to ont_tombo.egg-info/top_level.txt reading manifest file 'ont_tombo.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*' under directory 'cython' adding license file 'LICENSE.md' writing manifest file 'ont_tombo.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'tombo.R_scripts' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'tombo.R_scripts' 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 'tombo.R_scripts' 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 'tombo.R_scripts' to be distributed and are already explicitly excluding 'tombo.R_scripts' 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) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'tombo.tombo_models' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'tombo.tombo_models' 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 'tombo.tombo_models' 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 'tombo.tombo_models' to be distributed and are already explicitly excluding 'tombo.tombo_models' 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 running install_lib creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11 creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models/tombo.DNA.dam.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models/tombo.RNA.200mV.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models/tombo.DNA.5mC.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models/tombo.RNA.180mV.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models/tombo.DNA.6mA.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models/tombo.DNA.dcm.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models/tombo.DNA.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models/tombo.RNA.5mC.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models/tombo.DNA.CpG.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_default_parameters.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_filter_reads.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_plot_commands.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/resquiggle.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/__main__.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_option_parsers.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_c_helper.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/plotMultiReadCorr.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/plotSingleRun.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/plotROCPerRead.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/plotGroupComp.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/debugRawDP.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/plotROC.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/debugFit.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/plotSigMDS.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/plotModelComp.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/plotSingleRead.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/plotReadCorr.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/plotMotifStats.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/debugDP.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/plotPerReadStats.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/plotKmerDist.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_c_dynamic_programming.pyx -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_version.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_helper.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_c_dynamic_programming.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_event_resquiggle.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_c_helper.pyx -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_text_output_commands.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/__init__.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_preprocess.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_stats.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/_default_parameters.py to _default_parameters.cpython-311.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/_filter_reads.py to _filter_reads.cpython-311.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/_plot_commands.py to _plot_commands.cpython-311.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/resquiggle.py to resquiggle.cpython-311.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/__main__.py to __main__.cpython-311.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/_option_parsers.py to _option_parsers.cpython-311.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/_version.py to _version.cpython-311.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/tombo_helper.py to tombo_helper.cpython-311.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/_event_resquiggle.py to _event_resquiggle.cpython-311.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/_text_output_commands.py to _text_output_commands.cpython-311.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/_preprocess.py to _preprocess.cpython-311.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/tombo_stats.py to tombo_stats.cpython-311.pyc running install_egg_info Copying ont_tombo.egg-info to /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/ont_tombo-1.5.1.egg-info Skipping SOURCES.txt running install_scripts Installing tombo script to /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/bin dh_install -O--buildsystem=pybuild dh_installdocs -O--buildsystem=pybuild dh_sphinxdoc -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild debian/rules override_dh_python3 make[1]: Entering directory '/build/reproducible-path/tombo-1.5.1' dh_python3 I: dh_python3 tools:113: replacing shebang in debian/tombo/usr/share/tombo/scripts/dump_per_read_statistics.py dh_numpy3 make[1]: Leaving directory '/build/reproducible-path/tombo-1.5.1' dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/tombo-1.5.1' dh_fixperms find debian -name "*.model" -exec chmod -x \{\} \; make[1]: Leaving directory '/build/reproducible-path/tombo-1.5.1' dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package tombo-doc: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package tombo-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'tombo-dbgsym' in '../tombo-dbgsym_1.5.1-6_amd64.deb'. dpkg-deb: building package 'tombo-doc' in '../tombo-doc_1.5.1-6_all.deb'. dpkg-deb: building package 'tombo' in '../tombo_1.5.1-6_amd64.deb'. dpkg-genbuildinfo --build=binary -O../tombo_1.5.1-6_amd64.buildinfo dpkg-genchanges --build=binary -O../tombo_1.5.1-6_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/4189424 and its subdirectories I: Current time: Tue May 7 11:09:05 -12 2024 I: pbuilder-time-stamp: 1715123345 Tue May 7 23:09:07 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom02-amd64.debian.net. Tue May 7 23:09:07 UTC 2024 I: Preparing to do remote build '2' on infom02-amd64.debian.net. Tue May 7 23:13:19 UTC 2024 I: Deleting $TMPDIR on infom02-amd64.debian.net. Tue May 7 23:13:20 UTC 2024 I: tombo_1.5.1-6_amd64.changes: Format: 1.8 Date: Mon, 11 Dec 2023 21:22:16 +0100 Source: tombo Binary: tombo tombo-dbgsym tombo-doc Architecture: amd64 all Version: 1.5.1-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: tombo - identification of modified nucleotides from raw nanopore sequenci tombo-doc - identification of modified nucleotides from raw nanopore sequenci Closes: 1058010 Changes: tombo (1.5.1-6) unstable; urgency=medium . * No runtime dependency from cython Closes: #1058010 * execute dh_numpy3 after dh_python3 to assign python3-numpy-abi Checksums-Sha1: 631e7939d7d4145b89964fbab193b2704d43da4e 1067700 tombo-dbgsym_1.5.1-6_amd64.deb 1bd34891bbe47b7891102ee38f73f33020bb3631 21732384 tombo-doc_1.5.1-6_all.deb bfcde440bba1a381ae5c51dd14ea93d0f96d3c67 9104 tombo_1.5.1-6_amd64.buildinfo 6c6eb8e556f3f975fa4672af6eab09b6998c5b85 510784 tombo_1.5.1-6_amd64.deb Checksums-Sha256: f560e5e56191988c457ad47bf0036e21a1cae8a2743506c45d7ce38256166038 1067700 tombo-dbgsym_1.5.1-6_amd64.deb 838ee0f07edecc62fd0a0b2a88da70050cea139fc96aca3d6701de087b8aaff4 21732384 tombo-doc_1.5.1-6_all.deb 678c4f2e7e89f3ba4f55e87d3457dc23809dacdbfc3c8af188716ebe51b09c83 9104 tombo_1.5.1-6_amd64.buildinfo bcc8f50871438294e09138d4c4976f531447d815f260bb4c0e225ab7aa586475 510784 tombo_1.5.1-6_amd64.deb Files: 037dffef5749d0ade274478a4dc0683c 1067700 debug optional tombo-dbgsym_1.5.1-6_amd64.deb b54facc1fa8cd19ff3a26f8fef71b71f 21732384 doc optional tombo-doc_1.5.1-6_all.deb ae994f64a35917e38940c32f85a90c10 9104 science optional tombo_1.5.1-6_amd64.buildinfo 8392160b915a314daeb917f9521ab0dc 510784 science optional tombo_1.5.1-6_amd64.deb Tue May 7 23:13:21 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_33-11284.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.qcLXvUPe/tombo_1.5.1-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.qcLXvUPe/tombo_1.5.1-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.qcLXvUPe/tombo_1.5.1-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.qcLXvUPe/b1/tombo_1.5.1-6_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.qcLXvUPe/b2/tombo_1.5.1-6_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.617s) 0.617s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.260s) 0.260s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 955ms CPU time consumed: 954ms Tue May 7 23:13:22 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Tue May 7 23:13:22 UTC 2024 I: tombo from unstable built successfully and reproducibly on amd64. Tue May 7 23:13:23 UTC 2024 I: Submitting .buildinfo files to external archives: Tue May 7 23:13:23 UTC 2024 I: Submitting 12K b1/tombo_1.5.1-6_amd64.buildinfo.asc Tue May 7 23:13:25 UTC 2024 I: Submitting 12K b2/tombo_1.5.1-6_amd64.buildinfo.asc Tue May 7 23:13:26 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue May 7 23:13:26 UTC 2024 I: Done submitting .buildinfo files. Tue May 7 23:13:26 UTC 2024 I: Removing signed tombo_1.5.1-6_amd64.buildinfo.asc files: removed './b1/tombo_1.5.1-6_amd64.buildinfo.asc' removed './b2/tombo_1.5.1-6_amd64.buildinfo.asc'