Sun May 5 07:55:09 UTC 2024 I: starting to build tipp/unstable/amd64 on jenkins on '2024-05-05 07:54' Sun May 5 07:55:09 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_21/5619/console.log Sun May 5 07:55:09 UTC 2024 I: Downloading source for unstable/tipp=1.0+dfsg-3 --2024-05-05 07:55:09-- http://deb.debian.org/debian/pool/main/t/tipp/tipp_1.0%2bdfsg-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2040 (2.0K) [text/prs.lines.tag] Saving to: ‘tipp_1.0+dfsg-3.dsc’ 0K . 100% 288M=0s 2024-05-05 07:55:09 (288 MB/s) - ‘tipp_1.0+dfsg-3.dsc’ saved [2040/2040] Sun May 5 07:55:09 UTC 2024 I: tipp_1.0+dfsg-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: tipp Binary: tipp Architecture: any Version: 1.0+dfsg-3 Maintainer: Debian Med Packaging Team Uploaders: Pierre Gruet Homepage: https://github.com/TeraTrees/TIPP Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/tipp Vcs-Git: https://salsa.debian.org/med-team/tipp.git Build-Depends: debhelper-compat (= 13), dh-python, python3, python3-setuptools, python3-dendropy, ant, libjenkins-json-java, libgoogle-gson-java, ncbi-blast+, sepp (>= 4.5.1+really4.5.1+dfsg-1~) Package-List: tipp deb science optional arch=any Checksums-Sha1: 5383eb4919928d50ff9c5f92279b427565c8a854 67084 tipp_1.0+dfsg.orig.tar.xz 2a7838dd6028da7977a1a8055fa4a70e581f256e 10104 tipp_1.0+dfsg-3.debian.tar.xz Checksums-Sha256: 48bbabdc3b6267ad250dd60664dc2f76f0da924676a83aa4490e23219144a9eb 67084 tipp_1.0+dfsg.orig.tar.xz b3a1323d86bd96632775d43ef97227397569d76df5fd01fd43701bda9da78adc 10104 tipp_1.0+dfsg-3.debian.tar.xz Files: 71211248cd41a5e336e9aa6dcb1e1beb 67084 tipp_1.0+dfsg.orig.tar.xz 604dc65a78ed0878235cf4cb7c0ebd62 10104 tipp_1.0+dfsg-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEM8soQxPpC9J9y0UjYAMWptwndHYFAmN1Yg0ACgkQYAMWptwn dHbvUA/+OoWOOKdvuVluKCWBN69Zi76dur+SKVtqCoMBsPJ+NfFSlBW7jwzjUy25 6C8EXLE0DNXaMbP7IzFv24EPXDT0307etZZzU9O7jWfTiIzoUdXzPqa23pj/IDSu 45/Q9M8gFjrmLnfQvAlgjX67BU66GGos1bTmTYfDZ+VrslqUwE5YB3XH9i6fHfTV rBzHD46VYq5OBnl+nytKyf/kPyMalAXELfIU4+L4bGCnMzSFV30BHQRVSQDfkehb HT6TVmFjGlLS63f6HfBI5RABaH2j6idydpN70KBjjfvNKU6z/cARWbXbF+vsA7B/ sRwfOMhzWb+rmIgy/96DEfF+YJDw0Wa+Lql3WZ992oIIGTuH7yKpsrtQQDj3GiSb ZKzunAmXDWn3o33Z4IJLU3p6eJuIF6P7YuQdvffbQGgH139a8VEgxYacHg8r5+DY XwD0nvX+EcusJxjf2mabTalA3c45MV+aLi4JtoWIodNmwSRSc7Rc2DkdsjfCxV0f 47l/BXeb/xp37l6I/n3pg0PqX+1nEzWVIPh9GdEYnNyJ2fX0Pq5fka7UQ9wfWkTQ nAfmbvstgqElFZqAuQhoxfac4fpfkQHwmNoMjEabjichBYfunRWkZjasoh8mhajV iJdrQwzbuGRMkuSqREpUiV0MINaAClXlwjo72xa0C8T1oyAABIg= =xA82 -----END PGP SIGNATURE----- Sun May 5 07:55:09 UTC 2024 I: Checking whether the package is not for us Sun May 5 07:55:09 UTC 2024 I: Starting 1st build on remote node ionos11-amd64.debian.net. Sun May 5 07:55:09 UTC 2024 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Sun May 5 08:01:31 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat May 4 19:55:13 -12 2024 I: pbuilder-time-stamp: 1714895713 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 [tipp_1.0+dfsg-3.dsc] I: copying [./tipp_1.0+dfsg.orig.tar.xz] I: copying [./tipp_1.0+dfsg-3.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Nov 16 22:19:57 2022 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./tipp_1.0+dfsg-3.dsc: no acceptable signature found dpkg-source: info: extracting tipp in tipp-1.0+dfsg dpkg-source: info: unpacking tipp_1.0+dfsg.orig.tar.xz dpkg-source: info: unpacking tipp_1.0+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying setup.patch dpkg-source: info: applying use_debian_packaged_guppy_from_pplacer.patch dpkg-source: info: applying change_java_version_for_ant.patch dpkg-source: info: applying java_build.patch dpkg-source: info: applying configuration_files_in_etc_and_per_user.patch dpkg-source: info: applying using_python3_interpreter.patch dpkg-source: info: applying tipp_metagenomics.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3789512/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='896d6272f7e34cc5895a89552bd1f81f' 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='3789512' 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.57wAsRz2/pbuilderrc_06Da --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.57wAsRz2/b1 --logfile b1/build.log tipp_1.0+dfsg-3.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 5 07:43 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3789512/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, python3-setuptools, python3-dendropy, ant, libjenkins-json-java, libgoogle-gson-java, ncbi-blast+, sepp (>= 4.5.1+really4.5.1+dfsg-1~) 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; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-dendropy; however: Package python3-dendropy is not installed. pbuilder-satisfydepends-dummy depends on ant; however: Package ant is not installed. pbuilder-satisfydepends-dummy depends on libjenkins-json-java; however: Package libjenkins-json-java is not installed. pbuilder-satisfydepends-dummy depends on libgoogle-gson-java; however: Package libgoogle-gson-java is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+; however: Package ncbi-blast+ is not installed. pbuilder-satisfydepends-dummy depends on sepp (>= 4.5.1+really4.5.1+dfsg-1~); however: Package sepp 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: adwaita-icon-theme{a} ant{a} antlr{a} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} debhelper{a} default-jre{a} default-jre-headless{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} groovy{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} hmmer{a} intltool-debian{a} ivy{a} java-common{a} junit4{a} libantlr-java{a} libapache-pom-java{a} libarchive-zip-perl{a} libasm-java{a} libasound2-data{a} libasound2t64{a} libatk1.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbrotli1{a} libbsd0{a} libbsf-java{a} libcairo2{a} libcom-err2{a} libcommons-beanutils-java{a} libcommons-cli-java{a} libcommons-collections3-java{a} libcommons-lang-java{a} libcommons-logging-java{a} libcommons-parent-java{a} libcups2t64{a} libdatrie1{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libdivsufsort3{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libelf1t64{a} libexpat1{a} libezmorph-java{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgif7{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0t64{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgoogle-gson-java{a} libgraphite2-3{a} libgsl27{a} libgslcblas0{a} libgssapi-krb5-2{a} libgtk2.0-0t64{a} libgtk2.0-common{a} libhamcrest-java{a} libharfbuzz0b{a} libhawtjni-runtime-java{a} libicu72{a} libjansi-java{a} libjansi-native-java{a} libjansi1-java{a} libjaxen-java{a} libjbig0{a} libjenkins-json-java{a} libjline2-java{a} libjpeg62-turbo{a} libjson-java{a} libjsp-api-java{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} liblerc4{a} libllvm17t64{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libnspr4{a} libnss3{a} liboro-java{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpciaccess0{a} libpcsclite1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqdox-java{a} libreadline8t64{a} libsensors-config{a} libsensors5{a} libservlet-api-java{a} libsharpyuv0{a} libsub-override-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libvulkan1{a} libwebp7{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxerces2-java{a} libxext6{a} libxfixes3{a} libxi6{a} libxinerama1{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxom-java{a} libxpp3-java{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxstream-java{a} libxtst6{a} libxxf86vm1{a} libz3-4{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-data{a} netbase{a} openjdk-17-jre{a} openjdk-17-jre-headless{a} openssl{a} po-debconf{a} pplacer{a} python3{a} python3-dendropy{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-setuptools{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} sepp{a} shared-mime-info{a} tzdata{a} x11-common{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf ant-optional curl dbus fonts-dejavu-extra junit krb5-locales libarchive-cpio-perl libatk-wrapper-java-jni libgail-common libgdk-pixbuf2.0-bin libglib2.0-data libgpars-groovy-java libgtk2.0-bin libjcommander-java liblog4j1.2-java libltdl-dev libmail-sendmail-perl librsvg2-common lynx mesa-vulkan-drivers wget xdg-user-dirs 0 packages upgraded, 208 newly installed, 0 to remove and 0 not upgraded. Need to get 180 MB of archives. After unpacking 729 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-3 [307 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.80.0-9 [1481 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 shared-mime-info amd64 2.4-4 [759 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.3.2-0.4+b1 [108 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.3.2-0.4+b1 [308 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.10+dfsg-3+b3 [138 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 gtk-update-icon-cache amd64 3.24.41-4 [46.6 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 adwaita-icon-theme all 46.0-1 [614 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 java-common all 0.75 [6640 B] Get: 45 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libnspr4 amd64 2:4.35-1.1+b1 [109 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libnss3 amd64 2:3.99-1 [1408 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libpcsclite1 amd64 2.2.0-1 [54.7 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 openjdk-17-jre-headless amd64 17.0.11+9-1 [43.8 MB] Get: 50 http://deb.debian.org/debian unstable/main amd64 default-jre-headless amd64 2:1.17-75 [3068 B] Get: 51 http://deb.debian.org/debian unstable/main amd64 ant all 1.10.14-1 [2162 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libantlr-java all 2.7.7+dfsg-13 [458 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 antlr all 2.7.7+dfsg-13 [8272 B] Get: 54 http://deb.debian.org/debian unstable/main amd64 at-spi2-common all 2.52.0-1 [166 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 67 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libgtk2.0-common all 2.24.33-4 [2661 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libatk1.0-0t64 amd64 2.52.0-1 [50.8 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-1 [144 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-1 [114 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-1 [105 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.0-3+b1 [531 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-13+b2 [112 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-13+b2 [43.3 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.14.10-4+b1 [203 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-13+b2 [47.0 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1~rc2-1 [22.6 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 101 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.7-1.2+b1 [247 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.52.2+ds-1 [218 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.52.2+ds-1 [48.1 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.52.2+ds-1 [35.0 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libxcomposite1 amd64 1:0.4.5-1+b1 [14.9 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libxfixes3 amd64 1:6.0.0-2+b1 [20.3 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libxcursor1 amd64 1:1.2.1-1+b1 [36.2 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libxdamage1 amd64 1:1.1.6-1+b1 [15.5 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.8.1-1 [79.0 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libxinerama1 amd64 2:1.1.4-3+b1 [16.0 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libxrandr2 amd64 2:1.5.4-1 [36.1 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libgtk2.0-0t64 amd64 2.24.33-4 [1816 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libglvnd0 amd64 1.7.0-1+b1 [56.3 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.120-2 [7688 B] Get: 124 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libglapi-mesa amd64 24.0.6-1+b1 [36.6 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libx11-xcb1 amd64 2:1.8.7-1+b1 [232 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libxcb-dri2-0 amd64 1.17.0-1 [106 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libxcb-dri3-0 amd64 1.17.0-1 [106 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libxcb-glx0 amd64 1.17.0-1 [122 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libxcb-present0 amd64 1.17.0-1 [105 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libxcb-randr0 amd64 1.17.0-1 [116 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libxcb-sync1 amd64 1.17.0-1 [108 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libxcb-xfixes0 amd64 1.17.0-1 [109 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libxshmfence1 amd64 1.3-1+b1 [8852 B] Get: 135 http://deb.debian.org/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libvulkan1 amd64 1.3.280.0-1 [123 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libdrm-intel1 amd64 2.4.120-2 [62.7 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libdrm-nouveau2 amd64 2.4.120-2 [19.3 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libdrm-radeon1 amd64 2.4.120-2 [22.2 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20230828-1+b1 [93.5 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-11 [23.7 MB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libsensors-config all 1:3.6.0-9 [14.6 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libsensors5 amd64 1:3.6.0-9 [34.6 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libgl1-mesa-dri amd64 24.0.6-1+b1 [8279 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libglx-mesa0 amd64 24.0.6-1+b1 [151 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libglx0 amd64 1.7.0-1+b1 [35.0 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libgl1 amd64 1.7.0-1+b1 [89.8 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libasound2-data all 1.2.11-1 [20.9 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libasound2t64 amd64 1.2.11-1+b1 [369 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 libgif7 amd64 5.2.2-1 [43.9 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libxtst6 amd64 2:1.2.3-1.1+b1 [25.9 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 openjdk-17-jre amd64 17.0.11+9-1 [185 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 default-jre amd64 2:1.17-75 [1056 B] Get: 158 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 python3-distutils all 3.12.3-1 [131 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20240422 [107 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 ivy all 2.5.2-1 [1295 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libhamcrest-java all 2.2-2 [121 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 junit4 all 4.13.2-4 [349 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libasm-java all 9.7-1 [394 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libbsf-java all 1:2.4.0-8 [76.3 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libapache-pom-java all 29-2 [5276 B] Get: 170 http://deb.debian.org/debian unstable/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libjansi-java all 2.4.1-2 [100 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 libhawtjni-runtime-java all 1.18-1 [36.3 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 libjansi-native-java all 1.8-2 [26.0 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 libjansi1-java all 1.18-3 [66.5 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 libjline2-java all 2.14.6-5 [151 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 libqdox-java all 1.12.1-3 [172 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 libxpp3-java all 1.1.4c-3 [292 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 libxstream-java all 1.4.20-1 [565 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 groovy all 2.4.21-10 [12.8 MB] Get: 183 http://deb.debian.org/debian unstable/main amd64 libdivsufsort3 amd64 2.0.1-6 [45.6 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 hmmer amd64 3.4+dfsg-2 [1062 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 libcommons-beanutils-java all 1.9.4-2 [233 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 libcommons-lang-java all 2.6-10 [273 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 libezmorph-java all 1.0.6-4 [75.9 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.7.1+dfsg-6+b1 [107 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 libgsl27 amd64 2.7.1+dfsg-6+b1 [934 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 libjaxen-java all 1.1.6-4 [214 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 libjenkins-json-java all 2.4-jenkins-3-7 [139 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 liboro-java all 2.0.8a-14 [70.5 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 libxom-java all 1.3.9-1 [174 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 libjson-java all 2.4-3.1 [129 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 liblmdb0 amd64 0.9.31-1+b1 [44.8 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 ncbi-data all 6.1.20170106+dfsg2-2 [3544 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 ncbi-blast+ amd64 2.12.0+ds-4+b1 [12.5 MB] Get: 206 http://deb.debian.org/debian unstable/main amd64 pplacer amd64 1.1~alpha19-6 [2965 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 python3-dendropy all 4.6.1-1 [277 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 sepp amd64 4.5.1+really4.5.1+dfsg-5 [165 kB] Fetched 180 MB in 8s (21.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19699 files and directories currently installed.) 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. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20015 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../5-libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... 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 ... 21007 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 sensible-utils. 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Setting up libjaxen-java (1.1.6-4) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libnspr4:amd64 (2:4.35-1.1+b1) ... Setting up libjansi-java (2.4.1-2) ... Setting up libapache-pom-java (29-2) ... Setting up libavahi-common-data:amd64 (0.8-13+b2) ... Setting up libxpp3-java (1.1.4c-3) ... Setting up libdbus-1-3:amd64 (1.14.10-4+b1) ... Setting up libfribidi0:amd64 (1.0.13-3+b1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.43-5) ... Setting up libxml-commons-resolver1.1-java (1.2-11) ... Setting up autopoint (0.21-14) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libpcsclite1:amd64 (2.2.0-1) ... Setting up libsensors5:amd64 (1:3.6.0-9) ... Setting up libk5crypto3:amd64 (1.20.1-6+b1) ... Setting up libhamcrest-java (2.2-2) ... Setting up libglapi-mesa:amd64 (24.0.6-1+b1) ... Setting up libjsp-api-java (2.3.4-3) ... Setting up libvulkan1:amd64 (1.3.280.0-1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:amd64 (1.3.2-0.4+b1) ... Setting up libgif7:amd64 (5.2.2-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libxshmfence1:amd64 (1.3-1+b1) ... Setting up at-spi2-common (2.52.0-1) ... Setting up libtiff6:amd64 (4.5.1+git230720-4) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libxml-commons-external-java (1.4.01-6) ... Setting up libservlet-api-java (4.0.1-2) ... Setting up libsub-override-perl (0.10-1) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up libgtk2.0-common (2.24.33-4) ... Setting up libkrb5-3:amd64 (1.20.1-6+b1) ... Setting up libxerces2-java (2.12.2-1) ... Setting up libdivsufsort3:amd64 (2.0.1-6) ... Setting up libantlr-java (2.7.7+dfsg-13) ... Setting up openssl (3.2.1-3) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up libdrm-common (2.4.120-2) ... Setting up libezmorph-java (1.0.6-4) ... Setting up readline-common (8.2-4) ... Setting up libhawtjni-runtime-java (1.18-1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... 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 libxstream-java (1.4.20-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up libxcb1:amd64 (1.17.0-1) ... Setting up gettext (0.21-14+b1) ... Setting up libmbedx509-1t64:amd64 (2.28.8-1) ... Setting up libxcb-xfixes0:amd64 (1.17.0-1) ... Setting up libatk1.0-0t64:amd64 (2.52.0-1) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:amd64 (1.17.0-1) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libxcb-glx0:amd64 (1.17.0-1) ... Setting up libedit2:amd64 (3.1-20230828-1+b1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-13+b2) ... Setting up pplacer (1.1~alpha19-6) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libnss3:amd64 (2:3.99-1) ... Setting up libxcb-shm0:amd64 (1.17.0-1) ... Setting up libxom-java (1.3.9-1) ... Setting up libcommons-lang-java (2.6-10) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libxcb-present0:amd64 (1.17.0-1) ... Setting up dh-autoreconf (20) ... Setting up libthai0:amd64 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libllvm17t64:amd64 (1:17.0.6-11) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Setting up libxcb-sync1:amd64 (1.17.0-1) ... Setting up shared-mime-info (2.4-4) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up libxcb-dri2-0:amd64 (1.17.0-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libdrm2:amd64 (2.4.120-2) ... Setting up libjansi-native-java (1.8-2) ... Setting up libmbedtls14t64:amd64 (2.28.8-1) ... Setting up groff-base (1.23.0-4) ... Setting up libxcb-randr0:amd64 (1.17.0-1) ... Setting up hmmer (3.4+dfsg-2) ... Setting up libcommons-beanutils-java (1.9.4-2) ... Setting up libjansi1-java (1.18-3) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2+b1) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-3+b3) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libjline2-java (2.14.6-5) ... Setting up libxcomposite1:amd64 (1:0.4.5-1+b1) ... Setting up libjenkins-json-java (2.4-jenkins-3-7) ... Setting up libavahi-client3:amd64 (0.8-13+b2) ... Setting up libdrm-amdgpu1:amd64 (2.4.120-2) ... Setting up libxcb-dri3-0:amd64 (1.17.0-1) ... Setting up gtk-update-icon-cache (3.24.41-4) ... Setting up libx11-xcb1:amd64 (2:1.8.7-1+b1) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libdrm-nouveau2:amd64 (2.4.120-2) ... Setting up libxdamage1:amd64 (1:1.1.6-1+b1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up libdrm-radeon1:amd64 (2.4.120-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up libpango-1.0-0:amd64 (1.52.2+ds-1) ... Setting up libdrm-intel1:amd64 (2.4.120-2) ... Setting up libgl1-mesa-dri:amd64 (24.0.6-1+b1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.18.0-3+b1) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up adwaita-icon-theme (46.0-1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up libxfixes3:amd64 (1:6.0.0-2+b1) ... Setting up libxinerama1:amd64 (2:1.1.4-3+b1) ... Setting up libxrandr2:amd64 (2:1.5.4-1) ... Setting up openjdk-17-jre-headless:amd64 (17.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libpangoft2-1.0-0:amd64 (1.52.2+ds-1) ... Setting up libcups2t64:amd64 (2.4.7-1.2+b1) ... Setting up libpangocairo-1.0-0:amd64 (1.52.2+ds-1) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up libglx-mesa0:amd64 (24.0.6-1+b1) ... Setting up libxi6:amd64 (2:1.8.1-1) ... Setting up libglx0:amd64 (1.7.0-1+b1) ... Setting up libxtst6:amd64 (2:1.2.3-1.1+b1) ... Setting up libxcursor1:amd64 (1:1.2.1-1+b1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up ncbi-blast+ (2.12.0+ds-4+b1) ... Setting up libgl1:amd64 (1.7.0-1+b1) ... Setting up libgtk2.0-0t64:amd64 (2.24.33-4) ... Setting up python3-lib2to3 (3.12.3-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-dendropy (4.6.1-1) ... Setting up dh-python (6.20240422) ... Processing triggers for libc-bin (2.38-7) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up antlr (2.7.7+dfsg-13) ... Setting up ivy (2.5.2-1) ... Setting up ant (1.10.14-1) ... Setting up junit4 (4.13.2-4) ... Setting up groovy (2.4.21-10) ... update-alternatives: using /usr/share/groovy/bin/groovy to provide /usr/bin/groovy (groovy) in auto mode update-alternatives: using /usr/share/groovy/bin/groovyc to provide /usr/bin/groovyc (groovyc) in auto mode update-alternatives: using /usr/share/groovy/bin/grape to provide /usr/bin/grape (grape) in auto mode update-alternatives: using /usr/share/groovy/bin/startGroovy to provide /usr/bin/startGroovy (startGroovy) in auto mode update-alternatives: using /usr/share/groovy/bin/groovysh to provide /usr/bin/groovysh (groovysh) in auto mode update-alternatives: using /usr/share/groovy/bin/java2groovy to provide /usr/bin/java2groovy (java2groovy) in auto mode update-alternatives: using /usr/share/groovy/bin/groovyConsole to provide /usr/bin/groovyConsole (groovyConsole) in auto mode update-alternatives: using /usr/share/groovy/bin/groovydoc to provide /usr/bin/groovydoc (groovydoc) in auto mode Setting up default-jre-headless (2:1.17-75) ... Setting up openjdk-17-jre:amd64 (17.0.11+9-1) ... Setting up default-jre (2:1.17-75) ... Setting up libjson-java (2.4-3.1) ... Setting up sepp (4.5.1+really4.5.1+dfsg-5) ... 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. Processing triggers for ca-certificates-java (20240118) ... 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/tipp-1.0+dfsg/ && 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 > ../tipp_1.0+dfsg-3_source.changes dpkg-buildpackage: info: source package tipp dpkg-buildpackage: info: source version 1.0+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pierre Gruet dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/tipp-1.0+dfsg' dh_auto_clean I: pybuild base:311: python3.11 setup.py clean 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it rm -f -rf tools/bundled rm -f -rf tools/merge/build rm -f tipp.config find . -name "*.class" -delete find . -name "*.jar" -delete make[1]: Leaving directory '/build/reproducible-path/tipp-1.0+dfsg' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/tipp-1.0+dfsg' dh_auto_configure I: pybuild base:311: python3.11 setup.py config # Building the jar for tipp. cd tools/merge && \ CLASSPATH=/usr/share/java/jenkins-json-lib.jar:/usr/share/java/gson.jar ant -f tipp.xml Buildfile: /build/reproducible-path/tipp-1.0+dfsg/tools/merge/tipp.xml clean: compile: [mkdir] Created dir: /build/reproducible-path/tipp-1.0+dfsg/tools/merge/classes [javac] /build/reproducible-path/tipp-1.0+dfsg/tools/merge/tipp.xml:32: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 23 source files to /build/reproducible-path/tipp-1.0+dfsg/tools/merge/classes [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] /build/reproducible-path/tipp-1.0+dfsg/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/tree/util/Trees.java:32: warning: SunGraphicsEnvironment is internal proprietary API and may be removed in a future release [javac] import sun.java2d.SunGraphicsEnvironment; [javac] ^ [javac] /build/reproducible-path/tipp-1.0+dfsg/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/algos/lca/SchieberVishkinLCA.java:188: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal [javac] _tnode_idx_lookup.put(n, new Integer(i++)); [javac] ^ [javac] /build/reproducible-path/tipp-1.0+dfsg/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/tree/io/NewickReader.java:341: warning: [removal] Double(double) in Double has been deprecated and marked for removal [javac] node.setData(new Double(0)); [javac] ^ [javac] /build/reproducible-path/tipp-1.0+dfsg/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/tree/model/sti/STITree.java:221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal [javac] return _nodes.get(new Integer(id)); [javac] ^ [javac] /build/reproducible-path/tipp-1.0+dfsg/tools/merge/src/phylolab/taxonamic/JSONMerger.java:264: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal [javac] newRecord.set(locEdgeNum, new Integer(newLab)); [javac] ^ [javac] /build/reproducible-path/tipp-1.0+dfsg/tools/merge/src/phylolab/taxonamic/JSONMerger.java:275: warning: [removal] Double(double) in Double has been deprecated and marked for removal [javac] Double newLWR = new Double(prior * precord.getDouble(2)); [javac] ^ [javac] /build/reproducible-path/tipp-1.0+dfsg/tools/merge/src/phylolab/taxonamic/JSONMerger.java:519: warning: [removal] Double(String) in Double has been deprecated and marked for removal [javac] mainEdgeLen.put(edgeLenMatcher.group(2), new Double(edgeLenMatcher.group(1))); [javac] ^ [javac] /build/reproducible-path/tipp-1.0+dfsg/tools/merge/src/phylolab/taxonamic/JSONMerger.java:616: warning: [removal] Double(String) in Double has been deprecated and marked for removal [javac] cutoff = new Double(args[i]); [javac] ^ [javac] /build/reproducible-path/tipp-1.0+dfsg/tools/merge/src/phylolab/taxonamic/JSONMerger.java:656: warning: [removal] Double(String) in Double has been deprecated and marked for removal [javac] threshold = new Double(args[i]); [javac] ^ [javac] /build/reproducible-path/tipp-1.0+dfsg/tools/merge/src/phylolab/taxonamic/PPlacerJSONMerger.java:177: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal [javac] pr.set(locEdgeNum, new Integer(newLab)); [javac] ^ [javac] /build/reproducible-path/tipp-1.0+dfsg/tools/merge/src/phylolab/taxonamic/PPlacerJSONMerger.java:269: warning: [removal] Double(String) in Double has been deprecated and marked for removal [javac] Double len = new Double(matcher.group(1)); [javac] ^ [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 12 warnings jar: [jar] Building jar: /build/reproducible-path/tipp-1.0+dfsg/tools/merge/tippJsonMerger.jar BUILD SUCCESSFUL Total time: 5 seconds # Creating the config files. BLAST="/usr/bin/blastn" python3 setup.py tipp Creating main TIPP config file at /build/reproducible-path/tipp-1.0+dfsg/.tipp/tipp.config and tools at /build/reproducible-path/tipp-1.0+dfsg/.tipp Warning! REFERENCE variable is not defined. If you plan to run TIPP for abundance profiling, then have REFERENCE pointed to Reference directory. You can also change your config to point to the Reference directory by including the following line in your config: [reference] path=/location/of/reference_directory/ make[1]: Leaving directory '/build/reproducible-path/tipp-1.0+dfsg' dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/tipp-1.0+dfsg/.pybuild/cpython3_3.11/build; python3.11 -m unittest discover -v ---------------------------------------------------------------------- Ran 0 tests in 0.000s OK create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/tipp-1.0+dfsg' dh_auto_install I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/tipp-1.0+dfsg/debian/tipp /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() # Deleting upstream configuration file, which we are not packaging. rm -f debian/tipp/usr/home.path make[1]: Leaving directory '/build/reproducible-path/tipp-1.0+dfsg' dh_install -O--buildsystem=pybuild dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/tipp-1.0+dfsg' dh_installman --language=C make[1]: Leaving directory '/build/reproducible-path/tipp-1.0+dfsg' dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: Depends field of package tipp: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'tipp' in '../tipp_1.0+dfsg-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../tipp_1.0+dfsg-3_amd64.buildinfo dpkg-genchanges --build=binary -O../tipp_1.0+dfsg-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3789512 and its subdirectories I: Current time: Sat May 4 20:01:30 -12 2024 I: pbuilder-time-stamp: 1714896090 Sun May 5 08:01:31 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Sun May 5 08:01:31 UTC 2024 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Sun May 5 08:02:53 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Sun May 5 08:02:54 UTC 2024 I: tipp_1.0+dfsg-3_amd64.changes: Format: 1.8 Date: Wed, 16 Nov 2022 22:44:41 +0100 Source: tipp Binary: tipp Architecture: amd64 Version: 1.0+dfsg-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Pierre Gruet Description: tipp - tool for Taxonomic Identification and Phylogenetic Profiling Changes: tipp (1.0+dfsg-3) unstable; urgency=medium . * Updating d/watch after a change in the Github layout * Raising Standards version to 4.6.1 (no change) * Updating Lintian overrides after a change in their syntax Checksums-Sha1: c7ba8aac3197deb338506a84cb0189125f3dbea4 10506 tipp_1.0+dfsg-3_amd64.buildinfo 4bde96e3b302fe98ed8d848f59bc78ca44ff4d7d 130528 tipp_1.0+dfsg-3_amd64.deb Checksums-Sha256: 9d5542ad9b99cc4d172146ba27dd9b1eeadf136bc9348b59920257dcd8fd564b 10506 tipp_1.0+dfsg-3_amd64.buildinfo 0312fd316376a6ace009588862b67ac734ab2798859e22065c972e3954c0ef64 130528 tipp_1.0+dfsg-3_amd64.deb Files: de91f8beed5aa0d88e4d3f34e30c60ea 10506 science optional tipp_1.0+dfsg-3_amd64.buildinfo 20f626b841c0bc6411631bd40e323863 130528 science optional tipp_1.0+dfsg-3_amd64.deb Sun May 5 08:02:56 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_21-5619.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.57wAsRz2/tipp_1.0+dfsg-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.57wAsRz2/tipp_1.0+dfsg-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.57wAsRz2/tipp_1.0+dfsg-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.57wAsRz2/b1/tipp_1.0+dfsg-3_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.57wAsRz2/b2/tipp_1.0+dfsg-3_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.410s) 0.409s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.019s) 0.019s 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: 804ms CPU time consumed: 796ms Sun May 5 08:02:57 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Sun May 5 08:02:57 UTC 2024 I: tipp from unstable built successfully and reproducibly on amd64. Sun May 5 08:02:58 UTC 2024 I: Submitting .buildinfo files to external archives: Sun May 5 08:02:58 UTC 2024 I: Submitting 12K b1/tipp_1.0+dfsg-3_amd64.buildinfo.asc Sun May 5 08:02:59 UTC 2024 I: Submitting 12K b2/tipp_1.0+dfsg-3_amd64.buildinfo.asc Sun May 5 08:03:00 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun May 5 08:03:00 UTC 2024 I: Done submitting .buildinfo files. Sun May 5 08:03:00 UTC 2024 I: Removing signed tipp_1.0+dfsg-3_amd64.buildinfo.asc files: removed './b1/tipp_1.0+dfsg-3_amd64.buildinfo.asc' removed './b2/tipp_1.0+dfsg-3_amd64.buildinfo.asc'