Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/g/gubbins/gubbins_2.4.1-4_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/gubbins-2.4.1-4shnipi4z/gubbins_2.4.1-4_amd64.buildinfo Get source package info: gubbins=2.4.1-4 Source URL: http://snapshot.notset.fr/mr/package/gubbins/2.4.1-4/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.118 autoconf=2.69-14 automake=1:1.16.3-2 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=11 base-passwd=3.5.49 bash=5.1-2+b1 binutils=2.35.2-2 binutils-common=2.35.2-2 binutils-x86-64-linux-gnu=2.35.2-2 bsdextrautils=2.36.1-7 bsdutils=1:2.36.1-7 build-essential=12.9 bzip2=1.0.8-4 check=0.15.2-2 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.2.1-6 dash=0.5.11+git20210120+802ebd4-1 debconf=1.5.76 debhelper=13.3.4 debianutils=4.11.2 dh-autoreconf=20 dh-python=4.20201102+nmu1 dh-strip-nondeterminism=1.11.0-1 diffutils=1:3.7-5 dpkg=1.20.7.1 dpkg-dev=1.20.7.1 dwz=0.14-1 fasttree=2.1.11-2 file=1:5.39-3 findutils=4.8.0-1 g++=4:10.2.1-1 g++-10=10.2.1-6 gcc=4:10.2.1-1 gcc-10=10.2.1-6 gcc-10-base=10.2.1-6 gettext=0.21-4 gettext-base=0.21-4 grep=3.6-1 groff-base=1.22.4-6 gzip=1.10-4 hostname=3.23 ibverbs-providers=33.1-1 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 iqtree=1.6.12+dfsg-1 libacl1=2.2.53-10 libarchive-zip-perl=1.68-1 libasan6=10.2.1-6 libatomic1=10.2.1-6 libattr1=1:2.4.48-6 libaudit-common=1:3.0-2 libaudit1=1:3.0-2 libbinutils=2.35.2-2 libblas3=3.9.0-3 libblkid1=2.36.1-7 libbrotli1=1.0.9-2+b2 libbsd0=0.11.3-1 libbz2-1.0=1.0.8-4 libc-bin=2.31-10 libc-dev-bin=2.31-10 libc6=2.31-10 libc6-dev=2.31-10 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-6 libcom-err2=1.46.2-1 libcrypt-dev=1:4.4.18-2 libcrypt1=1:4.4.18-2 libctf-nobfd0=2.35.2-2 libctf0=2.35.2-2 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.257 libdebhelper-perl=13.3.4 libdeflate0=1.7-1 libdpkg-perl=1.20.7.1 libelf1=0.183-3 libevent-core-2.1-7=2.1.12-stable-1 libevent-pthreads-2.1-7=2.1.12-stable-1 libexpat1=2.2.10-2 libfabric1=1.11.0-2 libffi7=3.3-6 libfile-stripnondeterminism-perl=1.11.0-1 libfreetype6=2.10.4+dfsg-1 libgcc-10-dev=10.2.1-6 libgcc-s1=10.2.1-6 libgcrypt20=1.8.7-3 libgdbm-compat4=1.19-2 libgdbm6=1.19-2 libgfortran5=10.2.1-6 libglib2.0-0=2.66.8-1 libgmp10=2:6.2.1+dfsg-1 libgomp1=10.2.1-6 libgpg-error0=1.38-2 libgssapi-krb5-2=1.18.3-4 libhwloc-plugins=2.4.1+dfsg-1 libhwloc15=2.4.1+dfsg-1 libibverbs1=33.1-1 libicu67=67.1-6 libimagequant0=2.12.2-1.1 libisl23=0.23-1 libitm1=10.2.1-6 libjbig0=2.1-3.1+b2 libjpeg62-turbo=1:2.0.6-4 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 liblapack3=3.9.0-3 liblcms2-2=2.12~rc1-2 liblsan0=10.2.1-6 liblz4-1=1.9.3-1 liblzma5=5.2.5-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmd0=1.0.3-3 libmount1=2.36.1-7 libmpc3=1.2.0-1 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncursesw6=6.2+20201114-2 libnl-3-200=3.4.0-1+b1 libnl-route-3-200=3.4.0-1+b1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnuma1=2.0.12-1+b1 libopenmpi3=4.1.0-8 libpam-modules=1.4.0-7 libpam-modules-bin=1.4.0-7 libpam-runtime=1.4.0-7 libpam0g=1.4.0-7 libpciaccess0=0.16-1 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.1-3 libpipeline1=1.5.3-1 libpmix2=4.0.0-4 libpng16-16=1.6.37-3 libpsm-infinipath1=3.3+20.604758e7-6.1 libpsm2-2=11.2.185-1 libpython3-stdlib=3.9.2-2 libpython3.9-minimal=3.9.2-1 libpython3.9-stdlib=3.9.2-1 libquadmath0=10.2.1-6 librdmacm1=33.1-1 libreadline8=8.1-1 libseccomp2=2.5.1-1 libselinux1=3.1-3 libsemanage-common=3.1-1 libsemanage1=3.1-1+b2 libsepol1=3.1-1 libsigsegv2=2.13-1 libsmartcols1=2.36.1-7 libsqlite3-0=3.34.1-3 libssl1.1=1.1.1k-1 libstdc++-10-dev=10.2.1-6 libstdc++6=10.2.1-6 libsub-override-perl=0.09-2 libsubunit-dev=1.4.0-3 libsubunit0=1.4.0-3 libsystemd0=247.3-3 libtiff5=4.2.0-1 libtinfo6=6.2+20201114-2 libtirpc-common=1.3.1-1 libtirpc-dev=1.3.1-1 libtirpc3=1.3.1-1 libtool=2.4.6-15 libtsan0=10.2.1-6 libubsan1=10.2.1-6 libuchardet0=0.0.7-1 libucx0=1.10.0~rc1-7 libudev1=247.3-3 libunistring2=0.9.10-4 libuuid1=2.36.1-7 libwebp6=0.6.1-2+b1 libwebpdemux2=0.6.1-2+b1 libwebpmux3=0.6.1-2+b1 libx11-6=2:1.7.0-2 libx11-data=2:1.7.0-2 libxau6=1:1.0.9-1 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.3-1.1 libxml2=2.9.10+dfsg-6.3+b1 libxnvctrl0=460.56-1 libzstd1=1.4.8+dfsg-2.1 linux-libc-dev=5.10.26-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 mailcap=3.69 make=4.3-4 man-db=2.9.4-2 mawk=1.3.4.20200120-2 media-types=4.0.0 mime-support=3.66 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 ocl-icd-libopencl1=2.2.14-2 passwd=1:4.8.1-1 patch=2.7.6-7 perl=5.32.1-3 perl-base=5.32.1-3 perl-modules-5.32=5.32.1-3 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 python3=3.9.2-2 python3-biopython=1.78+dfsg-4 python3-dendropy=4.5.1-1 python3-distutils=3.9.2-1 python3-lib2to3=3.9.2-1 python3-minimal=3.9.2-2 python3-nose=1.3.7-7 python3-numpy=1:1.19.5-1 python3-pil=8.1.2-1 python3-pkg-resources=52.0.0-3 python3-reportlab=3.5.59-2 python3-reportlab-accel=3.5.59-2 python3-setuptools=52.0.0-3 python3.9=3.9.2-1 python3.9-minimal=3.9.2-1 raxml=8.2.12+dfsg-6+b4 readline-common=8.1-1 sed=4.7-1 sensible-utils=0.0.14 sysvinit-utils=2.96-6 tar=1.34+dfsg-1 tzdata=2021a-1 util-linux=2.36.1-7 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210331T212131Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d gubbins=2.4.1-4 && mkdir -p /build/gubbins-yvakmV && dpkg-source --no-check -x /*.dsc /build/gubbins-yvakmV/gubbins-2.4.1 && chown -R builduser:builduser /build/gubbins-yvakmV" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/gubbins-yvakmV/gubbins-2.4.1 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1617532863" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/gubbins-yvakmV /tmp/gubbins-2.4.1-4shnipi4z bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210331T212131Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.WnN5hiqcJB as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.WnN5hiqcJB Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-7). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20210331T212131Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210331T212131Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (671 kB/s) Selecting previously unselected package libfakeroot: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 ... 4663 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-10) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210331T212131Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.WnN5hiqcJB Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20210331T212131Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 20s (1116 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.WnN5hiqcJB I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d gubbins=2.4.1-4 && mkdir -p /build/gubbins-yvakmV && dpkg-source --no-check -x /*.dsc /build/gubbins-yvakmV/gubbins-2.4.1 && chown -R builduser:builduser /build/gubbins-yvakmV"' exec /tmp/mmdebstrap.WnN5hiqcJB Reading package lists... NOTICE: 'gubbins' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/gubbins.git Please use: git clone https://salsa.debian.org/med-team/gubbins.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 619 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main gubbins 2.4.1-4 (dsc) [2193 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main gubbins 2.4.1-4 (tar) [610 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main gubbins 2.4.1-4 (diff) [6988 B] Fetched 619 kB in 1s (1058 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'gubbins_2.4.1-4.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting gubbins in /build/gubbins-yvakmV/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: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/gubbins-yvakmV/gubbins-2.4.1 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1617532863" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.WnN5hiqcJB 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 amd64 debian/rules clean dh clean --with python3 debian/rules override_dh_clean make[1]: Entering directory '/build/gubbins-yvakmV/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-yvakmV/gubbins-2.4.1' debian/rules binary-arch dh binary-arch --with python3 dh_update_autotools_config -a dh_autoreconf -a 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 -a ./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 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... 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 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 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 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 -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 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 -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... 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... 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config.status: creating python/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build -a make -j4 make[1]: Entering directory '/build/gubbins-yvakmV/gubbins-2.4.1' make all-recursive make[2]: Entering directory '/build/gubbins-yvakmV/gubbins-2.4.1' Making all in src make[3]: Entering directory '/build/gubbins-yvakmV/gubbins-2.4.1/src' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-yvakmV/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-yvakmV/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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-Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-yvakmV/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c parse_phylip.c -o parse_phylip.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-yvakmV/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 -ffile-prefix-map=/build/gubbins-yvakmV/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snp_searching.lo snp_searching.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-yvakmV/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-yvakmV/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-yvakmV/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c seqUtil.c -o seqUtil.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-yvakmV/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snp_sites.lo snp_sites.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-yvakmV/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c snp_searching.c -o snp_searching.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-yvakmV/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-yvakmV/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o tree_statistics.lo tree_statistics.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-yvakmV/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c snp_sites.c -o 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-yvakmV/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c tree_statistics.c -fPIC -DPIC -o .libs/tree_statistics.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-yvakmV/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o tree_scaling.lo tree_scaling.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-yvakmV/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-yvakmV/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 -ffile-prefix-map=/build/gubbins-yvakmV/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 -ffile-prefix-map=/build/gubbins-yvakmV/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-yvakmV/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 -ffile-prefix-map=/build/gubbins-yvakmV/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c vcf.c -o vcf.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/gubbins-yvakmV/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-yvakmV/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-yvakmV/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-yvakmV/gubbins-2.4.1/src' Making all in release make[3]: Entering directory '/build/gubbins-yvakmV/gubbins-2.4.1/release' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/gubbins-yvakmV/gubbins-2.4.1/release' make[3]: Entering directory '/build/gubbins-yvakmV/gubbins-2.4.1' make[3]: Leaving directory '/build/gubbins-yvakmV/gubbins-2.4.1' make[2]: Leaving directory '/build/gubbins-yvakmV/gubbins-2.4.1' make[1]: Leaving directory '/build/gubbins-yvakmV/gubbins-2.4.1' debian/rules override_dh_auto_test make[1]: Entering directory '/build/gubbins-yvakmV/gubbins-2.4.1' dh_auto_test make -j4 check VERBOSE=1 make[2]: Entering directory '/build/gubbins-yvakmV/gubbins-2.4.1' Making check in src make[3]: Entering directory '/build/gubbins-yvakmV/gubbins-2.4.1/src' make run_all_tests make[4]: Entering directory '/build/gubbins-yvakmV/gubbins-2.4.1/src' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -ffile-prefix-map=/build/gubbins-yvakmV/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 -pthread -g -O2 -ffile-prefix-map=/build/gubbins-yvakmV/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 -pthread -g -O2 -ffile-prefix-map=/build/gubbins-yvakmV/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 -pthread -g -O2 -ffile-prefix-map=/build/gubbins-yvakmV/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 ../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_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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -ffile-prefix-map=/build/gubbins-yvakmV/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 -ffile-prefix-map=/build/gubbins-yvakmV/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 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"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -ffile-prefix-map=/build/gubbins-yvakmV/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 ../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"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -ffile-prefix-map=/build/gubbins-yvakmV/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/bash ../libtool --tag=CC --mode=link gcc -I../tests -pthread -g -O2 -ffile-prefix-map=/build/gubbins-yvakmV/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 -ffile-prefix-map=/build/gubbins-yvakmV/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-yvakmV/gubbins-2.4.1/src' make check-TESTS make[4]: Entering directory '/build/gubbins-yvakmV/gubbins-2.4.1/src' make[5]: Entering directory '/build/gubbins-yvakmV/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-yvakmV/gubbins-2.4.1/src' make[4]: Leaving directory '/build/gubbins-yvakmV/gubbins-2.4.1/src' make[3]: Leaving directory '/build/gubbins-yvakmV/gubbins-2.4.1/src' Making check in release make[3]: Entering directory '/build/gubbins-yvakmV/gubbins-2.4.1/release' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/gubbins-yvakmV/gubbins-2.4.1/release' make[3]: Entering directory '/build/gubbins-yvakmV/gubbins-2.4.1' make[3]: Leaving directory '/build/gubbins-yvakmV/gubbins-2.4.1' make[2]: Leaving directory '/build/gubbins-yvakmV/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-yvakmV/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-yvakmV/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-yvakmV/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 5033.290s OK make[1]: Leaving directory '/build/gubbins-yvakmV/gubbins-2.4.1' create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/gubbins-yvakmV/gubbins-2.4.1' dh_auto_install make -j1 install DESTDIR=/build/gubbins-yvakmV/gubbins-2.4.1/debian/gubbins AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/gubbins-yvakmV/gubbins-2.4.1' Making install in src make[3]: Entering directory '/build/gubbins-yvakmV/gubbins-2.4.1/src' make[4]: Entering directory '/build/gubbins-yvakmV/gubbins-2.4.1/src' /bin/mkdir -p '/build/gubbins-yvakmV/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-yvakmV/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-yvakmV/gubbins-2.4.1/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 libtool: install: (cd /build/gubbins-yvakmV/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-yvakmV/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-yvakmV/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-yvakmV/gubbins-2.4.1/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.a libtool: install: chmod 644 /build/gubbins-yvakmV/gubbins-2.4.1/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.a libtool: install: ranlib /build/gubbins-yvakmV/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-yvakmV/gubbins-2.4.1/debian/gubbins/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c gubbins '/build/gubbins-yvakmV/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-yvakmV/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-yvakmV/gubbins-2.4.1/src' make[3]: Leaving directory '/build/gubbins-yvakmV/gubbins-2.4.1/src' Making install in release make[3]: Entering directory '/build/gubbins-yvakmV/gubbins-2.4.1/release' make[4]: Entering directory '/build/gubbins-yvakmV/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-yvakmV/gubbins-2.4.1/release' make[3]: Leaving directory '/build/gubbins-yvakmV/gubbins-2.4.1/release' make[3]: Entering directory '/build/gubbins-yvakmV/gubbins-2.4.1' make[4]: Entering directory '/build/gubbins-yvakmV/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-yvakmV/gubbins-2.4.1' make[3]: Leaving directory '/build/gubbins-yvakmV/gubbins-2.4.1' make[2]: Leaving directory '/build/gubbins-yvakmV/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/PreProcessFasta.py -> build/lib/gubbins copying gubbins/__init__.py -> 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/ValidateFastaAlignment.py -> build/lib/gubbins creating build/lib/scripts copying scripts/gubbins_drawer.py -> build/lib/scripts copying scripts/run_gubbins.py -> build/lib/scripts copying scripts/__init__.py -> build/lib/scripts creating build/lib/gubbins/tests copying gubbins/tests/test_tree_methods.py -> build/lib/gubbins/tests copying gubbins/tests/__init__.py -> build/lib/gubbins/tests copying gubbins/tests/test_treebuilders.py -> build/lib/gubbins/tests copying gubbins/tests/test_validate_fasta_input.py -> build/lib/gubbins/tests copying gubbins/tests/test_pre_process_fasta.py -> build/lib/gubbins/tests copying gubbins/tests/test_utils.py -> build/lib/gubbins/tests copying gubbins/tests/test_alignment_python_methods.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_validate_starting_tree.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/PreProcessFasta.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/__init__.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/treebuilders.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/common.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/utils.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/__init__.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_validate_fasta_input.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_utils.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_dependencies.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_validate_starting_tree.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/ValidateFastaAlignment.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/run_gubbins.py -> ../debian/gubbins/usr/share/gubbins/scripts copying build/lib/scripts/__init__.py -> ../debian/gubbins/usr/share/gubbins/scripts byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/PreProcessFasta.py to PreProcessFasta.cpython-39.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/__init__.py to __init__.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/common.py to common.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/tests/test_tree_methods.py to test_tree_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_treebuilders.py to test_treebuilders.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_pre_process_fasta.py to test_pre_process_fasta.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_alignment_python_methods.py to test_alignment_python_methods.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/tests/test_converging_recombinations.py to test_converging_recombinations.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/ValidateFastaAlignment.py to ValidateFastaAlignment.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/run_gubbins.py to run_gubbins.cpython-39.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/scripts/__init__.py to __init__.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-yvakmV/gubbins-2.4.1' debian/rules override_dh_install make[1]: Entering directory '/build/gubbins-yvakmV/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-yvakmV/gubbins-2.4.1' dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_python3 -a dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a -a dh_strip -a -a dh_makeshlibs -a -a dh_shlibdeps -a -a 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 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 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 -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'gubbins-dbgsym' in '../gubbins-dbgsym_2.4.1-4_amd64.deb'. dpkg-deb: building package 'gubbins' in '../gubbins_2.4.1-4_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../gubbins_2.4.1-4_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/gubbins-yvakmV /tmp/gubbins-2.4.1-4shnipi4z I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.WnN5hiqcJB... I: success in 5432.8025 seconds md5: gubbins-dbgsym_2.4.1-4_amd64.deb: OK md5: gubbins_2.4.1-4_amd64.deb: OK sha1: gubbins-dbgsym_2.4.1-4_amd64.deb: OK sha1: gubbins_2.4.1-4_amd64.deb: OK sha256: gubbins-dbgsym_2.4.1-4_amd64.deb: OK sha256: gubbins_2.4.1-4_amd64.deb: OK Checksums: OK