Sun Jul 18 18:24:03 UTC 2021 I: starting to build gubbins/bullseye/i386 on jenkins on '2021-07-18 18:23' Sun Jul 18 18:24:03 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_4/14739/console.log Sun Jul 18 18:24:03 UTC 2021 I: Downloading source for bullseye/gubbins=2.4.1-4 --2021-07-18 18:24:04-- http://cdn-fastly.deb.debian.org/debian/pool/main/g/gubbins/gubbins_2.4.1-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2193 (2.1K) Saving to: ‘gubbins_2.4.1-4.dsc’ 0K .. 100% 21.2M=0s 2021-07-18 18:24:04 (21.2 MB/s) - ‘gubbins_2.4.1-4.dsc’ saved [2193/2193] Sun Jul 18 18:24:04 UTC 2021 I: gubbins_2.4.1-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: gubbins Binary: gubbins Architecture: any Version: 2.4.1-4 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://sanger-pathogens.github.io/gubbins/ Standards-Version: 4.5.0 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, fasttree, iqtree, raxml (>= 8.2.12+dfsg-5), python3-setuptools, zlib1g-dev, check, python3, python3-biopython, python3-dendropy, python3-reportlab, python3-nose, pkg-config Package-List: gubbins deb science optional arch=any Checksums-Sha1: 6bbbb5ce60a153b00f6eaaf3ac4a3c34c0591900 609778 gubbins_2.4.1.orig.tar.gz a444135f3956bef243fd7ce195b1af24c52eb069 6988 gubbins_2.4.1-4.debian.tar.xz Checksums-Sha256: df0f6f475ef402d6f2f67abb870dcb2c59f3333bf6a00af76251bb102f63e17b 609778 gubbins_2.4.1.orig.tar.gz 32ec94912079a05c0f3fdfc2e56f3807b21f16a75d2081dc2ae6422a8adc0a17 6988 gubbins_2.4.1-4.debian.tar.xz Files: 6b0f95ef9e2ff7a34b58dbbf53d5e593 609778 gubbins_2.4.1.orig.tar.gz 436dc6a3cbd3c71225f28cb3843d1df8 6988 gubbins_2.4.1-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAmBpmqsUHG5wYXRyYTk3 NEBnbWFpbC5jb20ACgkQALrnSzQzafHOzw//f5R1dZ7LuDXE1Q3zT9ngdVnlP6Zv 21DwsS0n/TJq2l0crFvVr9p8p0YDrZHqtNVE9jh4pDgLp4Wi8yGVexjHbmuc0yec EyvARe/LGyV1B2017rKS+l5f+OKP0H7r+ekLBEm5kEY6t0Mz83D8n6zznyRmTC4j +f5VBOwgtjIvEPr1wpoj+lYJSOEIF4DzHYsS/DCK4izgUgyisNqYhQyPUZ+aEHTd DjgSAuZD8NYDRlHDYPOS4awKkBK+sQAX46AsZZIRFpro5UlMddctDad0oydoYQxv PkCGAVbBktU2rDfIJ9NqWoLaFmwlfcjrC1HQKDa/+ZGV8sLNsRJ55RxN3367fakp ycSypCxC5O+TXdIsYs1YEXNimdzkd6tW9LXKgIN4kcKLgKd8w8rnMn1K6fn1tl+w yp3mLRFh1h9tpAzvOgQsVmxCZe2/cFsJq953NjnsrGGY812jKFEmfcI3Zh2CALsw O+eTbMmjCCFmUX95B4akUN4HkinITsw0IXEvO0GI53dlyX5amwYXk1CgxvHOkwX4 6NEvfLF+BSvpLi+dnhv6xSk352EI2Hb06rX9lAH0e3Czk29lOOF/HMk/aqYjmC8m 06JJ8mYi/bJRprMzHh+sq4ODJLm/ShVcno5Y2c+K7FkpQnzZNmzyQ5+UXex9yVRX t0ENRL3/Kffe0HI= =Krq7 -----END PGP SIGNATURE----- Sun Jul 18 18:24:04 UTC 2021 I: Checking whether the package is not for us Sun Jul 18 18:24:04 UTC 2021 I: Starting 1st build on remote node ionos16-i386.debian.net. Sun Jul 18 18:24:04 UTC 2021 I: Preparing to do remote build '1' on ionos16-i386.debian.net. Sun Jul 18 18:24:55 UTC 2021 I: Deleting $TMPDIR on ionos16-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Aug 20 12:47:05 -12 2022 I: pbuilder-time-stamp: 1661042825 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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: using eatmydata during job I: Copying source file I: copying [gubbins_2.4.1-4.dsc] I: copying [./gubbins_2.4.1.orig.tar.gz] I: copying [./gubbins_2.4.1-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.DyhyMJOv/trustedkeys.kbx': General error gpgv: Signature made Sat Apr 3 22:53:31 2021 -12 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./gubbins_2.4.1-4.dsc 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_2.4.1-4.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 spelling-error-in-binary.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/65183/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=18' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='b2dcd90e819b414284bba34993c2c185' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='65183' 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/tmp.OkaTSuw4yV/pbuilderrc_3nyz --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.OkaTSuw4yV/b1 --logfile b1/build.log gubbins_2.4.1-4.dsc' SUDO_GID='112' SUDO_UID='107' 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 ionos16-i386 4.19.0-17-amd64 #1 SMP Debian 4.19.194-2 (2021-06-21) x86_64 GNU/Linux I: ls -l /bin total 5776 -rwxr-xr-x 1 root root 1367848 Jun 21 2021 bash -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash -rwxr-xr-x 1 root root 124904 Sep 22 2020 date -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd -rwxr-xr-x 1 root root 100752 Sep 22 2020 df -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir -rwxr-xr-x 1 root root 83644 Feb 7 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 34664 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 71928 Feb 7 2021 findmnt -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 100952 Mar 2 2021 gzip -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln -rwxr-xr-x 1 root root 55572 Feb 7 2020 login -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls -rwxr-xr-x 1 root root 153124 Feb 7 2021 lsblk -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 58920 Feb 7 2021 more -rwsr-xr-x 1 root root 50720 Feb 7 2021 mount -rwxr-xr-x 1 root root 13856 Feb 7 2021 mountpoint -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Jun 21 2021 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 20 03:46 sh -> dash -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty -rwsr-xr-x 1 root root 79396 Feb 7 2021 su -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync -rwxr-xr-x 1 root root 602584 Feb 16 2021 tar -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch -rwxr-xr-x 1 root root 34664 Sep 22 2020 true -rwxr-xr-x 1 root root 17768 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30236 Feb 7 2021 umount -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir -rwxr-xr-x 1 root root 63024 Feb 7 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/65183/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: i386 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, fasttree, iqtree, raxml (>= 8.2.12+dfsg-5), python3-setuptools, zlib1g-dev, check, python3, python3-biopython, python3-dendropy, python3-reportlab, python3-nose, pkg-config dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19675 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 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-nose; however: Package python3-nose is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config 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} gettext{a} gettext-base{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} iqtree{a} libarchive-zip-perl{a} libblas3{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} libfabric1{a} libfile-stripnondeterminism-perl{a} libfreetype6{a} libgfortran5{a} libglib2.0-0{a} libhwloc-plugins{a} libhwloc15{a} libibverbs1{a} libicu67{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} liblapack3{a} liblcms2-2{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libmpdec3{a} libnl-3-200{a} libnl-route-3-200{a} libopenmpi3{a} libpciaccess0{a} libpipeline1{a} libpmix2{a} libpng16-16{a} libpsm-infinipath1{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} librdmacm1{a} libreadline8{a} libsigsegv2{a} libsub-override-perl{a} libsubunit-dev{a} libsubunit0{a} libtiff5{a} libtool{a} libuchardet0{a} libwebp6{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} m4{a} mailcap{a} man-db{a} media-types{a} mime-support{a} ocl-icd-libopencl1{a} pkg-config{a} po-debconf{a} python3{a} python3-biopython{a} python3-dendropy{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-nose{a} python3-numpy{a} python3-pil{a} python3-pkg-resources{a} python3-reportlab{a} python3-reportlab-accel{a} python3-setuptools{a} python3.9{a} python3.9-minimal{a} raxml{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx ncbi-blast+ python-biopython-doc python3-olefile python3-renderpm shared-mime-info wget xdg-user-dirs 0 packages upgraded, 105 newly installed, 0 to remove and 0 not upgraded. Need to get 48.1 MB of archives. After unpacking 192 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-7 [148 kB] Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB] Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB] Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB] Get: 6 http://deb.debian.org/debian bullseye/main i386 libpython3.9-minimal i386 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libexpat1 i386 2.2.10-2 [98.8 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 python3.9-minimal i386 3.9.2-1 [1956 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 python3-minimal i386 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 mailcap all 3.69 [31.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 mime-support all 3.66 [10.9 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 libmpdec3 i386 2.5.1-1 [91.9 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 readline-common all 8.1-1 [73.7 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 libreadline8 i386 8.1-1 [173 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 libpython3.9-stdlib i386 3.9.2-1 [1703 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 python3.9 i386 3.9.2-1 [466 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 libpython3-stdlib i386 3.9.2-3 [21.4 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 python3 i386 3.9.2-3 [37.9 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3 [273 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3 [133 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3 [69.0 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 libsubunit0 i386 1.4.0-3 [9884 B] Get: 32 http://deb.debian.org/debian bullseye/main i386 libsubunit-dev i386 1.4.0-3 [10.9 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 check i386 0.15.2-2 [118 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 42 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-7 [8775 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7 [728 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 python3-distutils all 3.9.2-1 [143 kB] Get: 51 http://deb.debian.org/debian bullseye/main i386 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 52 http://deb.debian.org/debian bullseye/main i386 fasttree i386 2.1.11-2 [183 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 libnl-3-200 i386 3.4.0-1+b1 [66.4 kB] Get: 54 http://deb.debian.org/debian bullseye/main i386 libnl-route-3-200 i386 3.4.0-1+b1 [168 kB] Get: 55 http://deb.debian.org/debian bullseye/main i386 libibverbs1 i386 33.2-1 [64.6 kB] Get: 56 http://deb.debian.org/debian bullseye/main i386 ibverbs-providers i386 33.2-1 [275 kB] Get: 57 http://deb.debian.org/debian bullseye/main i386 libevent-core-2.1-7 i386 2.1.12-stable-1 [148 kB] Get: 58 http://deb.debian.org/debian bullseye/main i386 libevent-pthreads-2.1-7 i386 2.1.12-stable-1 [57.3 kB] Get: 59 http://deb.debian.org/debian bullseye/main i386 libpsm-infinipath1 i386 3.3+20.604758e7-6.1 [178 kB] Get: 60 http://deb.debian.org/debian bullseye/main i386 librdmacm1 i386 33.2-1 [75.2 kB] Get: 61 http://deb.debian.org/debian bullseye/main i386 libfabric1 i386 1.11.0-2 [518 kB] Get: 62 http://deb.debian.org/debian bullseye/main i386 libhwloc15 i386 2.4.1+dfsg-1 [164 kB] Get: 63 http://deb.debian.org/debian bullseye/main i386 libpciaccess0 i386 0.16-1 [55.7 kB] Get: 64 http://deb.debian.org/debian bullseye/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 65 http://deb.debian.org/debian bullseye/main i386 libmd0 i386 1.0.3-3 [28.9 kB] Get: 66 http://deb.debian.org/debian bullseye/main i386 libbsd0 i386 0.11.3-1 [111 kB] Get: 67 http://deb.debian.org/debian bullseye/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 68 http://deb.debian.org/debian bullseye/main i386 libxcb1 i386 1.14-3 [144 kB] Get: 69 http://deb.debian.org/debian bullseye/main i386 libx11-data all 2:1.7.1-1 [310 kB] Get: 70 http://deb.debian.org/debian bullseye/main i386 libx11-6 i386 2:1.7.1-1 [796 kB] Get: 71 http://deb.debian.org/debian bullseye/main i386 libxext6 i386 2:1.3.3-1.1 [55.2 kB] Get: 72 http://deb.debian.org/debian bullseye/main i386 libxnvctrl0 i386 460.73.01-1 [26.8 kB] Get: 73 http://deb.debian.org/debian bullseye/main i386 ocl-icd-libopencl1 i386 2.2.14-2 [45.0 kB] Get: 74 http://deb.debian.org/debian bullseye/main i386 libhwloc-plugins i386 2.4.1+dfsg-1 [22.0 kB] Get: 75 http://deb.debian.org/debian bullseye/main i386 libpmix2 i386 4.0.0-4 [582 kB] Get: 76 http://deb.debian.org/debian bullseye/main i386 libopenmpi3 i386 4.1.0-10 [2144 kB] Get: 77 http://deb.debian.org/debian bullseye/main i386 iqtree i386 1.6.12+dfsg-1 [2595 kB] Get: 78 http://deb.debian.org/debian bullseye/main i386 libblas3 i386 3.9.0-3 [147 kB] Get: 79 http://deb.debian.org/debian bullseye/main i386 libbrotli1 i386 1.0.9-2+b2 [286 kB] Get: 80 http://deb.debian.org/debian bullseye/main i386 libdeflate0 i386 1.7-1 [48.4 kB] Get: 81 http://deb.debian.org/debian bullseye/main i386 libpng16-16 i386 1.6.37-3 [303 kB] Get: 82 http://deb.debian.org/debian bullseye/main i386 libfreetype6 i386 2.10.4+dfsg-1 [429 kB] Get: 83 http://deb.debian.org/debian bullseye/main i386 libgfortran5 i386 10.2.1-6 [643 kB] Get: 84 http://deb.debian.org/debian bullseye/main i386 libglib2.0-0 i386 2.66.8-1 [1437 kB] Get: 85 http://deb.debian.org/debian bullseye/main i386 libimagequant0 i386 2.12.2-1.1 [32.4 kB] Get: 86 http://deb.debian.org/debian bullseye/main i386 libjbig0 i386 2.1-3.1+b2 [31.5 kB] Get: 87 http://deb.debian.org/debian bullseye/main i386 libjpeg62-turbo i386 1:2.0.6-4 [160 kB] Get: 88 http://deb.debian.org/debian bullseye/main i386 liblapack3 i386 3.9.0-3 [1960 kB] Get: 89 http://deb.debian.org/debian bullseye/main i386 liblcms2-2 i386 2.12~rc1-2 [161 kB] Get: 90 http://deb.debian.org/debian bullseye/main i386 libwebp6 i386 0.6.1-2.1 [269 kB] Get: 91 http://deb.debian.org/debian bullseye/main i386 libtiff5 i386 4.2.0-1 [305 kB] Get: 92 http://deb.debian.org/debian bullseye/main i386 libwebpdemux2 i386 0.6.1-2.1 [88.2 kB] Get: 93 http://deb.debian.org/debian bullseye/main i386 libwebpmux3 i386 0.6.1-2.1 [99.0 kB] Get: 94 http://deb.debian.org/debian bullseye/main i386 pkg-config i386 0.29.2-1 [66.3 kB] Get: 95 http://deb.debian.org/debian bullseye/main i386 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 96 http://deb.debian.org/debian bullseye/main i386 python3-numpy i386 1:1.19.5-1 [3600 kB] Get: 97 http://deb.debian.org/debian bullseye/main i386 python3-reportlab-accel i386 3.5.59-2 [39.9 kB] Get: 98 http://deb.debian.org/debian bullseye/main i386 python3-pil i386 8.1.2+dfsg-0.2 [444 kB] Get: 99 http://deb.debian.org/debian bullseye/main i386 python3-reportlab all 3.5.59-2 [575 kB] Get: 100 http://deb.debian.org/debian bullseye/main i386 python3-biopython i386 1.78+dfsg-4 [1401 kB] Get: 101 http://deb.debian.org/debian bullseye/main i386 python3-dendropy all 4.5.1-1 [273 kB] Get: 102 http://deb.debian.org/debian bullseye/main i386 python3-nose all 1.3.7-7 [133 kB] Get: 103 http://deb.debian.org/debian bullseye/main i386 python3-setuptools all 52.0.0-4 [366 kB] Get: 104 http://deb.debian.org/debian bullseye/main i386 raxml i386 8.2.12+dfsg-6+b4 [973 kB] Get: 105 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2 [194 kB] Fetched 48.1 MB in 1s (86.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19675 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-7_i386.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../1-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_i386.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../3-libpipeline1_1.5.3-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_i386.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libpython3.9-minimal:i386. Preparing to unpack .../5-libpython3.9-minimal_3.9.2-1_i386.deb ... Unpacking libpython3.9-minimal:i386 (3.9.2-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../6-libexpat1_2.2.10-2_i386.deb ... Unpacking libexpat1:i386 (2.2.10-2) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../7-python3.9-minimal_3.9.2-1_i386.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:i386 (3.9.2-1) ... Setting up libexpat1:i386 (2.2.10-2) ... Setting up python3.9-minimal (3.9.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20542 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_i386.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package mailcap. Preparing to unpack .../2-mailcap_3.69_all.deb ... Unpacking mailcap (3.69) ... 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 libmpdec3:i386. Preparing to unpack .../4-libmpdec3_2.5.1-1_i386.deb ... Unpacking libmpdec3:i386 (2.5.1-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:i386. Preparing to unpack .../6-libreadline8_8.1-1_i386.deb ... Unpacking libreadline8:i386 (8.1-1) ... Selecting previously unselected package libpython3.9-stdlib:i386. Preparing to unpack .../7-libpython3.9-stdlib_3.9.2-1_i386.deb ... Unpacking libpython3.9-stdlib:i386 (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../8-python3.9_3.9.2-1_i386.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../9-libpython3-stdlib_3.9.2-3_i386.deb ... Unpacking libpython3-stdlib:i386 (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... 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 ... 20987 files and directories currently installed.) Preparing to unpack .../00-python3_3.9.2-3_i386.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.39-3_i386.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../03-libmagic1_1%3a5.39-3_i386.deb ... Unpacking libmagic1:i386 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.39-3_i386.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-4_i386.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../06-libsigsegv2_2.13-1_i386.deb ... Unpacking libsigsegv2:i386 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../07-m4_1.4.18-5_i386.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../08-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../09-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../10-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../11-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libsubunit0:i386. Preparing to unpack .../12-libsubunit0_1.4.0-3_i386.deb ... Unpacking libsubunit0:i386 (1.4.0-3) ... Selecting previously unselected package libsubunit-dev:i386. Preparing to unpack .../13-libsubunit-dev_1.4.0-3_i386.deb ... Unpacking libsubunit-dev:i386 (1.4.0-3) ... Selecting previously unselected package check:i386. Preparing to unpack .../14-check_0.15.2-2_i386.deb ... Unpacking check:i386 (0.15.2-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.11.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.11.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.11.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.11.0-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../22-libelf1_0.183-1_i386.deb ... Unpacking libelf1:i386 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.13+20210201-1_i386.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:i386. Preparing to unpack .../24-libicu67_67.1-7_i386.deb ... Unpacking libicu67:i386 (67.1-7) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../25-libxml2_2.9.10+dfsg-6.7_i386.deb ... Unpacking libxml2:i386 (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-4_i386.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../30-python3-lib2to3_3.9.2-1_all.deb ... Unpacking python3-lib2to3 (3.9.2-1) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../31-python3-distutils_3.9.2-1_all.deb ... Unpacking python3-distutils (3.9.2-1) ... Selecting previously unselected package dh-python. Preparing to unpack .../32-dh-python_4.20201102+nmu1_all.deb ... Unpacking dh-python (4.20201102+nmu1) ... Selecting previously unselected package fasttree. Preparing to unpack .../33-fasttree_2.1.11-2_i386.deb ... Unpacking fasttree (2.1.11-2) ... Selecting previously unselected package libnl-3-200:i386. Preparing to unpack .../34-libnl-3-200_3.4.0-1+b1_i386.deb ... Unpacking libnl-3-200:i386 (3.4.0-1+b1) ... Selecting previously unselected package libnl-route-3-200:i386. Preparing to unpack .../35-libnl-route-3-200_3.4.0-1+b1_i386.deb ... Unpacking libnl-route-3-200:i386 (3.4.0-1+b1) ... Selecting previously unselected package libibverbs1:i386. Preparing to unpack .../36-libibverbs1_33.2-1_i386.deb ... Unpacking libibverbs1:i386 (33.2-1) ... Selecting previously unselected package ibverbs-providers:i386. Preparing to unpack .../37-ibverbs-providers_33.2-1_i386.deb ... Unpacking ibverbs-providers:i386 (33.2-1) ... Selecting previously unselected package libevent-core-2.1-7:i386. Preparing to unpack .../38-libevent-core-2.1-7_2.1.12-stable-1_i386.deb ... Unpacking libevent-core-2.1-7:i386 (2.1.12-stable-1) ... Selecting previously unselected package libevent-pthreads-2.1-7:i386. Preparing to unpack .../39-libevent-pthreads-2.1-7_2.1.12-stable-1_i386.deb ... Unpacking libevent-pthreads-2.1-7:i386 (2.1.12-stable-1) ... Selecting previously unselected package libpsm-infinipath1. Preparing to unpack .../40-libpsm-infinipath1_3.3+20.604758e7-6.1_i386.deb ... Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.1) ... Selecting previously unselected package librdmacm1:i386. Preparing to unpack .../41-librdmacm1_33.2-1_i386.deb ... Unpacking librdmacm1:i386 (33.2-1) ... Selecting previously unselected package libfabric1. Preparing to unpack .../42-libfabric1_1.11.0-2_i386.deb ... Unpacking libfabric1 (1.11.0-2) ... Selecting previously unselected package libhwloc15:i386. Preparing to unpack .../43-libhwloc15_2.4.1+dfsg-1_i386.deb ... Unpacking libhwloc15:i386 (2.4.1+dfsg-1) ... Selecting previously unselected package libpciaccess0:i386. Preparing to unpack .../44-libpciaccess0_0.16-1_i386.deb ... Unpacking libpciaccess0:i386 (0.16-1) ... Selecting previously unselected package libxau6:i386. Preparing to unpack .../45-libxau6_1%3a1.0.9-1_i386.deb ... Unpacking libxau6:i386 (1:1.0.9-1) ... Selecting previously unselected package libmd0:i386. Preparing to unpack .../46-libmd0_1.0.3-3_i386.deb ... Unpacking libmd0:i386 (1.0.3-3) ... Selecting previously unselected package libbsd0:i386. Preparing to unpack .../47-libbsd0_0.11.3-1_i386.deb ... Unpacking libbsd0:i386 (0.11.3-1) ... Selecting previously unselected package libxdmcp6:i386. Preparing to unpack .../48-libxdmcp6_1%3a1.1.2-3_i386.deb ... Unpacking libxdmcp6:i386 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:i386. Preparing to unpack .../49-libxcb1_1.14-3_i386.deb ... Unpacking libxcb1:i386 (1.14-3) ... 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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 dpkg-buildpackage: info: source package gubbins dpkg-buildpackage: info: source version 2.4.1-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 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: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=i686-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/i386-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 thread-safe 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... i686-pc-linux-gnu checking host system type... i686-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 we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... 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 i686-pc-linux-gnu file names to i686-pc-linux-gnu format... func_convert_file_noop checking how to convert i686-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 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 how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.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) 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 we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (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 we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) 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) 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... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... 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 zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking math.h usability... yes checking math.h presence... 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... 3.9 checking for python3 platform... linux checking for python3 script directory... ${prefix}/lib/python3.9/site-packages checking for python3 extension module directory... ${exec_prefix}/lib/python3.9/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 -j18 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 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat 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-fstack-protector-strong -Wformat -Werror=format-security -c -o parse_vcf.lo parse_vcf.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylip_of_snp_sites.lo phylip_of_snp_sites.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o seqUtil.lo seqUtil.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snp_searching.lo snp_searching.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/gubbins-2.4.1=. 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alignment_file.c -fPIC -DPIC -o .libs/alignment_file.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c parse_vcf.c -fPIC -DPIC -o .libs/parse_vcf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c Newickform.c -fPIC -DPIC -o .libs/Newickform.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c gff_file.c -fPIC -DPIC -o .libs/gff_file.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c 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 -fdebug-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c gubbins.c -fPIC -DPIC -o .libs/gubbins.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c phylip_of_snp_sites.c -fPIC -DPIC -o .libs/phylip_of_snp_sites.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-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 -fdebug-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 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c vcf.c -fPIC -DPIC -o .libs/vcf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c tree_scaling.c -o tree_scaling.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 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-o branch_sequences.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -fdebug-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/i386-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 -fdebug-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 -fdebug-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 -j18 check 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 -pthread -g -O2 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-fdebug-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 -pthread -g -O2 -fdebug-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 -pthread -g -O2 -fdebug-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 -pthread -g -O2 -fdebug-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 -pthread -g -O2 -fdebug-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/check_branch_sequences.c: In function 'check_copy_and_concat_2d_integer_arrays_fn': ../tests/check_branch_sequences.c:67:16: 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"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check_snp_sites.c: In function 'valid_alignment_with_one_line_per_sequence_fn': ../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:42:133: 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:43:139: 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:44:153: 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"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../tests/check_gubbins.c:4: ../tests/check_gubbins.c: In function 'check_gubbins_no_recombinations_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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/bash ../libtool --tag=CC --mode=link gcc -I../tests -pthread -g -O2 -fdebug-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 -pthread -g -O2 -fdebug-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 -pthread 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' writing manifest file 'gubbins.egg-info/SOURCES.txt' running build_ext /build/gubbins-2.4.1/python/gubbins/common.py:538: DeprecationWarning: invalid escape sequence \d elif re.match('^\d', vcf_line) is not None: /build/gubbins-2.4.1/python/gubbins/common.py:613: DeprecationWarning: invalid escape sequence \d search_obj = re.search('misc_feature ([\d]+)..([\d]+)$', line) /build/gubbins-2.4.1/python/gubbins/common.py:620: DeprecationWarning: invalid escape sequence \= search_taxa = re.search('taxa\=\"([^"]+)\"', line) test_concatenate_fasta_files (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods) ... ok test_get_sequence_names_from_alignment (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods) ... ok test_number_of_sequences_in_alignment (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods) ... ok test_reconvert_fasta_file (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods) ... ok test_reinsert_gaps_into_fasta_file (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods) ... ok test_get_recombination_files (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations) ... ok test_multiple_files_have_one_match (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations) ... ok test_reading_embl_file (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations) ... ok test_two_files_are_different (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations) ... ok test_two_files_are_same (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations) ... ok test_cleanup (gubbins.tests.test_dependencies.TestExternalDependencies) ... ok test_fasttree (gubbins.tests.test_dependencies.TestExternalDependencies) ... ok test_hybrid (gubbins.tests.test_dependencies.TestExternalDependencies) ... ok test_iqtree (gubbins.tests.test_dependencies.TestExternalDependencies) ... ok test_raxml (gubbins.tests.test_dependencies.TestExternalDependencies) ... ok test_rename_final_output (gubbins.tests.test_dependencies.TestExternalDependencies) ... ok test_dont_filter_input_file_with_multiple_duplicate_sequences (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok test_filter_out_alignments_with_too_much_missing_data (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok test_input_file_with_all_duplicate_sequences (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok test_input_file_with_multiple_duplicate_sequences (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok test_input_file_with_no_duplicate_sequences (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok test_input_file_with_one_duplicate_sequences (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok test_filter_out_removed_taxa_from_tree (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok test_has_tree_been_seen_before (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok test_internal_node_taxons_removed_when_used_as_starting_tree (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok test_remove_internal_node_labels (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok test_reroot_tree (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok test_reroot_tree_at_midpoint (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok test_reroot_tree_with_outgroup (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok test_reroot_tree_with_outgroups (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok test_reroot_tree_with_outgroups_all_in_different_clade (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok test_reroot_tree_with_outgroups_all_in_one_clade (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok test_reroot_tree_with_outgroups_all_in_one_clade_large (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok test_reroot_tree_with_outgroups_with_two_mixed_clades (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok test_robinson_foulds_distance (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok test_root_tree (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok test_split_all_non_bi_nodes (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok test_transfer_internal_node_labels_to_tree (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok test_fasttree_treebuilding_command (gubbins.tests.test_treebuilders.TestStringConstruction) ... ok test_iqtree_convert_raw_ancestral_states_to_fasta (gubbins.tests.test_treebuilders.TestStringConstruction) ... ok test_iqtree_replace_internal_node_label (gubbins.tests.test_treebuilders.TestStringConstruction) ... ok test_iqtree_sequence_reconstruction_command (gubbins.tests.test_treebuilders.TestStringConstruction) ... ok test_iqtree_treebuilding_command (gubbins.tests.test_treebuilders.TestStringConstruction) ... ok test_raxml_convert_raw_ancestral_states_to_fasta (gubbins.tests.test_treebuilders.TestStringConstruction) ... ok test_raxml_replace_internal_node_label (gubbins.tests.test_treebuilders.TestStringConstruction) ... ok test_raxml_select_executable_based_on_threads (gubbins.tests.test_treebuilders.TestStringConstruction) ... ok test_raxml_sequence_reconstruction_command (gubbins.tests.test_treebuilders.TestStringConstruction) ... ok test_raxml_treebuilding_command (gubbins.tests.test_treebuilders.TestStringConstruction) ... ok test_check_and_fix_window_size (gubbins.tests.test_utils.TestUtilities) ... ok test_delete_files (gubbins.tests.test_utils.TestUtilities) ... ok test_do_files_exist (gubbins.tests.test_utils.TestUtilities) ... ok test_gubbins_command (gubbins.tests.test_utils.TestUtilities) ... ok test_is_executable (gubbins.tests.test_utils.TestUtilities) ... ok test_rename_files (gubbins.tests.test_utils.TestUtilities) ... ok test_replace_executable (gubbins.tests.test_utils.TestUtilities) ... ok test_translation_of_filenames_to_final_filenames (gubbins.tests.test_utils.TestUtilities) ... ok test_verbose_printer (gubbins.tests.test_utils.TestUtilities) ... ok test_which (gubbins.tests.test_utils.TestUtilities) ... ok test_are_all_sequence_names_unique (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile) ... ok test_are_all_sequences_the_same_length (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile) ... ok test_are_there_enough_sequences_to_build_a_tree (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile) ... ok test_does_each_sequence_have_a_name (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile) ... ok test_does_the_sequence_have_sensible_characters (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile) ... ok test_valid_fasta_file (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile) ... ok test_are_all_names_unique (gubbins.tests.test_validate_starting_tree.TestValidationOfStartingTree) ... ok test_do_the_names_match_the_fasta_file (gubbins.tests.test_validate_starting_tree.TestValidationOfStartingTree) ... ok test_is_it_a_valid_newick_tree (gubbins.tests.test_validate_starting_tree.TestValidationOfStartingTree) ... ok ---------------------------------------------------------------------- Ran 67 tests in 7.738s OK 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/i386-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libgubbins.la '/build/gubbins-2.4.1/debian/gubbins/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/libgubbins.so.0.0.1 /build/gubbins-2.4.1/debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.so.0.0.1 libtool: install: (cd /build/gubbins-2.4.1/debian/gubbins/usr/lib/i386-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/i386-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/i386-linux-gnu/libgubbins.la libtool: install: /usr/bin/install -c .libs/libgubbins.a /build/gubbins-2.4.1/debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.a libtool: install: chmod 644 /build/gubbins-2.4.1/debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.a libtool: install: ranlib /build/gubbins-2.4.1/debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.a libtool: warning: remember to run 'libtool --finish /usr/lib/i386-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/i386-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 running build running build_py creating build creating build/lib creating build/lib/gubbins copying gubbins/__init__.py -> build/lib/gubbins copying gubbins/utils.py -> build/lib/gubbins copying gubbins/ValidateFastaAlignment.py -> build/lib/gubbins copying gubbins/treebuilders.py -> build/lib/gubbins copying gubbins/PreProcessFasta.py -> build/lib/gubbins copying gubbins/common.py -> build/lib/gubbins creating build/lib/scripts copying scripts/gubbins_drawer.py -> build/lib/scripts copying scripts/__init__.py -> build/lib/scripts copying scripts/run_gubbins.py -> build/lib/scripts creating build/lib/gubbins/tests copying gubbins/tests/test_tree_methods.py -> build/lib/gubbins/tests copying gubbins/tests/test_validate_starting_tree.py -> build/lib/gubbins/tests copying gubbins/tests/test_utils.py -> build/lib/gubbins/tests copying gubbins/tests/test_pre_process_fasta.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 copying gubbins/tests/test_validate_fasta_input.py -> build/lib/gubbins/tests copying gubbins/tests/test_treebuilders.py -> build/lib/gubbins/tests copying gubbins/tests/test_dependencies.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 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/ValidateFastaAlignment.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/gubbins/tests copying build/lib/gubbins/tests/test_tree_methods.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/tests/test_utils.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_converging_recombinations.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/__init__.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_treebuilders.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/PreProcessFasta.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/common.py -> ../debian/gubbins/usr/share/gubbins/gubbins creating ../debian/gubbins/usr/share/gubbins/scripts copying build/lib/scripts/gubbins_drawer.py -> ../debian/gubbins/usr/share/gubbins/scripts copying build/lib/scripts/__init__.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/__init__.py to __init__.cpython-39.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/utils.py to utils.cpython-39.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/ValidateFastaAlignment.py to ValidateFastaAlignment.cpython-39.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/treebuilders.py to treebuilders.cpython-39.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_tree_methods.py to test_tree_methods.cpython-39.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_validate_starting_tree.py to test_validate_starting_tree.cpython-39.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_utils.py to test_utils.cpython-39.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_pre_process_fasta.py to test_pre_process_fasta.cpython-39.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_converging_recombinations.py to test_converging_recombinations.cpython-39.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_alignment_python_methods.py to test_alignment_python_methods.cpython-39.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/__init__.py to __init__.cpython-39.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_validate_fasta_input.py to test_validate_fasta_input.cpython-39.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_treebuilders.py to test_treebuilders.cpython-39.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_dependencies.py to test_dependencies.cpython-39.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/PreProcessFasta.py to PreProcessFasta.cpython-39.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/common.py to common.cpython-39.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/scripts/gubbins_drawer.py to gubbins_drawer.cpython-39.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/scripts/__init__.py to __init__.cpython-39.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/scripts/run_gubbins.py to run_gubbins.cpython-39.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' 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 dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: symbol gzopen used by debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzread used by debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzclose used by debian/gubbins/usr/lib/i386-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' in '../gubbins_2.4.1-4_i386.deb'. dpkg-deb: building package 'gubbins-dbgsym' in '../gubbins-dbgsym_2.4.1-4_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../gubbins_2.4.1-4_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/65183 and its subdirectories I: Current time: Sat Aug 20 12:47:55 -12 2022 I: pbuilder-time-stamp: 1661042875 Sun Jul 18 18:24:56 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos2-i386.debian.net. Sun Jul 18 18:24:56 UTC 2021 I: Preparing to do remote build '2' on ionos2-i386.debian.net. Sun Jul 18 18:36:05 UTC 2021 I: Deleting $TMPDIR on ionos2-i386.debian.net. Sun Jul 18 18:36:06 UTC 2021 I: gubbins_2.4.1-4_i386.changes: Format: 1.8 Date: Sun, 04 Apr 2021 16:11:03 +0530 Source: gubbins Binary: gubbins gubbins-dbgsym Architecture: i386 Version: 2.4.1-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: gubbins - phylogenetic analysis of genome sequences Closes: 986238 Changes: gubbins (2.4.1-4) unstable; urgency=medium . * Team upload. * Fix symlink to right place (Closes: #986238) Checksums-Sha1: 9498411799d155d03285625c26599420162ca701 59924 gubbins-dbgsym_2.4.1-4_i386.deb 7a576b0cdc96b50386942baa6843109c39654846 7179 gubbins_2.4.1-4_i386.buildinfo 24e505b53d53513441150d9ea3b6a069d6bf3374 59364 gubbins_2.4.1-4_i386.deb Checksums-Sha256: 00bb9c5f78f5a65d39f1f542f697c797842f7ff5faba27c1f27689838c662234 59924 gubbins-dbgsym_2.4.1-4_i386.deb e4faa747a2769494a97652f7f039dc792833725f9a1f50e8d9134302d8f36a12 7179 gubbins_2.4.1-4_i386.buildinfo adb7d87ba07dcf7d4dad528d643b82d6f51394498d3f3691c8952cda7fbbeae3 59364 gubbins_2.4.1-4_i386.deb Files: 2391cb4bf863dca83483d63f8a8dc20d 59924 debug optional gubbins-dbgsym_2.4.1-4_i386.deb 998011ef1f97ca5dc7e2a666e191e1ed 7179 science optional gubbins_2.4.1-4_i386.buildinfo 22ee01c78caca6258d311e568fd85c61 59364 science optional gubbins_2.4.1-4_i386.deb Sun Jul 18 18:36:17 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.OkaTSuw4yV/gubbins_2.4.1-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.OkaTSuw4yV/gubbins_2.4.1-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.OkaTSuw4yV/gubbins_2.4.1-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.OkaTSuw4yV/b1/gubbins_2.4.1-4_i386.changes /srv/reproducible-results/rbuild-debian/tmp.OkaTSuw4yV/b2/gubbins_2.4.1-4_i386.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: 0.284s) 0.284s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.069s) 0.068s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Sun Jul 18 19:08:18 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Sun Jul 18 19:08:18 UTC 2021 I: gubbins from bullseye built successfully and reproducibly on i386. Sun Jul 18 19:08:52 UTC 2021 I: Submitting .buildinfo files to external archives: Sun Jul 18 19:08:52 UTC 2021 I: Submitting 8.0K b1/gubbins_2.4.1-4_i386.buildinfo.asc Sun Jul 18 19:08:53 UTC 2021 I: Submitting 8.0K b2/gubbins_2.4.1-4_i386.buildinfo.asc Sun Jul 18 19:08:53 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Jul 18 19:08:53 UTC 2021 I: Done submitting .buildinfo files. Sun Jul 18 19:08:53 UTC 2021 I: Removing signed gubbins_2.4.1-4_i386.buildinfo.asc files: removed './b1/gubbins_2.4.1-4_i386.buildinfo.asc' removed './b2/gubbins_2.4.1-4_i386.buildinfo.asc'