Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/r/r-bioc-shortread/r-bioc-shortread_1.52.0-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/r-bioc-shortread-1.52.0-17rcuxlja/r-bioc-shortread_1.52.0-1_amd64.buildinfo Get source package info: r-bioc-shortread=1.52.0-1 Source URL: http://snapshot.notset.fr/mr/package/r-bioc-shortread/1.52.0-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.5-1.1 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.52 bash=5.1-3.1 binutils=2.37-10 binutils-common=2.37-10 binutils-x86-64-linux-gnu=2.37-10 bsdextrautils=2.37.2-4 bsdutils=1:2.37.2-4 build-essential=12.9 bzip2=1.0.8-4 ca-certificates=20211016 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-12 dash=0.5.11+git20210903+057cd650a4ed-3 dctrl-tools=2.24-3+b1 debconf=1.5.79 debhelper=13.5.2 debianutils=5.5-1 dh-autoreconf=20 dh-r=20210816 dh-strip-nondeterminism=1.12.1-1 diffutils=1:3.7-5 dpkg=1.20.9 dpkg-dev=1.20.9 dwz=0.14-1 file=1:5.41-2 findutils=4.8.0-1 fontconfig=2.13.1-4.2 fontconfig-config=2.13.1-4.2 fonts-dejavu-core=2.37-2 g++=4:11.2.0-2 g++-11=11.2.0-12 gcc=4:11.2.0-2 gcc-11=11.2.0-12 gcc-11-base=11.2.0-12 gettext=0.21-4 gettext-base=0.21-4 gfortran=4:11.2.0-2 gfortran-11=11.2.0-12 grep=3.7-1 groff-base=1.22.4-7 gzip=1.10-4 hostname=3.23 icu-devtools=67.1-7 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libalgorithm-c3-perl=0.11-1 libarchive-zip-perl=1.68-1 libasan6=11.2.0-12 libatomic1=11.2.0-12 libattr1=1:2.5.1-1 libaudit-common=1:3.0.6-1 libaudit1=1:3.0.6-1+b1 libb-hooks-endofscope-perl=0.25-1 libb-hooks-op-check-perl=0.22-1+b3 libbinutils=2.37-10 libblas-dev=3.10.0-1 libblas3=3.10.0-1 libblkid1=2.37.2-4 libboost-dev=1.74.0.3 libboost1.74-dev=1.74.0-13 libbrotli1=1.0.9-2+b3 libbsd0=0.11.3-1 libbz2-1.0=1.0.8-4 libbz2-dev=1.0.8-4 libc-bin=2.32-4 libc-dev-bin=2.32-4 libc6=2.32-4 libc6-dev=2.32-4 libcairo2=1.16.0-5 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcc1-0=11.2.0-12 libclass-c3-perl=0.35-1 libclass-load-perl=0.25-1 libclass-load-xs-perl=0.10-1+b5 libcom-err2=1.46.4-1 libcrypt-dev=1:4.4.26-1 libcrypt1=1:4.4.26-1 libctf-nobfd0=2.37-10 libctf0=2.37-10 libcurl3-gnutls=7.79.1-2 libcurl4=7.79.1-2 libdata-optlist-perl=0.112-1 libdatrie1=0.2.13-2 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.261 libdebhelper-perl=13.5.2 libdeflate0=1.8-1 libdevel-callchecker-perl=0.008-1+b2 libdevel-globaldestruction-perl=0.14-1.1 libdevel-overloadinfo-perl=0.007-1 libdevel-stacktrace-perl=2.0400-1 libdist-checkconflicts-perl=0.11-1.1 libdpkg-perl=1.20.9 libdynaloader-functions-perl=0.003-1.1 libelf1=0.186-1 libencode-locale-perl=1.05-1.1 libeval-closure-perl=0.14-1 libexpat1=2.4.1-3 libffi8=3.4.2-3 libfile-stripnondeterminism-perl=1.12.1-1 libfile-which-perl=1.23-1 libfontconfig1=2.13.1-4.2 libfreetype6=2.11.0+dfsg-1 libfribidi0=1.0.8-2 libgcc-11-dev=11.2.0-12 libgcc-s1=11.2.0-12 libgcrypt20=1.9.4-3+b1 libgdbm-compat4=1.22-1 libgdbm6=1.22-1 libgfortran-11-dev=11.2.0-12 libgfortran5=11.2.0-12 libglib2.0-0=2.70.1-1 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.2-2 libgomp1=11.2.0-12 libgpg-error0=1.42-3 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.18.3-7 libharfbuzz0b=2.7.4-1 libhogweed6=3.7.3-1 libhttp-date-perl=6.05-1 libhttp-message-perl=6.35-1 libice6=2:1.0.10-1 libicu-dev=67.1-7 libicu67=67.1-7 libidn2-0=2.3.2-2 libio-html-perl=1.004-2 libisl23=0.24-2 libitm1=11.2.0-12 libjbig0=2.1-3.1+b2 libjpeg-dev=1:2.1.1-2 libjpeg62-turbo=1:2.1.1-2 libjpeg62-turbo-dev=1:2.1.1-2 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 liblapack-dev=3.10.0-1 liblapack3=3.10.0-1 libldap-2.4-2=2.4.59+dfsg-1 liblsan0=11.2.0-12 liblwp-mediatypes-perl=6.04-1 liblz4-1=1.9.3-2 liblzma-dev=5.2.5-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.41-2 libmagic1=1:5.41-2 libmd0=1.0.4-1 libmodule-implementation-perl=0.09-1.1 libmodule-runtime-conflicts-perl=0.003-1.1 libmodule-runtime-perl=0.016-1 libmoose-perl=2.2200-1 libmount1=2.37.2-4 libmpc3=1.2.1-1 libmpfr6=4.1.0-3 libmro-compat-perl=0.13-1 libnamespace-clean-perl=0.27-1 libncurses-dev=6.3-1 libncurses5-dev=6.3-1 libncurses6=6.3-1 libncursesw6=6.3-1 libnettle8=3.7.3-1 libnghttp2-14=1.43.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libp11-kit0=0.24.0-5 libpackage-deprecationmanager-perl=0.17-1.1 libpackage-stash-perl=0.39-1 libpackage-stash-xs-perl=0.29-1+b2 libpam-modules=1.4.0-10 libpam-modules-bin=1.4.0-10 libpam-runtime=1.4.0-10 libpam0g=1.4.0-10 libpango-1.0-0=1.48.10+ds1-1 libpangocairo-1.0-0=1.48.10+ds1-1 libpangoft2-1.0-0=1.48.10+ds1-1 libpaper-utils=1.1.28+b1 libpaper1=1.1.28+b1 libparams-classify-perl=0.015-1+b3 libparams-util-perl=1.102-1+b1 libpcre16-3=2:8.39-13 libpcre2-16-0=10.39-3 libpcre2-32-0=10.39-3 libpcre2-8-0=10.39-3 libpcre2-dev=10.39-3 libpcre2-posix3=10.39-3 libpcre3=2:8.39-13 libpcre3-dev=2:8.39-13 libpcre32-3=2:8.39-13 libpcrecpp0v5=2:8.39-13 libperl5.32=5.32.1-6 libpipeline1=1.5.4-1 libpixman-1-0=0.40.0-1 libpng-dev=1.6.37-3 libpng16-16=1.6.37-3 libpsl5=0.21.0-1.2 libquadmath0=11.2.0-12 libreadline-dev=8.1-2 libreadline8=8.1-2 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg2-2 libsasl2-modules-db=2.1.27+dfsg2-2 libscalar-list-utils-perl=1:1.59-1 libseccomp2=2.5.3-2 libselinux1=3.3-1+b1 libsigsegv2=2.13-1 libsm6=2:1.2.3-1 libsmartcols1=2.37.2-4 libssh2-1=1.10.0-2 libssl1.1=1.1.1l-1 libstdc++-11-dev=11.2.0-12 libstdc++6=11.2.0-12 libsub-exporter-perl=0.988-1 libsub-exporter-progressive-perl=0.001013-1 libsub-identify-perl=0.14-1+b3 libsub-install-perl=0.928-1.1 libsub-name-perl=0.26-1+b1 libsub-override-perl=0.09-2 libswitch-perl=2.17-2.1 libsystemd0=249.7-1 libtasn1-6=4.18.0-4 libtcl8.6=8.6.12+dfsg-1 libthai-data=0.1.28-4.1 libthai0=0.1.28-4.1 libtiff5=4.3.0-2 libtimedate-perl=2.3300-2 libtinfo6=6.3-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtk8.6=8.6.12-1 libtool=2.4.6-15 libtry-tiny-perl=0.30-1 libtsan0=11.2.0-12 libubsan1=11.2.0-12 libuchardet0=0.0.7-1 libudev1=249.7-1 libunistring2=0.9.10-6 liburi-perl=5.10-1 libuuid1=2.37.2-4 libvariable-magic-perl=0.62-1+b3 libwebp6=0.6.1-2.1 libwww-curl-perl=4.17-7+b1 libwww-curl-simple-perl=0.100191-2 libx11-6=2:1.7.2-2+b1 libx11-data=2:1.7.2-2 libxau6=1:1.0.9-1 libxcb-render0=1.14-3 libxcb-shm0=1.14-3 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.4-1 libxft2=2.3.2-2 libxml2=2.9.12+dfsg-5+b1 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=1.4.8+dfsg-3 linux-libc-dev=5.15.3-1 login=1:4.8.1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.9.4-2 mawk=1.3.4.20200120-2 ncurses-base=6.3-1 ncurses-bin=6.3-1 openssl=1.1.1l-1 patch=2.7.6-7 perl=5.32.1-6 perl-base=5.32.1-6 perl-modules-5.32=5.32.1-6 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 r-base-core=4.1.2-1 r-base-dev=4.1.2-1 r-bioc-biobase=2.54.0-1 r-bioc-biocgenerics=0.40.0-1 r-bioc-biocparallel=1.28.1-1 r-bioc-biostrings=2.62.0-1 r-bioc-delayedarray=0.20.0+dfsg-1 r-bioc-genomeinfodb=1.30.0-1 r-bioc-genomeinfodbdata=1.2.6-1 r-bioc-genomicalignments=1.30.0-1 r-bioc-genomicranges=1.46.1+dfsg-1 r-bioc-iranges=2.28.0-1 r-bioc-matrixgenerics=1.6.0-1 r-bioc-rhtslib=1.26.0+dfsg-1 r-bioc-rsamtools=2.10.0-1 r-bioc-s4vectors=0.32.3-1 r-bioc-summarizedexperiment=1.24.0+dfsg-1 r-bioc-xvector=0.34.0-1 r-bioc-zlibbioc=1.40.0+dfsg-1 r-cran-bh=1.74.0-2 r-cran-bitops=1.0-7-1 r-cran-crayon=1.4.2-1 r-cran-formatr=1.11-1 r-cran-futile.logger=1.4.3-4 r-cran-futile.options=1.0.1-3 r-cran-hwriter=1.3.2-4 r-cran-jpeg=0.1-9-1 r-cran-lambda.r=1.2.4-2 r-cran-lattice=0.20-45-1 r-cran-latticeextra=0.6-29-3 r-cran-matrix=1.3-4-2 r-cran-matrixstats=0.61.0-1 r-cran-png=0.1-7-4 r-cran-rcolorbrewer=1.1-2-3 r-cran-rcurl=1.98-1.5-1 r-cran-snow=1:0.4.4-1 readline-common=8.1-2 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.00-1 tar=1.34+dfsg-1 tzdata=2021e-1 ucf=3.0043 unzip=6.0-26 util-linux=2.37.2-4 x11-common=1:7.7+23 xauth=1:1.1-1 xdg-utils=1.1.3-4.1 xz-utils=5.2.5-2 zip=3.0-12 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/20211125T203520Z/ unstable main deb-src http://snapshot.notset.fr/archive/debian/20211125T203520Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211126T150138Z/ 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-shortread=1.52.0-1 && mkdir -p /build/r-bioc-shortread-PCrLKh && dpkg-source --no-check -x /*.dsc /build/r-bioc-shortread-PCrLKh/r-bioc-shortread-1.52.0 && chown -R builduser:builduser /build/r-bioc-shortread-PCrLKh" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/r-bioc-shortread-PCrLKh/r-bioc-shortread-1.52.0 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1637848523" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/r-bioc-shortread-PCrLKh /tmp/r-bioc-shortread-1.52.0-17rcuxlja bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20211126T150138Z 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.mBHJmsIU5f 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.mBHJmsIU5f Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-4). 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/20211126T150138Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211126T150138Z unstable/main amd64 fakeroot amd64 1.26-1 [87.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1023 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 ... 4672 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.26-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.26-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.26-1_amd64.deb ... Unpacking fakeroot (1.26-1) ... Setting up libfakeroot:amd64 (1.26-1) ... Setting up fakeroot (1.26-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.32-4) ... 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/20211125T203520Z/ unstable main deb-src http://snapshot.notset.fr/archive/debian/20211125T203520Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211126T150138Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.mBHJmsIU5f Get:1 http://snapshot.notset.fr/archive/debian/20211125T203520Z unstable InRelease [165 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20211126T150138Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20211125T203520Z unstable/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211125T203520Z unstable/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20211125T203520Z unstable/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211125T203520Z unstable/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20211125T203520Z unstable/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211125T203520Z unstable/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20211125T203520Z unstable/main Sources [12.5 MB] Get:4 http://snapshot.notset.fr/archive/debian/20211125T203520Z unstable/main amd64 Packages [12.0 MB] Fetched 24.7 MB in 21s (1192 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.mBHJmsIU5f I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d r-bioc-shortread=1.52.0-1 && mkdir -p /build/r-bioc-shortread-PCrLKh && dpkg-source --no-check -x /*.dsc /build/r-bioc-shortread-PCrLKh/r-bioc-shortread-1.52.0 && chown -R builduser:builduser /build/r-bioc-shortread-PCrLKh"' exec /tmp/mmdebstrap.mBHJmsIU5f Reading package lists... NOTICE: 'r-bioc-shortread' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/r-pkg-team/r-bioc-shortread.git Please use: git clone https://salsa.debian.org/r-pkg-team/r-bioc-shortread.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 5193 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20211125T203520Z unstable/main r-bioc-shortread 1.52.0-1 (dsc) [2387 B] Get:2 http://snapshot.notset.fr/archive/debian/20211125T203520Z unstable/main r-bioc-shortread 1.52.0-1 (tar) [5185 kB] Get:3 http://snapshot.notset.fr/archive/debian/20211125T203520Z unstable/main r-bioc-shortread 1.52.0-1 (diff) [5616 B] Fetched 5193 kB in 4s (1275 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'r-bioc-shortread_1.52.0-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting r-bioc-shortread in /build/r-bioc-shortread-PCrLKh/r-bioc-shortread-1.52.0 dpkg-source: info: unpacking r-bioc-shortread_1.52.0.orig.tar.gz dpkg-source: info: unpacking r-bioc-shortread_1.52.0-1.debian.tar.xz I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/r-bioc-shortread-PCrLKh/r-bioc-shortread-1.52.0 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1637848523" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.mBHJmsIU5f dpkg-buildpackage: info: source package r-bioc-shortread dpkg-buildpackage: info: source version 1.52.0-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem R debian/rules override_dh_auto_clean make[1]: Entering directory '/build/r-bioc-shortread-PCrLKh/r-bioc-shortread-1.52.0' dh_auto_clean rm -f configure config.log config.status make[1]: Leaving directory '/build/r-bioc-shortread-PCrLKh/r-bioc-shortread-1.52.0' 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 configure.ac:14: warning: The macro `AC_ERROR' is obsolete. configure.ac:14: You should run autoupdate. ./lib/autoconf/oldnames.m4:34: AC_ERROR is expanded from... configure.ac:14: the top level configure.ac:17: warning: AC_OUTPUT should be used without arguments. configure.ac:17: You should run autoupdate. 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 dh_auto_install --destdir=debian/r-bioc-shortread/ -a -O--buildsystem=R I: R Package: ShortRead Version: 1.52.0 I: Building using R version 4.1.2-1 I: R API version: r-api-4.0 I: Using built-time from d/changelog: Thu, 25 Nov 2021 14:55:23 +0100 mkdir -p /build/r-bioc-shortread-PCrLKh/r-bioc-shortread-1.52.0/debian/r-bioc-shortread/usr/lib/R/site-library R CMD INSTALL -l /build/r-bioc-shortread-PCrLKh/r-bioc-shortread-1.52.0/debian/r-bioc-shortread/usr/lib/R/site-library --clean . "--built-timestamp='Thu, 25 Nov 2021 14:55:23 +0100'" * installing *source* package ‘ShortRead’ ... ** using staged installation checking for gcc... gcc -std=gnu99 -std=gnu11 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc -std=gnu99 -std=gnu11 accepts -g... yes checking for gcc -std=gnu99 -std=gnu11 option to enable C11 features... none needed checking for gzeof in -lz... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking size of unsigned long... 8 configure: creating ./config.status config.status: creating src/Makevars ** libs make[1]: Entering directory '/build/r-bioc-shortread-PCrLKh/r-bioc-shortread-1.52.0/src' gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-PT7Nxy/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-PT7Nxy/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c IRanges_stubs.c -o IRanges_stubs.o gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-PT7Nxy/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_init_ShortRead.c -o R_init_ShortRead.o gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-PT7Nxy/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-PT7Nxy/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c XVector_stubs.c -o XVector_stubs.o gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-PT7Nxy/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c alphabet.c -o alphabet.o gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-PT7Nxy/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c count.c -o count.o gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-PT7Nxy/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c io.c -o io.o gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-PT7Nxy/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c io_bowtie.c -o io_bowtie.o gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-PT7Nxy/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c io_soap.c -o io_soap.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic -g -O2 -ffile-prefix-map=/build/r-base-PT7Nxy/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c readBfaToc.cc -o readBfaToc.o readBfaToc.cc: In function ‘SEXPREC* readBfaToc(SEXP)’: readBfaToc.cc:35:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 35 | (void) fread( seq_name, sizeof(char), name_len, fp ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readBfaToc.cc:36:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 36 | (void) fread( &seq_ori_len, sizeof(int), 1, fp ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readBfaToc.cc:37:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | (void) fread( &seq_len, sizeof(int), 1, fp ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic -g -O2 -ffile-prefix-map=/build/r-base-PT7Nxy/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c read_maq_map.cc -o read_maq_map.o gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-PT7Nxy/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sampler.c -o sampler.o gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-PT7Nxy/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c trim.c -o trim.o gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-PT7Nxy/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c util.c -o util.o gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-PT7Nxy/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xsnap.c -o xsnap.o g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-z,relro -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o count.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -lz -fopenmp -L/usr/lib/R/lib -lR make[1]: Leaving directory '/build/r-bioc-shortread-PCrLKh/r-bioc-shortread-1.52.0/src' make[1]: Entering directory '/build/r-bioc-shortread-PCrLKh/r-bioc-shortread-1.52.0/src' make[1]: Leaving directory '/build/r-bioc-shortread-PCrLKh/r-bioc-shortread-1.52.0/src' installing to /build/r-bioc-shortread-PCrLKh/r-bioc-shortread-1.52.0/debian/r-bioc-shortread/usr/lib/R/site-library/00LOCK-r-bioc-shortread-1.52.0/00new/ShortRead/libs ** R ** inst ** byte-compile and prepare package for lazy loading code for methods in class “ShortReadFile” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “FastqFileReader” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “QAData” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Snapshot” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “SpTrellis” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “FastqSampler” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “FastqStreamer” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) ** 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 (ShortRead) Use of uninitialized value $dep_line in substitution (s///) at /usr/share/perl5/Dpkg/Deps.pm line 299. Use of uninitialized value $dep_line in substitution (s///) at /usr/share/perl5/Dpkg/Deps.pm line 300. Use of uninitialized value $dep_line in split at /usr/share/perl5/Dpkg/Deps.pm line 303. I: Using r-bioc-biocgenerics for Depends:BiocGenerics (>= 0.23.3) I: Using r-bioc-biocparallel for Depends:BiocParallel I: Using r-bioc-biostrings for Depends:Biostrings (>= 2.47.6) I: Using r-bioc-rsamtools for Depends:Rsamtools (>= 1.31.2) I: Using r-bioc-genomicalignments for Depends:GenomicAlignments (>= 1.15.6) I: Using r-bioc-biocstyle for Suggests:BiocStyle I: Using r-cran-runit for Suggests:RUnit I: Using r-bioc-biomart for Suggests:biomaRt I: Using r-bioc-genomicfeatures for Suggests:GenomicFeatures W: Cannot find a debian package for Suggests:yeastNagalakshmi I: Using r-bioc-biobase for Imports:Biobase I: Using r-bioc-s4vectors for Imports:S4Vectors (>= 0.17.25) I: Using r-bioc-iranges for Imports:IRanges (>= 2.13.12) I: Using r-bioc-genomeinfodb for Imports:GenomeInfoDb (>= 1.15.2) I: Using r-bioc-genomicranges for Imports:GenomicRanges (>= 1.31.8) I: Using r-cran-hwriter for Imports:hwriter I: Using r-bioc-zlibbioc for Imports:zlibbioc I: Using r-cran-lattice for Imports:lattice I: Using r-cran-latticeextra for Imports:latticeExtra I: Using r-bioc-s4vectors for LinkingTo:S4Vectors I: Using r-bioc-iranges for LinkingTo:IRanges I: Using r-bioc-xvector for LinkingTo:XVector I: Using r-bioc-biostrings for LinkingTo:Biostrings I: Using r-bioc-rhtslib for LinkingTo:Rhtslib I: Using r-bioc-zlibbioc for LinkingTo:zlibbioc I: BioConductor API version: r-api-bioc-3.14 I: Use r-bioc-shortread as Debian binary package for variables substitution 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 -O--buildsystem=R dh_strip -a -O--buildsystem=R dh_makeshlibs -a -O--buildsystem=R dh_shlibdeps -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-shortread' in '../r-bioc-shortread_1.52.0-1_amd64.deb'. dpkg-deb: building package 'r-bioc-shortread-dbgsym' in '../r-bioc-shortread-dbgsym_1.52.0-1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../r-bioc-shortread_1.52.0-1_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-shortread-PCrLKh /tmp/r-bioc-shortread-1.52.0-17rcuxlja I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.mBHJmsIU5f... I: success in 3377.9176 seconds md5: r-bioc-shortread-dbgsym_1.52.0-1_amd64.deb: OK md5: r-bioc-shortread_1.52.0-1_amd64.deb: OK sha1: r-bioc-shortread-dbgsym_1.52.0-1_amd64.deb: OK sha1: r-bioc-shortread_1.52.0-1_amd64.deb: OK sha256: r-bioc-shortread-dbgsym_1.52.0-1_amd64.deb: OK sha256: r-bioc-shortread_1.52.0-1_amd64.deb: OK Checksums: OK