Sun Apr 16 05:28:58 UTC 2023 I: starting to build gubbins/bookworm/amd64 on jenkins on '2023-04-16 05:28' Sun Apr 16 05:28:58 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_14/18884/console.log Sun Apr 16 05:28:58 UTC 2023 I: Downloading source for bookworm/gubbins=2.4.1-5 --2023-04-16 05:28:59-- http://cdn-fastly.deb.debian.org/debian/pool/main/g/gubbins/gubbins_2.4.1-5.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2269 (2.2K) [text/prs.lines.tag] Saving to: ‘gubbins_2.4.1-5.dsc’ 0K .. 100% 190M=0s 2023-04-16 05:28:59 (190 MB/s) - ‘gubbins_2.4.1-5.dsc’ saved [2269/2269] Sun Apr 16 05:28:59 UTC 2023 I: gubbins_2.4.1-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: gubbins Binary: gubbins Architecture: any Version: 2.4.1-5 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://sanger-pathogens.github.io/gubbins/ Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/gubbins Vcs-Git: https://salsa.debian.org/med-team/gubbins.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-python, pkg-config, fasttree, iqtree, raxml (>= 8.2.12+dfsg-5), python3-setuptools, zlib1g-dev, check, python3, python3-biopython, python3-dendropy, python3-reportlab, python3-pytest, python3-scipy , python3-multiprocess , python3-wheel Package-List: gubbins deb science optional arch=any Checksums-Sha1: 6bbbb5ce60a153b00f6eaaf3ac4a3c34c0591900 609778 gubbins_2.4.1.orig.tar.gz 89fcfa7af8f8f9969ced267c183a16ccc4b845f1 7744 gubbins_2.4.1-5.debian.tar.xz Checksums-Sha256: df0f6f475ef402d6f2f67abb870dcb2c59f3333bf6a00af76251bb102f63e17b 609778 gubbins_2.4.1.orig.tar.gz 75930a6941347dbbff34c11efcb00d10f5afee3c7e549e5c39a6edeca4bfa45c 7744 gubbins_2.4.1-5.debian.tar.xz Files: 6b0f95ef9e2ff7a34b58dbbf53d5e593 609778 gubbins_2.4.1.orig.tar.gz e28ed05f8817dfe3746f39168d2fdd21 7744 gubbins_2.4.1-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmIJFJ4RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEYLw//aXHeC25hACP7lox5eiBZHgQPEDzWGwHW ZMlxorN9g2RSmFIk5OHjqkK7MBwAUPp0bqOnGZoisUcbs/XRw0/slLNLSigBHjqg MrRB/jpYxMEUvCQHk0EZu0AKxaFQdbeJ0xNkgGZVm7K7MdPqIQsr+z3iuIintGwZ vh9gDQj+hwZvhsy8xeeRVtaDM6XPGk2TOFXFV+ipRCZrKFF7AMXrqfu3VZYUQlcH OGvMxgEog/QRjOdKSwUrnkNUfOOiZQpLD1fDX8JMBU2QCB98nmm5OCnUzsgz2ieQ nvnd+gA8Gon+L/wAgudhi4aObnLNK0YtUb6nJcKY1YB967TpdfzPZ4WQTaoxN2UR p+SwVdDXXh3tRUNu/SNQgzrBPD2OuzvfSb61leDFuAu+dsk1YwgqzWZnrjNc0Esd 94AIxIqqtogWSGVMaYkJth9DPINvc3ZdugTJdxtz5tB6nHdbo7zrlHkjSHbN8+6l /TSfw5YBlQuc1emRIepW3OWSUKZWlXGsjPGpQ4P1cCKS35BxQfdLmDxqvHzjvrY1 N5WCq0bHAvlaw/4LjcjzMNqNuIH+Ro9Gcl8A5cuoGwEyvebHm3kZaMoFQFK3Yq3f vG90KypEaruoNwW3rvVcgMjy9gKH5xq2uG2Q4Dc4ptIjon+Vq+GbolZVlQxeBYYD I2nsC53g2UA= =t2Ak -----END PGP SIGNATURE----- Sun Apr 16 05:28:59 UTC 2023 I: Checking whether the package is not for us Sun Apr 16 05:28:59 UTC 2023 I: Starting 1st build on remote node ionos5-amd64.debian.net. Sun Apr 16 05:28:59 UTC 2023 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Sun Apr 16 05:31:05 UTC 2023 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri May 17 23:52:01 -12 2024 I: pbuilder-time-stamp: 1716033121 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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 [gubbins_2.4.1-5.dsc] I: copying [./gubbins_2.4.1.orig.tar.gz] I: copying [./gubbins_2.4.1-5.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Feb 13 02:24:30 2022 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./gubbins_2.4.1-5.dsc: no acceptable signature found dpkg-source: info: extracting gubbins in gubbins-2.4.1 dpkg-source: info: unpacking gubbins_2.4.1.orig.tar.gz dpkg-source: info: unpacking gubbins_2.4.1-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying do_not_handle_python_by_upstream_build_system.patch dpkg-source: info: applying gubbins_exe_in_usr_lib.patch dpkg-source: info: applying port-to-pytest.patch dpkg-source: info: applying spelling-error-in-binary.patch dpkg-source: info: applying iqtree2.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3484544/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' 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=16' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='5373289701624ec1906743a90ba91073' 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='3484544' 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.whOOMsYZ/pbuilderrc_vUxK --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.whOOMsYZ/b1 --logfile b1/build.log gubbins_2.4.1-5.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos5-amd64 6.1.0-0.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Feb 12 2023 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 2023 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 2023 more -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Feb 12 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 2023 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/3484544/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, pkg-config, fasttree, iqtree, raxml (>= 8.2.12+dfsg-5), python3-setuptools, zlib1g-dev, check, python3, python3-biopython, python3-dendropy, python3-reportlab, python3-pytest, python3-scipy, python3-multiprocess, python3-wheel dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19596 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 pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on fasttree; however: Package fasttree is not installed. pbuilder-satisfydepends-dummy depends on iqtree; however: Package iqtree is not installed. pbuilder-satisfydepends-dummy depends on raxml (>= 8.2.12+dfsg-5); however: Package raxml is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on check; however: Package check is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-dendropy; however: Package python3-dendropy is not installed. pbuilder-satisfydepends-dummy depends on python3-reportlab; however: Package python3-reportlab is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-multiprocess; however: Package python3-multiprocess is not installed. pbuilder-satisfydepends-dummy depends on python3-wheel; however: Package python3-wheel is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} check{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} fasttree{a} file{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} iqtree{a} libarchive-zip-perl{a} libblas3{a} libboost-dev{a} libboost1.74-dev{a} libbrotli1{a} libbsd0{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libevent-core-2.1-7{a} libevent-pthreads-2.1-7{a} libexpat1{a} libexpat1-dev{a} libfabric1{a} libfile-stripnondeterminism-perl{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libhwloc-plugins{a} libhwloc15{a} libibverbs1{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} liblerc4{a} libmagic-mgc{a} libmagic1{a} libmunge2{a} libnl-3-200{a} libnl-route-3-200{a} libnuma1{a} libopenblas-dev{a} libopenblas-pthread-dev{a} libopenblas0{a} libopenblas0-pthread{a} libopenjp2-7{a} libopenmpi3{a} libpciaccess0{a} libpipeline1{a} libpkgconf3{a} libpmix2{a} libpng16-16{a} libpsm-infinipath1{a} libpsm2-2{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libraqm0{a} librdmacm1{a} libreadline8{a} libsub-override-perl{a} libsubunit-dev{a} libsubunit0{a} libtiff6{a} libtool{a} libuchardet0{a} libucx0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} libxsimd-dev{a} m4{a} mailcap{a} man-db{a} media-types{a} mime-support{a} ocl-icd-libopencl1{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-all{a} python3-all-dev{a} python3-attr{a} python3-beniget{a} python3-biopython{a} python3-decorator{a} python3-dendropy{a} python3-dev{a} python3-dill{a} python3-distutils{a} python3-gast{a} python3-iniconfig{a} python3-lib2to3{a} python3-minimal{a} python3-more-itertools{a} python3-multiprocess{a} python3-numpy{a} python3-packaging{a} python3-pil{a} python3-pkg-resources{a} python3-pluggy{a} python3-ply{a} python3-py{a} python3-pytest{a} python3-pythran{a} python3-renderpm{a} python3-reportlab{a} python3-reportlab-accel{a} python3-scipy{a} python3-setuptools{a} python3-wheel{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} raxml{a} readline-common{a} sensible-utils{a} sgml-base{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx ncbi-blast+ python-biopython-doc python3-olefile python3-pygments shared-mime-info wget xdg-user-dirs 0 packages upgraded, 159 newly installed, 0 to remove and 0 not upgraded. Need to get 115 MB of archives. After unpacking 605 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 mailcap all 3.70+nmu1 [32.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 mime-support all 3.66 [10.9 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 13 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 sgml-base all 1.31 [15.4 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 libsubunit0 amd64 1.4.0-3 [9724 B] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libsubunit-dev amd64 1.4.0-3 [10.7 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 check amd64 0.15.2-2+b1 [113 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-2 [76.2 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-2 [131 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 dh-python all 5.20230130 [104 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 fasttree amd64 2.1.11-2 [181 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libfontenc1 amd64 1:1.1.4-1 [24.3 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-4 [399 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 fonts-urw-base35 all 20200910-7 [10.8 MB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libnl-3-200 amd64 3.7.0-0.2+b1 [63.1 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 libnl-route-3-200 amd64 3.7.0-0.2+b1 [185 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libibverbs1 amd64 44.0-2 [60.7 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 ibverbs-providers amd64 44.0-2 [335 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-8 [131 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-8 [53.6 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.2 [168 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 libnuma1 amd64 2.0.16-1 [21.0 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 librdmacm1 amd64 44.0-2 [68.6 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 libfabric1 amd64 1.17.0-3 [627 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 libhwloc15 amd64 2.9.0-1 [154 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 libmunge2 amd64 0.5.15-2 [19.5 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2 [292 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2 [759 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 libxnvctrl0 amd64 525.85.05-1 [13.3 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 ocl-icd-libopencl1 amd64 2.3.1-1 [43.0 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 libhwloc-plugins amd64 2.9.0-1 [17.5 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 libpmix2 amd64 4.2.2-1+b1 [622 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 libucx0 amd64 1.13.1-1 [860 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 libopenmpi3 amd64 4.1.4-3+b1 [2422 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 iqtree amd64 2.0.7+dfsg-1 [3458 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-20 [9510 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get: 91 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 libexpat1-dev amd64 2.5.0-1 [150 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-1 [1397 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 libimagequant0 amd64 2.17.0-1 [32.5 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 102 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 libopenblas0-pthread amd64 0.3.21+ds-4 [6709 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1 [28.9 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get: 109 http://deb.debian.org/debian bookworm/main amd64 libopenblas0 amd64 0.3.21+ds-4 [32.6 kB] Get: 110 http://deb.debian.org/debian bookworm/main amd64 libopenblas-pthread-dev amd64 0.3.21+ds-4 [4971 kB] Get: 111 http://deb.debian.org/debian bookworm/main amd64 libopenblas-dev amd64 0.3.21+ds-4 [44.9 kB] Get: 112 http://deb.debian.org/debian bookworm/main amd64 libopenjp2-7 amd64 2.5.0-1+b1 [189 kB] Get: 113 http://deb.debian.org/debian bookworm/main amd64 libpkgconf3 amd64 1.8.1-1 [36.1 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 libpython3.11 amd64 3.11.2-6 [1988 kB] Get: 115 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 116 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-dev amd64 3.11.2-6 [4738 kB] Get: 117 http://deb.debian.org/debian bookworm/main amd64 libpython3-dev amd64 3.11.2-1+b1 [9572 B] Get: 118 http://deb.debian.org/debian bookworm/main amd64 libpython3-all-dev amd64 3.11.2-1+b1 [1068 B] Get: 119 http://deb.debian.org/debian bookworm/main amd64 libraqm0 amd64 0.7.0-4.1 [10.6 kB] Get: 120 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.1 [285 kB] Get: 121 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-5 [316 kB] Get: 122 http://deb.debian.org/debian bookworm/main amd64 libwebpdemux2 amd64 1.2.4-0.1 [99.2 kB] Get: 123 http://deb.debian.org/debian bookworm/main amd64 libwebpmux3 amd64 1.2.4-0.1 [109 kB] Get: 124 http://deb.debian.org/debian bookworm/main amd64 libxsimd-dev amd64 8.1.0-7 [88.8 kB] Get: 125 http://deb.debian.org/debian bookworm/main amd64 pkgconf-bin amd64 1.8.1-1 [29.5 kB] Get: 126 http://deb.debian.org/debian bookworm/main amd64 pkgconf amd64 1.8.1-1 [25.9 kB] Get: 127 http://deb.debian.org/debian bookworm/main amd64 pkg-config amd64 1.8.1-1 [13.7 kB] Get: 128 http://deb.debian.org/debian bookworm/main amd64 python3-all amd64 3.11.2-1+b1 [1056 B] Get: 129 http://deb.debian.org/debian bookworm/main amd64 python3.11-dev amd64 3.11.2-6 [615 kB] Get: 130 http://deb.debian.org/debian bookworm/main amd64 python3-dev amd64 3.11.2-1+b1 [26.2 kB] Get: 131 http://deb.debian.org/debian bookworm/main amd64 python3-all-dev amd64 3.11.2-1+b1 [1072 B] Get: 132 http://deb.debian.org/debian bookworm/main amd64 python3-attr all 22.2.0-1 [65.4 kB] Get: 133 http://deb.debian.org/debian bookworm/main amd64 python3-gast all 0.5.2-2 [9364 B] Get: 134 http://deb.debian.org/debian bookworm/main amd64 python3-beniget all 0.4.1-3 [9920 B] Get: 135 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 136 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB] Get: 137 http://deb.debian.org/debian bookworm/main amd64 python3-renderpm amd64 3.6.12-1+b1 [79.2 kB] Get: 138 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab-accel amd64 3.6.12-1+b1 [38.6 kB] Get: 139 http://deb.debian.org/debian bookworm/main amd64 python3-pil amd64 9.4.0-1.1+b1 [472 kB] Get: 140 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab all 3.6.12-1 [564 kB] Get: 141 http://deb.debian.org/debian bookworm/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get: 142 http://deb.debian.org/debian bookworm/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 143 http://deb.debian.org/debian bookworm/main amd64 python3-biopython amd64 1.80+dfsg-4+b1 [1593 kB] Get: 144 http://deb.debian.org/debian bookworm/main amd64 python3-decorator all 5.1.1-3 [14.9 kB] Get: 145 http://deb.debian.org/debian bookworm/main amd64 python3-dendropy all 4.5.2-1 [275 kB] Get: 146 http://deb.debian.org/debian bookworm/main amd64 python3-dill all 0.3.6-1 [79.5 kB] Get: 147 http://deb.debian.org/debian bookworm/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 148 http://deb.debian.org/debian bookworm/main amd64 python3-more-itertools all 8.10.0-2 [53.0 kB] Get: 149 http://deb.debian.org/debian bookworm/main amd64 python3-multiprocess all 0.70.12.2-1 [103 kB] Get: 150 http://deb.debian.org/debian bookworm/main amd64 python3-packaging all 23.0-1 [32.5 kB] Get: 151 http://deb.debian.org/debian bookworm/main amd64 python3-pluggy all 1.0.0+repack-1 [19.7 kB] Get: 152 http://deb.debian.org/debian bookworm/main amd64 python3-ply all 3.11-5 [65.8 kB] Get: 153 http://deb.debian.org/debian bookworm/main amd64 python3-py all 1.11.0-1 [89.2 kB] Get: 154 http://deb.debian.org/debian bookworm/main amd64 python3-pytest all 7.2.1-2 [236 kB] Get: 155 http://deb.debian.org/debian bookworm/main amd64 python3-pythran amd64 0.11.0+ds-7 [427 kB] Get: 156 http://deb.debian.org/debian bookworm/main amd64 python3-scipy amd64 1.10.1-2 [15.2 MB] Get: 157 http://deb.debian.org/debian bookworm/main amd64 python3-setuptools all 66.1.1-1 [521 kB] Get: 158 http://deb.debian.org/debian bookworm/main amd64 python3-wheel all 0.38.4-1 [30.8 kB] Get: 159 http://deb.debian.org/debian bookworm/main amd64 raxml amd64 8.2.12+dfsg-8+b2 [1481 kB] Fetched 115 MB in 1s (98.9 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 ... 19596 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... 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 ... 19912 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_amd64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package mailcap. Preparing to unpack .../2-mailcap_3.70+nmu1_all.deb ... Unpacking mailcap (3.70+nmu1) ... Selecting previously unselected package mime-support. Preparing to unpack .../3-mime-support_3.66_all.deb ... Unpacking mime-support (3.66) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../5-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... 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 ... 20370 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... 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Setting up libglib2.0-0:amd64 (2.74.6-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libmagic1:amd64 (1:5.44-3) ... Setting up libdeflate0:amd64 (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libsubunit0:amd64 (1.4.0-3) ... Setting up libjbig0:amd64 (2.1-6.1) ... Setting up libxsimd-dev:amd64 (8.1.0-7) ... Setting up libfontenc1:amd64 (1:1.1.4-1) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libpkgconf3:amd64 (1.8.1-1) ... 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Setting up libopenjp2-7:amd64 (2.5.0-1+b1) ... Setting up libsub-override-perl (0.09-4) ... Setting up fasttree (2.1.11-2) ... Setting up sgml-base (1.31) ... Setting up libboost-dev:amd64 (1.74.0.3) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.2) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libwebpmux3:amd64 (1.2.4-0.1) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up mailcap (3.70+nmu1) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.1+b3) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libevent-pthreads-2.1-7:amd64 (2.1.12-stable-8) ... Setting up raxml (8.2.12+dfsg-8+b2) ... 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 libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libopenblas0-pthread:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-x86_64-linux-gnu) in auto mode Setting up mime-support (3.66) ... Setting up libtool (2.4.7-5) ... Setting up libwebpdemux2:amd64 (1.2.4-0.1) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libsubunit-dev:amd64 (1.4.0-3) ... Setting up pkgconf:amd64 (1.8.1-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.2+b1) ... Setting up dh-autoreconf (20) ... 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Setting up libopenblas-pthread-dev:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/x86_64-linux-gnu/libopenblas.so (libopenblas.so-x86_64-linux-gnu) in auto mode Setting up libibverbs1:amd64 (44.0-2) ... Setting up ibverbs-providers:amd64 (44.0-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxnvctrl0:amd64 (525.85.05-1) ... 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Setting up python3-distutils (3.11.2-2) ... Setting up dh-python (5.20230130) ... Setting up python3-more-itertools (8.10.0-2) ... Setting up libfabric1:amd64 (1.17.0-3) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-attr (22.2.0-1) ... Setting up libpython3-dev:amd64 (3.11.2-1+b1) ... Setting up python3-renderpm:amd64 (3.6.12-1+b1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3-py (1.11.0-1) ... Setting up libpmix2:amd64 (4.2.2-1+b1) ... Setting up python3.11-dev (3.11.2-6) ... Setting up python3-pytest (7.2.1-2) ... Setting up libopenmpi3:amd64 (4.1.4-3+b1) ... Setting up python3-ply (3.11-5) ... Setting up python3-gast (0.5.2-2) ... Setting up python3-all (3.11.2-1+b1) ... Setting up iqtree (2.0.7+dfsg-1) ... Setting up python3-wheel (0.38.4-1) ... Setting up python3-beniget (0.4.1-3) ... Setting up libpython3-all-dev:amd64 (3.11.2-1+b1) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up python3-dendropy (4.5.2-1) ... Setting up python3-all-dev (3.11.2-1+b1) ... Setting up python3-pythran (0.11.0+ds-7) ... Setting up python3-scipy (1.10.1-2) ... Processing triggers for libc-bin (2.36-8) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.80+dfsg-4+b1) ... 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/gubbins-2.4.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../gubbins_2.4.1-5_source.changes dpkg-buildpackage: info: source package gubbins dpkg-buildpackage: info: source version 2.4.1-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 debian/rules override_dh_clean make[1]: Entering directory '/build/gubbins-2.4.1' dh_clean rm -rf python/*.egg-info python/build python/Makefile find . -name "*.pyc" -delete rm -rf python/output_alignment python/tmp* make[1]: Leaving directory '/build/gubbins-2.4.1' debian/rules binary dh binary --with python3 dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:1: warning: AC_INIT: unsafe as a filename: "$(PACKAGE_NAME)$(AC_PACKAGE_VERSION)" configure.ac:20: warning: The macro `AC_PROG_LIBTOOL' is obsolete. configure.ac:20: You should run autoupdate. m4/libtool.m4:100: AC_PROG_LIBTOOL is expanded from... configure.ac:20: the top level configure.ac:20: installing './compile' configure.ac:10: installing './config.guess' configure.ac:10: installing './config.sub' configure.ac:3: installing './install-sh' configure.ac:3: installing './missing' src/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' dh_auto_configure ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking how to create a pax tar archive... gnutar checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking dependency style of gcc... (cached) none checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking if compiler needs -Werror to reject unknown flags... no checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for zlib... yes checking for zlib.h... yes checking for math.h... yes checking for a Python interpreter with version >= 3.0... python3 checking for python3... /usr/bin/python3 checking for python3 version... 3.11 checking for python3 platform... linux checking for GNU default python3 prefix... ${prefix} checking for GNU default python3 exec_prefix... ${exec_prefix} checking for python3 script directory (pythondir)... ${PYTHON_PREFIX}/lib/python3.11/site-packages checking for python3 extension module directory (pyexecdir)... ${PYTHON_EXEC_PREFIX}/lib/python3.11/site-packages checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating release/Makefile config.status: creating python/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build make -j16 make[1]: Entering directory '/build/gubbins-2.4.1' make all-recursive make[2]: Entering directory '/build/gubbins-2.4.1' Making all in src make[3]: Entering directory '/build/gubbins-2.4.1/src' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o main.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Newickform.lo Newickform.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 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fasta_of_snp_sites.c -fPIC -DPIC -o .libs/fasta_of_snp_sites.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c seqUtil.c -fPIC -DPIC -o .libs/seqUtil.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c snp_searching.c -fPIC -DPIC -o .libs/snp_searching.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c tree_statistics.c -fPIC -DPIC -o .libs/tree_statistics.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c snp_sites.c -fPIC -DPIC -o .libs/snp_sites.o /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o tree_scaling.lo tree_scaling.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c string_cat.c -o string_cat.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c gff_file.c -o gff_file.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c block_tab_file.c -o block_tab_file.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c fasta_of_snp_sites.c -o fasta_of_snp_sites.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c phylip_of_snp_sites.c -o phylip_of_snp_sites.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c seqUtil.c -o seqUtil.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c tree_statistics.c -o tree_statistics.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c gubbins.c -o gubbins.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcf.lo vcf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c parse_vcf.c -o parse_vcf.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c tree_scaling.c -fPIC -DPIC -o .libs/tree_scaling.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 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branch_sequences.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:1 -Wl,-z,relro -Wl,-z,now -o libgubbins.la -rpath /usr/lib/x86_64-linux-gnu Newickform.lo alignment_file.lo block_tab_file.lo branch_sequences.lo string_cat.lo fasta_of_snp_sites.lo gff_file.lo gubbins.lo parse_phylip.lo parse_vcf.lo phylip_of_snp_sites.lo seqUtil.lo snp_searching.lo snp_sites.lo tree_statistics.lo tree_scaling.lo vcf.lo -lm libtool: link: gcc -shared -fPIC -DPIC .libs/Newickform.o .libs/alignment_file.o .libs/block_tab_file.o .libs/branch_sequences.o .libs/string_cat.o .libs/fasta_of_snp_sites.o .libs/gff_file.o .libs/gubbins.o .libs/parse_phylip.o .libs/parse_vcf.o .libs/phylip_of_snp_sites.o .libs/seqUtil.o .libs/snp_searching.o .libs/snp_sites.o .libs/tree_statistics.o .libs/tree_scaling.o .libs/vcf.o -lm -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libgubbins.so.0 -o .libs/libgubbins.so.0.0.1 libtool: link: (cd ".libs" && rm -f "libgubbins.so.0" && ln -s "libgubbins.so.0.0.1" "libgubbins.so.0") libtool: link: (cd ".libs" && rm -f "libgubbins.so" && ln -s "libgubbins.so.0.0.1" "libgubbins.so") libtool: link: ar cr .libs/libgubbins.a Newickform.o alignment_file.o block_tab_file.o branch_sequences.o string_cat.o fasta_of_snp_sites.o gff_file.o gubbins.o parse_phylip.o parse_vcf.o phylip_of_snp_sites.o seqUtil.o snp_searching.o snp_sites.o tree_statistics.o tree_scaling.o vcf.o libtool: link: ranlib .libs/libgubbins.a libtool: link: ( cd ".libs" && rm -f "libgubbins.la" && ln -s "../libgubbins.la" "libgubbins.la" ) /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gubbins main.o libgubbins.la -lz -lm libtool: link: gcc -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/gubbins main.o ./.libs/libgubbins.so -lz -lm make[3]: Leaving directory '/build/gubbins-2.4.1/src' Making all in release make[3]: Entering directory '/build/gubbins-2.4.1/release' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/gubbins-2.4.1/release' make[3]: Entering directory '/build/gubbins-2.4.1' make[3]: Leaving directory '/build/gubbins-2.4.1' make[2]: Leaving directory '/build/gubbins-2.4.1' make[1]: Leaving directory '/build/gubbins-2.4.1' debian/rules override_dh_auto_test make[1]: Entering directory '/build/gubbins-2.4.1' dh_auto_test make -j16 check "TESTSUITEFLAGS=-j16 --verbose" VERBOSE=1 make[2]: Entering directory '/build/gubbins-2.4.1' Making check in src make[3]: Entering directory '/build/gubbins-2.4.1/src' make run_all_tests make[4]: Entering directory '/build/gubbins-2.4.1/src' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_branch_sequences.o `test -f '../tests/check_branch_sequences.c' || echo './'`../tests/check_branch_sequences.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_gubbins.o `test -f '../tests/check_gubbins.c' || echo './'`../tests/check_gubbins.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_parse_phylip.o `test -f '../tests/check_parse_phylip.c' || echo './'`../tests/check_parse_phylip.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_snp_searching.o `test -f '../tests/check_snp_searching.c' || echo './'`../tests/check_snp_searching.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_snp_sites.o `test -f '../tests/check_snp_sites.c' || echo './'`../tests/check_snp_sites.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_vcf_parsing.o `test -f '../tests/check_vcf_parsing.c' || echo './'`../tests/check_vcf_parsing.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-helper_methods.o `test -f '../tests/helper_methods.c' || echo './'`../tests/helper_methods.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-run_all_tests.o `test -f '../tests/run_all_tests.c' || echo './'`../tests/run_all_tests.c ../tests/helper_methods.c: In function 'compare_files': ../tests/helper_methods.c:27:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | fread(expected_buffer, sizeof(char), numbytes, expected_output_fh); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/helper_methods.c:34:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 34 | fread(actual_buffer, sizeof(char), numbytes, actual_output_fh); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check_branch_sequences.c: In function 'check_copy_and_concat_2d_integer_arrays_fn': ../tests/check_branch_sequences.c:67:23: warning: implicit declaration of function 'copy_and_concat_2d_integer_arrays'; did you mean 'copy_and_concat_integer_arrays'? [-Wimplicit-function-declaration] 67 | output_size = copy_and_concat_2d_integer_arrays(block_coords, 3, block_coords_2, 2, block_coords_out) ; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | copy_and_concat_integer_arrays In file included from ../tests/check_snp_sites.c:5: ../tests/check_snp_sites.c: In function 'valid_alignment_with_large_numbers_of_snps_fn': ../tests/check_snp_sites.c:16:155: warning: too many arguments for format [-Wformat-extra-args] 16 | fail_unless( compare_files("../tests/data/alignment_file_with_large_number_of_snps.aln.vcf", "alignment_file_with_large_number_of_snps.aln.vcf" ) == 1, "Invalid VCF file for 1 line per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check_snp_sites.c:17:161: warning: too many arguments for format [-Wformat-extra-args] 17 | fail_unless( compare_files("../tests/data/alignment_file_with_large_number_of_snps.aln.phylip", "alignment_file_with_large_number_of_snps.aln.phylip" ) == 1, "Invalid Phylip file for 1 line per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check_snp_sites.c:18:175: warning: too many arguments for format [-Wformat-extra-args] 18 | fail_unless( compare_files("../tests/data/alignment_file_with_large_number_of_snps.aln.snp_sites.aln","alignment_file_with_large_number_of_snps.aln.snp_sites.aln" ) == 1 , "Invalid ALN file for 1 line per seq"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../tests/check_gubbins.c:4: ../tests/check_gubbins.c: In function 'check_gubbins_no_recombinations_fn': ../tests/check_snp_sites.c: In function 'valid_alignment_with_one_line_per_sequence_fn': ../tests/check_gubbins.c:21:15: warning: implicit declaration of function 'number_of_recombinations_in_file' [-Wimplicit-function-declaration] 21 | fail_unless(number_of_recombinations_in_file("../tests/data/no_recombinations.tre.tab") == 0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check_snp_sites.c:29:153: warning: too many arguments for format [-Wformat-extra-args] 29 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.phylip", "alignment_file_one_line_per_sequence.aln.phylip" ) == 1, "Invalid Phylip file for 1 line per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check_snp_sites.c:30:147: warning: too many arguments for format [-Wformat-extra-args] 30 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.vcf", "alignment_file_one_line_per_sequence.aln.vcf" ) == 1, "Invalid VCF file for 1 line per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check_snp_sites.c:31:167: warning: too many arguments for format [-Wformat-extra-args] 31 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","alignment_file_one_line_per_sequence.aln.snp_sites.aln" ) == 1 , "Invalid ALN file for 1 line per seq"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check_snp_sites.c: In function 'valid_alignment_with_n_as_gap_fn': ../tests/check_snp_sites.c:42:140: warning: too many arguments for format [-Wformat-extra-args] 42 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.vcf", "alignment_file_with_n.aln.vcf" ) == 1, "Invalid VCF file for 1 line per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check_snp_sites.c:43:146: warning: too many arguments for format [-Wformat-extra-args] 43 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.phylip", "alignment_file_with_n.aln.phylip" ) == 1, "Invalid Phylip file for 1 line per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check_snp_sites.c:44:160: warning: too many arguments for format [-Wformat-extra-args] 44 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","alignment_file_with_n.aln.snp_sites.aln" ) == 1 , "Invalid ALN file for 1 line per seq"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check_snp_sites.c: In function 'valid_alignment_with_one_line_per_sequence_gzipped_fn': ../tests/check_snp_sites.c:56:150: warning: too many arguments for format [-Wformat-extra-args] 56 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.vcf", "alignment_file_one_line_per_sequence.aln.gz.vcf" ) == 1, "Invalid VCF file for 1 line per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check_snp_sites.c:57:156: warning: too many arguments for format [-Wformat-extra-args] 57 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.phylip", "alignment_file_one_line_per_sequence.aln.gz.phylip" ) == 1, "Invalid Phylip file for 1 line per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check_snp_sites.c:58:170: warning: too many arguments for format [-Wformat-extra-args] 58 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","alignment_file_one_line_per_sequence.aln.gz.snp_sites.aln" ) == 1 , "Invalid ALN file for 1 line per seq"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check_snp_sites.c: In function 'valid_alignment_with_multiple_lines_per_sequence_fn': ../tests/check_snp_sites.c:71:161: warning: too many arguments for format [-Wformat-extra-args] 71 | fail_unless( compare_files("../tests/data/alignment_file_multiple_lines_per_sequence.aln.vcf", "alignment_file_multiple_lines_per_sequence.aln.vcf" ) == 1, "Invalid VCF file for multiple lines per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check_snp_sites.c:72:167: warning: too many arguments for format [-Wformat-extra-args] 72 | fail_unless( compare_files("../tests/data/alignment_file_multiple_lines_per_sequence.aln.phylip", "alignment_file_multiple_lines_per_sequence.aln.phylip" ) == 1, "Invalid Phylip file for multiple lines per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check_snp_sites.c:73:180: warning: too many arguments for format [-Wformat-extra-args] 73 | fail_unless( compare_files("../tests/data/alignment_file_multiple_lines_per_sequence.aln.snp_sites.aln","alignment_file_multiple_lines_per_sequence.aln.snp_sites.aln" ) == 1 ,"Invalid ALN file for multiple lines per seq"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check_snp_sites.c: In function 'two_sequences_fn': ../tests/check_snp_sites.c:83:103: warning: too many arguments for format [-Wformat-extra-args] 83 | fail_unless( compare_files("../tests/data/two_sequences.aln.vcf", "two_sequences.aln.vcf" ) == 1, "Invalid VCF file for multiple lines per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check_snp_sites.c:84:109: warning: too many arguments for format [-Wformat-extra-args] 84 | fail_unless( compare_files("../tests/data/two_sequences.aln.phylip", "two_sequences.aln.phylip" ) == 1, "Invalid Phylip file for multiple lines per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check_snp_sites.c:85:122: warning: too many arguments for format [-Wformat-extra-args] 85 | fail_unless( compare_files("../tests/data/two_sequences.aln.snp_sites.aln","two_sequences.aln.snp_sites.aln" ) == 1 ,"Invalid ALN file for multiple lines per seq"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/bash ../libtool --tag=CC --mode=link gcc -I../tests -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o run_all_tests ../tests/run_all_tests-check_branch_sequences.o ../tests/run_all_tests-check_gubbins.o ../tests/run_all_tests-check_parse_phylip.o ../tests/run_all_tests-check_snp_searching.o ../tests/run_all_tests-check_snp_sites.o ../tests/run_all_tests-check_vcf_parsing.o ../tests/run_all_tests-helper_methods.o ../tests/run_all_tests-run_all_tests.o -lcheck libgubbins.la -lz -lm -lrt -lsubunit libtool: link: gcc -I../tests -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/run_all_tests ../tests/run_all_tests-check_branch_sequences.o ../tests/run_all_tests-check_gubbins.o ../tests/run_all_tests-check_parse_phylip.o ../tests/run_all_tests-check_snp_searching.o ../tests/run_all_tests-check_snp_sites.o ../tests/run_all_tests-check_vcf_parsing.o ../tests/run_all_tests-helper_methods.o ../tests/run_all_tests-run_all_tests.o -lcheck ./.libs/libgubbins.so -lz -lm -lrt -lsubunit make[4]: Leaving directory '/build/gubbins-2.4.1/src' make check-TESTS make[4]: Entering directory '/build/gubbins-2.4.1/src' make[5]: Entering directory '/build/gubbins-2.4.1/src' PASS: run_all_tests ============================================================================ Testsuite summary for gubbins 2.4.1 ============================================================================ # TOTAL: 1 # PASS: 1 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/build/gubbins-2.4.1/src' make[4]: Leaving directory '/build/gubbins-2.4.1/src' make[3]: Leaving directory '/build/gubbins-2.4.1/src' Making check in release make[3]: Entering directory '/build/gubbins-2.4.1/release' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/gubbins-2.4.1/release' make[3]: Entering directory '/build/gubbins-2.4.1' make[3]: Leaving directory '/build/gubbins-2.4.1' make[2]: Leaving directory '/build/gubbins-2.4.1' cd python && \ PATH="$PATH:../src" python3 setup.py test running test WARNING: Testing via this command is deprecated and will be removed in a future version. Users looking for a generic test entry point independent of test runner are encouraged to use tox. running egg_info creating gubbins.egg-info writing gubbins.egg-info/PKG-INFO writing dependency_links to gubbins.egg-info/dependency_links.txt writing entry points to gubbins.egg-info/entry_points.txt writing requirements to gubbins.egg-info/requires.txt writing top-level names to gubbins.egg-info/top_level.txt writing manifest file 'gubbins.egg-info/SOURCES.txt' reading manifest file 'gubbins.egg-info/SOURCES.txt' adding license file 'LICENSE.txt' writing manifest file 'gubbins.egg-info/SOURCES.txt' running build_ext test_are_all_names_unique (gubbins.tests.test_validate_starting_tree.TestValidationOfStartingTree.test_are_all_names_unique) ... ok test_do_the_names_match_the_fasta_file (gubbins.tests.test_validate_starting_tree.TestValidationOfStartingTree.test_do_the_names_match_the_fasta_file) ... ok test_is_it_a_valid_newick_tree (gubbins.tests.test_validate_starting_tree.TestValidationOfStartingTree.test_is_it_a_valid_newick_tree) ... ok test_are_all_sequence_names_unique (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile.test_are_all_sequence_names_unique) ... ok test_are_all_sequences_the_same_length (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile.test_are_all_sequences_the_same_length) ... ok test_are_there_enough_sequences_to_build_a_tree (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile.test_are_there_enough_sequences_to_build_a_tree) ... ok test_does_each_sequence_have_a_name (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile.test_does_each_sequence_have_a_name) ... ok test_does_the_sequence_have_sensible_characters (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile.test_does_the_sequence_have_sensible_characters) ... ok test_valid_fasta_file (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile.test_valid_fasta_file) ... ok test_check_and_fix_window_size (gubbins.tests.test_utils.TestUtilities.test_check_and_fix_window_size) ... ok test_delete_files (gubbins.tests.test_utils.TestUtilities.test_delete_files) ... ok test_do_files_exist (gubbins.tests.test_utils.TestUtilities.test_do_files_exist) ... ok test_gubbins_command (gubbins.tests.test_utils.TestUtilities.test_gubbins_command) ... ok test_is_executable (gubbins.tests.test_utils.TestUtilities.test_is_executable) ... ok test_rename_files (gubbins.tests.test_utils.TestUtilities.test_rename_files) ... ok test_replace_executable (gubbins.tests.test_utils.TestUtilities.test_replace_executable) ... ok test_translation_of_filenames_to_final_filenames (gubbins.tests.test_utils.TestUtilities.test_translation_of_filenames_to_final_filenames) ... ok test_verbose_printer (gubbins.tests.test_utils.TestUtilities.test_verbose_printer) ... ok test_which (gubbins.tests.test_utils.TestUtilities.test_which) ... ok test_fasttree_treebuilding_command (gubbins.tests.test_treebuilders.TestStringConstruction.test_fasttree_treebuilding_command) ... ok test_iqtree_convert_raw_ancestral_states_to_fasta (gubbins.tests.test_treebuilders.TestStringConstruction.test_iqtree_convert_raw_ancestral_states_to_fasta) ... ok test_iqtree_replace_internal_node_label (gubbins.tests.test_treebuilders.TestStringConstruction.test_iqtree_replace_internal_node_label) ... ok test_iqtree_sequence_reconstruction_command (gubbins.tests.test_treebuilders.TestStringConstruction.test_iqtree_sequence_reconstruction_command) ... ok test_iqtree_treebuilding_command (gubbins.tests.test_treebuilders.TestStringConstruction.test_iqtree_treebuilding_command) ... ok test_raxml_convert_raw_ancestral_states_to_fasta (gubbins.tests.test_treebuilders.TestStringConstruction.test_raxml_convert_raw_ancestral_states_to_fasta) ... ok test_raxml_replace_internal_node_label (gubbins.tests.test_treebuilders.TestStringConstruction.test_raxml_replace_internal_node_label) ... ok test_raxml_select_executable_based_on_threads (gubbins.tests.test_treebuilders.TestStringConstruction.test_raxml_select_executable_based_on_threads) ... ok test_raxml_sequence_reconstruction_command (gubbins.tests.test_treebuilders.TestStringConstruction.test_raxml_sequence_reconstruction_command) ... ok test_raxml_treebuilding_command (gubbins.tests.test_treebuilders.TestStringConstruction.test_raxml_treebuilding_command) ... ok test_filter_out_removed_taxa_from_tree (gubbins.tests.test_tree_methods.TestTreeMethods.test_filter_out_removed_taxa_from_tree) ... ok test_has_tree_been_seen_before (gubbins.tests.test_tree_methods.TestTreeMethods.test_has_tree_been_seen_before) ... ok test_internal_node_taxons_removed_when_used_as_starting_tree (gubbins.tests.test_tree_methods.TestTreeMethods.test_internal_node_taxons_removed_when_used_as_starting_tree) ... ok test_remove_internal_node_labels (gubbins.tests.test_tree_methods.TestTreeMethods.test_remove_internal_node_labels) ... ok test_reroot_tree (gubbins.tests.test_tree_methods.TestTreeMethods.test_reroot_tree) ... ok test_reroot_tree_at_midpoint (gubbins.tests.test_tree_methods.TestTreeMethods.test_reroot_tree_at_midpoint) ... ok test_reroot_tree_with_outgroup (gubbins.tests.test_tree_methods.TestTreeMethods.test_reroot_tree_with_outgroup) ... ok test_reroot_tree_with_outgroups (gubbins.tests.test_tree_methods.TestTreeMethods.test_reroot_tree_with_outgroups) ... ok test_reroot_tree_with_outgroups_all_in_different_clade (gubbins.tests.test_tree_methods.TestTreeMethods.test_reroot_tree_with_outgroups_all_in_different_clade) ... ok test_reroot_tree_with_outgroups_all_in_one_clade (gubbins.tests.test_tree_methods.TestTreeMethods.test_reroot_tree_with_outgroups_all_in_one_clade) ... ok test_reroot_tree_with_outgroups_all_in_one_clade_large (gubbins.tests.test_tree_methods.TestTreeMethods.test_reroot_tree_with_outgroups_all_in_one_clade_large) ... ok test_reroot_tree_with_outgroups_with_two_mixed_clades (gubbins.tests.test_tree_methods.TestTreeMethods.test_reroot_tree_with_outgroups_with_two_mixed_clades) ... ok test_robinson_foulds_distance (gubbins.tests.test_tree_methods.TestTreeMethods.test_robinson_foulds_distance) ... ok test_root_tree (gubbins.tests.test_tree_methods.TestTreeMethods.test_root_tree) ... ok test_split_all_non_bi_nodes (gubbins.tests.test_tree_methods.TestTreeMethods.test_split_all_non_bi_nodes) ... ok test_transfer_internal_node_labels_to_tree (gubbins.tests.test_tree_methods.TestTreeMethods.test_transfer_internal_node_labels_to_tree) ... ok test_dont_filter_input_file_with_multiple_duplicate_sequences (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta.test_dont_filter_input_file_with_multiple_duplicate_sequences) ... ok test_filter_out_alignments_with_too_much_missing_data (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta.test_filter_out_alignments_with_too_much_missing_data) ... ok test_input_file_with_all_duplicate_sequences (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta.test_input_file_with_all_duplicate_sequences) ... ok test_input_file_with_multiple_duplicate_sequences (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta.test_input_file_with_multiple_duplicate_sequences) ... ok test_input_file_with_no_duplicate_sequences (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta.test_input_file_with_no_duplicate_sequences) ... ok test_input_file_with_one_duplicate_sequences (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta.test_input_file_with_one_duplicate_sequences) ... ok test_cleanup (gubbins.tests.test_dependencies.TestExternalDependencies.test_cleanup) ... NOTE: gubbins_drawer.py is no longer supported. Instead we recommend using Phandango[1] (http://phandango.net/) to visualise the outputs of Gubbins. [1] James Hadfield, Nicholas J Croucher, Richard J Goater, Khalil Abudahab, David M Aanensen, Simon R Harris. "Phandango: an interactive viewer for bacterial population genomics". Bioinformatics, Volume 34, Issue 2, 15 January 2018, Pages 292–293, https://doi.org/10.1093/bioinformatics/btx610 Error with the input starting tree: Is it a valid Newick file? Error with the input starting tree: Is it a valid Newick file? All sequence names in the fasta file must be unique Unexpected error: Error with the input FASTA file: It is in the wrong format so check its an alignment Unexpected error: Error with the input FASTA file: It is in the wrong format so check its an alignment Each sequence must be the same length Error with input FASTA file: you need more than 3 sequences to build a meaningful tree Each sequence must have a name and some genomic data Error with the input FASTA file: One of the sequence names is blank Error with the input FASTA file: One of the sequence names is blank Each sequence must have a name and some genomic data Error with the input FASTA file: One of the sequences contains odd characters, only ACGTNacgtn- are permitted Error with the input FASTA file: One of the sequences contains odd characters, only ACGTNacgtn- are permitted Each sequence must have a name and some genomic data Trying multithreaded version of RAxML because no single threaded version of RAxML could be found. Just to warn you, this requires 2 threads. Your outgroups do not form a clade. Using the first taxon A as the outgroup. Taxon C is in the clade but not in your list of outgroups. Your outgroups do not form a clade. Using the first taxon A as the outgroup. Taxon C is in the clade but not in your list of outgroups. Your outgroups do not form a clade. Using the first taxon A as the outgroup. Taxon E is in the clade but not in your list of outgroups. Your outgroups do not form a clade. Using the first taxon A as the outgroup. Taxon E is in the clade but not in your list of outgroups. Sequences in sample1 and sample3 are identical, removing sample1 from analysis Sequences in sample2 and sample4 are identical, removing sample2 from analysis Excluded sequence sample2 because it had 28.571428571428573 percentage missing data while a maximum of 5 is allowed Excluded sequence sample4 because it had 28.571428571428573 percentage missing data while a maximum of 5 is allowed Sequences in sample1 and sample4 are identical, removing sample1 from analysis Sequences in sample2 and sample4 are identical, removing sample2 from analysis Sequences in sample3 and sample4 are identical, removing sample3 from analysis Sequences in sample1 and sample3 are identical, removing sample1 from analysis Sequences in sample2 and sample4 are identical, removing sample2 from analysis Sequences in sample1 and sample3 are identical, removing sample1 from analysis Sequences in sample2 and sample4 are identical, removing sample2 from analysis Sequences in sample1 and sample3 are identical, removing sample1 from analysis Sequences in sample1 and sample3 are identical, removing sample1 from analysis --- Gubbins 2.4.1 --- Checking dependencies... ...done. Run time: 0.00 s Checking input files... ...done. Run time: 0.00 s Filtering input alignment... ...done. Run time: 0.01 s Running Gubbins to detect SNPs... gubbins /build/gubbins-2.4.1/python/tmpgsreag7f/multiple_recombinations.aln ...done. Run time: 0.02 s Entering the main loop. *** Iteration 1 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_1 > /dev/null 2>&1 ...done. Run time: 0.28 s Reconstructing ancestral sequences with raxmlHPC... raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_1.internal -t /build/gubbins-2.4.1/python/tmpgsreag7f/multiple_recombinations.iteration_1.tre.rooted > /dev/null 2>&1 ...done. Run time: 0.35 s Reinserting gaps into the alignment... ...done. Run time: 0.36 s Running Gubbins to detect recombinations... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpgsreag7f/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 0.38 s Checking for convergence... ...done. Run time: 0.38 s *** Iteration 2 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre.phylip -n multiple_recombinations.iteration_2 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre > /dev/null 2>&1 ...done. Run time: 0.54 s Reconstructing ancestral sequences with raxmlHPC... raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_2.internal -t /build/gubbins-2.4.1/python/tmpgsreag7f/multiple_recombinations.iteration_2.tre.rooted > /dev/null 2>&1 ...done. Run time: 0.68 s Reinserting gaps into the alignment... ...done. Run time: 0.68 s Running Gubbins to detect recombinations... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpgsreag7f/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 0.71 s Checking for convergence... ...done. Run time: 0.71 s *** Iteration 3 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre.phylip -n multiple_recombinations.iteration_3 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre > /dev/null 2>&1 ...done. Run time: 0.86 s Reconstructing ancestral sequences with raxmlHPC... raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_3.internal -t /build/gubbins-2.4.1/python/tmpgsreag7f/multiple_recombinations.iteration_3.tre.rooted > /dev/null 2>&1 ...done. Run time: 0.92 s Reinserting gaps into the alignment... ...done. Run time: 0.93 s Running Gubbins to detect recombinations... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpgsreag7f/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 0.95 s Checking for convergence... ...done. Run time: 0.96 s *** Iteration 4 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre.phylip -n multiple_recombinations.iteration_4 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre > /dev/null 2>&1 ...done. Run time: 1.23 s Reconstructing ancestral sequences with raxmlHPC... raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_4.internal -t /build/gubbins-2.4.1/python/tmpgsreag7f/multiple_recombinations.iteration_4.tre.rooted > /dev/null 2>&1 ...done. Run time: 1.29 s Reinserting gaps into the alignment... ...done. Run time: 1.29 s Running Gubbins to detect recombinations... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpgsreag7f/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 1.31 s Checking for convergence... ...done. Run time: 1.32 s *** Iteration 5 *** Constructing the phylogenetic tree with raxmlHPC... ok test_fasttree (gubbins.tests.test_dependencies.TestExternalDependencies.test_fasttree) ... ok test_hybrid (gubbins.tests.test_dependencies.TestExternalDependencies.test_hybrid) ... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre.phylip -n multiple_recombinations.iteration_5 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre > /dev/null 2>&1 ...done. Run time: 1.61 s Reconstructing ancestral sequences with raxmlHPC... raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_5.internal -t /build/gubbins-2.4.1/python/tmpgsreag7f/multiple_recombinations.iteration_5.tre.rooted > /dev/null 2>&1 ...done. Run time: 1.67 s Reinserting gaps into the alignment... ...done. Run time: 1.67 s Running Gubbins to detect recombinations... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpgsreag7f/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 1.69 s Checking for convergence... ...done. Run time: 1.70 s Maximum number of iterations (5) reached. Exiting the main loop. Creating the final output... ...finished. Total run time: 1.71 s --- Gubbins 2.4.1 --- Checking dependencies... ...done. Run time: 0.00 s Checking input files... ...done. Run time: 0.00 s Filtering input alignment... ...done. Run time: 0.01 s Running Gubbins to detect SNPs... gubbins /build/gubbins-2.4.1/python/tmpsuo7cx_b/multiple_recombinations.aln ...done. Run time: 0.02 s Entering the main loop. *** Iteration 1 *** Constructing the phylogenetic tree with FastTree... FastTree -nosupport -gtr -gamma -nt -out multiple_recombinations.iteration_1.tre /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln > /dev/null 2>&1 ...done. Run time: 0.13 s Reconstructing ancestral sequences with raxmlHPC... raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_1.internal -t /build/gubbins-2.4.1/python/tmpsuo7cx_b/multiple_recombinations.iteration_1.tre.rooted > /dev/null 2>&1 ...done. Run time: 0.19 s Reinserting gaps into the alignment... ...done. Run time: 0.19 s Running Gubbins to detect recombinations... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpsuo7cx_b/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 0.21 s Checking for convergence... ...done. Run time: 0.21 s *** Iteration 2 *** Constructing the phylogenetic tree with FastTree... FastTree -nosupport -gtr -gamma -nt -intree /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre -out multiple_recombinations.iteration_2.tre /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre.snp_sites.aln > /dev/null 2>&1 ...done. Run time: 0.25 s Reconstructing ancestral sequences with raxmlHPC... raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_2.internal -t /build/gubbins-2.4.1/python/tmpsuo7cx_b/multiple_recombinations.iteration_2.tre.rooted > /dev/null 2>&1 ...done. Run time: 0.31 s Reinserting gaps into the alignment... ...done. Run time: 0.31 s Running Gubbins to detect recombinations... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpsuo7cx_b/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 0.33 s Checking for convergence... ...done. Run time: 0.33 s *** Iteration 3 *** Constructing the phylogenetic tree with FastTree... FastTree -nosupport -gtr -gamma -nt -intree /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre -out multiple_recombinations.iteration_3.tre /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre.snp_sites.aln > /dev/null 2>&1 ...done. Run time: 0.39 s Reconstructing ancestral sequences with raxmlHPC... raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_3.internal -t /build/gubbins-2.4.1/python/tmpsuo7cx_b/multiple_recombinations.iteration_3.tre.rooted > /dev/null 2>&1 ...done. Run time: 0.44 s Reinserting gaps into the alignment... ...done. Run time: 0.45 s Running Gubbins to detect recombinations... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpsuo7cx_b/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 0.47 s Checking for convergence... ...done. Run time: 0.47 s *** Iteration 4 *** Constructing the phylogenetic tree with FastTree... FastTree -nosupport -gtr -gamma -nt -intree /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre -out multiple_recombinations.iteration_4.tre /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre.snp_sites.aln > /dev/null 2>&1 ...done. Run time: 0.54 s Reconstructing ancestral sequences with raxmlHPC... raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_4.internal -t /build/gubbins-2.4.1/python/tmpsuo7cx_b/multiple_recombinations.iteration_4.tre.rooted > /dev/null 2>&1 ...done. Run time: 0.60 s Reinserting gaps into the alignment... ...done. Run time: 0.60 s Running Gubbins to detect recombinations... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpsuo7cx_b/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 0.62 s Checking for convergence... ...done. Run time: 0.63 s *** Iteration 5 *** Constructing the phylogenetic tree with FastTree... FastTree -nosupport -gtr -gamma -nt -intree /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre -out multiple_recombinations.iteration_5.tre /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre.snp_sites.aln > /dev/null 2>&1 ...done. Run time: 0.69 s Reconstructing ancestral sequences with raxmlHPC... raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_5.internal -t /build/gubbins-2.4.1/python/tmpsuo7cx_b/multiple_recombinations.iteration_5.tre.rooted > /dev/null 2>&1 ...done. Run time: 0.74 s Reinserting gaps into the alignment... ...done. Run time: 0.74 s Running Gubbins to detect recombinations... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpsuo7cx_b/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 0.76 s Checking for convergence... Convergence after 5 iterations: Tree observed before. Exiting the main loop. Creating the final output... ...finished. Total run time: 0.77 s --- Gubbins 2.4.1 --- Checking dependencies... ...done. Run time: 0.00 s Checking input files... ...done. Run time: 0.00 s Filtering input alignment... ...done. Run time: 0.01 s Running Gubbins to detect SNPs... gubbins /build/gubbins-2.4.1/python/tmpj586geap/multiple_recombinations.aln ...done. Run time: 0.02 s Entering the main loop. *** Iteration 1 *** Constructing the phylogenetic tree with FastTree... FastTree -nosupport -gtr -gamma -nt -out multiple_recombinations.iteration_1.tre /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln > /dev/null 2>&1 ...done. Run time: 0.12 s Reconstructing ancestral sequences with raxmlHPC... raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_1.internal -t /build/gubbins-2.4.1/python/tmpj586geap/multiple_recombinations.iteration_1.tre.rooted > /dev/null 2>&1 ...done. Run time: 0.18 s Reinserting gaps into the alignment... ...done. Run time: 0.18 s Running Gubbins to detect recombinations... ok test_iqtree (gubbins.tests.test_dependencies.TestExternalDependencies.test_iqtree) ... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpj586geap/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 0.20 s Checking for convergence... ...done. Run time: 0.21 s *** Iteration 2 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre.phylip -n multiple_recombinations.iteration_2 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre > /dev/null 2>&1 ...done. Run time: 0.33 s Reconstructing ancestral sequences with raxmlHPC... raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_2.internal -t /build/gubbins-2.4.1/python/tmpj586geap/multiple_recombinations.iteration_2.tre.rooted > /dev/null 2>&1 ...done. Run time: 0.39 s Reinserting gaps into the alignment... ...done. Run time: 0.39 s Running Gubbins to detect recombinations... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpj586geap/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 0.42 s Checking for convergence... ...done. Run time: 0.42 s *** Iteration 3 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre.phylip -n multiple_recombinations.iteration_3 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre > /dev/null 2>&1 ...done. Run time: 0.60 s Reconstructing ancestral sequences with raxmlHPC... raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_3.internal -t /build/gubbins-2.4.1/python/tmpj586geap/multiple_recombinations.iteration_3.tre.rooted > /dev/null 2>&1 ...done. Run time: 0.67 s Reinserting gaps into the alignment... ...done. Run time: 0.67 s Running Gubbins to detect recombinations... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpj586geap/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 0.69 s Checking for convergence... ...done. Run time: 0.70 s *** Iteration 4 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre.phylip -n multiple_recombinations.iteration_4 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre > /dev/null 2>&1 ...done. Run time: 0.94 s Reconstructing ancestral sequences with raxmlHPC... raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_4.internal -t /build/gubbins-2.4.1/python/tmpj586geap/multiple_recombinations.iteration_4.tre.rooted > /dev/null 2>&1 ...done. Run time: 1.00 s Reinserting gaps into the alignment... ...done. Run time: 1.00 s Running Gubbins to detect recombinations... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpj586geap/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 1.02 s Checking for convergence... ...done. Run time: 1.03 s *** Iteration 5 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre.phylip -n multiple_recombinations.iteration_5 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre > /dev/null 2>&1 ...done. Run time: 1.12 s Reconstructing ancestral sequences with raxmlHPC... raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_5.internal -t /build/gubbins-2.4.1/python/tmpj586geap/multiple_recombinations.iteration_5.tre.rooted > /dev/null 2>&1 ...done. Run time: 1.17 s Reinserting gaps into the alignment... ...done. Run time: 1.17 s Running Gubbins to detect recombinations... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpj586geap/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 1.19 s Checking for convergence... ...done. Run time: 1.20 s Maximum number of iterations (5) reached. Exiting the main loop. Creating the final output... ...finished. Total run time: 1.20 s --- Gubbins 2.4.1 --- Checking dependencies... ...done. Run time: 0.00 s Checking input files... ...done. Run time: 0.00 s Filtering input alignment... ...done. Run time: 0.00 s Running Gubbins to detect SNPs... gubbins /build/gubbins-2.4.1/python/tmpr6__2_cl/multiple_recombinations.aln ...done. Run time: 0.02 s Entering the main loop. *** Iteration 1 *** Constructing the phylogenetic tree with iqtree2... iqtree2 -safe -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_1 -nt 1 -quiet ...done. Run time: 0.96 s Reconstructing ancestral sequences with iqtree2... iqtree2 -safe -asr -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_1.internal -nt 1 -te /build/gubbins-2.4.1/python/tmpr6__2_cl/multiple_recombinations.iteration_1.tre.rooted -quiet ...done. Run time: 1.02 s Reinserting gaps into the alignment... ...done. Run time: 1.03 s Running Gubbins to detect recombinations... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpr6__2_cl/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 1.05 s Checking for convergence... ...done. Run time: 1.05 s *** Iteration 2 *** Constructing the phylogenetic tree with iqtree2... iqtree2 -safe -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre.phylip -pre multiple_recombinations.iteration_2 -nt 1 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre -quiet ...done. Run time: 1.42 s Reconstructing ancestral sequences with iqtree2... iqtree2 -safe -asr -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_2.internal -nt 1 -te /build/gubbins-2.4.1/python/tmpr6__2_cl/multiple_recombinations.iteration_2.tre.rooted -quiet ...done. Run time: 1.47 s Reinserting gaps into the alignment... ...done. Run time: 1.48 s Running Gubbins to detect recombinations... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpr6__2_cl/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 1.50 s Checking for convergence... ...done. Run time: 1.50 s *** Iteration 3 *** Constructing the phylogenetic tree with iqtree2... iqtree2 -safe -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre.phylip -pre multiple_recombinations.iteration_3 -nt 1 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre -quiet ...done. Run time: 1.60 s Reconstructing ancestral sequences with iqtree2... iqtree2 -safe -asr -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_3.internal -nt 1 -te /build/gubbins-2.4.1/python/tmpr6__2_cl/multiple_recombinations.iteration_3.tre.rooted -quiet ...done. Run time: 1.65 s Reinserting gaps into the alignment... ...done. Run time: 1.65 s Running Gubbins to detect recombinations... ok test_raxml (gubbins.tests.test_dependencies.TestExternalDependencies.test_raxml) ... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpr6__2_cl/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 1.68 s Checking for convergence... ...done. Run time: 1.68 s *** Iteration 4 *** Constructing the phylogenetic tree with iqtree2... iqtree2 -safe -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre.phylip -pre multiple_recombinations.iteration_4 -nt 1 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre -quiet ...done. Run time: 2.13 s Reconstructing ancestral sequences with iqtree2... iqtree2 -safe -asr -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_4.internal -nt 1 -te /build/gubbins-2.4.1/python/tmpr6__2_cl/multiple_recombinations.iteration_4.tre.rooted -quiet ...done. Run time: 2.24 s Reinserting gaps into the alignment... ...done. Run time: 2.24 s Running Gubbins to detect recombinations... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpr6__2_cl/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 2.26 s Checking for convergence... ...done. Run time: 2.27 s *** Iteration 5 *** Constructing the phylogenetic tree with iqtree2... iqtree2 -safe -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre.phylip -pre multiple_recombinations.iteration_5 -nt 1 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre -quiet ...done. Run time: 3.28 s Reconstructing ancestral sequences with iqtree2... iqtree2 -safe -asr -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_5.internal -nt 1 -te /build/gubbins-2.4.1/python/tmpr6__2_cl/multiple_recombinations.iteration_5.tre.rooted -quiet ...done. Run time: 3.33 s Reinserting gaps into the alignment... ...done. Run time: 3.33 s Running Gubbins to detect recombinations... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpr6__2_cl/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 3.35 s Checking for convergence... ...done. Run time: 3.36 s Maximum number of iterations (5) reached. Exiting the main loop. Creating the final output... ...finished. Total run time: 3.36 s --- Gubbins 2.4.1 --- Checking dependencies... ...done. Run time: 0.00 s Checking input files... ...done. Run time: 0.01 s Filtering input alignment... ...done. Run time: 0.01 s Running Gubbins to detect SNPs... gubbins /build/gubbins-2.4.1/python/tmppy_1dwz8/multiple_recombinations.aln ...done. Run time: 0.03 s Entering the main loop. *** Iteration 1 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_1 > /dev/null 2>&1 ...done. Run time: 0.28 s Reconstructing ancestral sequences with raxmlHPC... raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_1.internal -t /build/gubbins-2.4.1/python/tmppy_1dwz8/multiple_recombinations.iteration_1.tre.rooted > /dev/null 2>&1 ...done. Run time: 0.36 s Reinserting gaps into the alignment... ...done. Run time: 0.37 s Running Gubbins to detect recombinations... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmppy_1dwz8/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 0.39 s Checking for convergence... ...done. Run time: 0.39 s *** Iteration 2 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre.phylip -n multiple_recombinations.iteration_2 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre > /dev/null 2>&1 ...done. Run time: 0.54 s Reconstructing ancestral sequences with raxmlHPC... raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_2.internal -t /build/gubbins-2.4.1/python/tmppy_1dwz8/multiple_recombinations.iteration_2.tre.rooted > /dev/null 2>&1 ...done. Run time: 0.67 s Reinserting gaps into the alignment... ...done. Run time: 0.68 s Running Gubbins to detect recombinations... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmppy_1dwz8/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 0.70 s Checking for convergence... ...done. Run time: 0.70 s *** Iteration 3 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre.phylip -n multiple_recombinations.iteration_3 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre > /dev/null 2>&1 ...done. Run time: 0.81 s Reconstructing ancestral sequences with raxmlHPC... raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_3.internal -t /build/gubbins-2.4.1/python/tmppy_1dwz8/multiple_recombinations.iteration_3.tre.rooted > /dev/null 2>&1 ...done. Run time: 0.87 s Reinserting gaps into the alignment... ...done. Run time: 0.88 s Running Gubbins to detect recombinations... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmppy_1dwz8/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 0.90 s Checking for convergence... ...done. Run time: 0.91 s *** Iteration 4 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre.phylip -n multiple_recombinations.iteration_4 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre > /dev/null 2>&1 ...done. Run time: 1.17 s Reconstructing ancestral sequences with raxmlHPC... raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_4.internal -t /build/gubbins-2.4.1/python/tmppy_1dwz8/multiple_recombinations.iteration_4.tre.rooted > /dev/null 2>&1 ...done. Run time: 1.23 s Reinserting gaps into the alignment... ...done. Run time: 1.24 s Running Gubbins to detect recombinations... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmppy_1dwz8/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 1.26 s Checking for convergence... ...done. Run time: 1.27 s *** Iteration 5 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre.phylip -n multiple_recombinations.iteration_5 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre > /dev/null 2>&1 ...done. Run time: 1.55 s Reconstructing ancestral sequences with raxmlHPC... raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_5.internal -t /build/gubbins-2.4.1/python/tmppy_1dwz8/multiple_recombinations.iteration_5.tre.rooted > /dev/null 2>&1 ...done. Run time: 1.62 s Reinserting gaps into the alignment... ...done. Run time: 1.63 s Running Gubbins to detect recombinations... ok test_rename_final_output (gubbins.tests.test_dependencies.TestExternalDependencies.test_rename_final_output) ... ok test_get_recombination_files (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations.test_get_recombination_files) ... ok test_multiple_files_have_one_match (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations.test_multiple_files_have_one_match) ... ok test_reading_embl_file (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations.test_reading_embl_file) ... ok test_two_files_are_different (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations.test_two_files_are_different) ... ok test_two_files_are_same (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations.test_two_files_are_same) ... ok test_concatenate_fasta_files (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods.test_concatenate_fasta_files) ... ok test_get_sequence_names_from_alignment (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods.test_get_sequence_names_from_alignment) ... ok test_number_of_sequences_in_alignment (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods.test_number_of_sequences_in_alignment) ... ok test_reconvert_fasta_file (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods.test_reconvert_fasta_file) ... ok test_reinsert_gaps_into_fasta_file (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods.test_reinsert_gaps_into_fasta_file) ... ok ---------------------------------------------------------------------- Ran 67 tests in 10.475s OK gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmppy_1dwz8/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 1.65 s Checking for convergence... ...done. Run time: 1.66 s Maximum number of iterations (5) reached. Exiting the main loop. Creating the final output... ...finished. Total run time: 1.66 s --- Gubbins 2.4.1 --- Checking dependencies... ...done. Run time: 0.00 s Checking input files... ...done. Run time: 0.00 s Filtering input alignment... ...done. Run time: 0.01 s Running Gubbins to detect SNPs... gubbins /build/gubbins-2.4.1/python/tmpokvpx6vk/multiple_recombinations.aln ...done. Run time: 0.02 s Entering the main loop. *** Iteration 1 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_1 > /dev/null 2>&1 ...done. Run time: 0.29 s Reconstructing ancestral sequences with raxmlHPC... raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_1.internal -t /build/gubbins-2.4.1/python/tmpokvpx6vk/multiple_recombinations.iteration_1.tre.rooted > /dev/null 2>&1 ...done. Run time: 0.37 s Reinserting gaps into the alignment... ...done. Run time: 0.37 s Running Gubbins to detect recombinations... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpokvpx6vk/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 0.40 s Checking for convergence... ...done. Run time: 0.40 s *** Iteration 2 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre.phylip -n multiple_recombinations.iteration_2 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre > /dev/null 2>&1 ...done. Run time: 0.56 s Reconstructing ancestral sequences with raxmlHPC... raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_2.internal -t /build/gubbins-2.4.1/python/tmpokvpx6vk/multiple_recombinations.iteration_2.tre.rooted > /dev/null 2>&1 ...done. Run time: 0.72 s Reinserting gaps into the alignment... ...done. Run time: 0.72 s Running Gubbins to detect recombinations... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpokvpx6vk/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 0.74 s Checking for convergence... ...done. Run time: 0.75 s *** Iteration 3 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre.phylip -n multiple_recombinations.iteration_3 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre > /dev/null 2>&1 ...done. Run time: 0.91 s Reconstructing ancestral sequences with raxmlHPC... raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_3.internal -t /build/gubbins-2.4.1/python/tmpokvpx6vk/multiple_recombinations.iteration_3.tre.rooted > /dev/null 2>&1 ...done. Run time: 0.97 s Reinserting gaps into the alignment... ...done. Run time: 0.97 s Running Gubbins to detect recombinations... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpokvpx6vk/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 1.00 s Checking for convergence... ...done. Run time: 1.00 s *** Iteration 4 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre.phylip -n multiple_recombinations.iteration_4 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre > /dev/null 2>&1 ...done. Run time: 1.27 s Reconstructing ancestral sequences with raxmlHPC... raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_4.internal -t /build/gubbins-2.4.1/python/tmpokvpx6vk/multiple_recombinations.iteration_4.tre.rooted > /dev/null 2>&1 ...done. Run time: 1.33 s Reinserting gaps into the alignment... ...done. Run time: 1.33 s Running Gubbins to detect recombinations... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpokvpx6vk/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 1.36 s Checking for convergence... ...done. Run time: 1.37 s *** Iteration 5 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre.phylip -n multiple_recombinations.iteration_5 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre > /dev/null 2>&1 ...done. Run time: 1.57 s Reconstructing ancestral sequences with raxmlHPC... raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_5.internal -t /build/gubbins-2.4.1/python/tmpokvpx6vk/multiple_recombinations.iteration_5.tre.rooted > /dev/null 2>&1 ...done. Run time: 1.63 s Reinserting gaps into the alignment... ...done. Run time: 1.63 s Running Gubbins to detect recombinations... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpokvpx6vk/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln ...done. Run time: 1.66 s Checking for convergence... ...done. Run time: 1.67 s Maximum number of iterations (5) reached. Exiting the main loop. Creating the final output... ...finished. Total run time: 1.67 s make[1]: Leaving directory '/build/gubbins-2.4.1' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/gubbins-2.4.1' dh_auto_install make -j1 install DESTDIR=/build/gubbins-2.4.1/debian/gubbins AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/gubbins-2.4.1' Making install in src make[3]: Entering directory '/build/gubbins-2.4.1/src' make[4]: Entering directory '/build/gubbins-2.4.1/src' /bin/mkdir -p '/build/gubbins-2.4.1/debian/gubbins/usr/lib/x86_64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libgubbins.la '/build/gubbins-2.4.1/debian/gubbins/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libgubbins.so.0.0.1 /build/gubbins-2.4.1/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 libtool: install: (cd /build/gubbins-2.4.1/debian/gubbins/usr/lib/x86_64-linux-gnu && { ln -s -f libgubbins.so.0.0.1 libgubbins.so.0 || { rm -f libgubbins.so.0 && ln -s libgubbins.so.0.0.1 libgubbins.so.0; }; }) libtool: install: (cd /build/gubbins-2.4.1/debian/gubbins/usr/lib/x86_64-linux-gnu && { ln -s -f libgubbins.so.0.0.1 libgubbins.so || { rm -f libgubbins.so && ln -s libgubbins.so.0.0.1 libgubbins.so; }; }) libtool: install: /usr/bin/install -c .libs/libgubbins.lai /build/gubbins-2.4.1/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.la libtool: install: /usr/bin/install -c .libs/libgubbins.a /build/gubbins-2.4.1/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.a libtool: install: chmod 644 /build/gubbins-2.4.1/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.a libtool: install: ranlib /build/gubbins-2.4.1/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /bin/mkdir -p '/build/gubbins-2.4.1/debian/gubbins/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c gubbins '/build/gubbins-2.4.1/debian/gubbins/usr/bin' libtool: warning: 'libgubbins.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/gubbins /build/gubbins-2.4.1/debian/gubbins/usr/bin/gubbins make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/gubbins-2.4.1/src' make[3]: Leaving directory '/build/gubbins-2.4.1/src' Making install in release make[3]: Entering directory '/build/gubbins-2.4.1/release' make[4]: Entering directory '/build/gubbins-2.4.1/release' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/gubbins-2.4.1/release' make[3]: Leaving directory '/build/gubbins-2.4.1/release' make[3]: Entering directory '/build/gubbins-2.4.1' make[4]: Entering directory '/build/gubbins-2.4.1' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/gubbins-2.4.1' make[3]: Leaving directory '/build/gubbins-2.4.1' make[2]: Leaving directory '/build/gubbins-2.4.1' # pybuild --install --system=distutils cd python && \ python3 setup.py install --root=../debian/gubbins --install-layout=deb --install-lib=/usr/share/gubbins --install-scripts=/usr/share/gubbins running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py creating build creating build/lib creating build/lib/scripts copying scripts/run_gubbins.py -> build/lib/scripts copying scripts/gubbins_drawer.py -> build/lib/scripts copying scripts/__init__.py -> build/lib/scripts creating build/lib/gubbins copying gubbins/treebuilders.py -> build/lib/gubbins copying gubbins/common.py -> build/lib/gubbins copying gubbins/utils.py -> build/lib/gubbins copying gubbins/__init__.py -> build/lib/gubbins copying gubbins/ValidateFastaAlignment.py -> build/lib/gubbins copying gubbins/PreProcessFasta.py -> build/lib/gubbins creating build/lib/gubbins/tests copying gubbins/tests/test_validate_starting_tree.py -> build/lib/gubbins/tests copying gubbins/tests/test_validate_fasta_input.py -> build/lib/gubbins/tests copying gubbins/tests/test_utils.py -> build/lib/gubbins/tests copying gubbins/tests/test_treebuilders.py -> build/lib/gubbins/tests copying gubbins/tests/test_tree_methods.py -> build/lib/gubbins/tests copying gubbins/tests/test_pre_process_fasta.py -> build/lib/gubbins/tests copying gubbins/tests/test_dependencies.py -> build/lib/gubbins/tests copying gubbins/tests/test_converging_recombinations.py -> build/lib/gubbins/tests copying gubbins/tests/test_alignment_python_methods.py -> build/lib/gubbins/tests copying gubbins/tests/__init__.py -> build/lib/gubbins/tests running install_lib creating ../debian/gubbins/usr/share creating ../debian/gubbins/usr/share/gubbins creating ../debian/gubbins/usr/share/gubbins/gubbins creating ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/__init__.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_alignment_python_methods.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_converging_recombinations.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_dependencies.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_pre_process_fasta.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_tree_methods.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_treebuilders.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_utils.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_validate_fasta_input.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_validate_starting_tree.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/PreProcessFasta.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/ValidateFastaAlignment.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/__init__.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/utils.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/common.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/treebuilders.py -> ../debian/gubbins/usr/share/gubbins/gubbins creating ../debian/gubbins/usr/share/gubbins/scripts copying build/lib/scripts/__init__.py -> ../debian/gubbins/usr/share/gubbins/scripts copying build/lib/scripts/gubbins_drawer.py -> ../debian/gubbins/usr/share/gubbins/scripts copying build/lib/scripts/run_gubbins.py -> ../debian/gubbins/usr/share/gubbins/scripts byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/__init__.py to __init__.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_alignment_python_methods.py to test_alignment_python_methods.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_converging_recombinations.py to test_converging_recombinations.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_dependencies.py to test_dependencies.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_pre_process_fasta.py to test_pre_process_fasta.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_tree_methods.py to test_tree_methods.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_treebuilders.py to test_treebuilders.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_utils.py to test_utils.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_validate_fasta_input.py to test_validate_fasta_input.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_validate_starting_tree.py to test_validate_starting_tree.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/PreProcessFasta.py to PreProcessFasta.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/ValidateFastaAlignment.py to ValidateFastaAlignment.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/__init__.py to __init__.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/utils.py to utils.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/common.py to common.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/treebuilders.py to treebuilders.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/scripts/__init__.py to __init__.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/scripts/gubbins_drawer.py to gubbins_drawer.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/scripts/run_gubbins.py to run_gubbins.cpython-311.pyc running install_egg_info running egg_info writing gubbins.egg-info/PKG-INFO writing dependency_links to gubbins.egg-info/dependency_links.txt writing entry points to gubbins.egg-info/entry_points.txt writing requirements to gubbins.egg-info/requires.txt writing top-level names to gubbins.egg-info/top_level.txt reading manifest file 'gubbins.egg-info/SOURCES.txt' adding license file 'LICENSE.txt' writing manifest file 'gubbins.egg-info/SOURCES.txt' Copying gubbins.egg-info to ../debian/gubbins/usr/share/gubbins/gubbins-2.4.1.egg-info Skipping SOURCES.txt running install_scripts Installing run_gubbins.py script to ../debian/gubbins/usr/share/gubbins make[1]: Leaving directory '/build/gubbins-2.4.1' debian/rules override_dh_install make[1]: Entering directory '/build/gubbins-2.4.1' dh_install find debian -name "*.la" -delete find debian -name "*.a" -delete mkdir -p debian/gubbins/usr/lib/gubbins mv debian/gubbins/usr/bin/gubbins debian/gubbins/usr/lib/gubbins make[1]: Leaving directory '/build/gubbins-2.4.1' dh_installdocs dh_installchangelogs dh_installman dh_python3 dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dwz: debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1: DWARF compression not beneficial - old size 67489 new size 68435 dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: symbol gzread used by debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzclose used by debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzopen used by debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/gubbins/usr/lib/gubbins/gubbins was not linked against libz.so.1 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'gubbins-dbgsym' in '../gubbins-dbgsym_2.4.1-5_amd64.deb'. dpkg-deb: building package 'gubbins' in '../gubbins_2.4.1-5_amd64.deb'. dpkg-genbuildinfo --build=binary -O../gubbins_2.4.1-5_amd64.buildinfo dpkg-genchanges --build=binary -O../gubbins_2.4.1-5_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/3484544 and its subdirectories I: Current time: Fri May 17 23:54:06 -12 2024 I: pbuilder-time-stamp: 1716033246 Sun Apr 16 05:31:05 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Sun Apr 16 05:31:05 UTC 2023 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Sun Apr 16 05:42:32 UTC 2023 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Sun Apr 16 05:42:33 UTC 2023 I: gubbins_2.4.1-5_amd64.changes: Format: 1.8 Date: Sun, 13 Feb 2022 15:17:59 +0100 Source: gubbins Binary: gubbins gubbins-dbgsym Architecture: amd64 Version: 2.4.1-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: gubbins - phylogenetic analysis of genome sequences Closes: 1005476 Changes: gubbins (2.4.1-5) unstable; urgency=medium . * Team Upload. [ Andreas Tille ] * New upstream version * Standards-Version: 4.6.0 (routine-update) * Build-Depends: python3-scipy , python3-multiprocess , python3-wheel * Remove trailing whitespace in debian/changelog (routine-update) * Adapt test to iqtree2 Closes: #1005476 . [ Étienne Mollier ] * d/control: update uploader address * d/watch: bump to uscan version 4 and fix broken link to github . [ Nilesh Patra ] * Switch from nosetest -> pytest Checksums-Sha1: d264fa6205df601997514c4a9b4eac2d9850e601 72572 gubbins-dbgsym_2.4.1-5_amd64.deb 6b08521168f1e8ba6e6ebb67e15c931220f61386 9164 gubbins_2.4.1-5_amd64.buildinfo a4f2af8ee8ea53a6e22a9992add590f1ac76d719 57512 gubbins_2.4.1-5_amd64.deb Checksums-Sha256: 86814c24bb05972c14ca567daa6223f6f31b127a37ec2792d06825b4c12497b6 72572 gubbins-dbgsym_2.4.1-5_amd64.deb 05e249d0ba529ea1ced95ff161c13eb8872bf5e0c5a39d2ca3bd430d67c77dae 9164 gubbins_2.4.1-5_amd64.buildinfo 625efd0bd87bfd94644fde510281d3b6f53c504a18437137c8202e819b3e357c 57512 gubbins_2.4.1-5_amd64.deb Files: f57566ed6becccc641d85d1f4a342e94 72572 debug optional gubbins-dbgsym_2.4.1-5_amd64.deb 7274fb8fad40d8706c9ee696a0dbd61f 9164 science optional gubbins_2.4.1-5_amd64.buildinfo f34b4d16f1a40a6a907f110195b3b359 57512 science optional gubbins_2.4.1-5_amd64.deb Sun Apr 16 05:42:34 UTC 2023 I: diffoscope 240 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.whOOMsYZ/gubbins_2.4.1-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.whOOMsYZ/gubbins_2.4.1-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.whOOMsYZ/gubbins_2.4.1-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.whOOMsYZ/b1/gubbins_2.4.1-5_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.whOOMsYZ/b2/gubbins_2.4.1-5_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: 0.443s) 0.443s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.041s) 0.041s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Sun Apr 16 05:42:35 UTC 2023 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists. Sun Apr 16 05:42:35 UTC 2023 I: gubbins from bookworm built successfully and reproducibly on amd64. Sun Apr 16 05:42:43 UTC 2023 I: Submitting .buildinfo files to external archives: Sun Apr 16 05:42:43 UTC 2023 I: Submitting 12K b1/gubbins_2.4.1-5_amd64.buildinfo.asc Sun Apr 16 05:42:45 UTC 2023 I: Submitting 12K b2/gubbins_2.4.1-5_amd64.buildinfo.asc Sun Apr 16 05:42:47 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Apr 16 05:42:47 UTC 2023 I: Done submitting .buildinfo files. Sun Apr 16 05:42:47 UTC 2023 I: Removing signed gubbins_2.4.1-5_amd64.buildinfo.asc files: removed './b1/gubbins_2.4.1-5_amd64.buildinfo.asc' removed './b2/gubbins_2.4.1-5_amd64.buildinfo.asc'