Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/r/r-bioc-ioniser/r-bioc-ioniser_2.20.0+dfsg-1_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/r-bioc-ioniser-2.20.0+dfsg-10w1k34ts/r-bioc-ioniser_2.20.0+dfsg-1_all.buildinfo Get source package info: r-bioc-ioniser=2.20.0+dfsg-1 Source URL: http://snapshot.notset.fr/mr/package/r-bioc-ioniser/2.20.0+dfsg-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.5-1.3 autopoint=0.21-6 autotools-dev=20220109.1 base-files=12.2 base-passwd=3.5.52 bash=5.1-6+b1 binutils=2.38-4 binutils-common=2.38-4 binutils-x86-64-linux-gnu=2.38-4 bsdextrautils=2.38-4 bsdutils=1:2.38-4 build-essential=12.9 bzip2=1.0.8-5 ca-certificates=20211016 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.3.0-1 dash=0.5.11+git20210903+057cd650a4ed-8 dctrl-tools=2.24-3+b1 debconf=1.5.79 debhelper=13.7.1 debianutils=5.7-0.2 dh-autoreconf=20 dh-r=20210816 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 dpkg=1.21.7 dpkg-dev=1.21.7 dwz=0.14-1 file=1:5.41-4 findutils=4.9.0-3 fontconfig=2.13.1-4.4 fontconfig-config=2.13.1-4.4 fonts-dejavu-core=2.37-2 fonts-font-awesome=5.0.10+really4.7.0~dfsg-4.1 fonts-glyphicons-halflings=1.009~3.4.1+dfsg-2 fonts-lmodern=2.005-1 fonts-mathjax=2.7.9+dfsg-1 g++=4:11.2.0-2 g++-11=11.3.0-1 gcc=4:11.2.0-2 gcc-11=11.3.0-1 gcc-11-base=11.3.0-1 gcc-12-base=12.1.0-2 gettext=0.21-6 gettext-base=0.21-6 gfortran=4:11.2.0-2 gfortran-11=11.3.0-1 grep=3.7-1 groff-base=1.22.4-8 gzip=1.12-1 hdf5-helpers=1.10.7+repack-4+b1 hostname=3.23 icu-devtools=71.1-3 init-system-helpers=1.62 intltool-debian=0.35.0+20060710.5 javascript-common=11+nmu1 libacl1=2.3.1-1 libaec-dev=1.0.6-1 libaec0=1.0.6-1 libalgorithm-c3-perl=0.11-1 libarchive-zip-perl=1.68-1 libasan6=11.3.0-1 libatomic1=12.1.0-2 libattr1=1:2.5.1-1 libaudit-common=1:3.0.7-1 libaudit1=1:3.0.7-1+b1 libb-hooks-endofscope-perl=0.26-1 libb-hooks-op-check-perl=0.22-1+b4 libbinutils=2.38-4 libblas-dev=3.10.1-1 libblas3=3.10.1-1 libblkid1=2.38-4 libblosc1=1.21.1+ds2-2 libboost-dev=1.74.0.3 libboost1.74-dev=1.74.0-14+b1 libbrotli1=1.0.9-2+b3 libbsd0=0.11.6-1 libbz2-1.0=1.0.8-5 libbz2-dev=1.0.8-5 libc-bin=2.33-7 libc-dev-bin=2.33-7 libc6=2.33-7 libc6-dev=2.33-7 libcairo2=1.16.0-5 libcap-ng0=0.7.9-2.2+b2 libcap2=1:2.44-1 libcc1-0=12.1.0-2 libclass-c3-perl=0.35-1 libclass-load-perl=0.25-1 libclass-load-xs-perl=0.10-1+b6 libcmark-gfm-extensions0.29.0.gfm.3=0.29.0.gfm.3-3+b1 libcmark-gfm0.29.0.gfm.3=0.29.0.gfm.3-3+b1 libcom-err2=1.46.5-2 libcrypt-dev=1:4.4.27-1.1 libcrypt1=1:4.4.27-1.1 libctf-nobfd0=2.38-4 libctf0=2.38-4 libcurl3-gnutls=7.83.1-1+b1 libcurl4=7.83.1-1+b1 libcurl4-openssl-dev=7.83.1-1+b1 libdata-optlist-perl=0.112-1 libdatrie1=0.2.13-2 libdb5.3=5.3.28+dfsg1-0.9 libdebconfclient0=0.262 libdebhelper-perl=13.7.1 libdeflate0=1.10-2 libdevel-callchecker-perl=0.008-1+b3 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=1.21.7 libdynaloader-functions-perl=0.003-1.1 libelf1=0.187-1 libencode-locale-perl=1.05-1.1 libeval-closure-perl=0.14-1 libexpat1=2.4.8-1 libffi8=3.4.2-4 libfile-stripnondeterminism-perl=1.13.0-1 libfile-which-perl=1.27-1 libfontconfig1=2.13.1-4.4 libfreetype6=2.12.1+dfsg-1 libfribidi0=1.0.8-2.1 libgcc-11-dev=11.3.0-1 libgcc-s1=12.1.0-2 libgcrypt20=1.10.1-2 libgdbm-compat4=1.23-1 libgdbm6=1.23-1 libgfortran-11-dev=11.3.0-1 libgfortran5=12.1.0-2 libglib2.0-0=2.72.1-1 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.4-2 libgomp1=12.1.0-2 libgpg-error0=1.45-2 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.19.2-2+b2 libharfbuzz0b=2.7.4-1+b1 libhdf5-103-1=1.10.7+repack-4+b1 libhdf5-cpp-103-1=1.10.7+repack-4+b1 libhdf5-dev=1.10.7+repack-4+b1 libhdf5-fortran-102=1.10.7+repack-4+b1 libhdf5-hl-100=1.10.7+repack-4+b1 libhdf5-hl-cpp-100=1.10.7+repack-4+b1 libhdf5-hl-fortran-100=1.10.7+repack-4+b1 libhogweed6=3.7.3-1 libhttp-date-perl=6.05-1 libhttp-message-perl=6.36-1 libice6=2:1.0.10-1 libicu-dev=71.1-3 libicu71=71.1-3 libidn2-0=2.3.2-2 libio-html-perl=1.004-3 libisl23=0.24-2 libitm1=12.1.0-2 libjbig0=2.1-3.1+b2 libjpeg-dev=1:2.1.2-1 libjpeg62-turbo=1:2.1.2-1 libjpeg62-turbo-dev=1:2.1.2-1 libjs-bootstrap=3.4.1+dfsg-2 libjs-bootstrap4=4.6.1+dfsg1-1 libjs-d3=3.5.17-4 libjs-es5-shim=4.6.7-1 libjs-highlight.js=9.18.5+dfsg1-2 libjs-jquery=3.6.0+dfsg+~3.5.13-1 libjs-jquery-datatables=1.11.5+dfsg-2 libjs-jquery-selectize.js=0.12.6+dfsg-1.1 libjs-jquery-ui=1.13.1+dfsg-1 libjs-json=0~20210531+~1.0.8-1 libjs-lunr=2.3.9~dfsg-1 libjs-mathjax=2.7.9+dfsg-1 libjs-microplugin.js=0.0.3+dfsg-1.1 libjs-modernizr=2.6.2+ds1-4 libjs-popper.js=1.16.1+ds-5 libjs-prettify=2015.12.04+dfsg-1.1 libjs-sifter.js=0.6.0+dfsg-2 libjs-twitter-bootstrap-datepicker=1.3.1+dfsg1-4.1 libk5crypto3=1.19.2-2+b2 libkeyutils1=1.6.1-3 libkpathsea6=2021.20210626.59705-1+b1 libkrb5-3=1.19.2-2+b2 libkrb5support0=1.19.2-2+b2 liblapack-dev=3.10.1-1 liblapack3=3.10.1-1 libldap-2.5-0=2.5.12+dfsg-1 liblsan0=12.1.0-2 liblwp-mediatypes-perl=6.04-1 liblz4-1=1.9.3-2 liblzma-dev=5.2.5-2.1 liblzma5=5.2.5-2.1 libmagic-mgc=1:5.41-4 libmagic1=1:5.41-4 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+b1 libmount1=2.38-4 libmpc3=1.2.1-2 libmpfr6=4.1.0-3 libmro-compat-perl=0.15-1 libnamespace-clean-perl=0.27-1 libncurses-dev=6.3+20220423-2 libncurses5-dev=6.3+20220423-2 libncurses6=6.3+20220423-2 libncursesw6=6.3+20220423-2 libnettle8=3.7.3-1 libnghttp2-14=1.47.0-1+b1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libp11-kit0=0.24.1-1 libpackage-deprecationmanager-perl=0.17-1.1 libpackage-stash-perl=0.40-1 libpackage-stash-xs-perl=0.29-1+b3 libpam-modules=1.4.0-13 libpam-modules-bin=1.4.0-13 libpam-runtime=1.4.0-13 libpam0g=1.4.0-13 libpango-1.0-0=1.50.7+ds-1 libpangocairo-1.0-0=1.50.7+ds-1 libpangoft2-1.0-0=1.50.7+ds-1 libpaper-utils=1.1.28+b1 libpaper1=1.1.28+b1 libparams-classify-perl=0.015-1+b4 libparams-util-perl=1.102-1+b2 libpcre16-3=2:8.39-14 libpcre2-16-0=10.40-1 libpcre2-32-0=10.40-1 libpcre2-8-0=10.40-1 libpcre2-dev=10.40-1 libpcre2-posix3=10.40-1 libpcre3=2:8.39-14 libpcre3-dev=2:8.39-14 libpcre32-3=2:8.39-14 libpcrecpp0v5=2:8.39-14 libperl5.34=5.34.0-4 libpipeline1=1.5.6-1 libpixman-1-0=0.40.0-1 libpng-dev=1.6.37-5 libpng16-16=1.6.37-5 libpsl5=0.21.0-1.2 libptexenc1=2021.20210626.59705-1+b1 libquadmath0=12.1.0-2 libreadline-dev=8.1.2-1.2 libreadline8=8.1.2-1.2 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.28+dfsg-5 libsasl2-modules-db=2.1.28+dfsg-5 libscalar-list-utils-perl=1:1.62-1 libseccomp2=2.5.4-1 libselinux1=3.3-1+b2 libsigsegv2=2.14-1 libsm6=2:1.2.3-1 libsmartcols1=2.38-4 libsnappy1v5=1.1.9-2 libssh2-1=1.10.0-3+b1 libssl-dev=3.0.3-3 libssl3=3.0.3-3 libstdc++-11-dev=11.3.0-1 libstdc++6=12.1.0-2 libsub-exporter-perl=0.988-1 libsub-exporter-progressive-perl=0.001013-1 libsub-identify-perl=0.14-1+b4 libsub-install-perl=0.928-1.1 libsub-name-perl=0.26-1+b2 libsub-override-perl=0.09-2 libswitch-perl=2.17-2.1 libsynctex2=2021.20210626.59705-1+b1 libsystemd0=250.4-1 libsz2=1.0.6-1 libtasn1-6=4.18.0-4 libtcl8.6=8.6.12+dfsg-1 libteckit0=2.5.11+ds1-1 libtexlua53=2021.20210626.59705-1+b1 libtexluajit2=2021.20210626.59705-1+b1 libthai-data=0.1.29-1 libthai0=0.1.29-1 libtiff5=4.3.0-7 libtimedate-perl=2.3300-2 libtinfo6=6.3+20220423-2 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtk8.6=8.6.12-1 libtool=2.4.7-4 libtry-tiny-perl=0.31-1 libtsan0=11.3.0-1 libubsan1=12.1.0-2 libuchardet0=0.0.7-1 libudev1=250.4-1 libunistring2=1.0-1 liburi-perl=5.10-1 libuuid1=2.38-4 libuv1=1.44.1-2 libvariable-magic-perl=0.62-1+b4 libwebp7=1.2.2-2+b1 libwww-curl-perl=4.17-7+b2 libwww-curl-simple-perl=0.100191-2 libx11-6=2:1.7.5-1 libx11-data=2:1.7.5-1 libxau6=1:1.0.9-1 libxaw7=2:1.0.14-1 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=2.3.4-1 libxi6=2:1.8-1 libxml2=2.9.14+dfsg-1 libxmu6=2:1.1.3-3 libxmuu1=2:1.1.3-3 libxpm4=1:3.5.12-1 libxrender1=1:0.9.10-1 libxss1=1:1.2.3-1 libxt6=1:1.2.1-1 libzstd1=1.5.2+dfsg-1 libzzip-0-13=0.13.72+dfsg.1-1.1 linux-libc-dev=5.17.6-1+b1 littler=0.3.15-1 login=1:4.11.1+dfsg1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.10.2-1 mawk=1.3.4.20200120-3+b1 ncurses-base=6.3+20220423-2 ncurses-bin=6.3+20220423-2 node-bootstrap-sass=3.4.3-2 node-html5shiv=3.7.3+dfsg-4 node-normalize.css=8.0.1-5 openssl=3.0.3-3 pandoc=2.9.2.1-3+b2 pandoc-data=2.9.2.1-3 patch=2.7.6-7 perl=5.34.0-4 perl-base=5.34.0-4 perl-modules-5.34=5.34.0-4 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 r-base-core=4.2.0-1+b1 r-base-dev=4.2.0-1 r-bioc-biobase=2.56.0-1 r-bioc-biocgenerics=0.42.0-1 r-bioc-biocparallel=1.30.0-1 r-bioc-biocstyle=2.24.0+dfsg-1 r-bioc-biostrings=2.64.0-1 r-bioc-delayedarray=0.22.0+dfsg-1 r-bioc-genomeinfodb=1.32.1-1 r-bioc-genomeinfodbdata=1.2.7-1 r-bioc-genomicalignments=1.32.0-1 r-bioc-genomicranges=1.48.0+dfsg-1 r-bioc-iranges=2.30.0-1 r-bioc-matrixgenerics=1.8.0-1 r-bioc-rhdf5=2.40.0+dfsg-1 r-bioc-rhdf5filters=1.8.0+dfsg-1 r-bioc-rhdf5lib=1.18.0+dfsg-2 r-bioc-rhtslib=1.28.0+dfsg-1 r-bioc-rsamtools=2.12.0-1 r-bioc-s4vectors=0.34.0-1 r-bioc-shortread=1.54.0-1 r-bioc-summarizedexperiment=1.26.1+dfsg-1 r-bioc-xvector=0.36.0-1 r-bioc-zlibbioc=1.42.0+dfsg-1 r-cran-base64enc=0.1-3-3 r-cran-bh=1.74.0-2 r-cran-biocmanager=1.30.17+dfsg-1 r-cran-bit=4.0.4+dfsg-1 r-cran-bit64=4.0.5-1 r-cran-bitops=1.0-7-1 r-cran-bookdown=0.21+dfsg-1 r-cran-bslib=0.3.1+dfsg-2 r-cran-cachem=1.0.6-1 r-cran-cli=3.3.0-1 r-cran-colorspace=2.0-3+dfsg-1 r-cran-commonmark=1.8.0-1 r-cran-cpp11=0.4.2-1 r-cran-crayon=1.5.1-1 r-cran-digest=0.6.29-1 r-cran-dplyr=1.0.8-2 r-cran-ellipsis=0.3.2-2 r-cran-evaluate=0.15-1 r-cran-fansi=1.0.3-1 r-cran-farver=2.1.0-1 r-cran-fastmap=1.1.0-1 r-cran-formatr=1.12-1 r-cran-fs=1.5.2+dfsg-1 r-cran-futile.logger=1.4.3-4 r-cran-futile.options=1.0.1-3 r-cran-generics=0.1.2-1 r-cran-ggplot2=3.3.6+dfsg-1 r-cran-glue=1.6.2-1 r-cran-gtable=0.3.0+dfsg-2 r-cran-highr=0.9+dfsg-1 r-cran-htmltools=0.5.2-1 r-cran-httpuv=1.6.5+dfsg-1 r-cran-hwriter=1.3.2.1-1 r-cran-isoband=0.2.5-1 r-cran-jpeg=0.1-9-1 r-cran-jquerylib=0.1.4+dfsg-3 r-cran-jsonlite=1.8.0+dfsg-1 r-cran-knitr=1.39+dfsg-1 r-cran-labeling=0.4.2-1 r-cran-lambda.r=1.2.4-2 r-cran-later=1.3.0+dfsg-1 r-cran-lattice=0.20-45-3 r-cran-latticeextra=0.6-29-3 r-cran-lifecycle=1.0.1-1 r-cran-littler=0.3.15-1 r-cran-magrittr=2.0.3-1 r-cran-markdown=1.1+dfsg-1+b1 r-cran-mass=7.3-57-1 r-cran-matrix=1.4-1-1 r-cran-matrixstats=0.61.0-1 r-cran-mgcv=1.8-40-1 r-cran-mime=0.12-1 r-cran-munsell=0.5.0-2 r-cran-nlme=3.1.157-1 r-cran-pillar=1.7.0+dfsg-1 r-cran-pkgconfig=2.0.3-2 r-cran-pkgkitten=0.2.2-2 r-cran-png=0.1-7-4 r-cran-promises=1.2.0.1+dfsg-1 r-cran-purrr=0.3.4-1+b1 r-cran-r6=2.5.1-1 r-cran-rappdirs=0.3.3-1 r-cran-rcolorbrewer=1.1-3-1 r-cran-rcpp=1.0.8.3-1 r-cran-rcurl=1.98-1.6-1 r-cran-rlang=1.0.2-1 r-cran-rmarkdown=2.14+dfsg-2 r-cran-sass=0.4.1+dfsg-1 r-cran-scales=1.2.0-1 r-cran-shiny=1.6.0+dfsg-1 r-cran-snow=1:0.4.4-2 r-cran-sourcetools=0.1.7-3 r-cran-stringi=1.7.6-1+b2 r-cran-stringr=1.4.0-2 r-cran-tibble=3.1.7+dfsg-1 r-cran-tidyr=1.2.0-1 r-cran-tidyselect=1.1.2+dfsg-1 r-cran-tinytex=0.37-1 r-cran-utf8=1.2.2-1 r-cran-vctrs=0.4.1-1 r-cran-viridislite=0.4.0-2 r-cran-withr=2.5.0-1 r-cran-xfun=0.30-1 r-cran-xtable=1:1.8-4-2 r-cran-yaml=2.3.5-1 readline-common=8.1.2-1.2 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.03-1 t1utils=1.41-4 tar=1.34+dfsg-1 tex-common=6.17 texlive-base=2021.20220204-1 texlive-bibtex-extra=2021.20220204-1 texlive-binaries=2021.20210626.59705-1+b1 texlive-latex-base=2021.20220204-1 tzdata=2022a-1 ucf=3.0043 unzip=6.0-26 util-linux=2.38-4 util-linux-extra=2.38-4 x11-common=1:7.7+23 xauth=1:1.1.1-1 xdg-utils=1.1.3-4.1 xz-utils=5.2.5-2.1 zip=3.0-12 zlib1g=1:1.2.11.dfsg-4 zlib1g-dev=1:1.2.11.dfsg-4 --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/20220524T030904Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220524T030904Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220516T154358Z/ 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-ioniser=2.20.0+dfsg-1 && mkdir -p /build/r-bioc-ioniser-yfZ4MZ && dpkg-source --no-check -x /*.dsc /build/r-bioc-ioniser-yfZ4MZ/r-bioc-ioniser-2.20.0+dfsg && chown -R builduser:builduser /build/r-bioc-ioniser-yfZ4MZ" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/r-bioc-ioniser-yfZ4MZ/r-bioc-ioniser-2.20.0+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1652704902" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/r-bioc-ioniser-yfZ4MZ /tmp/r-bioc-ioniser-2.20.0+dfsg-10w1k34ts bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220516T154358Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.cb4a4XtNBR 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.cb4a4XtNBR Reading package lists... Building dependency tree... util-linux is already the newest version (2.38-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 135 kB of archives. After this operation, 406 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220516T154358Z unstable/main amd64 libfakeroot amd64 1.28-1 [48.2 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220516T154358Z unstable/main amd64 fakeroot amd64 1.28-1 [87.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 135 kB in 0s (1038 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 ... 4628 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.28-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.28-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.28-1_amd64.deb ... Unpacking fakeroot (1.28-1) ... Setting up libfakeroot:amd64 (1.28-1) ... Setting up fakeroot (1.28-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-7) ... 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/20220524T030904Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220524T030904Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220516T154358Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.cb4a4XtNBR Get:1 http://snapshot.notset.fr/archive/debian/20220524T030904Z bookworm InRelease [130 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20220516T154358Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20220524T030904Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220524T030904Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20220524T030904Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220524T030904Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20220524T030904Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220524T030904Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20220524T030904Z bookworm/main Sources [12.0 MB] Get:4 http://snapshot.notset.fr/archive/debian/20220524T030904Z bookworm/main amd64 Packages [11.5 MB] Fetched 23.5 MB in 20s (1181 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.cb4a4XtNBR I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d r-bioc-ioniser=2.20.0+dfsg-1 && mkdir -p /build/r-bioc-ioniser-yfZ4MZ && dpkg-source --no-check -x /*.dsc /build/r-bioc-ioniser-yfZ4MZ/r-bioc-ioniser-2.20.0+dfsg && chown -R builduser:builduser /build/r-bioc-ioniser-yfZ4MZ"' exec /tmp/mmdebstrap.cb4a4XtNBR Reading package lists... NOTICE: 'r-bioc-ioniser' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/r-pkg-team/r-bioc-ioniser.git Please use: git clone https://salsa.debian.org/r-pkg-team/r-bioc-ioniser.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1093 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20220524T030904Z bookworm/main r-bioc-ioniser 2.20.0+dfsg-1 (dsc) [2411 B] Get:2 http://snapshot.notset.fr/archive/debian/20220524T030904Z bookworm/main r-bioc-ioniser 2.20.0+dfsg-1 (tar) [1087 kB] Get:3 http://snapshot.notset.fr/archive/debian/20220524T030904Z bookworm/main r-bioc-ioniser 2.20.0+dfsg-1 (diff) [3544 B] Fetched 1093 kB in 1s (1254 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'r-bioc-ioniser_2.20.0+dfsg-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting r-bioc-ioniser in /build/r-bioc-ioniser-yfZ4MZ/r-bioc-ioniser-2.20.0+dfsg dpkg-source: info: unpacking r-bioc-ioniser_2.20.0+dfsg.orig.tar.xz dpkg-source: info: unpacking r-bioc-ioniser_2.20.0+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying IONiseR.Rmd-fix.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/r-bioc-ioniser-yfZ4MZ/r-bioc-ioniser-2.20.0+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1652704902" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.cb4a4XtNBR dpkg-buildpackage: info: source package r-bioc-ioniser dpkg-buildpackage: info: source version 2.20.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . 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-indep dh binary-indep --buildsystem R dh_update_autotools_config -i -O--buildsystem=R dh_autoreconf -i -O--buildsystem=R dh_auto_configure -i -O--buildsystem=R dh_auto_build -i -O--buildsystem=R debian/rules execute_after_dh_auto_build make[1]: Entering directory '/build/r-bioc-ioniser-yfZ4MZ/r-bioc-ioniser-2.20.0+dfsg' cd inst/doc && Rscript -e "require(knitr); require(markdown); knit('IONiseR.Rmd', 'IONiseR.md'); markdownToHTML('IONiseR.md', 'IONiseR.html', options=c('use_xhtml', 'base64_images'));" && rm -f IONiseR.md Warning message: In normalizePath("~") : path[1]="/nonexistent": No such file or directory Warning message: In normalizePath("~") : path[1]="/nonexistent": No such file or directory Loading required package: knitr Loading required package: markdown processing file: IONiseR.Rmd | | | 0% | |.. | 3% inline R code fragments | |.... | 5% label: style (with options) List of 2 $ echo : logi FALSE $ results: chr "asis" | |...... | 8% ordinary text without R code | |........ | 11% label: loadLibs (with options) List of 2 $ message: logi FALSE $ warning: logi FALSE | |......... | 14% ordinary text without R code | |........... | 16% label: readData (with options) List of 1 $ eval: logi FALSE | |............. | 19% ordinary text without R code | |............... | 22% label: loadData | |................. | 24% ordinary text without R code | |................... | 27% label: exampleData | |..................... | 30% ordinary text without R code | |....................... | 32% label: extractData1 (with options) List of 1 $ warning: logi FALSE | |......................... | 35% ordinary text without R code | |.......................... | 38% label: extractData2 (with options) List of 1 $ warning: logi FALSE | |............................ | 41% ordinary text without R code | |.............................. | 43% label: summaryPlots1 (with options) List of 4 $ fig.height: num 5 $ fig.width : num 12.5 $ dev : chr "png" $ warning : logi FALSE | |................................ | 46% ordinary text without R code | |.................................. | 49% label: readCategories (with options) List of 4 $ fig.height: num 5 $ fig.width : num 12.5 $ dev : chr "png" $ warning : logi FALSE | |.................................... | 51% ordinary text without R code | |...................................... | 54% label: summaryPlots2 (with options) List of 4 $ fig.height: num 5 $ fig.width : num 12.5 $ dev : chr "png" $ warning : logi FALSE | |........................................ | 57% ordinary text without R code | |.......................................... | 59% label: numReads (with options) List of 4 $ fig.height: num 4.8 $ fig.width : num 14.5 $ dev : chr "png" $ warning : logi FALSE | |............................................ | 62% ordinary text without R code | |............................................. | 65% label: heatmapExample (with options) List of 5 $ fig.height: num 4.8 $ fig.width : num 14.5 $ dev : chr "png" $ message : logi FALSE $ warning : logi FALSE Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union | |............................................... | 68% ordinary text without R code | |................................................. | 70% label: channelActivity (with options) List of 5 $ fig.height: num 4.8 $ fig.width : num 10 $ dev : chr "png" $ message : logi FALSE $ warning : logi FALSE | |................................................... | 73% ordinary text without R code | |..................................................... | 76% label: pentamerCorrelation (with options) List of 5 $ fig.height: num 5 $ fig.width : num 6.5 $ dev : chr "png" $ message : logi FALSE $ warning : logi FALSE | |....................................................... | 78% ordinary text without R code | |......................................................... | 81% label: combinedplots (with options) List of 1 $ eval: logi FALSE | |........................................................... | 84% ordinary text without R code | |............................................................. | 86% label: writefastq (with options) List of 1 $ message: logi FALSE Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:dplyr': combine, intersect, setdiff, union The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: BiocParallel Loading required package: Biostrings Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:dplyr': first, rename The following objects are masked from 'package:base': expand.grid, I, unname Loading required package: IRanges Attaching package: 'IRanges' The following objects are masked from 'package:dplyr': collapse, desc, slice Loading required package: XVector Loading required package: GenomeInfoDb Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: Rsamtools Loading required package: GenomicRanges Loading required package: GenomicAlignments Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'matrixStats' The following object is masked from 'package:dplyr': count Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Attaching package: 'GenomicAlignments' The following object is masked from 'package:dplyr': last Attaching package: 'ShortRead' The following object is masked from 'package:dplyr': id | |.............................................................. | 89% ordinary text without R code | |................................................................ | 92% label: writefastq2 | |.................................................................. | 95% ordinary text without R code | |.................................................................... | 97% label: fast5toFastq | |......................................................................| 100% ordinary text without R code output file: IONiseR.md [1] "IONiseR.md" make[1]: Leaving directory '/build/r-bioc-ioniser-yfZ4MZ/r-bioc-ioniser-2.20.0+dfsg' dh: command-omitted: The call to "dh_auto_test -i -O--buildsystem=R" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_testroot -i -O--buildsystem=R dh_prep -i -O--buildsystem=R dh_auto_install --destdir=debian/r-bioc-ioniser/ -i -O--buildsystem=R I: R packages needed for DEP8: testthat I: R Package: IONiseR Version: 2.20.0 I: Building using R version 4.2.0-1 I: R API version: r-api-4.0 I: Using built-time from d/changelog: Mon, 16 May 2022 14:41:42 +0200 mkdir -p /build/r-bioc-ioniser-yfZ4MZ/r-bioc-ioniser-2.20.0\+dfsg/debian/r-bioc-ioniser/usr/lib/R/site-library R CMD INSTALL -l /build/r-bioc-ioniser-yfZ4MZ/r-bioc-ioniser-2.20.0\+dfsg/debian/r-bioc-ioniser/usr/lib/R/site-library --clean . "--built-timestamp='Mon, 16 May 2022 14:41:42 +0200'" * installing *source* package ‘IONiseR’ ... ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (IONiseR) rm -f /build/r-bioc-ioniser-yfZ4MZ/r-bioc-ioniser-2.20.0\+dfsg/debian/r-bioc-ioniser/usr/lib/R/site-library/IONiseR/LICENSE W: Ignoring specified R dependency: R (>= 3.4) I: Using r-cran-testthat for Recommends:testthat I: Using r-bioc-biocstyle for Suggests:BiocStyle I: Using r-cran-knitr for Suggests:knitr I: Using r-cran-rmarkdown for Suggests:rmarkdown I: Using r-cran-gridextra for Suggests:gridExtra W: Cannot find a debian package for Suggests:minionSummaryData I: Using r-bioc-rhdf5 for Imports:rhdf5 I: Using r-cran-dplyr for Imports:dplyr I: Using r-cran-magrittr for Imports:magrittr I: Using r-cran-tidyr for Imports:tidyr I: Using r-bioc-shortread for Imports:ShortRead I: Using r-bioc-biostrings for Imports:Biostrings I: Using r-cran-ggplot2 for Imports:ggplot2 I: Using r-bioc-biocgenerics for Imports:BiocGenerics I: Using r-bioc-xvector for Imports:XVector I: Using r-cran-tibble for Imports:tibble I: Using r-bioc-biocparallel for Imports:BiocParallel I: Using r-cran-bit64 for Imports:bit64 I: Using r-cran-stringr for Imports:stringr I: BioConductor API version: r-api-bioc-3.15 I: Use r-bioc-ioniser as Debian binary package for variables substitution dh_installdocs -i -O--buildsystem=R dh_installchangelogs -i -O--buildsystem=R dh_installsystemduser -i -O--buildsystem=R dh_perl -i -O--buildsystem=R dh_link -i -O--buildsystem=R dh_strip_nondeterminism -i -O--buildsystem=R dh_compress -i -O--buildsystem=R debian/rules override_dh_fixperms make[1]: Entering directory '/build/r-bioc-ioniser-yfZ4MZ/r-bioc-ioniser-2.20.0+dfsg' dh_fixperms find debian -name '*.fast5' | xargs chmod -x make[1]: Leaving directory '/build/r-bioc-ioniser-yfZ4MZ/r-bioc-ioniser-2.20.0+dfsg' dh_missing -i -O--buildsystem=R dh_installdeb -i -O--buildsystem=R dh_gencontrol -i -O--buildsystem=R dh_md5sums -i -O--buildsystem=R dh_builddeb -i -O--buildsystem=R dpkg-deb: building package 'r-bioc-ioniser' in '../r-bioc-ioniser_2.20.0+dfsg-1_all.deb'. dpkg-genbuildinfo --build=all -O../r-bioc-ioniser_2.20.0+dfsg-1_all.buildinfo dpkg-genchanges --build=all -O../r-bioc-ioniser_2.20.0+dfsg-1_all.changes dpkg-genchanges: info: binary-only arch-indep upload (source code and arch-specific 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-ioniser-yfZ4MZ /tmp/r-bioc-ioniser-2.20.0+dfsg-10w1k34ts I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.cb4a4XtNBR... I: success in 849.4832 seconds md5: r-bioc-ioniser_2.20.0+dfsg-1_all.deb: OK sha1: r-bioc-ioniser_2.20.0+dfsg-1_all.deb: OK sha256: r-bioc-ioniser_2.20.0+dfsg-1_all.deb: OK Checksums: OK