Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/r/r-bioc-shortread/r-bioc-shortread_1.48.0-2_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/r-bioc-shortread-1.48.0-2di1ttekx/r-bioc-shortread_1.48.0-2_amd64.buildinfo Get source package info: r-bioc-shortread=1.48.0-2 Source URL: http://snapshot.notset.fr/mr/package/r-bioc-shortread/1.48.0-2/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-14 automake=1:1.16.3-2 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=11 base-passwd=3.5.48 bash=5.1-2 binutils=2.35.1-7 binutils-common=2.35.1-7 binutils-x86-64-linux-gnu=2.35.1-7 bsdextrautils=2.36.1-6 bsdutils=1:2.36.1-6 build-essential=12.9 bzip2=1.0.8-4 ca-certificates=20210119 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.2.1-6 dash=0.5.11+git20200708+dd9ef66-5 dctrl-tools=2.24-3+b1 debconf=1.5.74 debhelper=13.3.3 debianutils=4.11.2 dh-autoreconf=20 dh-r=20201129 dh-strip-nondeterminism=1.11.0-1 diffutils=1:3.7-5 dpkg=1.20.7.1 dpkg-dev=1.20.7.1 dwz=0.13+20210201-1 file=1:5.39-3 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++=4:10.2.1-1 g++-10=10.2.1-6 gcc=4:10.2.1-1 gcc-10=10.2.1-6 gcc-10-base=10.2.1-6 gettext=0.21-4 gettext-base=0.21-4 gfortran=4:10.2.1-1 gfortran-10=10.2.1-6 grep=3.6-1 groff-base=1.22.4-6 gzip=1.10-2 hostname=3.23 icu-devtools=67.1-6 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-10 libalgorithm-c3-perl=0.11-1 libarchive-zip-perl=1.68-1 libasan6=10.2.1-6 libatomic1=10.2.1-6 libattr1=1:2.4.48-6 libaudit-common=1:3.0-2 libaudit1=1:3.0-2 libb-hooks-endofscope-perl=0.24-1.1 libb-hooks-op-check-perl=0.22-1+b3 libbinutils=2.35.1-7 libblas-dev=3.9.0-3 libblas3=3.9.0-3 libblkid1=2.36.1-6 libboost-dev=1.74.0.3 libboost1.74-dev=1.74.0-8 libbrotli1=1.0.9-2+b2 libbsd0=0.11.1-1 libbz2-1.0=1.0.8-4 libbz2-dev=1.0.8-4 libc-bin=2.31-9 libc-dev-bin=2.31-9 libc6=2.31-9 libc6-dev=2.31-9 libcairo2=1.16.0-5 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-6 libclass-c3-perl=0.35-1 libclass-load-perl=0.25-1 libclass-load-xs-perl=0.10-1+b5 libcom-err2=1.45.7-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-7 libctf0=2.35.1-7 libcurl3-gnutls=7.74.0-1 libcurl4=7.74.0-1 libdata-optlist-perl=0.110-1.1 libdatrie1=0.2.13-1 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.256 libdebhelper-perl=13.3.3 libdeflate0=1.7-1 libdevel-callchecker-perl=0.008-1+b2 libdevel-globaldestruction-perl=0.14-1.1 libdevel-overloadinfo-perl=0.005-1 libdevel-stacktrace-perl=2.0400-1 libdist-checkconflicts-perl=0.11-1.1 libdpkg-perl=1.20.7.1 libdynaloader-functions-perl=0.003-1.1 libelf1=0.182+20210205-1 libencode-locale-perl=1.05-1.1 libeval-closure-perl=0.14-1 libexpat1=2.2.10-1 libffi7=3.3-5 libfile-stripnondeterminism-perl=1.11.0-1 libfile-which-perl=1.23-1 libfontconfig1=2.13.1-4.2 libfreetype6=2.10.4+dfsg-1 libfribidi0=1.0.8-2 libgcc-10-dev=10.2.1-6 libgcc-s1=10.2.1-6 libgcrypt20=1.8.7-2 libgdbm-compat4=1.19-2 libgdbm6=1.19-2 libgfortran-10-dev=10.2.1-6 libgfortran5=10.2.1-6 libglib2.0-0=2.66.6-1 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.7.0-5 libgomp1=10.2.1-6 libgpg-error0=1.38-2 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.18.3-4 libharfbuzz0b=2.7.4-1 libhogweed6=3.7-2 libhttp-date-perl=6.05-1 libhttp-message-perl=6.27-1 libice6=2:1.0.10-1 libicu-dev=67.1-6 libicu67=67.1-6 libidn2-0=2.3.0-5 libio-html-perl=1.004-1 libisl23=0.23-1 libitm1=10.2.1-6 libjbig0=2.1-3.1+b2 libjpeg-dev=1:2.0.5-2 libjpeg62-turbo=1:2.0.5-2 libjpeg62-turbo-dev=1:2.0.5-2 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 liblapack-dev=3.9.0-3 liblapack3=3.9.0-3 libldap-2.4-2=2.4.57+dfsg-1 liblsan0=10.2.1-6 liblwp-mediatypes-perl=6.04-1 liblz4-1=1.9.3-1 liblzma-dev=5.2.5-1.0 liblzma5=5.2.5-1.0 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmd0=1.0.3-1 libmodule-implementation-perl=0.09-1.1 libmodule-runtime-conflicts-perl=0.003-1.1 libmodule-runtime-perl=0.016-1 libmoose-perl=2.2014-2 libmount1=2.36.1-6 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libmro-compat-perl=0.13-1 libnamespace-clean-perl=0.27-1 libncurses-dev=6.2+20201114-2 libncurses5-dev=6.2+20201114-2 libncurses6=6.2+20201114-2 libncursesw6=6.2+20201114-2 libnettle8=3.7-2 libnghttp2-14=1.42.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libp11-kit0=0.23.22-1 libpackage-deprecationmanager-perl=0.17-1.1 libpackage-stash-perl=0.39-1 libpackage-stash-xs-perl=0.29-1+b2 libpam-modules=1.4.0-4 libpam-modules-bin=1.4.0-4 libpam-runtime=1.4.0-4 libpam0g=1.4.0-4 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 libparams-classify-perl=0.015-1+b3 libparams-util-perl=1.102-1+b1 libpcre16-3=2:8.39-13 libpcre2-16-0=10.36-2 libpcre2-32-0=10.36-2 libpcre2-8-0=10.36-2 libpcre2-dev=10.36-2 libpcre2-posix2=10.36-2 libpcre3=2:8.39-13 libpcre3-dev=2:8.39-13 libpcre32-3=2:8.39-13 libpcrecpp0v5=2:8.39-13 libperl5.32=5.32.1-2 libpipeline1=1.5.3-1 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=10.2.1-6 libreadline-dev=8.1-1 libreadline8=8.1-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2 libsasl2-modules-db=2.1.27+dfsg-2 libseccomp2=2.5.1-1 libselinux1=3.1-2+b2 libsigsegv2=2.13-1 libsm6=2:1.2.3-1 libsmartcols1=2.36.1-6 libssh2-1=1.9.0-2 libssl1.1=1.1.1i-3 libstdc++-10-dev=10.2.1-6 libstdc++6=10.2.1-6 libsub-exporter-perl=0.987-1 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=247.3-1 libtasn1-6=4.16.0-2 libtcl8.6=8.6.11+dfsg-1 libthai-data=0.1.28-3 libthai0=0.1.28-3 libtiff5=4.2.0-1 libtimedate-perl=2.3300-1 libtinfo6=6.2+20201114-2 libtirpc-common=1.3.1-1 libtirpc-dev=1.3.1-1 libtirpc3=1.3.1-1 libtk8.6=8.6.11-2 libtool=2.4.6-15 libtry-tiny-perl=0.30-1 libtsan0=10.2.1-6 libubsan1=10.2.1-6 libuchardet0=0.0.7-1 libudev1=247.3-1 libunistring2=0.9.10-4 liburi-perl=5.07-1 libuuid1=2.36.1-6 libvariable-magic-perl=0.62-1+b3 libwebp6=0.6.1-2+b1 libwww-curl-perl=4.17-7+b1 libwww-curl-simple-perl=0.100191-2 libx11-6=2:1.7.0-2 libx11-data=2:1.7.0-2 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=2:1.3.3-1.1 libxft2=2.3.2-2 libxml2=2.9.10+dfsg-6.3+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-1 linux-libc-dev=5.10.12-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 openssl=1.1.1i-3 patch=2.7.6-7 perl=5.32.1-2 perl-base=5.32.1-2 perl-modules-5.32=5.32.1-2 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 r-base-core=4.0.3-1 r-base-dev=4.0.3-1 r-bioc-biobase=2.50.0-1 r-bioc-biocgenerics=0.36.0-1 r-bioc-biocparallel=1.24.1-1 r-bioc-biostrings=2.58.0-1 r-bioc-delayedarray=0.16.1+dfsg-1 r-bioc-genomeinfodb=1.26.2-1 r-bioc-genomeinfodbdata=1.2.4-1 r-bioc-genomicalignments=1.26.0-1 r-bioc-genomicranges=1.42.0+dfsg-1 r-bioc-iranges=2.24.1-1 r-bioc-matrixgenerics=1.2.1-1 r-bioc-rhtslib=1.22.0+dfsg-1 r-bioc-rsamtools=2.6.0-1 r-bioc-s4vectors=0.28.1-1 r-bioc-summarizedexperiment=1.20.0+dfsg-1 r-bioc-xvector=0.30.0-1 r-bioc-zlibbioc=1.36.0+dfsg-1 r-cran-bh=1.74.0-1 r-cran-bitops=1.0-6-5 r-cran-crayon=1.4.0-1 r-cran-formatr=1.7-2 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=0.1-8.1-1+b1 r-cran-lambda.r=1.2.4-2 r-cran-lattice=0.20-41-1+b1 r-cran-latticeextra=0.6-29-3 r-cran-matrix=1.3-2-1 r-cran-matrixstats=0.58.0-1 r-cran-png=0.1-7-4 r-cran-rcolorbrewer=1.1-2-3 r-cran-rcurl=1.98-1.2-1+b1 r-cran-snow=1:0.4.3-2 readline-common=8.1-1 sed=4.7-1 sensible-utils=0.0.14 sysvinit-utils=2.96-5 tar=1.32+dfsg-1 tzdata=2021a-1 ucf=3.0043 unzip=6.0-26 util-linux=2.36.1-6 x11-common=1:7.7+21 xauth=1:1.1-1 xdg-utils=1.1.3-4 xz-utils=5.2.5-1.0 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/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210208T033121Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20210205T151755Z/ 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=1.48.0-2 && mkdir -p /build/r-bioc-shortread-HJCJR2 && dpkg-source --no-check -x /*.dsc /build/r-bioc-shortread-HJCJR2/r-bioc-shortread-1.48.0 && chown -R builduser:builduser /build/r-bioc-shortread-HJCJR2" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/r-bioc-shortread-HJCJR2/r-bioc-shortread-1.48.0 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1612697312" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/r-bioc-shortread-HJCJR2 /tmp/r-bioc-shortread-1.48.0-2di1ttekx bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210205T151755Z 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.JkS9hFEeFr 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.JkS9hFEeFr Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-6). 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/20210205T151755Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210205T151755Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1080 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4663 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-9) ... 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/20210208T033121Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20210205T151755Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.JkS9hFEeFr Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210208T033121Z unstable InRelease [153 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20210205T151755Z 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/20210208T033121Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20210208T033121Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20210208T033121Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20210208T033121Z unstable/main amd64 Packages [11.7 MB] Fetched 34.4 MB in 28s (1212 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.JkS9hFEeFr I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d r-bioc-shortread=1.48.0-2 && mkdir -p /build/r-bioc-shortread-HJCJR2 && dpkg-source --no-check -x /*.dsc /build/r-bioc-shortread-HJCJR2/r-bioc-shortread-1.48.0 && chown -R builduser:builduser /build/r-bioc-shortread-HJCJR2"' exec /tmp/mmdebstrap.JkS9hFEeFr 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/20210814T212851Z bookworm/main r-bioc-shortread 1.48.0-2 (dsc) [2531 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main r-bioc-shortread 1.48.0-2 (tar) [5185 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main r-bioc-shortread 1.48.0-2 (diff) [5548 B] Fetched 5193 kB in 4s (1214 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'r-bioc-shortread_1.48.0-2.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-HJCJR2/r-bioc-shortread-1.48.0 dpkg-source: info: unpacking r-bioc-shortread_1.48.0.orig.tar.gz dpkg-source: info: unpacking r-bioc-shortread_1.48.0-2.debian.tar.xz I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/r-bioc-shortread-HJCJR2/r-bioc-shortread-1.48.0 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1612697312" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.JkS9hFEeFr dpkg-buildpackage: info: source package r-bioc-shortread dpkg-buildpackage: info: source version 1.48.0-2 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 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 dh_auto_install -a -O--buildsystem=R I: R packages needed for DEP8: runit I: R Package: ShortRead Version: 1.48.0 I: Building using R version 4.0.3-1 I: R API version: r-api-4.0 I: Using built-time from d/changelog: Sun, 07 Feb 2021 12:28:32 +0100 mkdir -p /build/r-bioc-shortread-HJCJR2/r-bioc-shortread-1.48.0/debian/r-bioc-shortread/usr/lib/R/site-library R CMD INSTALL -l /build/r-bioc-shortread-HJCJR2/r-bioc-shortread-1.48.0/debian/r-bioc-shortread/usr/lib/R/site-library --clean . "--built-timestamp='Sun, 07 Feb 2021 12:28:32 +0100'" * installing *source* package ‘ShortRead’ ... ** using staged installation checking for gcc... gcc -std=gnu99 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed checking for gzeof in -lz... yes checking how to run the C preprocessor... gcc -std=gnu99 -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking size of unsigned long... 8 configure: creating ./config.status config.status: creating src/Makevars ** libs make[1]: Entering directory '/build/r-bioc-shortread-HJCJR2/r-bioc-shortread-1.48.0/src' gcc -std=gnu99 -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 -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 Biostrings_stubs.c -o Biostrings_stubs.o gcc -std=gnu99 -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 -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 IRanges_stubs.c -o IRanges_stubs.o gcc -std=gnu99 -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 -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 R_init_ShortRead.c -o R_init_ShortRead.o gcc -std=gnu99 -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 -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 S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -std=gnu99 -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 -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 XVector_stubs.c -o XVector_stubs.o gcc -std=gnu99 -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 -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 alphabet.c -o alphabet.o gcc -std=gnu99 -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 -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 count.c -o count.o gcc -std=gnu99 -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 -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 io.c -o io.o gcc -std=gnu99 -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 -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 io_bowtie.c -o io_bowtie.o gcc -std=gnu99 -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 -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 io_soap.c -o io_soap.o g++ -std=gnu++11 -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -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 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++11 -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -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 read_maq_map.cc -o read_maq_map.o gcc -std=gnu99 -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 -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 sampler.c -o sampler.o gcc -std=gnu99 -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 -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 trim.c -o trim.o gcc -std=gnu99 -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 -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 util.c -o util.o gcc -std=gnu99 -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 -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 xsnap.c -o xsnap.o g++ -std=gnu++11 -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-HJCJR2/r-bioc-shortread-1.48.0/src' make[1]: Entering directory '/build/r-bioc-shortread-HJCJR2/r-bioc-shortread-1.48.0/src' make[1]: Leaving directory '/build/r-bioc-shortread-HJCJR2/r-bioc-shortread-1.48.0/src' installing to /build/r-bioc-shortread-HJCJR2/r-bioc-shortread-1.48.0/debian/r-bioc-shortread/usr/lib/R/site-library/00LOCK-r-bioc-shortread-1.48.0/00new/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) 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-cran-runit for Recommends:runit I: Using r-bioc-biocstyle for Suggests:BiocStyle 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-3.12 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 -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-shortread-dbgsym' in '../r-bioc-shortread-dbgsym_1.48.0-2_amd64.deb'. dpkg-deb: building package 'r-bioc-shortread' in '../r-bioc-shortread_1.48.0-2_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../r-bioc-shortread_1.48.0-2_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-HJCJR2 /tmp/r-bioc-shortread-1.48.0-2di1ttekx I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.JkS9hFEeFr... I: success in 592.4187 seconds md5: r-bioc-shortread-dbgsym_1.48.0-2_amd64.deb: OK md5: r-bioc-shortread_1.48.0-2_amd64.deb: OK sha1: r-bioc-shortread-dbgsym_1.48.0-2_amd64.deb: OK sha1: r-bioc-shortread_1.48.0-2_amd64.deb: OK sha256: r-bioc-shortread-dbgsym_1.48.0-2_amd64.deb: OK sha256: r-bioc-shortread_1.48.0-2_amd64.deb: OK Checksums: OK