Wed May 1 06:47:40 UTC 2024 I: starting to build sepp/unstable/amd64 on jenkins on '2024-05-01 06:47' Wed May 1 06:47:40 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_5/5592/console.log Wed May 1 06:47:40 UTC 2024 I: Downloading source for unstable/sepp=4.5.1+really4.5.1+dfsg-5 --2024-05-01 06:47:41-- http://deb.debian.org/debian/pool/main/s/sepp/sepp_4.5.1%2breally4.5.1%2bdfsg-5.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2213 (2.2K) [text/prs.lines.tag] Saving to: ‘sepp_4.5.1+really4.5.1+dfsg-5.dsc’ 0K .. 100% 317M=0s 2024-05-01 06:47:41 (317 MB/s) - ‘sepp_4.5.1+really4.5.1+dfsg-5.dsc’ saved [2213/2213] Wed May 1 06:47:41 UTC 2024 I: sepp_4.5.1+really4.5.1+dfsg-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: sepp Binary: sepp Architecture: any Version: 4.5.1+really4.5.1+dfsg-5 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Pierre Gruet Homepage: https://github.com/smirarab/sepp/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/sepp Vcs-Git: https://salsa.debian.org/med-team/sepp.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-python, python3, python3-setuptools, python3-dendropy, ant, libjenkins-json-java, libgoogle-gson-java, ncbi-blast+ , pplacer , hmmer Package-List: sepp deb science optional arch=any Checksums-Sha1: e096dbf8273f11f802ee7ff6bcabf7ea218c8aa4 4302024 sepp_4.5.1+really4.5.1+dfsg.orig.tar.xz 188247eca96a2168212ea2e63464152644fe03bf 13336 sepp_4.5.1+really4.5.1+dfsg-5.debian.tar.xz Checksums-Sha256: 49c7a823633bcb0c70dcb944c0b8e7e32abf946cdd8c2fa7c2ca239a61f4acbe 4302024 sepp_4.5.1+really4.5.1+dfsg.orig.tar.xz 99b138510fcdf28bb82d20fb07d34f6120db5d3925d4cc3769e0db36ae5f5f53 13336 sepp_4.5.1+really4.5.1+dfsg-5.debian.tar.xz Files: 1ab4c63b1a4352e980d01823e4303526 4302024 sepp_4.5.1+really4.5.1+dfsg.orig.tar.xz 78749b505bbd5252e6ef4aeddd7f5ebd 13336 sepp_4.5.1+really4.5.1+dfsg-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEM8soQxPpC9J9y0UjYAMWptwndHYFAmPRGV0ACgkQYAMWptwn dHY9uBAAid0Xl5BOW11JdW7lG4iPf7It57ly2ql2gNU8KZhnFMHjINEyqvpc48kp c5lGRUuHOME35cQavKNpBjGG0wOcSkfNI98nLSB7iCACdQBt1wTk3DWDBq0OqBz8 EHJjfNq88IDrZDOO33beZPMhoC47/v6FAnBLi9xcWBlKnGUq29wFOox3Kua4pZOp 3yskh/LxpQuWHaPdAtz97I3GKT4II1THgl3lDY2wOTs7OzmwMrAYNKeORQR/UyWR vnvXz7n3cyWMJLPZmFUVHX0h5rj3jyXZK4TWUeHG+uWNPn3kV4mVmmIVp3IiuiXy DANr0tSLaxLBJZEpI/0ak0MLH20CMu24cH4hLBR0Jytv0blpcLTsrYHp2QhiTkQW TkFyTM2j3TbijZESD80VILW/qjW3pftHbCQBm0RUiQxykXZjro8P4LVJnVMwMNEt FDKtYEGJA9IcNu0kIJy7sTUDbnkpkP/6lgsqutQfP6FYMHjvuOziP0SlohZKo7XW JfkVfwVYVc+GfQUv/vDbHOptL2ZbxafOYzy/Ml6frZzspG9dF2rGGjZcxDmnJ3+9 KzpuOlJeKmDOLZSEXXSr/+cWyEe3uwOBTxm2k4pTGtaunlvDFwFq0+EB4dXQZ8gr fKQwhQ1PCFqRM9bXuoRWBio1wQMjm/wwE4oMBfFegsebcCZqzUQ= =wwcW -----END PGP SIGNATURE----- Wed May 1 06:47:41 UTC 2024 I: Checking whether the package is not for us Wed May 1 06:47:41 UTC 2024 I: Starting 1st build on remote node ionos11-amd64.debian.net. Wed May 1 06:47:41 UTC 2024 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Wed May 1 06:50:51 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Apr 30 18:47:43 -12 2024 I: pbuilder-time-stamp: 1714546063 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 [sepp_4.5.1+really4.5.1+dfsg-5.dsc] I: copying [./sepp_4.5.1+really4.5.1+dfsg.orig.tar.xz] I: copying [./sepp_4.5.1+really4.5.1+dfsg-5.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Jan 25 11:58:21 2023 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./sepp_4.5.1+really4.5.1+dfsg-5.dsc: no acceptable signature found dpkg-source: info: extracting sepp in sepp-4.5.1+really4.5.1+dfsg dpkg-source: info: unpacking sepp_4.5.1+really4.5.1+dfsg.orig.tar.xz dpkg-source: info: unpacking sepp_4.5.1+really4.5.1+dfsg-5.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 deactivating_log_test.patch dpkg-source: info: applying using_python3_interpreter.patch dpkg-source: info: applying hmmbuild_path_for_testUPP.patch dpkg-source: info: applying py310_collections_import.patch dpkg-source: info: applying open-U-obsolete.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3188862/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='b22f2299a48045229c3b82d3e55adebc' 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='3188862' 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.phq64Ny9/pbuilderrc_rKQ8 --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.phq64Ny9/b1 --logfile b1/build.log sepp_4.5.1+really4.5.1+dfsg-5.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 Apr 27 07:43 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3188862/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+, pplacer, hmmer dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19694 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 pplacer; however: Package pplacer is not installed. pbuilder-satisfydepends-dummy depends on hmmer; however: Package hmmer 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: ant{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} debhelper{a} default-jre-headless{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} hmmer{a} intltool-debian{a} java-common{a} libapache-pom-java{a} libarchive-zip-perl{a} libcommons-beanutils-java{a} libcommons-collections3-java{a} libcommons-lang-java{a} libcommons-logging-java{a} libcommons-parent-java{a} libdebhelper-perl{a} libdivsufsort3{a} libelf1t64{a} libexpat1{a} libezmorph-java{a} libfile-stripnondeterminism-perl{a} libgoogle-gson-java{a} libgsl27{a} libgslcblas0{a} libicu72{a} libjenkins-json-java{a} libjpeg62-turbo{a} liblcms2-2{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libnspr4{a} libnss3{a} libpcsclite1{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-data{a} netbase{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} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ant-optional curl groovy junit libarchive-cpio-perl libasound2t64 libcups2t64 libfontconfig1 libfreetype6 libharfbuzz0b liblog4j1.2-java libltdl-dev libmail-sendmail-perl liboro-java liboss4-salsa-asound2 libxom-java lynx wget 0 packages upgraded, 81 newly installed, 0 to remove and 0 not upgraded. Need to get 98.9 MB of archives. After unpacking 420 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-3 [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 ca-certificates-java all 20240118 [11.6 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 java-common all 0.75 [6640 B] Get: 28 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libnspr4 amd64 2:4.35-1.1+b1 [109 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libnss3 amd64 2:3.99-1 [1408 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libpcsclite1 amd64 2.0.3-1 [51.0 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 openjdk-17-jre-headless amd64 17.0.11+9-1 [43.8 MB] Get: 34 http://deb.debian.org/debian unstable/main amd64 default-jre-headless amd64 2:1.17-75 [3068 B] Get: 35 http://deb.debian.org/debian unstable/main amd64 ant all 1.10.14-1 [2162 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 48 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 python3-distutils all 3.12.3-1 [131 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20240422 [107 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libdivsufsort3 amd64 2.0.1-6 [45.6 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 hmmer amd64 3.4+dfsg-2 [1062 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libapache-pom-java all 29-2 [5276 B] Get: 64 http://deb.debian.org/debian unstable/main amd64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libcommons-beanutils-java all 1.9.4-2 [233 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libcommons-lang-java all 2.6-10 [273 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libezmorph-java all 1.0.6-4 [75.9 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.7.1+dfsg-6+b1 [107 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libgsl27 amd64 2.7.1+dfsg-6+b1 [934 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libjenkins-json-java all 2.4-jenkins-3-7 [139 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 liblmdb0 amd64 0.9.31-1+b1 [44.8 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 ncbi-data all 6.1.20170106+dfsg2-2 [3544 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 ncbi-blast+ amd64 2.12.0+ds-4+b1 [12.5 MB] Get: 80 http://deb.debian.org/debian unstable/main amd64 pplacer amd64 1.1~alpha19-6 [2965 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 python3-dendropy all 4.6.1-1 [277 kB] Fetched 98.9 MB in 6s (17.8 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 ... 19694 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. 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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. 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Setting up gettext-base (0.21-14+b1) ... Setting up libgsl27:amd64 (2.7.1+dfsg-6+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' Local time is now: Wed May 1 06:49:47 UTC 2024. Universal Time is now: Wed May 1 06:49:47 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libcommons-collections3-java (3.2.2-3) ... Setting up autotools-dev (20220109.1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3) ... Setting up libnspr4:amd64 (2:4.35-1.1+b1) ... Setting up libapache-pom-java (29-2) ... Setting up autopoint (0.21-14) ... Setting up libpcsclite1:amd64 (2.0.3-1) ... Setting up autoconf (2.71-3) ... 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 libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up libdivsufsort3:amd64 (2.0.1-6) ... Setting up openssl (3.2.1-3) ... Setting up libezmorph-java (1.0.6-4) ... Setting up readline-common (8.2-4) ... 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 gettext (0.21-14+b1) ... Setting up libmbedx509-1t64:amd64 (2.28.8-1) ... Setting up libtool (2.4.7-7) ... Setting up libcommons-parent-java (56-1) ... 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 libcommons-lang-java (2.6-10) ... 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 libreadline8t64:amd64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libmbedtls14t64:amd64 (2.28.8-1) ... Setting up groff-base (1.23.0-4) ... Setting up hmmer (3.4+dfsg-2) ... Setting up libcommons-beanutils-java (1.9.4-2) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libjenkins-json-java (2.4-jenkins-3-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib: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 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 libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... 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 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 (2.37-19) ... 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 default-jre-headless (2:1.17-75) ... Setting up ant (1.10.14-1) ... 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. 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/sepp-4.5.1+really4.5.1+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 > ../sepp_4.5.1+really4.5.1+dfsg-5_source.changes dpkg-buildpackage: info: source package sepp dpkg-buildpackage: info: source version 4.5.1+really4.5.1+dfsg-5 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/sepp-4.5.1+really4.5.1+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 sepp.config upp.config find . -name "*.class" -delete find . -name "*.jar" -delete rm -f home.path sepp.egg-info/PKG-INFO sepp.egg-info/SOURCES.txt sepp.egg-info/dependency_links.txt sepp.egg-info/requires.txt sepp.egg-info/top_level.txt make[1]: Leaving directory '/build/reproducible-path/sepp-4.5.1+really4.5.1+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/sepp-4.5.1+really4.5.1+dfsg' mkdir -p tools/bundled/Linux mkdir -p tools/merge/lib # Building the jar for sepp. cd tools/merge && \ CLASSPATH=/usr/share/java/jenkins-json-lib.jar:/usr/share/java/gson.jar ant Buildfile: /build/reproducible-path/sepp-4.5.1+really4.5.1+dfsg/tools/merge/build.xml clean: compile: [mkdir] Created dir: /build/reproducible-path/sepp-4.5.1+really4.5.1+dfsg/tools/merge/classes [javac] /build/reproducible-path/sepp-4.5.1+really4.5.1+dfsg/tools/merge/build.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/sepp-4.5.1+really4.5.1+dfsg/tools/merge/classes [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] /build/reproducible-path/sepp-4.5.1+really4.5.1+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/sepp-4.5.1+really4.5.1+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/sepp-4.5.1+really4.5.1+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/sepp-4.5.1+really4.5.1+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/sepp-4.5.1+really4.5.1+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/sepp-4.5.1+really4.5.1+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/sepp-4.5.1+really4.5.1+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/sepp-4.5.1+really4.5.1+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/sepp-4.5.1+really4.5.1+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/sepp-4.5.1+really4.5.1+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/sepp-4.5.1+really4.5.1+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/sepp-4.5.1+really4.5.1+dfsg/tools/merge/seppJsonMerger.jar BUILD SUCCESSFUL Total time: 6 seconds dh_auto_configure I: pybuild base:311: python3.11 setup.py config Creating main sepp config file at /build/reproducible-path/sepp-4.5.1+really4.5.1+dfsg/.pybuild/cpython3_3.11/.sepp/main.config and tools at /build/reproducible-path/sepp-4.5.1+really4.5.1+dfsg/.pybuild/cpython3_3.11/.sepp # dh_auto_configure only calls the config for sepp, we need it for upp as well. pybuild --configure --configure-args "upp" I: pybuild base:311: python3.11 setup.py config upp Creating main sepp config file at /build/reproducible-path/sepp-4.5.1+really4.5.1+dfsg/.pybuild/cpython3_3.11/.sepp/main.config and tools at /build/reproducible-path/sepp-4.5.1+really4.5.1+dfsg/.pybuild/cpython3_3.11/.sepp Creating main UPP config file at /build/reproducible-path/sepp-4.5.1+really4.5.1+dfsg/.pybuild/cpython3_3.11/.sepp/upp.config and tools at /build/reproducible-path/sepp-4.5.1+really4.5.1+dfsg/.pybuild/cpython3_3.11/.sepp make[1]: Leaving directory '/build/reproducible-path/sepp-4.5.1+really4.5.1+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/sepp-4.5.1+really4.5.1+dfsg' dh_auto_build I: pybuild base:311: /usr/bin/python3 setup.py build # Preparing a conffile with Debian paths for sepp. sed 's,path=.*\(pplacer\)$,path=/usr/bin/\1,' `find . -name main.config` | \ sed 's,path=.*\(hmm[a-z]*\)$,path=/usr/bin/\1,' | \ sed 's,path=.*\(seppJsonMerger.jar\)$,path=/usr/share/sepp/\1,' > sepp.config # Preparing a conffile with Debian paths for upp. sed 's,path=.*\(pplacer\)$,path=/usr/bin/\1,' `find . -name upp.config` | \ sed 's,path=.*\(hmm[a-z]*\)$,path=/usr/bin/\1,' | \ sed 's,path=.*\(seppJsonMerger.jar\)$,path=/usr/share/sepp/\1,' > upp.config make[1]: Leaving directory '/build/reproducible-path/sepp-4.5.1+really4.5.1+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/sepp-4.5.1+really4.5.1+dfsg' ORIGIN_FOLDER=`pwd` && \ TEST_FOLDER=`mktemp -d` && \ cp -r test/ $TEST_FOLDER && \ cd $TEST_FOLDER && \ mkdir sepp/ && \ for F in $(ls $ORIGIN_FOLDER/sepp/*.py); do \ sed "s,/etc/sepp,$TEST_FOLDER," $F > sepp/${F##*/}; \ done && \ for F in $(ls $ORIGIN_FOLDER/*.config); do \ sed "s,/usr/share/sepp,$ORIGIN_FOLDER/tools/merge," $F > ${F##*/}; \ done && \ cd test/unittest/ && \ sed "s,\".*\.jar\",\"$ORIGIN_FOLDER/tools/merge/seppJsonMerger.jar\"," testMerge.py > testMergeCp.py && \ mv testMergeCp.py testMerge.py && \ PYTHONPATH=$PYTHONPATH:../../ python3 -m unittest discover -v testAlignmentReadFasta (testAlignment.Test.testAlignmentReadFasta) ... /tmp/tmp.dmpGTwkJ4k/test/unittest/testAlignment.py:38: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.dmpGTwkJ4k/test/unittest/data/mock/pyrg/sate.fasta' mode='r' encoding='UTF-8'> alg.read_filepath(get_data_path("mock/pyrg/sate.fasta")) ResourceWarning: Enable tracemalloc to get the object allocation traceback ok testExtendedAlignment (testAlignment.Test.testExtendedAlignment) ... /tmp/tmp.dmpGTwkJ4k/test/unittest/testAlignment.py:107: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.dmpGTwkJ4k/test/unittest/data/simulated/test.fasta' mode='r' encoding='UTF-8'> alg.read_filepath(get_data_path("simulated/test.fasta")) ResourceWarning: Enable tracemalloc to get the object allocation traceback /tmp/tmp.dmpGTwkJ4k/test/unittest/testAlignment.py:112: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.dmpGTwkJ4k/test/unittest/data/simulated/test.fas' mode='r' encoding='UTF-8'> frg.read_filepath(get_data_path("simulated/test.fas")) ResourceWarning: Enable tracemalloc to get the object allocation traceback /tmp/tmp.dmpGTwkJ4k/test/unittest/testAlignment.py:130: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpbo42_u32' mode='r' encoding='UTF-8'> tmp = MutableAlignment().read_filepath(self.fp_dummy1) ResourceWarning: Enable tracemalloc to get the object allocation traceback /tmp/tmp.dmpGTwkJ4k/test/unittest/testAlignment.py:133: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpx6vb4r68' mode='r' encoding='UTF-8'> tmp = MutableAlignment().read_filepath(self.fp_dummy2) ResourceWarning: Enable tracemalloc to get the object allocation traceback /tmp/tmp.dmpGTwkJ4k/sepp/alignment.py:555: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpbo42_u32' mode='r' encoding='UTF-8'> self.read_filepath(base_alignment, "FASTA") ResourceWarning: Enable tracemalloc to get the object allocation traceback /tmp/tmp.dmpGTwkJ4k/sepp/alignment.py:566: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.dmpGTwkJ4k/test/unittest/data/tmp/cp1.extended.sto' mode='r' encoding='UTF-8'> ext.read_extended_alignment(path) ResourceWarning: Enable tracemalloc to get the object allocation traceback [18:50:45] alignment.py (line 567): INFO: Merging extension sto file (/tmp/tmp.dmpGTwkJ4k/test/unittest/data/tmp/cp1.extended.sto) into base alignment (/tmp/tmpbo42_u32). /tmp/tmp.dmpGTwkJ4k/sepp/alignment.py:555: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpx6vb4r68' mode='r' encoding='UTF-8'> self.read_filepath(base_alignment, "FASTA") ResourceWarning: Enable tracemalloc to get the object allocation traceback /tmp/tmp.dmpGTwkJ4k/sepp/alignment.py:566: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.dmpGTwkJ4k/test/unittest/data/tmp/cp2.extended.sto' mode='r' encoding='UTF-8'> ext.read_extended_alignment(path) ResourceWarning: Enable tracemalloc to get the object allocation traceback [18:50:45] alignment.py (line 567): INFO: Merging extension sto file (/tmp/tmp.dmpGTwkJ4k/test/unittest/data/tmp/cp2.extended.sto) into base alignment (/tmp/tmpx6vb4r68). ok testReadOnlySubAlignment (testAlignment.Test.testReadOnlySubAlignment) ... /tmp/tmp.dmpGTwkJ4k/test/unittest/testAlignment.py:46: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.dmpGTwkJ4k/test/unittest/data/mock/pyrg/sate.fasta' mode='r' encoding='UTF-8'> alg.read_filepath(get_data_path("mock/pyrg/sate.fasta")) ResourceWarning: Enable tracemalloc to get the object allocation traceback ok testCheckPoint (unittest.loader._FailedTest.testCheckPoint) ... ERROR testConfigFile (testConfig.Test.testConfigFile) ... /usr/lib/python3.11/argparse.py:971: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.dmpGTwkJ4k/test/unittest/data/configs/test.config' mode='r' encoding='UTF-8'> setattr(namespace, self.dest, values) ResourceWarning: Enable tracemalloc to get the object allocation traceback [18:50:46] config.py (line 371): INFO: Seed number: 297834 ok testConfigFileMissingFile (testConfig.Test.testConfigFileMissingFile) ... /tmp/tmp.dmpGTwkJ4k/test/unittest/testConfig.py:66: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.dmpGTwkJ4k/test/unittest/data/configs/test.config' mode='r' encoding='UTF-8'> config._options_singelton = None ResourceWarning: Enable tracemalloc to get the object allocation traceback /usr/lib/python3.11/argparse.py:971: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.dmpGTwkJ4k/test/unittest/data/configs/test2.config' mode='r' encoding='UTF-8'> setattr(namespace, self.dest, values) ResourceWarning: Enable tracemalloc to get the object allocation traceback /usr/lib/python3.11/argparse.py:971: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.dmpGTwkJ4k/test/unittest/data/simulated/test.fas' mode='r' encoding='UTF-8'> setattr(namespace, self.dest, values) ResourceWarning: Enable tracemalloc to get the object allocation traceback /usr/lib/python3.11/argparse.py:971: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.dmpGTwkJ4k/test/unittest/data/simulated/test.small.fas' mode='r' encoding='UTF-8'> setattr(namespace, self.dest, values) ResourceWarning: Enable tracemalloc to get the object allocation traceback [18:50:46] config.py (line 371): INFO: Seed number: 297834 ok testCpuCount (testConfig.Test.testCpuCount) ... /tmp/tmp.dmpGTwkJ4k/test/unittest/testConfig.py:120: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.dmpGTwkJ4k/test/unittest/data/configs/test2.config' mode='r' encoding='UTF-8'> config._options_singelton = None ResourceWarning: Enable tracemalloc to get the object allocation traceback /tmp/tmp.dmpGTwkJ4k/test/unittest/testConfig.py:120: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.dmpGTwkJ4k/test/unittest/data/simulated/test.small.fas' mode='r' encoding='UTF-8'> config._options_singelton = None ResourceWarning: Enable tracemalloc to get the object allocation traceback /tmp/tmp.dmpGTwkJ4k/test/unittest/testConfig.py:120: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.dmpGTwkJ4k/test/unittest/data/simulated/test.fas' mode='r' encoding='UTF-8'> config._options_singelton = None ResourceWarning: Enable tracemalloc to get the object allocation traceback [18:50:47] config.py (line 371): INFO: Seed number: 297834 [18:50:47] config.py (line 371): INFO: Seed number: 297834 ok testLog (testConfig.Test.testLog) ... ERROR testMainConfigFile (testConfig.Test.testMainConfigFile) ... [18:50:47] config.py (line 337): WARNING: Main configuration file was not found at: /tmp/tmpfdijotqm Proceeding without the main configuration... [18:50:47] config.py (line 371): INFO: Seed number: 297834 ok testExternalJobs (unittest.loader._FailedTest.testExternalJobs) ... ERROR testMerge (unittest.loader._FailedTest.testMerge) ... ERROR testMidpoint (unittest.loader._FailedTest.testMidpoint) ... ERROR testSepp (unittest.loader._FailedTest.testSepp) ... ERROR testUPP (unittest.loader._FailedTest.testUPP) ... ERROR ====================================================================== ERROR: testCheckPoint (unittest.loader._FailedTest.testCheckPoint) ---------------------------------------------------------------------- ImportError: Failed to import test module: testCheckPoint Traceback (most recent call last): File "/usr/lib/python3.11/unittest/loader.py", line 419, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name __import__(name) File "/tmp/tmp.dmpGTwkJ4k/test/unittest/testCheckPoint.py", line 15, in from sepp.exhaustive import ExhaustiveAlgorithm File "/tmp/tmp.dmpGTwkJ4k/sepp/exhaustive.py", line 6, in from sepp.algorithm import AbstractAlgorithm File "/tmp/tmp.dmpGTwkJ4k/sepp/algorithm.py", line 12, in from sepp.tree import PhylogeneticTree File "/tmp/tmp.dmpGTwkJ4k/sepp/tree.py", line 25, in from dendropy.datamodel.treemodel import _convert_node_to_root_polytomy as \ ImportError: cannot import name '_convert_node_to_root_polytomy' from 'dendropy.datamodel.treemodel' (/usr/lib/python3/dist-packages/dendropy/datamodel/treemodel/__init__.py) ====================================================================== ERROR: testLog (testConfig.Test.testLog) ---------------------------------------------------------------------- Traceback (most recent call last): File "/tmp/tmp.dmpGTwkJ4k/test/unittest/testConfig.py", line 141, in testLog import sepp.jobs File "/tmp/tmp.dmpGTwkJ4k/sepp/jobs.py", line 16, in from sepp.tree import PhylogeneticTree File "/tmp/tmp.dmpGTwkJ4k/sepp/tree.py", line 25, in from dendropy.datamodel.treemodel import _convert_node_to_root_polytomy as \ ImportError: cannot import name '_convert_node_to_root_polytomy' from 'dendropy.datamodel.treemodel' (/usr/lib/python3/dist-packages/dendropy/datamodel/treemodel/__init__.py) ====================================================================== ERROR: testExternalJobs (unittest.loader._FailedTest.testExternalJobs) ---------------------------------------------------------------------- ImportError: Failed to import test module: testExternalJobs Traceback (most recent call last): File "/usr/lib/python3.11/unittest/loader.py", line 419, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name __import__(name) File "/tmp/tmp.dmpGTwkJ4k/test/unittest/testExternalJobs.py", line 7, in from sepp.jobs import ExternalSeppJob File "/tmp/tmp.dmpGTwkJ4k/sepp/jobs.py", line 16, in from sepp.tree import PhylogeneticTree File "/tmp/tmp.dmpGTwkJ4k/sepp/tree.py", line 25, in from dendropy.datamodel.treemodel import _convert_node_to_root_polytomy as \ ImportError: cannot import name '_convert_node_to_root_polytomy' from 'dendropy.datamodel.treemodel' (/usr/lib/python3/dist-packages/dendropy/datamodel/treemodel/__init__.py) ====================================================================== ERROR: testMerge (unittest.loader._FailedTest.testMerge) ---------------------------------------------------------------------- ImportError: Failed to import test module: testMerge Traceback (most recent call last): File "/usr/lib/python3.11/unittest/loader.py", line 419, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name __import__(name) File "/tmp/tmp.dmpGTwkJ4k/test/unittest/testMerge.py", line 7, in from sepp.jobs import MergeJsonJob File "/tmp/tmp.dmpGTwkJ4k/sepp/jobs.py", line 16, in from sepp.tree import PhylogeneticTree File "/tmp/tmp.dmpGTwkJ4k/sepp/tree.py", line 25, in from dendropy.datamodel.treemodel import _convert_node_to_root_polytomy as \ ImportError: cannot import name '_convert_node_to_root_polytomy' from 'dendropy.datamodel.treemodel' (/usr/lib/python3/dist-packages/dendropy/datamodel/treemodel/__init__.py) ====================================================================== ERROR: testMidpoint (unittest.loader._FailedTest.testMidpoint) ---------------------------------------------------------------------- ImportError: Failed to import test module: testMidpoint Traceback (most recent call last): File "/usr/lib/python3.11/unittest/loader.py", line 419, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name __import__(name) File "/tmp/tmp.dmpGTwkJ4k/test/unittest/testMidpoint.py", line 16, in from sepp.exhaustive import ExhaustiveAlgorithm File "/tmp/tmp.dmpGTwkJ4k/sepp/exhaustive.py", line 6, in from sepp.algorithm import AbstractAlgorithm File "/tmp/tmp.dmpGTwkJ4k/sepp/algorithm.py", line 12, in from sepp.tree import PhylogeneticTree File "/tmp/tmp.dmpGTwkJ4k/sepp/tree.py", line 25, in from dendropy.datamodel.treemodel import _convert_node_to_root_polytomy as \ ImportError: cannot import name '_convert_node_to_root_polytomy' from 'dendropy.datamodel.treemodel' (/usr/lib/python3/dist-packages/dendropy/datamodel/treemodel/__init__.py) ====================================================================== ERROR: testSepp (unittest.loader._FailedTest.testSepp) ---------------------------------------------------------------------- ImportError: Failed to import test module: testSepp Traceback (most recent call last): File "/usr/lib/python3.11/unittest/loader.py", line 419, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name __import__(name) File "/tmp/tmp.dmpGTwkJ4k/test/unittest/testSepp.py", line 15, in from sepp.exhaustive import ExhaustiveAlgorithm File "/tmp/tmp.dmpGTwkJ4k/sepp/exhaustive.py", line 6, in from sepp.algorithm import AbstractAlgorithm File "/tmp/tmp.dmpGTwkJ4k/sepp/algorithm.py", line 12, in from sepp.tree import PhylogeneticTree File "/tmp/tmp.dmpGTwkJ4k/sepp/tree.py", line 25, in from dendropy.datamodel.treemodel import _convert_node_to_root_polytomy as \ ImportError: cannot import name '_convert_node_to_root_polytomy' from 'dendropy.datamodel.treemodel' (/usr/lib/python3/dist-packages/dendropy/datamodel/treemodel/__init__.py) ====================================================================== ERROR: testUPP (unittest.loader._FailedTest.testUPP) ---------------------------------------------------------------------- ImportError: Failed to import test module: testUPP Traceback (most recent call last): File "/usr/lib/python3.11/unittest/loader.py", line 419, in _find_test_path module = self._get_module_from_name(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name __import__(name) File "/tmp/tmp.dmpGTwkJ4k/test/unittest/testUPP.py", line 11, in from sepp.exhaustive_upp import UPPExhaustiveAlgorithm File "/tmp/tmp.dmpGTwkJ4k/sepp/exhaustive_upp.py", line 13, in from sepp.exhaustive import JoinAlignJobs, ExhaustiveAlgorithm File "/tmp/tmp.dmpGTwkJ4k/sepp/exhaustive.py", line 6, in from sepp.algorithm import AbstractAlgorithm File "/tmp/tmp.dmpGTwkJ4k/sepp/algorithm.py", line 12, in from sepp.tree import PhylogeneticTree File "/tmp/tmp.dmpGTwkJ4k/sepp/tree.py", line 25, in from dendropy.datamodel.treemodel import _convert_node_to_root_polytomy as \ ImportError: cannot import name '_convert_node_to_root_polytomy' from 'dendropy.datamodel.treemodel' (/usr/lib/python3/dist-packages/dendropy/datamodel/treemodel/__init__.py) ---------------------------------------------------------------------- Ran 14 tests in 2.977s FAILED (errors=7) /usr/lib/python3.11/multiprocessing/pool.py:268: ResourceWarning: unclosed running multiprocessing pool sys:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.dmpGTwkJ4k/test/unittest/data/configs/test2.config' mode='r' encoding='UTF-8'> make[1]: *** [debian/rules:61: override_dh_auto_test] Error 1 make[1]: Leaving directory '/build/reproducible-path/sepp-4.5.1+really4.5.1+dfsg' make: *** [debian/rules:8: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package 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/3188862 and its subdirectories Wed May 1 06:50:52 UTC 2024 W: No second build log, what happened?