Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/r/r-bioc-rhdf5/r-bioc-rhdf5_2.34.0+dfsg-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/r-bioc-rhdf5-2.34.0+dfsg-1u_bprck1/r-bioc-rhdf5_2.34.0+dfsg-1_amd64.buildinfo Get source package info: r-bioc-rhdf5=2.34.0+dfsg-1 Source URL: http://snapshot.notset.fr/mr/package/r-bioc-rhdf5/2.34.0+dfsg-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11.1 automake=1:1.16.2-4 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.48 bash=5.1~rc2-1 binutils=2.35.1-2 binutils-common=2.35.1-2 binutils-x86-64-linux-gnu=2.35.1-2 bsdextrautils=2.36.1-1 bsdutils=1:2.36-3+b2 build-essential=12.8 bzip2=1.0.8-4 ca-certificates=20200601 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.0-17 dash=0.5.11+git20200708+dd9ef66-2 dctrl-tools=2.24-3+b1 debconf=1.5.74 debhelper=13.2.1 debianutils=4.11.2 dh-autoreconf=19 dh-r=20200923 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-3 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13-5 file=1:5.38-5 findutils=4.7.0+git20201010-2 fontconfig=2.13.1-4.2 fontconfig-config=2.13.1-4.2 fonts-dejavu-core=2.37-2 g++=4:10.2.0-1 g++-10=10.2.0-17 gcc=4:10.2.0-1 gcc-10=10.2.0-17 gcc-10-base=10.2.0-17 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 gfortran=4:10.2.0-1 gfortran-10=10.2.0-17 grep=3.6-1 groff-base=1.22.4-5 gzip=1.10-2 hdf5-helpers=1.10.6+repack-2 hostname=3.23 icu-devtools=67.1-4 init-system-helpers=1.58 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-8 libaec-dev=1.0.4-1 libaec0=1.0.4-1 libarchive-zip-perl=1.68-1 libasan6=10.2.0-17 libatomic1=10.2.0-17 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3.1 libaudit1=1:2.8.5-3.1 libbinutils=2.35.1-2 libblas-dev=3.9.0-3 libblas3=3.9.0-3 libblkid1=2.36-3+b2 libbrotli1=1.0.9-2+b1 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-4 libbz2-dev=1.0.8-4 libc-bin=2.31-4 libc-dev-bin=2.31-4 libc6=2.31-4 libc6-dev=2.31-4 libcairo2=1.16.0-4 libcap-ng0=0.7.9-2.2 libcc1-0=10.2.0-17 libcom-err2=1.45.6-1 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-2 libctf0=2.35.1-2 libcurl4=7.72.0-1 libdatrie1=0.2.12-3 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.255 libdebhelper-perl=13.2.1 libdpkg-perl=1.20.5 libelf1=0.182-1 libexpat1=2.2.10-1 libffi7=3.3-5 libfile-stripnondeterminism-perl=1.9.0-1 libfile-which-perl=1.23-1 libfontconfig1=2.13.1-4.2 libfreetype6=2.10.2+dfsg-4 libfribidi0=1.0.8-2 libgcc-10-dev=10.2.0-17 libgcc-s1=10.2.0-17 libgcrypt20=1.8.7-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libgfortran-10-dev=10.2.0-17 libgfortran5=10.2.0-17 libglib2.0-0=2.66.2-1 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.6.15-4 libgomp1=10.2.0-17 libgpg-error0=1.38-2 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.17-10 libharfbuzz0b=2.6.7-1 libhdf5-103-1=1.10.6+repack-2 libhdf5-cpp-103-1=1.10.6+repack-2 libhdf5-dev=1.10.6+repack-2 libhdf5-fortran-102=1.10.6+repack-2 libhdf5-hl-100=1.10.6+repack-2 libhdf5-hl-cpp-100=1.10.6+repack-2 libhdf5-hl-fortran-100=1.10.6+repack-2 libhogweed6=3.6-2 libice6=2:1.0.10-1 libicu-dev=67.1-4 libicu67=67.1-4 libidn2-0=2.3.0-3 libisl22=0.22.1-1 libitm1=10.2.0-17 libjbig0=2.1-3.1+b2 libjpeg-dev=1:2.0.5-1.1 libjpeg62-turbo=1:2.0.5-1.1 libjpeg62-turbo-dev=1:2.0.5-1.1 libk5crypto3=1.17-10 libkeyutils1=1.6.1-2 libkrb5-3=1.17-10 libkrb5support0=1.17-10 liblapack-dev=3.9.0-3 liblapack3=3.9.0-3 libldap-2.4-2=2.4.56+dfsg-1 liblsan0=10.2.0-17 liblz4-1=1.9.2-2 liblzma-dev=5.2.4-1+b1 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.38-5 libmagic1=1:5.38-5 libmount1=2.36-3+b2 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libncurses-dev=6.2+20200918-1 libncurses5-dev=6.2+20200918-1 libncurses6=6.2+20200918-1 libncursesw6=6.2+20200918-1 libnettle8=3.6-2 libnghttp2-14=1.41.0-3 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnss-nis=3.1-4 libnss-nisplus=1.3-4 libp11-kit0=0.23.21-2 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpango-1.0-0=1.46.2-3 libpangocairo-1.0-0=1.46.2-3 libpangoft2-1.0-0=1.46.2-3 libpaper-utils=1.1.28+b1 libpaper1=1.1.28+b1 libpcre16-3=2:8.39-13 libpcre2-16-0=10.34-7 libpcre2-32-0=10.34-7 libpcre2-8-0=10.34-7 libpcre2-dev=10.34-7 libpcre2-posix2=10.34-7 libpcre3=2:8.39-13 libpcre3-dev=2:8.39-13 libpcre32-3=2:8.39-13 libpcrecpp0v5=2:8.39-13 libperl5.32=5.32.0-5 libpipeline1=1.5.3-1 libpixman-1-0=0.36.0-1 libpng-dev=1.6.37-3 libpng16-16=1.6.37-3 libpsl5=0.21.0-1.1 libquadmath0=10.2.0-17 libreadline-dev=8.1~rc2-2 libreadline8=8.1~rc2-2 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2 libsasl2-modules-db=2.1.27+dfsg-2 libseccomp2=2.5.0-3 libselinux1=3.1-2+b1 libsigsegv2=2.12-2 libsm6=2:1.2.3-1 libsmartcols1=2.36-3+b2 libssh2-1=1.8.0-2.1 libssl1.1=1.1.1h-1 libstdc++-10-dev=10.2.0-17 libstdc++6=10.2.0-17 libsub-override-perl=0.09-2 libswitch-perl=2.17-2 libsystemd0=246.6-2 libsz2=1.0.4-1 libtasn1-6=4.16.0-2 libtcl8.6=8.6.10+dfsg-1 libthai-data=0.1.28-3 libthai0=0.1.28-3 libtiff5=4.1.0+git191117-2 libtinfo6=6.2+20200918-1 libtirpc-common=1.2.6-3 libtirpc-dev=1.2.6-3 libtirpc3=1.2.6-3 libtk8.6=8.6.10-1 libtool=2.4.6-14 libtsan0=10.2.0-17 libubsan1=10.2.0-17 libuchardet0=0.0.7-1 libudev1=246.6-2 libunistring2=0.9.10-4 libuuid1=2.36-3+b2 libwebp6=0.6.1-2+b1 libx11-6=2:1.6.12-1 libx11-data=2:1.6.12-1 libxau6=1:1.0.8-1+b2 libxcb-render0=1.14-2 libxcb-shm0=1.14-2 libxcb1=1.14-2 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.3-1+b2 libxft2=2.3.2-2 libxml2=2.9.10+dfsg-6.2 libxmuu1=2:1.1.2-2+b3 libxrender1=1:0.9.10-1 libxss1=1:1.2.3-1 libxt6=1:1.2.0-1 libzstd1=1.4.5+dfsg-4 linux-libc-dev=5.9.6-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 ncurses-base=6.2+20200918-1 ncurses-bin=6.2+20200918-1 openssl=1.1.1h-1 patch=2.7.6-6 perl=5.32.0-5 perl-base=5.32.0-5 perl-modules-5.32=5.32.0-5 pkg-config=0.29.2-1 po-debconf=1.0.21 r-base-core=4.0.3-1 r-base-dev=4.0.3-1 r-bioc-biocgenerics=0.36.0-1 r-bioc-rhdf5filters=1.2.0+dfsg-4 r-bioc-rhdf5lib=1.12.0+dfsg-1 readline-common=8.1~rc2-2 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-5 tar=1.30+dfsg-7 tzdata=2020d-1 ucf=3.0043 unzip=6.0-25 util-linux=2.36-3+b2 x11-common=1:7.7+21 xauth=1:1.0.10-1 xdg-utils=1.1.3-2 xz-utils=5.2.4-1+b1 zip=3.0-11+b1 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/20201117T094129Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201116T092020Z/ 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 r-bioc-rhdf5=2.34.0+dfsg-1 && mkdir -p /build/r-bioc-rhdf5-vwxH1S && dpkg-source --no-check -x /*.dsc /build/r-bioc-rhdf5-vwxH1S/r-bioc-rhdf5-2.34.0+dfsg && chown -R builduser:builduser /build/r-bioc-rhdf5-vwxH1S" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/r-bioc-rhdf5-vwxH1S/r-bioc-rhdf5-2.34.0+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1605612230" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/r-bioc-rhdf5-vwxH1S /tmp/r-bioc-rhdf5-2.34.0+dfsg-1u_bprck1 bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20201116T092020Z 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.fkFse8dp_B 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.fkFse8dp_B Reading package lists... Building dependency tree... util-linux is already the newest version (2.36-3+b2). 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/20201116T092020Z unstable/main amd64 libfakeroot amd64 1.25.3-1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201116T092020Z unstable/main amd64 fakeroot amd64 1.25.3-1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (907 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 ... 4695 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1_amd64.deb ... Unpacking fakeroot (1.25.3-1) ... Setting up libfakeroot:amd64 (1.25.3-1) ... Setting up fakeroot (1.25.3-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-4) ... 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/20201117T094129Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201116T092020Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.fkFse8dp_B Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201117T094129Z unstable InRelease [146 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20201116T092020Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20201117T094129Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201117T094129Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201117T094129Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20201117T094129Z unstable/main amd64 Packages [11.5 MB] Fetched 34.3 MB in 28s (1213 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.fkFse8dp_B I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d r-bioc-rhdf5=2.34.0+dfsg-1 && mkdir -p /build/r-bioc-rhdf5-vwxH1S && dpkg-source --no-check -x /*.dsc /build/r-bioc-rhdf5-vwxH1S/r-bioc-rhdf5-2.34.0+dfsg && chown -R builduser:builduser /build/r-bioc-rhdf5-vwxH1S"' exec /tmp/mmdebstrap.fkFse8dp_B Reading package lists... NOTICE: 'r-bioc-rhdf5' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/r-pkg-team/r-bioc-rhdf5.git Please use: git clone https://salsa.debian.org/r-pkg-team/r-bioc-rhdf5.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 240 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main r-bioc-rhdf5 2.34.0+dfsg-1 (dsc) [2175 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main r-bioc-rhdf5 2.34.0+dfsg-1 (tar) [209 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main r-bioc-rhdf5 2.34.0+dfsg-1 (diff) [29.1 kB] Fetched 240 kB in 0s (736 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'r-bioc-rhdf5_2.34.0+dfsg-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting r-bioc-rhdf5 in /build/r-bioc-rhdf5-vwxH1S/r-bioc-rhdf5-2.34.0+dfsg dpkg-source: info: unpacking r-bioc-rhdf5_2.34.0+dfsg.orig.tar.xz dpkg-source: info: unpacking r-bioc-rhdf5_2.34.0+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hack_to_use_H5private.h.patch dpkg-source: info: applying use_debian_packaged_libhdf5.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/r-bioc-rhdf5-vwxH1S/r-bioc-rhdf5-2.34.0+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1605612230" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.fkFse8dp_B dpkg-buildpackage: info: source package r-bioc-rhdf5 dpkg-buildpackage: info: source version 2.34.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem R dh_auto_clean -O--buildsystem=R dh_autoreconf_clean -O--buildsystem=R dh_clean -O--buildsystem=R debian/rules binary-arch dh binary-arch --buildsystem R dh_update_autotools_config -a -O--buildsystem=R dh_autoreconf -a -O--buildsystem=R dh_auto_configure -a -O--buildsystem=R dh_auto_build -a -O--buildsystem=R dh_auto_test -a -O--buildsystem=R create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=R dh_prep -a -O--buildsystem=R debian/rules override_dh_auto_install make[1]: Entering directory '/build/r-bioc-rhdf5-vwxH1S/r-bioc-rhdf5-2.34.0+dfsg' # see debian/hdf5-private/README ln -s /build/r-bioc-rhdf5-vwxH1S/r-bioc-rhdf5-2.34.0+dfsg/debian/hdf5-private/H5private.h /build/r-bioc-rhdf5-vwxH1S/r-bioc-rhdf5-2.34.0+dfsg/src/H5private.h ln -s /build/r-bioc-rhdf5-vwxH1S/r-bioc-rhdf5-2.34.0+dfsg/debian/hdf5-private/H5TSprivate.h /build/r-bioc-rhdf5-vwxH1S/r-bioc-rhdf5-2.34.0+dfsg/src/H5TSprivate.h dh_auto_install # --no-parallel ... does not help I: R packages needed for DEP8: testthat, bit64 I: R Package: rhdf5 Version: 2.34.0 I: Building using R version 4.0.3-1 I: R API version: r-api-4.0 I: Using built-time from d/changelog: Tue, 17 Nov 2020 12:23:50 +0100 mkdir -p /build/r-bioc-rhdf5-vwxH1S/r-bioc-rhdf5-2.34.0\+dfsg/debian/r-bioc-rhdf5/usr/lib/R/site-library R CMD INSTALL -l /build/r-bioc-rhdf5-vwxH1S/r-bioc-rhdf5-2.34.0\+dfsg/debian/r-bioc-rhdf5/usr/lib/R/site-library --clean . "--built-timestamp='Tue, 17 Nov 2020 12:23:50 +0100'" * installing *source* package ‘rhdf5’ ... ** using staged installation configure: creating ./config.status config.status: creating src/external_filters.h ** libs make[2]: Entering directory '/build/r-bioc-rhdf5-vwxH1S/r-bioc-rhdf5-2.34.0+dfsg/src' gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c H5.c -o H5.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c H5A.c -o H5A.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c H5D.c -o H5D.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c H5E.c -o H5E.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c H5F.c -o H5F.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c H5G.c -o H5G.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c H5I.c -o H5I.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c H5L.c -o H5L.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c H5O.c -o H5O.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c H5P.c -o H5P.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c H5S.c -o H5S.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c H5T.c -o H5T.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c H5Z.c -o H5Z.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c H5constants.c -o H5constants.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c HandleList.cpp -o HandleList.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c HandleListWrap.c -o HandleListWrap.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c external_filters.c -o external_filters.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c h5dump.c -o h5dump.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c h5ls.c -o h5ls.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c h5testLock.c -o h5testLock.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c h5writeDataFrame.c -o h5writeDataFrame.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c printdatatype.c -o printdatatype.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oKyfjH/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c wrap.c -o wrap.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-z,relro -o rhdf5.so H5.o H5A.o H5D.o H5E.o H5F.o H5G.o H5I.o H5L.o H5O.o H5P.o H5S.o H5T.o H5Z.o H5constants.o HandleList.o HandleListWrap.o external_filters.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o utils.o wrap.o /usr/lib/R/site-library/Rhdf5lib/libs/Rhdf5lib.so -L/usr/lib/x86_64-linux-gnu/hdf5/serial/ -lhdf5 -L/usr/lib/R/lib -lR make[2]: Leaving directory '/build/r-bioc-rhdf5-vwxH1S/r-bioc-rhdf5-2.34.0+dfsg/src' make[2]: Entering directory '/build/r-bioc-rhdf5-vwxH1S/r-bioc-rhdf5-2.34.0+dfsg/src' make[2]: Leaving directory '/build/r-bioc-rhdf5-vwxH1S/r-bioc-rhdf5-2.34.0+dfsg/src' installing to /build/r-bioc-rhdf5-vwxH1S/r-bioc-rhdf5-2.34.0+dfsg/debian/r-bioc-rhdf5/usr/lib/R/site-library/00LOCK-r-bioc-rhdf5-2.34.0+dfsg/00new/rhdf5/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rhdf5) W: Ignoring specified R dependency: R (>= 3.5.0) I: Using r-cran-testthat for Recommends:testthat I: Using r-cran-bit64 for Recommends:bit64 I: Using r-bioc-biocstyle for Suggests:BiocStyle I: Using r-cran-knitr for Suggests:knitr I: Using r-cran-rmarkdown for Suggests:rmarkdown W: Cannot find a debian package for Suggests:microbenchmark I: Using r-cran-dplyr for Suggests:dplyr I: Using r-cran-ggplot2 for Suggests:ggplot2 I: Using r-bioc-rhdf5lib for Imports:Rhdf5lib (>= 1.11.0) I: Using r-bioc-rhdf5filters for Imports:rhdf5filters I: Using r-bioc-rhdf5lib for LinkingTo:Rhdf5lib I: BioConductor API version: r-api-bioc-3.12 I: Use r-bioc-rhdf5 as Debian binary package for variables substitution rm src/H5private.h src/H5TSprivate.h make[1]: Leaving directory '/build/r-bioc-rhdf5-vwxH1S/r-bioc-rhdf5-2.34.0+dfsg' dh_installdocs -a -O--buildsystem=R dh_installchangelogs -a -O--buildsystem=R dh_installsystemduser -a -O--buildsystem=R dh_perl -a -O--buildsystem=R dh_link -a -O--buildsystem=R dh_strip_nondeterminism -a -O--buildsystem=R dh_compress -a -O--buildsystem=R dh_fixperms -a -O--buildsystem=R dh_missing -a -O--buildsystem=R dh_dwz -a -a -O--buildsystem=R dh_strip -a -a -O--buildsystem=R dh_makeshlibs -a -a -O--buildsystem=R dh_shlibdeps -a -a -O--buildsystem=R dh_installdeb -a -O--buildsystem=R dh_gencontrol -a -O--buildsystem=R dh_md5sums -a -O--buildsystem=R dh_builddeb -a -O--buildsystem=R dpkg-deb: building package 'r-bioc-rhdf5-dbgsym' in '../r-bioc-rhdf5-dbgsym_2.34.0+dfsg-1_amd64.deb'. dpkg-deb: building package 'r-bioc-rhdf5' in '../r-bioc-rhdf5_2.34.0+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../r-bioc-rhdf5_2.34.0+dfsg-1_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/r-bioc-rhdf5-vwxH1S /tmp/r-bioc-rhdf5-2.34.0+dfsg-1u_bprck1 I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.fkFse8dp_B... I: success in 674.4712 seconds md5: r-bioc-rhdf5-dbgsym_2.34.0+dfsg-1_amd64.deb: OK md5: r-bioc-rhdf5_2.34.0+dfsg-1_amd64.deb: OK sha1: r-bioc-rhdf5-dbgsym_2.34.0+dfsg-1_amd64.deb: OK sha1: r-bioc-rhdf5_2.34.0+dfsg-1_amd64.deb: OK sha256: r-bioc-rhdf5-dbgsym_2.34.0+dfsg-1_amd64.deb: OK sha256: r-bioc-rhdf5_2.34.0+dfsg-1_amd64.deb: OK Checksums: OK