Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/f/fast5/fast5_0.6.5-4_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/fast5-0.6.5-4rw6s56rm/fast5_0.6.5-4_all.buildinfo Get source package info: fast5=0.6.5-4 Source URL: http://snapshot.notset.fr/mr/package/fast5/0.6.5-4/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11 automake=1:1.16.1-4 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.46 bash=5.0-5 binutils=2.33.1-2 binutils-common=2.33.1-2 binutils-x86-64-linux-gnu=2.33.1-2 bsdmainutils=11.1.2+b1 bsdutils=1:2.34-0.1 build-essential=12.8 bzip2=1.0.8-2 coreutils=8.30-3+b1 cpp=4:9.2.1-3.1 cpp-9=9.2.1-19 cython3=0.29.14-0.1+b1 dash=0.5.10.2-6 debconf=1.5.73 debhelper=12.7.1 debianutils=4.9 dh-autoreconf=19 dh-python=4.20191017 dh-strip-nondeterminism=1.6.2-1 diffutils=1:3.7-3 dpkg=1.19.7 dpkg-dev=1.19.7 dwz=0.13-2 fdisk=2.34-0.1 file=1:5.37-6 findutils=4.7.0-1 g++=4:9.2.1-3.1 g++-9=9.2.1-19 gcc=4:9.2.1-3.1 gcc-9=9.2.1-19 gcc-9-base=9.2.1-19 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 grep=3.3-1 groff-base=1.22.4-3 gzip=1.9-3+b1 hdf5-helpers=1.10.4+repack-10 hostname=3.23 init-system-helpers=1.57 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-5 libaec-dev=1.0.4-1 libaec0=1.0.4-1 libarchive-zip-perl=1.67-1 libasan5=9.2.1-19 libatomic1=9.2.1-19 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-2 libaudit1=1:2.8.5-2+b1 libbinutils=2.33.1-2 libblkid1=2.34-0.1 libboost-python-dev=1.67.0.2 libboost-python1.67-dev=1.67.0-13+b1 libboost-python1.67.0=1.67.0-13+b1 libboost1.67-dev=1.67.0-13+b1 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-2 libc-bin=2.29-3 libc-dev-bin=2.29-3 libc6=2.29-3 libc6-dev=2.29-3 libcap-ng0=0.7.9-2.1+b1 libcc1-0=9.2.1-19 libcroco3=0.6.13-1 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.250 libdebhelper-perl=12.7.1 libdpkg-perl=1.19.7 libelf1=0.176-1.1 libexpat1=2.2.9-1 libexpat1-dev=2.2.9-1 libfdisk1=2.34-0.1 libffi6=3.2.1-9 libfile-stripnondeterminism-perl=1.6.2-1 libgcc-9-dev=9.2.1-19 libgcc1=1:9.2.1-19 libgcrypt20=1.8.5-3 libgdbm-compat4=1.18.1-5 libgdbm6=1.18.1-5 libgfortran5=9.2.1-19 libglib2.0-0=2.62.2-3 libgmp10=2:6.1.2+dfsg-4 libgomp1=9.2.1-19 libgpg-error0=1.36-7 libhdf5-103=1.10.4+repack-10 libhdf5-cpp-103=1.10.4+repack-10 libhdf5-dev=1.10.4+repack-10 libicu63=63.2-2 libisl21=0.21-2 libitm1=9.2.1-19 libjpeg-dev=1:1.5.2-2 libjpeg62-turbo=1:1.5.2-2+b1 libjpeg62-turbo-dev=1:1.5.2-2+b1 liblsan0=9.2.1-19 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.37-6 libmagic1=1:5.37-6 libmount1=2.34-0.1 libmpc3=1.1.0-1 libmpdec2=2.4.2-2 libmpfr6=4.0.2-1 libncursesw6=6.1+20191019-1 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpcre2-8-0=10.32-5+b1 libpcre3=2:8.39-12+b1 libperl5.30=5.30.0-9 libpipeline1=1.5.1-2 libpython-dev=2.7.17-2 libpython-stdlib=2.7.17-2 libpython2-dev=2.7.17-2 libpython2-stdlib=2.7.17-2 libpython2.7=2.7.17-1 libpython2.7-dev=2.7.17-1 libpython2.7-minimal=2.7.17-1 libpython2.7-stdlib=2.7.17-1 libpython3-all-dev=3.7.5-3 libpython3-dev=3.7.5-3 libpython3-stdlib=3.7.5-3 libpython3.7=3.7.5-2 libpython3.7-dev=3.7.5-2 libpython3.7-minimal=3.7.5-2 libpython3.7-stdlib=3.7.5-2 libpython3.8=3.8.0-4 libpython3.8-dev=3.8.0-4 libpython3.8-minimal=3.8.0-4 libpython3.8-stdlib=3.8.0-4 libquadmath0=9.2.1-19 libreadline8=8.0-3 libseccomp2=2.4.2-2 libselinux1=2.9-3+b1 libsigsegv2=2.12-2 libsmartcols1=2.34-0.1 libsqlite3-0=3.30.1-1 libssl1.1=1.1.1d-2 libstdc++-9-dev=9.2.1-19 libstdc++6=9.2.1-19 libsub-override-perl=0.09-2 libsystemd0=243-8 libsz2=1.0.4-1 libtinfo6=6.1+20191019-1 libtool=2.4.6-11 libtsan0=9.2.1-19 libubsan1=9.2.1-19 libuchardet0=0.0.6-3 libudev1=243-8 libunistring2=0.9.10-2 libuuid1=2.34-0.1 libxml2=2.9.4+dfsg1-8 linux-libc-dev=5.3.9-3 login=1:4.7-2 lsb-base=11.1.0 m4=1.4.18-4 make=4.2.1-1.2 man-db=2.9.0-1 mawk=1.3.3-17+b3 mime-support=3.64 ncurses-base=6.1+20191019-1 ncurses-bin=6.1+20191019-1 patch=2.7.6-6 perl=5.30.0-9 perl-base=5.30.0-9 perl-modules-5.30=5.30.0-9 po-debconf=1.0.21 python=2.7.17-2 python-dev=2.7.17-2 python-minimal=2.7.17-2 python2=2.7.17-2 python2-dev=2.7.17-2 python2-minimal=2.7.17-2 python2.7=2.7.17-1 python2.7-dev=2.7.17-1 python2.7-minimal=2.7.17-1 python3=3.7.5-3 python3-all=3.7.5-3 python3-all-dev=3.7.5-3 python3-dev=3.7.5-3 python3-distutils=3.8.0-1 python3-lib2to3=3.8.0-1 python3-minimal=3.7.5-3 python3-pkg-resources=41.4.0-1 python3-setuptools=41.4.0-1 python3.7=3.7.5-2 python3.7-dev=3.7.5-2 python3.7-minimal=3.7.5-2 python3.8=3.8.0-4 python3.8-dev=3.8.0-4 python3.8-minimal=3.8.0-4 readline-common=8.0-3 sed=4.7-1 sensible-utils=0.0.12 sysvinit-utils=2.96-1 tar=1.30+dfsg-6+b1 util-linux=2.34-0.1 xz-utils=5.2.4-1+b1 zlib1g=1:1.2.11.dfsg-1+b1 zlib1g-dev=1:1.2.11.dfsg-1+b1 --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/20191121T152004Z/ 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 fast5=0.6.5-4 && mkdir -p /build/fast5-U1iShs && dpkg-source --no-check -x /*.dsc /build/fast5-U1iShs/fast5-0.6.5 && chown -R builduser:builduser /build/fast5-U1iShs" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/fast5-U1iShs/fast5-0.6.5 && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1574324057" dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/fast5-U1iShs /tmp/fast5-0.6.5-4rw6s56rm bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20191121T152004Z 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.AqOY1KkzTS 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.AqOY1KkzTS Reading package lists... Building dependency tree... util-linux is already the newest version (2.34-0.1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 132 kB of archives. After this operation, 393 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20191121T152004Z unstable/main amd64 libfakeroot amd64 1.24-1 [45.7 kB] Get:2 http://snapshot.notset.fr/archive/debian/20191121T152004Z unstable/main amd64 fakeroot amd64 1.24-1 [85.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 132 kB in 0s (944 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 ... 4508 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.24-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.24-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.24-1_amd64.deb ... Unpacking fakeroot (1.24-1) ... Setting up libfakeroot:amd64 (1.24-1) ... Setting up fakeroot (1.24-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.29-3) ... 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/20191121T152004Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.AqOY1KkzTS Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20191121T152004Z 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 19s (1159 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.AqOY1KkzTS I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d fast5=0.6.5-4 && mkdir -p /build/fast5-U1iShs && dpkg-source --no-check -x /*.dsc /build/fast5-U1iShs/fast5-0.6.5 && chown -R builduser:builduser /build/fast5-U1iShs"' exec /tmp/mmdebstrap.AqOY1KkzTS Reading package lists... NOTICE: 'fast5' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/fast5.git Please use: git clone https://salsa.debian.org/med-team/fast5.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 100 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main fast5 0.6.5-4 (dsc) [2173 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main fast5 0.6.5-4 (tar) [93.6 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main fast5 0.6.5-4 (diff) [4608 B] Fetched 100 kB in 0s (554 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'fast5_0.6.5-4.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting fast5 in /build/fast5-U1iShs/fast5-0.6.5 dpkg-source: info: unpacking fast5_0.6.5.orig.tar.gz dpkg-source: info: unpacking fast5_0.6.5-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying rpath.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/fast5-U1iShs/fast5-0.6.5 && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1574324057" dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.AqOY1KkzTS dpkg-buildpackage: info: source package fast5 dpkg-buildpackage: info: source version 0.6.5-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-source: info: using options from fast5-0.6.5/debian/source/options: --extend-diff-ignore=^[^/]+\.egg-info/|python/fast5/fast5.cpp fakeroot debian/rules clean dh clean --with python3 --buildsystem=pybuild \ --sourcedirectory=python debian/rules override_dh_auto_clean make[1]: Entering directory '/build/fast5-U1iShs/fast5-0.6.5' cd src && /usr/bin/make clean make[2]: Entering directory '/build/fast5-U1iShs/fast5-0.6.5/src' rm -rf f5ls f5ls-full hdf5-mod f5-mod f5dump f5pack make[2]: Leaving directory '/build/fast5-U1iShs/fast5-0.6.5/src' dh_auto_clean I: pybuild base:217: python3.8 setup.py clean Compiling fast5/fast5.pyx because it changed. [1/1] Cythonizing fast5/fast5.pyx running clean removing '/build/fast5-U1iShs/fast5-0.6.5/.pybuild/cpython3_3.8_fast5/build' (and everything under it) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/fast5-U1iShs/fast5-0.6.5/python/fast5/fast5.pyx tree = Parsing.p_module(s, pxd, full_module_name) 'build/bdist.linux-amd64' does not exist -- can't clean it 'build/scripts-3.8' does not exist -- can't clean it I: pybuild base:217: python3.7 setup.py clean running clean removing '/build/fast5-U1iShs/fast5-0.6.5/.pybuild/cpython3_3.7_fast5/build' (and everything under it) 'build/bdist.linux-amd64' does not exist -- can't clean it 'build/scripts-3.7' does not exist -- can't clean it rm -rf python/fast5/fast5.cpp make[1]: Leaving directory '/build/fast5-U1iShs/fast5-0.6.5' dh_autoreconf_clean -O--buildsystem=pybuild -O--sourcedirectory=python dh_clean -O--buildsystem=pybuild -O--sourcedirectory=python debian/rules build-indep dh build-indep --with python3 --buildsystem=pybuild \ --sourcedirectory=python dh_update_autotools_config -i -O--buildsystem=pybuild -O--sourcedirectory=python dh_autoreconf -i -O--buildsystem=pybuild -O--sourcedirectory=python dh_auto_configure -i -O--buildsystem=pybuild -O--sourcedirectory=python I: pybuild base:217: python3.8 setup.py config Compiling fast5/fast5.pyx because it changed. [1/1] Cythonizing fast5/fast5.pyx running config /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/fast5-U1iShs/fast5-0.6.5/python/fast5/fast5.pyx tree = Parsing.p_module(s, pxd, full_module_name) I: pybuild base:217: python3.7 setup.py config running config dh_auto_build -i -O--buildsystem=pybuild -O--sourcedirectory=python I: pybuild base:217: /usr/bin/python3.8 setup.py build running build running build_ext building 'fast5' extension creating build creating build/temp.linux-amd64-3.8 creating build/temp.linux-amd64-3.8/fast5 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/fast5-U1iShs/fast5-0.6.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I../include -I../src -I/usr/include/python3.8 -c fast5/fast5.cpp -o build/temp.linux-amd64-3.8/fast5/fast5.o -std=c++11 -Wall -Wextra -Wpedantic -isystem /usr/include/hdf5/serial x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/fast5-U1iShs/fast5-0.6.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.8/fast5/fast5.o -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -o /build/fast5-U1iShs/fast5-0.6.5/.pybuild/cpython3_3.8_fast5/build/fast5.cpython-38-x86_64-linux-gnu.so running build_scripts creating build/scripts-3.8 copying and adjusting bin/f5ls -> build/scripts-3.8 copying and adjusting bin/f5pack -> build/scripts-3.8 changing mode of build/scripts-3.8/f5ls from 644 to 755 changing mode of build/scripts-3.8/f5pack from 644 to 755 I: pybuild base:217: /usr/bin/python3 setup.py build running build running build_ext building 'fast5' extension creating build/temp.linux-amd64-3.7 creating build/temp.linux-amd64-3.7/fast5 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/fast5-U1iShs/fast5-0.6.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I../include -I../src -I/usr/include/python3.7m -c fast5/fast5.cpp -o build/temp.linux-amd64-3.7/fast5/fast5.o -std=c++11 -Wall -Wextra -Wpedantic -isystem /usr/include/hdf5/serial x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/fast5-U1iShs/fast5-0.6.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.7/fast5/fast5.o -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -o /build/fast5-U1iShs/fast5-0.6.5/.pybuild/cpython3_3.7_fast5/build/fast5.cpython-37m-x86_64-linux-gnu.so running build_scripts creating build/scripts-3.7 copying and adjusting bin/f5ls -> build/scripts-3.7 copying and adjusting bin/f5pack -> build/scripts-3.7 changing mode of build/scripts-3.7/f5ls from 644 to 755 changing mode of build/scripts-3.7/f5pack from 644 to 755 debian/rules override_dh_auto_test make[1]: Entering directory '/build/fast5-U1iShs/fast5-0.6.5' cd src && /usr/bin/make make[2]: Entering directory '/build/fast5-U1iShs/fast5-0.6.5/src' g++ -std=c++11 -O0 -g3 -ggdb -fno-eliminate-unused-debug-types -Wall -Wextra -Wpedantic -isystem /usr/include/hdf5/serial -I /build/fast5-U1iShs/fast5-0.6.5/src/../include -o f5ls f5ls.cpp -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,--rpath=/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -lpthread -lz -ldl In file included from /usr/include/c++/9/cassert:44, from /build/fast5-U1iShs/fast5-0.6.5/src/../include/fast5/hdf5_tools.hpp:11, from /build/fast5-U1iShs/fast5-0.6.5/src/../include/fast5.hpp:27, from f5ls.cpp:12: /build/fast5-U1iShs/fast5-0.6.5/src/../include/fast5/hdf5_tools.hpp: In member function ‘void hdf5_tools::detail::Writer_Helper<3, std::__cxx11::basic_string >::operator()(hid_t, const string&, bool, hid_t, size_t, const string*, hid_t) const’: /build/fast5-U1iShs/fast5-0.6.5/src/../include/fast5/hdf5_tools.hpp:1633:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 1633 | assert(slen <= std::numeric_limits::max()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from f5ls.cpp:12: /build/fast5-U1iShs/fast5-0.6.5/src/../include/fast5.hpp: In static member function ‘static fast5::Basecall_Alignment_Pack fast5::File::pack_al(const std::vector&, const string&)’: /build/fast5-U1iShs/fast5-0.6.5/src/../include/fast5.hpp:2317:32: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘signed char’ [-Wsign-compare] 2317 | if (next_pos - pos > std::numeric_limits< int8_t >::max()) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -O0 -g3 -ggdb -fno-eliminate-unused-debug-types -Wall -Wextra -Wpedantic -isystem /usr/include/hdf5/serial -I /build/fast5-U1iShs/fast5-0.6.5/src/../include -o f5ls-full f5ls-full.cpp -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,--rpath=/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -lpthread -lz -ldl In file included from /usr/include/c++/9/cassert:44, from /build/fast5-U1iShs/fast5-0.6.5/src/../include/fast5/hdf5_tools.hpp:11, from /build/fast5-U1iShs/fast5-0.6.5/src/../include/fast5.hpp:27, from f5ls-full.cpp:12: /build/fast5-U1iShs/fast5-0.6.5/src/../include/fast5/hdf5_tools.hpp: In member function ‘void hdf5_tools::detail::Writer_Helper<3, std::__cxx11::basic_string >::operator()(hid_t, const string&, bool, hid_t, size_t, const string*, hid_t) const’: /build/fast5-U1iShs/fast5-0.6.5/src/../include/fast5/hdf5_tools.hpp:1633:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 1633 | assert(slen <= std::numeric_limits::max()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from f5ls-full.cpp:12: /build/fast5-U1iShs/fast5-0.6.5/src/../include/fast5.hpp: In static member function ‘static fast5::Basecall_Alignment_Pack fast5::File::pack_al(const std::vector&, const string&)’: /build/fast5-U1iShs/fast5-0.6.5/src/../include/fast5.hpp:2317:32: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘signed char’ [-Wsign-compare] 2317 | if (next_pos - pos > std::numeric_limits< int8_t >::max()) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -O0 -g3 -ggdb -fno-eliminate-unused-debug-types -Wall -Wextra -Wpedantic -isystem /usr/include/hdf5/serial -I /build/fast5-U1iShs/fast5-0.6.5/src/../include -o hdf5-mod hdf5-mod.cpp -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,--rpath=/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -lpthread -lz -ldl In file included from /usr/include/c++/9/cassert:44, from /build/fast5-U1iShs/fast5-0.6.5/src/../include/fast5/hdf5_tools.hpp:11, from hdf5-mod.cpp:12: /build/fast5-U1iShs/fast5-0.6.5/src/../include/fast5/hdf5_tools.hpp: In member function ‘void hdf5_tools::detail::Writer_Helper<3, std::__cxx11::basic_string >::operator()(hid_t, const string&, bool, hid_t, size_t, const string*, hid_t) const’: /build/fast5-U1iShs/fast5-0.6.5/src/../include/fast5/hdf5_tools.hpp:1633:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 1633 | assert(slen <= std::numeric_limits::max()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -O0 -g3 -ggdb -fno-eliminate-unused-debug-types -Wall -Wextra -Wpedantic -isystem /usr/include/hdf5/serial -I /build/fast5-U1iShs/fast5-0.6.5/src/../include -o f5-mod f5-mod.cpp -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,--rpath=/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -lpthread -lz -ldl In file included from /usr/include/c++/9/cassert:44, from /build/fast5-U1iShs/fast5-0.6.5/src/../include/fast5/hdf5_tools.hpp:11, from /build/fast5-U1iShs/fast5-0.6.5/src/../include/fast5.hpp:27, from f5-mod.cpp:12: /build/fast5-U1iShs/fast5-0.6.5/src/../include/fast5/hdf5_tools.hpp: In member function ‘void hdf5_tools::detail::Writer_Helper<3, std::__cxx11::basic_string >::operator()(hid_t, const string&, bool, hid_t, size_t, const string*, hid_t) const’: /build/fast5-U1iShs/fast5-0.6.5/src/../include/fast5/hdf5_tools.hpp:1633:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 1633 | assert(slen <= std::numeric_limits::max()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from f5-mod.cpp:12: /build/fast5-U1iShs/fast5-0.6.5/src/../include/fast5.hpp: In static member function ‘static fast5::Basecall_Alignment_Pack fast5::File::pack_al(const std::vector&, const string&)’: /build/fast5-U1iShs/fast5-0.6.5/src/../include/fast5.hpp:2317:32: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘signed char’ [-Wsign-compare] 2317 | if (next_pos - pos > std::numeric_limits< int8_t >::max()) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/build/fast5-U1iShs/fast5-0.6.5/src' make[1]: Leaving directory '/build/fast5-U1iShs/fast5-0.6.5' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-indep dh binary-indep --with python3 --buildsystem=pybuild \ --sourcedirectory=python dh_testroot -i -O--buildsystem=pybuild -O--sourcedirectory=python dh_prep -i -O--buildsystem=pybuild -O--sourcedirectory=python dh_auto_install -i -O--buildsystem=pybuild -O--sourcedirectory=python I: pybuild base:217: /usr/bin/python3.8 setup.py install --root /build/fast5-U1iShs/fast5-0.6.5/debian/python3-fast5 running install running build running build_ext running build_scripts running install_lib creating /build/fast5-U1iShs/fast5-0.6.5/debian/python3-fast5 creating /build/fast5-U1iShs/fast5-0.6.5/debian/python3-fast5/usr creating /build/fast5-U1iShs/fast5-0.6.5/debian/python3-fast5/usr/lib creating /build/fast5-U1iShs/fast5-0.6.5/debian/python3-fast5/usr/lib/python3.8 creating /build/fast5-U1iShs/fast5-0.6.5/debian/python3-fast5/usr/lib/python3.8/dist-packages copying /build/fast5-U1iShs/fast5-0.6.5/.pybuild/cpython3_3.8_fast5/build/fast5.cpython-38-x86_64-linux-gnu.so -> /build/fast5-U1iShs/fast5-0.6.5/debian/python3-fast5/usr/lib/python3.8/dist-packages running install_egg_info running egg_info creating fast5.egg-info writing fast5.egg-info/PKG-INFO writing dependency_links to fast5.egg-info/dependency_links.txt writing top-level names to fast5.egg-info/top_level.txt writing manifest file 'fast5.egg-info/SOURCES.txt' reading manifest file 'fast5.egg-info/SOURCES.txt' writing manifest file 'fast5.egg-info/SOURCES.txt' Copying fast5.egg-info to /build/fast5-U1iShs/fast5-0.6.5/debian/python3-fast5/usr/lib/python3.8/dist-packages/fast5-0.6.2.egg-info Skipping SOURCES.txt running install_scripts creating /build/fast5-U1iShs/fast5-0.6.5/debian/python3-fast5/usr/bin copying build/scripts-3.8/f5pack -> /build/fast5-U1iShs/fast5-0.6.5/debian/python3-fast5/usr/bin copying build/scripts-3.8/f5ls -> /build/fast5-U1iShs/fast5-0.6.5/debian/python3-fast5/usr/bin changing mode of /build/fast5-U1iShs/fast5-0.6.5/debian/python3-fast5/usr/bin/f5pack to 755 changing mode of /build/fast5-U1iShs/fast5-0.6.5/debian/python3-fast5/usr/bin/f5ls to 755 I: pybuild base:217: /usr/bin/python3 setup.py install --root /build/fast5-U1iShs/fast5-0.6.5/debian/python3-fast5 running install running build running build_ext running build_scripts running install_lib creating /build/fast5-U1iShs/fast5-0.6.5/debian/python3-fast5/usr/lib/python3.7 creating /build/fast5-U1iShs/fast5-0.6.5/debian/python3-fast5/usr/lib/python3.7/dist-packages copying /build/fast5-U1iShs/fast5-0.6.5/.pybuild/cpython3_3.7_fast5/build/fast5.cpython-37m-x86_64-linux-gnu.so -> /build/fast5-U1iShs/fast5-0.6.5/debian/python3-fast5/usr/lib/python3.7/dist-packages running install_egg_info running egg_info writing fast5.egg-info/PKG-INFO writing dependency_links to fast5.egg-info/dependency_links.txt writing top-level names to fast5.egg-info/top_level.txt reading manifest file 'fast5.egg-info/SOURCES.txt' writing manifest file 'fast5.egg-info/SOURCES.txt' Copying fast5.egg-info to /build/fast5-U1iShs/fast5-0.6.5/debian/python3-fast5/usr/lib/python3.7/dist-packages/fast5-0.6.2.egg-info Skipping SOURCES.txt running install_scripts copying build/scripts-3.7/f5pack -> /build/fast5-U1iShs/fast5-0.6.5/debian/python3-fast5/usr/bin copying build/scripts-3.7/f5ls -> /build/fast5-U1iShs/fast5-0.6.5/debian/python3-fast5/usr/bin changing mode of /build/fast5-U1iShs/fast5-0.6.5/debian/python3-fast5/usr/bin/f5pack to 755 changing mode of /build/fast5-U1iShs/fast5-0.6.5/debian/python3-fast5/usr/bin/f5ls to 755 debian/rules override_dh_install make[1]: Entering directory '/build/fast5-U1iShs/fast5-0.6.5' dh_install mkdir -p debian/fast5/usr/bin/ mv debian/python3-fast5/usr/bin/* debian/fast5/usr/bin/ make[1]: Leaving directory '/build/fast5-U1iShs/fast5-0.6.5' dh_installdocs -i -O--buildsystem=pybuild -O--sourcedirectory=python dh_installchangelogs -i -O--buildsystem=pybuild -O--sourcedirectory=python dh_installexamples -i -O--buildsystem=pybuild -O--sourcedirectory=python dh_python3 -i -O--buildsystem=pybuild -O--sourcedirectory=python dh_installinit -i -O--buildsystem=pybuild -O--sourcedirectory=python dh_installsystemduser -i -O--buildsystem=pybuild -O--sourcedirectory=python dh_perl -i -O--buildsystem=pybuild -O--sourcedirectory=python dh_link -i -O--buildsystem=pybuild -O--sourcedirectory=python dh_strip_nondeterminism -i -O--buildsystem=pybuild -O--sourcedirectory=python debian/rules override_dh_compress make[1]: Entering directory '/build/fast5-U1iShs/fast5-0.6.5' cd src && /usr/bin/make clean make[2]: Entering directory '/build/fast5-U1iShs/fast5-0.6.5/src' rm -rf f5ls f5ls-full hdf5-mod f5-mod f5dump f5pack make[2]: Leaving directory '/build/fast5-U1iShs/fast5-0.6.5/src' dh_compress -X .cpp -X .hpp make[1]: Leaving directory '/build/fast5-U1iShs/fast5-0.6.5' dh_fixperms -i -O--buildsystem=pybuild -O--sourcedirectory=python dh_missing -i -O--buildsystem=pybuild -O--sourcedirectory=python dh_installdeb -i -O--buildsystem=pybuild -O--sourcedirectory=python dh_gencontrol -i -O--buildsystem=pybuild -O--sourcedirectory=python dh_md5sums -i -O--buildsystem=pybuild -O--sourcedirectory=python dh_builddeb -i -O--buildsystem=pybuild -O--sourcedirectory=python dpkg-deb: building package 'fast5' in '../fast5_0.6.5-4_all.deb'. dpkg-deb: building package 'libfast5-dev' in '../libfast5-dev_0.6.5-4_all.deb'. dpkg-genbuildinfo --build=all dpkg-genchanges --build=all >../fast5_0.6.5-4_all.changes dpkg-genchanges: info: binary-only arch-indep upload (source code and arch-specific packages not included) dpkg-source --after-build . dpkg-source: info: using options from fast5-0.6.5/debian/source/options: --extend-diff-ignore=^[^/]+\.egg-info/|python/fast5/fast5.cpp dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/fast5-U1iShs /tmp/fast5-0.6.5-4rw6s56rm I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.AqOY1KkzTS... I: success in 620.7953 seconds md5: fast5_0.6.5-4_all.deb: OK md5: libfast5-dev_0.6.5-4_all.deb: OK sha1: fast5_0.6.5-4_all.deb: OK sha1: libfast5-dev_0.6.5-4_all.deb: OK sha256: fast5_0.6.5-4_all.deb: OK sha256: libfast5-dev_0.6.5-4_all.deb: OK Checksums: OK