Build log for r-bioc-shortread (1.54.0-1) on armhf

r-bioc-shortread → 1.54.0-1 → armhf → 2022-05-25 10:57:47

sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019

+==============================================================================+
| r-bioc-shortread 1.54.0-1 (armhf)            Wed, 25 May 2022 10:34:08 +0000 |
+==============================================================================+

Package: r-bioc-shortread
Version: 1.54.0-1
Source Version: 1.54.0-1
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-dbb40622-8138-4f77-9f9b-4927412b8fb1' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-shortread-6SmSPO/resolver-0DtmUF' with '<<RESOLVERDIR>>'

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.0 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [13.9 MB]
Fetched 26.9 MB in 11s (2550 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/bookworm-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Check APT
---------

Checking available source versions...

Download source files with APT
------------------------------

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://172.17.4.1/private bookworm-staging/main r-bioc-shortread 1.54.0-1 (dsc) [2387 B]
Get:2 http://172.17.4.1/private bookworm-staging/main r-bioc-shortread 1.54.0-1 (tar) [5185 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main r-bioc-shortread 1.54.0-1 (diff) [5636 B]
Fetched 5193 kB in 1s (7586 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/r-bioc-shortread-6SmSPO/r-bioc-shortread-1.54.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-shortread-6SmSPO' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper-compat (= 13), dh-r, r-base-dev, r-bioc-biocgenerics, r-bioc-biocparallel, r-bioc-biostrings, r-bioc-rsamtools, r-bioc-genomicalignments, r-bioc-biobase, r-bioc-s4vectors, r-bioc-iranges, r-bioc-genomeinfodb, r-bioc-genomicranges, r-cran-hwriter, r-bioc-zlibbioc, r-cran-lattice, r-cran-latticeextra, r-bioc-xvector, r-bioc-rhtslib, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), dh-r, r-base-dev, r-bioc-biocgenerics, r-bioc-biocparallel, r-bioc-biostrings, r-bioc-rsamtools, r-bioc-genomicalignments, r-bioc-biobase, r-bioc-s4vectors, r-bioc-iranges, r-bioc-genomeinfodb, r-bioc-genomicranges, r-cran-hwriter, r-bioc-zlibbioc, r-cran-lattice, r-cran-latticeextra, r-bioc-xvector, r-bioc-rhtslib, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [488 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [572 B]
Fetched 2017 B in 0s (52.5 kB/s)
Reading package lists...
Reading package lists...

Install main build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bsdextrautils ca-certificates
  cpp-11 dctrl-tools debhelper dh-autoreconf dh-r dh-strip-nondeterminism dwz
  file fontconfig fontconfig-config fonts-dejavu-core g++-11 gcc-11
  gcc-11-base gcc-12-base gettext gettext-base gfortran gfortran-11 groff-base
  icu-devtools intltool-debian libalgorithm-c3-perl libarchive-zip-perl
  libasan6 libatomic1 libb-hooks-endofscope-perl libb-hooks-op-check-perl
  libblas-dev libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0
  libbz2-dev libcairo2 libcc1-0 libclass-c3-perl libclass-load-perl
  libclass-load-xs-perl libcurl3-gnutls libcurl4 libdata-optlist-perl
  libdatrie1 libdebhelper-perl libdeflate0 libdevel-callchecker-perl
  libdevel-globaldestruction-perl libdevel-overloadinfo-perl
  libdevel-stacktrace-perl libdist-checkconflicts-perl
  libdynaloader-functions-perl libelf1 libencode-locale-perl
  libeval-closure-perl libexpat1 libfile-stripnondeterminism-perl
  libfile-which-perl libfontconfig1 libfreetype6 libfribidi0 libgcc-11-dev
  libgcc-s1 libgfortran-11-dev libgfortran5 libglib2.0-0 libgomp1
  libgraphite2-3 libharfbuzz0b libhttp-date-perl libhttp-message-perl libice6
  libicu-dev libicu71 libio-html-perl libjbig0 libjpeg-dev libjpeg62-turbo
  libjpeg62-turbo-dev liblapack-dev liblapack3 liblwp-mediatypes-perl
  liblzma-dev libmagic-mgc libmagic1 libmd0 libmodule-implementation-perl
  libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoose-perl
  libmro-compat-perl libnamespace-clean-perl libncurses-dev libncurses5-dev
  libncurses6 libncursesw6 libnghttp2-14 libpackage-deprecationmanager-perl
  libpackage-stash-perl libpackage-stash-xs-perl libpango-1.0-0
  libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1
  libparams-classify-perl libparams-util-perl libpcre16-3 libpcre2-16-0
  libpcre2-32-0 libpcre2-8-0 libpcre2-dev libpcre2-posix3 libpcre3-dev
  libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0 libpng-dev libpng16-16
  libpsl5 libreadline-dev librtmp1 libscalar-list-utils-perl libsigsegv2
  libsm6 libssh2-1 libstdc++-11-dev libstdc++6 libsub-exporter-perl
  libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl
  libsub-name-perl libsub-override-perl libswitch-perl libtcl8.6 libthai-data
  libthai0 libtiff5 libtimedate-perl libtinfo6 libtk8.6 libtool
  libtry-tiny-perl libubsan1 libuchardet0 liburi-perl libvariable-magic-perl
  libwebp7 libwww-curl-perl libwww-curl-simple-perl libx11-6 libx11-data
  libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2
  libxml2 libxmuu1 libxrender1 libxss1 libxt6 m4 man-db openssl pkg-config
  po-debconf r-base-core r-base-dev r-bioc-biobase r-bioc-biocgenerics
  r-bioc-biocparallel r-bioc-biostrings r-bioc-delayedarray
  r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments
  r-bioc-genomicranges r-bioc-iranges r-bioc-matrixgenerics r-bioc-rhtslib
  r-bioc-rsamtools r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-xvector
  r-bioc-zlibbioc r-cran-bh r-cran-bitops r-cran-codetools r-cran-crayon
  r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-hwriter
  r-cran-jpeg r-cran-lambda.r r-cran-lattice r-cran-latticeextra r-cran-matrix
  r-cran-matrixstats r-cran-png r-cran-rcolorbrewer r-cran-rcurl r-cran-snow
  sgml-base ucf unzip x11-common xauth xdg-utils zip zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc gcc-11-locales debtags dh-make
  postgresql-client-common gcc-11-doc gettext-doc libasprintf-dev
  libgettextpo-dev gfortran-doc gfortran-11-doc libcoarrays-dev groff
  liblapack-doc libboost-doc libboost1.74-doc libboost-atomic1.74-dev
  libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev
  libboost-contract1.74-dev libboost-coroutine1.74-dev
  libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev
  libboost-filesystem1.74-dev libboost-graph1.74-dev
  libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev
  libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev
  libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev
  libboost-program-options1.74-dev libboost-python1.74-dev
  libboost-random1.74-dev libboost-regex1.74-dev
  libboost-serialization1.74-dev libboost-stacktrace1.74-dev
  libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev
  libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev
  libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev
  icu-doc liblzma-doc ncurses-doc libscalar-number-perl readline-doc
  libstdc++-11-doc tcl8.6 tk8.6 libtool-doc gcj-jdk libbusiness-isbn-perl
  libwww-perl libcurl4-gnutls-dev m4-doc apparmor less www-browser
  libmail-box-perl elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html
  texlive-base texlive-latex-base texlive-plain-generic
  texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils
  texlive-latex-recommended texlive-latex-extra texinfo r-bioc-all
  r-bioc-annotationdbi r-bioc-affy r-bioc-deseq2 r-bioc-annotate
  r-cran-foreach r-cran-bbmisc r-bioc-variantannotation r-bioc-shortread
  r-bioc-biocstyle r-cran-knitr r-cran-data.table r-bioc-bsgenome
  r-bioc-genomicfeatures r-cran-runit r-bioc-hdf5array r-bioc-genefilter
  r-cran-lobstr r-bioc-delayedmatrixstats r-cran-rmarkdown r-bioc-rtracklayer
  r-bioc-edger r-bioc-gviz r-bioc-annotationhub r-bioc-dexseq r-bioc-keggrest
  r-cran-digest r-bioc-sparsematrixstats r-cran-testthat r-bioc-graph
  r-cran-jsonlite r-bioc-rhdf5 r-cran-rstudioapi r-cran-shiny r-cran-base64enc
  r-cran-ggplot2 r-cran-markdown r-cran-r.devices r-cran-r.rsp r-cran-xml
  r-cran-rmpi r-cran-rlecuyer sgml-base-doc
Recommended packages:
  devscripts cme git-buildpackage curl | wget | lynx bzip2-doc
  libclass-c3-xs-perl libdevel-lexalias-perl libarchive-cpio-perl
  libglib2.0-data shared-mime-info xdg-user-dirs libclone-perl
  libdevel-partialdump-perl libgpm2 libpng-tools publicsuffix libltdl-dev
  libmail-sendmail-perl r-recommended r-doc-html r-cran-runit r-cran-batchjobs
  r-cran-doparallel r-cran-batchtools r-cran-rmpi r-cran-testthat r-cran-withr
  r-cran-mockery r-cran-testit r-cran-survival libfile-mimeinfo-perl
  libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bsdextrautils ca-certificates
  dctrl-tools debhelper dh-autoreconf dh-r dh-strip-nondeterminism dwz file
  fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base gfortran
  gfortran-11 groff-base icu-devtools intltool-debian libalgorithm-c3-perl
  libarchive-zip-perl libb-hooks-endofscope-perl libb-hooks-op-check-perl
  libblas-dev libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0
  libbz2-dev libcairo2 libclass-c3-perl libclass-load-perl
  libclass-load-xs-perl libcurl3-gnutls libcurl4 libdata-optlist-perl
  libdatrie1 libdebhelper-perl libdeflate0 libdevel-callchecker-perl
  libdevel-globaldestruction-perl libdevel-overloadinfo-perl
  libdevel-stacktrace-perl libdist-checkconflicts-perl
  libdynaloader-functions-perl libelf1 libencode-locale-perl
  libeval-closure-perl libexpat1 libfile-stripnondeterminism-perl
  libfile-which-perl libfontconfig1 libfreetype6 libfribidi0
  libgfortran-11-dev libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b
  libhttp-date-perl libhttp-message-perl libice6 libicu-dev libicu71
  libio-html-perl libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev
  liblapack-dev liblapack3 liblwp-mediatypes-perl liblzma-dev libmagic-mgc
  libmagic1 libmd0 libmodule-implementation-perl
  libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoose-perl
  libmro-compat-perl libnamespace-clean-perl libncurses-dev libncurses5-dev
  libncurses6 libnghttp2-14 libpackage-deprecationmanager-perl
  libpackage-stash-perl libpackage-stash-xs-perl libpango-1.0-0
  libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1
  libparams-classify-perl libparams-util-perl libpcre16-3 libpcre2-16-0
  libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpcre3-dev libpcre32-3
  libpcrecpp0v5 libpipeline1 libpixman-1-0 libpng-dev libpng16-16 libpsl5
  libreadline-dev librtmp1 libscalar-list-utils-perl libsigsegv2 libsm6
  libssh2-1 libsub-exporter-perl libsub-exporter-progressive-perl
  libsub-identify-perl libsub-install-perl libsub-name-perl
  libsub-override-perl libswitch-perl libtcl8.6 libthai-data libthai0 libtiff5
  libtimedate-perl libtk8.6 libtool libtry-tiny-perl libuchardet0 liburi-perl
  libvariable-magic-perl libwebp7 libwww-curl-perl libwww-curl-simple-perl
  libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6
  libxext6 libxft2 libxml2 libxmuu1 libxrender1 libxss1 libxt6 m4 man-db
  openssl pkg-config po-debconf r-base-core r-base-dev r-bioc-biobase
  r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biostrings
  r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata
  r-bioc-genomicalignments r-bioc-genomicranges r-bioc-iranges
  r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-s4vectors
  r-bioc-summarizedexperiment r-bioc-xvector r-bioc-zlibbioc r-cran-bh
  r-cran-bitops r-cran-codetools r-cran-crayon r-cran-formatr
  r-cran-futile.logger r-cran-futile.options r-cran-hwriter r-cran-jpeg
  r-cran-lambda.r r-cran-lattice r-cran-latticeextra r-cran-matrix
  r-cran-matrixstats r-cran-png r-cran-rcolorbrewer r-cran-rcurl r-cran-snow
  sbuild-build-depends-main-dummy sgml-base ucf unzip x11-common xauth
  xdg-utils zip zlib1g-dev
The following packages will be upgraded:
  cpp-11 g++-11 gcc-11 gcc-11-base gcc-12-base libasan6 libatomic1 libcc1-0
  libgcc-11-dev libgcc-s1 libgomp1 libncursesw6 libpcre2-8-0 libstdc++-11-dev
  libstdc++6 libtinfo6 libubsan1
17 upgraded, 206 newly installed, 0 to remove and 38 not upgraded.
Need to get 196 MB of archives.
After this operation, 486 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [996 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf sgml-base all 1.30 [15.1 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libatomic1 armhf 12.1.0-2+rpi1 [8196 B]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf libubsan1 armhf 12.1.0-2+rpi1 [860 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf gcc-12-base armhf 12.1.0-2+rpi1 [207 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf libstdc++6 armhf 12.1.0-2+rpi1 [504 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libgomp1 armhf 12.1.0-2+rpi1 [95.4 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libcc1-0 armhf 12.1.0-2+rpi1 [32.1 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf libgcc-s1 armhf 12.1.0-2+rpi1 [36.1 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf libtinfo6 armhf 6.3+20220423-2 [337 kB]
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Get:17 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.10.2-1 [1362 kB]
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Get:23 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-6 [171 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.14-1 [36.6 kB]
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Get:27 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
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Get:29 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-6 [510 kB]
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Get:38 http://172.17.4.1/private bookworm-staging/main armhf dctrl-tools armhf 2.24-3 [94.2 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.7.1 [195 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-4 [526 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
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Get:43 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
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Get:48 http://172.17.4.1/private bookworm-staging/main armhf libicu71 armhf 71.1-3 [8855 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1 [591 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-6 [1214 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.7.1 [1071 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf zip armhf 3.0-12 [209 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf unzip armhf 6.0-26 [151 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf libpaper1 armhf 1.1.28 [20.5 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf libpaper-utils armhf 1.1.28 [17.7 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf xdg-utils all 1.1.3-4.1 [75.5 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf libblas3 armhf 3.10.1-2 [109 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.8-1 [84.1 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf libpng16-16 armhf 1.6.37-5 [272 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf libfreetype6 armhf 2.12.1+dfsg-2 [352 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf fontconfig-config all 2.13.1-4.4 [281 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libfontconfig1 armhf 2.13.1-4.4 [331 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libpixman-1-0 armhf 0.40.0-1 [463 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-1 [28.9 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.6-1 [109 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf libxcb1 armhf 1.14-3 [136 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf libx11-data all 2:1.7.5-1 [308 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libx11-6 armhf 2:1.7.5-1 [706 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libxcb-render0 armhf 1.14-3 [110 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libxcb-shm0 armhf 1.14-3 [101 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf libcairo2 armhf 1.16.0-5 [602 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.47.0-1 [65.0 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-3 [161 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf libcurl4 armhf 7.83.0-1 [316 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.72.1-1 [1231 kB]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo armhf 1:2.1.2-1 [144 kB]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf libgfortran5 armhf 12.1.0-2+rpi1 [238 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf liblapack3 armhf 3.10.1-2 [1587 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf fontconfig armhf 2.13.1-4.4 [416 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf libfribidi0 armhf 1.0.8-2.1 [63.7 kB]
Get:91 http://172.17.4.1/private bookworm-staging/main armhf libgraphite2-3 armhf 1.3.14-1 [70.3 kB]
Get:92 http://172.17.4.1/private bookworm-staging/main armhf libharfbuzz0b armhf 2.7.4-1+b1 [1420 kB]
Get:93 http://172.17.4.1/private bookworm-staging/main armhf libthai-data all 0.1.29-1 [176 kB]
Get:94 http://172.17.4.1/private bookworm-staging/main armhf libdatrie1 armhf 0.2.13-2+b2 [39.9 kB]
Get:95 http://172.17.4.1/private bookworm-staging/main armhf libthai0 armhf 0.1.29-1 [54.5 kB]
Get:96 http://172.17.4.1/private bookworm-staging/main armhf libpango-1.0-0 armhf 1.50.7+ds-1 [214 kB]
Get:97 http://172.17.4.1/private bookworm-staging/main armhf libpangoft2-1.0-0 armhf 1.50.7+ds-1 [70.1 kB]
Get:98 http://172.17.4.1/private bookworm-staging/main armhf libpangocairo-1.0-0 armhf 1.50.7+ds-1 [60.1 kB]
Get:99 http://172.17.4.1/private bookworm-staging/main armhf libtcl8.6 armhf 8.6.12+dfsg-1 [906 kB]
Get:100 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.10-2 [55.4 kB]
Get:101 http://172.17.4.1/private bookworm-staging/main armhf libjbig0 armhf 2.1-3.1+b2 [27.6 kB]
Get:102 http://172.17.4.1/private bookworm-staging/main armhf libwebp7 armhf 1.2.2-2 [237 kB]
Get:103 http://172.17.4.1/private bookworm-staging/main armhf libtiff5 armhf 4.3.0-8 [273 kB]
Get:104 http://172.17.4.1/private bookworm-staging/main armhf libxft2 armhf 2.3.4-1 [50.2 kB]
Get:105 http://172.17.4.1/private bookworm-staging/main armhf x11-common all 1:7.7+23 [252 kB]
Get:106 http://172.17.4.1/private bookworm-staging/main armhf libxss1 armhf 1:1.2.3-1 [17.3 kB]
Get:107 http://172.17.4.1/private bookworm-staging/main armhf libtk8.6 armhf 8.6.12-1 [680 kB]
Get:108 http://172.17.4.1/private bookworm-staging/main armhf libice6 armhf 2:1.0.10-1 [51.7 kB]
Get:109 http://172.17.4.1/private bookworm-staging/main armhf libsm6 armhf 2:1.2.3-1 [32.9 kB]
Get:110 http://172.17.4.1/private bookworm-staging/main armhf libxt6 armhf 1:1.2.1-1 [159 kB]
Get:111 http://172.17.4.1/private bookworm-staging/main armhf r-base-core armhf 4.2.0-1 [27.7 MB]
Get:112 http://172.17.4.1/private bookworm-staging/main armhf libgfortran-11-dev armhf 11.3.0-1+rpi1 [280 kB]
Get:113 http://172.17.4.1/private bookworm-staging/main armhf gfortran-11 armhf 11.3.0-1+rpi1 [7580 kB]
Get:114 http://172.17.4.1/private bookworm-staging/main armhf gfortran armhf 4:11.2.0-2+rpi1 [1428 B]
Get:115 http://172.17.4.1/private bookworm-staging/main armhf libblas-dev armhf 3.10.1-2 [114 kB]
Get:116 http://172.17.4.1/private bookworm-staging/main armhf liblapack-dev armhf 3.10.1-2 [2847 kB]
Get:117 http://172.17.4.1/private bookworm-staging/main armhf libncurses6 armhf 6.3+20220423-2 [79.6 kB]
Get:118 http://172.17.4.1/private bookworm-staging/main armhf libncurses-dev armhf 6.3+20220423-2 [289 kB]
Get:119 http://172.17.4.1/private bookworm-staging/main armhf libncurses5-dev armhf 6.3+20220423-2 [940 B]
Get:120 http://172.17.4.1/private bookworm-staging/main armhf libreadline-dev armhf 8.1.2-1.2 [120 kB]
Get:121 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo-dev armhf 1:2.1.2-1 [261 kB]
Get:122 http://172.17.4.1/private bookworm-staging/main armhf libjpeg-dev armhf 1:2.1.2-1 [74.7 kB]
Get:123 http://172.17.4.1/private bookworm-staging/main armhf libpcre2-16-0 armhf 10.40-1 [208 kB]
Get:124 http://172.17.4.1/private bookworm-staging/main armhf libpcre2-32-0 armhf 10.40-1 [199 kB]
Get:125 http://172.17.4.1/private bookworm-staging/main armhf libpcre2-posix3 armhf 10.40-1 [53.4 kB]
Get:126 http://172.17.4.1/private bookworm-staging/main armhf libpcre2-dev armhf 10.40-1 [637 kB]
Get:127 http://172.17.4.1/private bookworm-staging/main armhf libpcre16-3 armhf 2:8.39-14 [239 kB]
Get:128 http://172.17.4.1/private bookworm-staging/main armhf libpcre32-3 armhf 2:8.39-14 [232 kB]
Get:129 http://172.17.4.1/private bookworm-staging/main armhf libpcrecpp0v5 armhf 2:8.39-14 [150 kB]
Get:130 http://172.17.4.1/private bookworm-staging/main armhf libpcre3-dev armhf 2:8.39-14 [569 kB]
Get:131 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-4 [183 kB]
Get:132 http://172.17.4.1/private bookworm-staging/main armhf libpng-dev armhf 1.6.37-5 [272 kB]
Get:133 http://172.17.4.1/private bookworm-staging/main armhf libbz2-dev armhf 1.0.8-5 [26.8 kB]
Get:134 http://172.17.4.1/private bookworm-staging/main armhf liblzma-dev armhf 5.2.5-2.1 [218 kB]
Get:135 http://172.17.4.1/private bookworm-staging/main armhf icu-devtools armhf 71.1-3 [177 kB]
Get:136 http://172.17.4.1/private bookworm-staging/main armhf libicu-dev armhf 71.1-3 [9799 kB]
Get:137 http://172.17.4.1/private bookworm-staging/main armhf libxmuu1 armhf 2:1.1.3-3 [23.3 kB]
Get:138 http://172.17.4.1/private bookworm-staging/main armhf xauth armhf 1:1.1.1-1 [36.9 kB]
Get:139 http://172.17.4.1/private bookworm-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
Get:140 http://172.17.4.1/private bookworm-staging/main armhf r-base-dev all 4.2.0-1 [4488 B]
Get:141 http://172.17.4.1/private bookworm-staging/main armhf libfile-which-perl all 1.27-1 [17.3 kB]
Get:142 http://172.17.4.1/private bookworm-staging/main armhf libswitch-perl all 2.17-2.1 [20.0 kB]
Get:143 http://172.17.4.1/private bookworm-staging/main armhf libencode-locale-perl all 1.05-1.1 [13.2 kB]
Get:144 http://172.17.4.1/private bookworm-staging/main armhf libtimedate-perl all 2.3300-2 [39.3 kB]
Get:145 http://172.17.4.1/private bookworm-staging/main armhf libhttp-date-perl all 6.05-1 [10.4 kB]
Get:146 http://172.17.4.1/private bookworm-staging/main armhf libio-html-perl all 1.004-3 [16.2 kB]
Get:147 http://172.17.4.1/private bookworm-staging/main armhf liblwp-mediatypes-perl all 6.04-1 [19.9 kB]
Get:148 http://172.17.4.1/private bookworm-staging/main armhf liburi-perl all 5.10-1 [91.0 kB]
Get:149 http://172.17.4.1/private bookworm-staging/main armhf libhttp-message-perl all 6.36-1 [80.6 kB]
Get:150 http://172.17.4.1/private bookworm-staging/main armhf libparams-util-perl armhf 1.102-1+b2 [24.5 kB]
Get:151 http://172.17.4.1/private bookworm-staging/main armhf libsub-install-perl all 0.928-1.1 [10.8 kB]
Get:152 http://172.17.4.1/private bookworm-staging/main armhf libdata-optlist-perl all 0.112-1 [11.8 kB]
Get:153 http://172.17.4.1/private bookworm-staging/main armhf libb-hooks-op-check-perl armhf 0.22-1+b5 [10.9 kB]
Get:154 http://172.17.4.1/private bookworm-staging/main armhf libdynaloader-functions-perl all 0.003-1.1 [12.7 kB]
Get:155 http://172.17.4.1/private bookworm-staging/main armhf libdevel-callchecker-perl armhf 0.008-1+b3 [15.7 kB]
Get:156 http://172.17.4.1/private bookworm-staging/main armhf libparams-classify-perl armhf 0.015-1+b4 [24.6 kB]
Get:157 http://172.17.4.1/private bookworm-staging/main armhf libmodule-runtime-perl all 0.016-1 [19.4 kB]
Get:158 http://172.17.4.1/private bookworm-staging/main armhf libtry-tiny-perl all 0.31-1 [24.2 kB]
Get:159 http://172.17.4.1/private bookworm-staging/main armhf libmodule-implementation-perl all 0.09-1.1 [12.4 kB]
Get:160 http://172.17.4.1/private bookworm-staging/main armhf libscalar-list-utils-perl armhf 1:1.62-1 [61.6 kB]
Get:161 http://172.17.4.1/private bookworm-staging/main armhf libpackage-stash-perl all 0.40-1 [22.0 kB]
Get:162 http://172.17.4.1/private bookworm-staging/main armhf libclass-load-perl all 0.25-1 [16.1 kB]
Get:163 http://172.17.4.1/private bookworm-staging/main armhf libclass-load-xs-perl armhf 0.10-1+b5 [14.2 kB]
Get:164 http://172.17.4.1/private bookworm-staging/main armhf libsub-exporter-progressive-perl all 0.001013-1 [7588 B]
Get:165 http://172.17.4.1/private bookworm-staging/main armhf libdevel-globaldestruction-perl all 0.14-1.1 [8312 B]
Get:166 http://172.17.4.1/private bookworm-staging/main armhf libalgorithm-c3-perl all 0.11-1 [11.7 kB]
Get:167 http://172.17.4.1/private bookworm-staging/main armhf libclass-c3-perl all 0.35-1 [22.9 kB]
Get:168 http://172.17.4.1/private bookworm-staging/main armhf libmro-compat-perl all 0.15-1 [12.6 kB]
Get:169 http://172.17.4.1/private bookworm-staging/main armhf libdevel-overloadinfo-perl all 0.007-1 [7896 B]
Get:170 http://172.17.4.1/private bookworm-staging/main armhf libdevel-stacktrace-perl all 2.0400-1 [28.6 kB]
Get:171 http://172.17.4.1/private bookworm-staging/main armhf libsub-exporter-perl all 0.988-1 [51.9 kB]
Get:172 http://172.17.4.1/private bookworm-staging/main armhf libeval-closure-perl all 0.14-1 [11.5 kB]
Get:173 http://172.17.4.1/private bookworm-staging/main armhf libdist-checkconflicts-perl all 0.11-1.1 [10.2 kB]
Get:174 http://172.17.4.1/private bookworm-staging/main armhf libmodule-runtime-conflicts-perl all 0.003-1.1 [7156 B]
Get:175 http://172.17.4.1/private bookworm-staging/main armhf libsub-name-perl armhf 0.26-1+b2 [13.2 kB]
Get:176 http://172.17.4.1/private bookworm-staging/main armhf libpackage-deprecationmanager-perl all 0.17-1.1 [16.6 kB]
Get:177 http://172.17.4.1/private bookworm-staging/main armhf libpackage-stash-xs-perl armhf 0.29-1+b3 [18.4 kB]
Get:178 http://172.17.4.1/private bookworm-staging/main armhf libmoose-perl armhf 2.2200-1+b1 [802 kB]
Get:179 http://172.17.4.1/private bookworm-staging/main armhf libvariable-magic-perl armhf 0.62-1+b4 [43.1 kB]
Get:180 http://172.17.4.1/private bookworm-staging/main armhf libb-hooks-endofscope-perl all 0.26-1 [19.6 kB]
Get:181 http://172.17.4.1/private bookworm-staging/main armhf libsub-identify-perl armhf 0.14-1+b4 [11.6 kB]
Get:182 http://172.17.4.1/private bookworm-staging/main armhf libnamespace-clean-perl all 0.27-1 [17.3 kB]
Get:183 http://172.17.4.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.83.0-1 [313 kB]
Get:184 http://172.17.4.1/private bookworm-staging/main armhf libwww-curl-perl armhf 4.17-7+b2 [60.5 kB]
Get:185 http://172.17.4.1/private bookworm-staging/main armhf libwww-curl-simple-perl all 0.100191-2 [12.5 kB]
Get:186 http://172.17.4.1/private bookworm-staging/main armhf dh-r all 20210816 [41.6 kB]
Get:187 http://172.17.4.1/private bookworm-staging/main armhf libboost1.74-dev armhf 1.74.0-14+b2 [9533 kB]
Get:188 http://172.17.4.1/private bookworm-staging/main armhf libboost-dev armhf 1.74.0.3+b4 [4824 B]
Get:189 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-biocgenerics all 0.42.0-1 [589 kB]
Get:190 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-biobase armhf 2.56.0-1 [2094 kB]
Get:191 http://172.17.4.1/private bookworm-staging/main armhf r-cran-formatr all 1.12-1 [151 kB]
Get:192 http://172.17.4.1/private bookworm-staging/main armhf r-cran-lambda.r all 1.2.4-2 [118 kB]
Get:193 http://172.17.4.1/private bookworm-staging/main armhf r-cran-futile.options all 1.0.1-3 [20.0 kB]
Get:194 http://172.17.4.1/private bookworm-staging/main armhf r-cran-futile.logger all 1.4.3-4 [98.4 kB]
Get:195 http://172.17.4.1/private bookworm-staging/main armhf r-cran-snow all 1:0.4.4-2 [98.9 kB]
Get:196 http://172.17.4.1/private bookworm-staging/main armhf r-cran-bh all 1.74.0-2 [5524 B]
Get:197 http://172.17.4.1/private bookworm-staging/main armhf r-cran-codetools all 0.2-18-1 [91.8 kB]
Get:198 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-biocparallel armhf 1.30.2-2 [1451 kB]
Get:199 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-s4vectors armhf 0.34.0-1 [2015 kB]
Get:200 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-iranges armhf 2.30.0-1 [2211 kB]
Get:201 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-zlibbioc all 1.42.0+dfsg-1 [9136 B]
Get:202 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-xvector armhf 0.36.0-1 [617 kB]
Get:203 http://172.17.4.1/private bookworm-staging/main armhf r-cran-bitops armhf 1.0-7-1 [30.1 kB]
Get:204 http://172.17.4.1/private bookworm-staging/main armhf r-cran-rcurl armhf 1.98-1.6-1 [795 kB]
Get:205 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-genomeinfodbdata all 1.2.8-1 [11.5 MB]
Get:206 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-genomeinfodb all 1.32.2-1 [3891 kB]
Get:207 http://172.17.4.1/private bookworm-staging/main armhf r-cran-crayon all 1.5.1-1 [162 kB]
Get:208 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-biostrings armhf 2.64.0-1 [13.9 MB]
Get:209 http://172.17.4.1/private bookworm-staging/main armhf r-cran-lattice armhf 0.20-45-3 [1176 kB]
Get:210 http://172.17.4.1/private bookworm-staging/main armhf r-cran-matrix armhf 1.4-1-1 [4290 kB]
Get:211 http://172.17.4.1/private bookworm-staging/main armhf r-cran-matrixstats armhf 0.62.0-1 [449 kB]
Get:212 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-matrixgenerics all 1.8.0-1 [299 kB]
Get:213 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-delayedarray armhf 0.22.0+dfsg-1 [1923 kB]
Get:214 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-genomicranges armhf 1.48.0+dfsg-1 [1796 kB]
Get:215 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-summarizedexperiment all 1.26.1+dfsg-1 [2003 kB]
Get:216 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-rhtslib armhf 1.28.0+dfsg-1 [947 kB]
Get:217 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-rsamtools armhf 2.12.0-1 [3535 kB]
Get:218 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-genomicalignments armhf 1.32.0-1 [2098 kB]
Get:219 http://172.17.4.1/private bookworm-staging/main armhf r-cran-hwriter all 1.3.2.1-1 [110 kB]
Get:220 http://172.17.4.1/private bookworm-staging/main armhf r-cran-jpeg armhf 0.1-9-1 [29.6 kB]
Get:221 http://172.17.4.1/private bookworm-staging/main armhf r-cran-png armhf 0.1-7-4 [39.9 kB]
Get:222 http://172.17.4.1/private bookworm-staging/main armhf r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB]
Get:223 http://172.17.4.1/private bookworm-staging/main armhf r-cran-latticeextra all 0.6-29-3 [2192 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package sgml-base.
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Preparing to unpack .../sgml-base_1.30_all.deb ...
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Unpacking libatomic1:armhf (12.1.0-2+rpi1) over (12-20220319-1+rpi1) ...
Preparing to unpack .../libubsan1_12.1.0-2+rpi1_armhf.deb ...
Unpacking libubsan1:armhf (12.1.0-2+rpi1) over (12-20220319-1+rpi1) ...
Preparing to unpack .../gcc-12-base_12.1.0-2+rpi1_armhf.deb ...
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invoke-rc.d: could not determine current runlevel
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Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libncurses6:armhf (6.3+20220423-2) ...
Setting up libsigsegv2:armhf (2.14-1) ...
Setting up libfribidi0:armhf (1.0.8-2.1) ...
Setting up libpng16-16:armhf (1.6.37-5) ...
Setting up libpcre32-3:armhf (2:8.39-14) ...
Setting up libatomic1:armhf (12.1.0-2+rpi1) ...
Setting up libvariable-magic-perl (0.62-1+b4) ...
Setting up libio-html-perl (1.004-3) ...
Setting up libtcl8.6:armhf (8.6.12+dfsg-1) ...
Setting up autopoint (0.21-6) ...
Setting up libb-hooks-op-check-perl (0.22-1+b5) ...
Setting up icu-devtools (71.1-3) ...
Setting up pkg-config (0.29.2-1) ...
Setting up fonts-dejavu-core (2.37-2) ...
Setting up ucf (3.0043) ...
Setting up libparams-util-perl (1.102-1+b2) ...
Setting up libgfortran5:armhf (12.1.0-2+rpi1) ...
Setting up libsub-exporter-progressive-perl (0.001013-1) ...
Setting up libwebp7:armhf (1.2.2-2) ...
Setting up libtimedate-perl (2.3300-2) ...
Setting up liblzma-dev:armhf (5.2.5-2.1) ...
Setting up libubsan1:armhf (12.1.0-2+rpi1) ...
Setting up libsub-name-perl (0.26-1+b2) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-4) ...
Setting up libpcre2-posix3:armhf (10.40-1) ...
Setting up libgcc-11-dev:armhf (11.3.0-1+rpi1) ...
Setting up libmd0:armhf (1.0.4-1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libthai-data (0.1.29-1) ...
Setting up libdevel-globaldestruction-perl (0.14-1.1) ...
Setting up libssh2-1:armhf (1.10.0-3) ...
Setting up sgml-base (1.30) ...
Setting up libdevel-stacktrace-perl (2.0400-1) ...
Setting up libtiff5:armhf (4.3.0-8) ...
Setting up openssl (1.1.1o-1) ...
Setting up libbsd0:armhf (0.11.6-1) ...
Setting up libelf1:armhf (0.187-1) ...
Setting up libicu-dev:armhf (71.1-3) ...
Setting up libxml2:armhf (2.9.14+dfsg-1) ...
Setting up xdg-utils (1.1.3-4.1) ...
update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
Setting up libcc1-0:armhf (12.1.0-2+rpi1) ...
Setting up liburi-perl (5.10-1) ...
Setting up dctrl-tools (2.24-3) ...
Setting up libbz2-dev:armhf (1.0.8-5) ...
Setting up libfile-stripnondeterminism-perl (1.13.0-1) ...
Setting up cpp-11 (11.3.0-1+rpi1) ...
Setting up libpaper1:armhf (1.1.28) ...

Creating config file /etc/papersize with new version
Setting up libice6:armhf (2:1.0.10-1) ...
Setting up libhttp-date-perl (6.05-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up libncurses-dev:armhf (6.3+20220423-2) ...
Setting up libxcb1:armhf (1.14-3) ...
Setting up gettext (0.21-6) ...
Setting up libpcre2-dev:armhf (10.40-1) ...
Setting up libtool (2.4.7-4) ...
Setting up libxcb-render0:armhf (1.14-3) ...
Setting up libpcre3-dev:armhf (2:8.39-14) ...
Setting up libgfortran-11-dev:armhf (11.3.0-1+rpi1) ...
Setting up fontconfig-config (2.13.1-4.4) ...
Setting up libpng-dev:armhf (1.6.37-5) ...
Setting up libjpeg-dev:armhf (1:2.1.2-1) ...
Setting up m4 (1.4.18-5) ...
Setting up libcurl3-gnutls:armhf (7.83.0-1) ...
Setting up libxcb-shm0:armhf (1.14-3) ...
Setting up libpaper-utils (1.1.28) ...
Setting up libclass-c3-perl (0.35-1) ...
Setting up libreadline-dev:armhf (8.1.2-1.2) ...
Setting up libdevel-callchecker-perl (0.008-1+b3) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libthai0:armhf (0.1.29-1) ...
Setting up ca-certificates (20211016) ...
Updating certificates in /etc/ssl/certs...
127 added, 0 removed; done.
Setting up libblas3:armhf (3.10.1-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libfreetype6:armhf (2.12.1+dfsg-2) ...
Setting up libdata-optlist-perl (0.112-1) ...
Setting up autoconf (2.71-2) ...
Setting up libstdc++-11-dev:armhf (11.3.0-1+rpi1) ...
Setting up dh-strip-nondeterminism (1.13.0-1) ...
Setting up dwz (0.14-1) ...
Setting up gcc-11 (11.3.0-1+rpi1) ...
Setting up groff-base (1.22.4-8) ...
Setting up libncurses5-dev:armhf (6.3+20220423-2) ...
Setting up libcurl4:armhf (7.83.0-1) ...
Setting up libx11-6:armhf (2:1.7.5-1) ...
Setting up libharfbuzz0b:armhf (2.7.4-1+b1) ...
Setting up libfontconfig1:armhf (2.13.1-4.4) ...
Setting up libmro-compat-perl (0.15-1) ...
Setting up libsm6:armhf (2:1.2.3-1) ...
Setting up libxmuu1:armhf (2:1.1.3-3) ...
Setting up libblas-dev:armhf (3.10.1-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up libsub-exporter-perl (0.988-1) ...
Setting up libhttp-message-perl (6.36-1) ...
Setting up libeval-closure-perl (0.14-1) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up fontconfig (2.13.1-4.4) ...
Regenerating fonts cache... done.
Setting up liblapack3:armhf (3.10.1-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libboost1.74-dev:armhf (1.74.0-14+b2) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up g++-11 (11.3.0-1+rpi1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libparams-classify-perl (0.015-1+b4) ...
Setting up libpango-1.0-0:armhf (1.50.7+ds-1) ...
Setting up libxext6:armhf (2:1.3.4-1) ...
Setting up libwww-curl-perl (4.17-7+b2) ...
Setting up man-db (2.10.2-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libcairo2:armhf (1.16.0-5) ...
Setting up dh-autoreconf (20) ...
Setting up libmodule-runtime-perl (0.016-1) ...
Setting up liblapack-dev:armhf (3.10.1-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up libdist-checkconflicts-perl (0.11-1.1) ...
Setting up libxt6:armhf (1:1.2.1-1) ...
Setting up gfortran-11 (11.3.0-1+rpi1) ...
Setting up xauth (1:1.1.1-1) ...
Setting up libboost-dev:armhf (1.74.0.3+b4) ...
Setting up libxss1:armhf (1:1.2.3-1) ...
Setting up libpangoft2-1.0-0:armhf (1.50.7+ds-1) ...
Setting up libpangocairo-1.0-0:armhf (1.50.7+ds-1) ...
Setting up r-cran-bh (1.74.0-2) ...
Setting up libxft2:armhf (2.3.4-1) ...
Setting up libmodule-implementation-perl (0.09-1.1) ...
Setting up libpackage-stash-perl (0.40-1) ...
Setting up libtk8.6:armhf (8.6.12-1) ...
Setting up debhelper (13.7.1) ...
Setting up libmodule-runtime-conflicts-perl (0.003-1.1) ...
Setting up gfortran (4:11.2.0-2+rpi1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up libclass-load-perl (0.25-1) ...
Setting up r-base-core (4.2.0-1) ...

Creating config file /etc/R/Renviron with new version
Setting up r-cran-crayon (1.5.1-1) ...
Setting up r-cran-futile.options (1.0.1-3) ...
Setting up r-cran-lattice (0.20-45-3) ...
Setting up r-cran-formatr (1.12-1) ...
Setting up libpackage-deprecationmanager-perl (0.17-1.1) ...
Setting up libdevel-overloadinfo-perl (0.007-1) ...
Setting up libclass-load-xs-perl (0.10-1+b5) ...
Setting up r-cran-jpeg (0.1-9-1) ...
Setting up libb-hooks-endofscope-perl (0.26-1) ...
Setting up r-bioc-genomeinfodbdata (1.2.8-1) ...
Setting up r-cran-codetools (0.2-18-1) ...
Setting up r-bioc-biocgenerics (0.42.0-1) ...
Setting up r-cran-matrixstats (0.62.0-1) ...
Setting up r-base-dev (4.2.0-1) ...
Setting up r-bioc-matrixgenerics (1.8.0-1) ...
Setting up libmoose-perl:armhf (2.2200-1+b1) ...
Setting up r-cran-lambda.r (1.2.4-2) ...
Setting up r-cran-snow (1:0.4.4-2) ...
Setting up r-cran-bitops (1.0-7-1) ...
Setting up r-bioc-zlibbioc (1.42.0+dfsg-1) ...
Setting up r-cran-png (0.1-7-4) ...
Setting up r-bioc-biobase (2.56.0-1) ...
Setting up r-cran-hwriter (1.3.2.1-1) ...
Setting up r-cran-rcolorbrewer (1.1-3-1) ...
Setting up r-bioc-s4vectors (0.34.0-1) ...
Setting up r-cran-futile.logger (1.4.3-4) ...
Setting up libnamespace-clean-perl (0.27-1) ...
Setting up r-cran-matrix (1.4-1-1) ...
Setting up r-bioc-iranges (2.30.0-1) ...
Setting up r-cran-rcurl (1.98-1.6-1) ...
Setting up r-bioc-delayedarray (0.22.0+dfsg-1) ...
Setting up r-bioc-biocparallel (1.30.2-2) ...
Setting up libwww-curl-simple-perl (0.100191-2) ...
Setting up r-bioc-rhtslib (1.28.0+dfsg-1) ...
Setting up r-cran-latticeextra (0.6-29-3) ...
Setting up r-bioc-genomeinfodb (1.32.2-1) ...
Setting up r-bioc-xvector (0.36.0-1) ...
Setting up dh-r (20210816) ...
Setting up r-bioc-genomicranges (1.48.0+dfsg-1) ...
Setting up r-bioc-biostrings (2.64.0-1) ...
Setting up r-bioc-rsamtools (2.12.0-1) ...
Setting up r-bioc-summarizedexperiment (1.26.1+dfsg-1) ...
Setting up r-bioc-genomicalignments (1.32.0-1) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.33-7+rpi1) ...
Processing triggers for ca-certificates (20211016) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (armhf included in any)

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.38-3+rpi1 dpkg-dev_1.21.7+rpi1 g++-11_11.3.0-1+rpi1 gcc-11_11.3.0-1+rpi1 libc6-dev_2.33-7+rpi1 libstdc++-11-dev_11.3.0-1+rpi1 libstdc++6_12.1.0-2+rpi1 linux-libc-dev_5.16.18-1+rpi1
Package versions: adduser_3.121 apt_2.4.5 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-6 autotools-dev_20220109.1 base-files_12.2+rpi1 base-passwd_3.5.52 bash_5.1-6 binutils_2.38-3+rpi1 binutils-arm-linux-gnueabihf_2.38-3+rpi1 binutils-common_2.38-3+rpi1 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+rpi1 cpp-11_11.3.0-1+rpi1 dash_0.5.11+git20210903+057cd650a4ed-8 dctrl-tools_2.24-3 debconf_1.5.79 debhelper_13.7.1 debianutils_5.7-0.1 dh-autoreconf_20 dh-r_20210816 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-3+b1 dpkg_1.21.7+rpi1 dpkg-dev_1.21.7+rpi1 dwz_0.14-1 e2fsprogs_1.46.5-2 fakeroot_1.28-1 file_1:5.41-4 findutils_4.9.0-2 fontconfig_2.13.1-4.4 fontconfig-config_2.13.1-4.4 fonts-dejavu-core_2.37-2 g++_4:11.2.0-2+rpi1 g++-11_11.3.0-1+rpi1 gcc_4:11.2.0-2+rpi1 gcc-11_11.3.0-1+rpi1 gcc-11-base_11.3.0-1+rpi1 gcc-12-base_12.1.0-2+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-6 gettext-base_0.21-6 gfortran_4:11.2.0-2+rpi1 gfortran-11_11.3.0-1+rpi1 gnupg_2.2.27-3 gnupg-l10n_2.2.27-3 gnupg-utils_2.2.27-3+b1 gpg_2.2.27-3+b1 gpg-agent_2.2.27-3+b1 gpg-wks-client_2.2.27-3+b1 gpg-wks-server_2.2.27-3+b1 gpgconf_2.2.27-3+b1 gpgsm_2.2.27-3+b1 gpgv_2.2.27-3+b1 grep_3.7-1 groff-base_1.22.4-8 gzip_1.12-1 hostname_3.23 icu-devtools_71.1-3 init-system-helpers_1.62 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libalgorithm-c3-perl_0.11-1 libapt-pkg6.0_2.4.5 libarchive-zip-perl_1.68-1 libasan6_11.3.0-1+rpi1 libassuan0_2.5.5-1 libatomic1_12.1.0-2+rpi1 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+b5 libbinutils_2.38-3+rpi1 libblas-dev_3.10.1-2 libblas3_3.10.1-2 libblkid1_2.38-4 libboost-dev_1.74.0.3+b4 libboost1.74-dev_1.74.0-14+b2 libbrotli1_1.0.9-2+b2 libbsd0_0.11.6-1 libbz2-1.0_1.0.8-5 libbz2-dev_1.0.8-5 libc-bin_2.33-7+rpi1 libc-dev-bin_2.33-7+rpi1 libc6_2.33-7+rpi1 libc6-dev_2.33-7+rpi1 libcairo2_1.16.0-5 libcap-ng0_0.7.9-2.2+b2 libcap2_1:2.44-1 libcc1-0_12.1.0-2+rpi1 libclass-c3-perl_0.35-1 libclass-load-perl_0.25-1 libclass-load-xs-perl_0.10-1+b5 libcom-err2_1.46.5-2 libcrypt-dev_1:4.4.27-1.1 libcrypt1_1:4.4.27-1.1 libctf-nobfd0_2.38-3+rpi1 libctf0_2.38-3+rpi1 libcurl3-gnutls_7.83.0-1 libcurl4_7.83.0-1 libdata-optlist-perl_0.112-1 libdatrie1_0.2.13-2+b2 libdb5.3_5.3.28+dfsg1-0.8 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+rpi1 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 libext2fs2_1.46.5-2 libfakeroot_1.28-1 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-2 libfribidi0_1.0.8-2.1 libgcc-11-dev_11.3.0-1+rpi1 libgcc-s1_12.1.0-2+rpi1 libgcrypt20_1.10.1-2 libgdbm-compat4_1.23-1 libgdbm6_1.23-1 libgfortran-11-dev_11.3.0-1+rpi1 libgfortran5_12.1.0-2+rpi1 libglib2.0-0_2.72.1-1 libgmp10_2:6.2.1+dfsg-3 libgnutls30_3.7.4-2 libgomp1_12.1.0-2+rpi1 libgpg-error0_1.43-3 libgraphite2-3_1.3.14-1 libgssapi-krb5-2_1.19.2-2+b2 libharfbuzz0b_2.7.4-1+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 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 libk5crypto3_1.19.2-2+b2 libkeyutils1_1.6.1-3+rpi1 libkrb5-3_1.19.2-2+b2 libkrb5support0_1.19.2-2+b2 libksba8_1.6.0-2 liblapack-dev_3.10.1-2 liblapack3_3.10.1-2 libldap-2.5-0_2.5.11+dfsg-1+rpi1 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 libnpth0_1.6-3 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_1.4.0-11 libpam-modules-bin_1.4.0-11 libpam-runtime_1.4.0-11 libpam0g_1.4.0-11 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 libpaper1_1.1.28 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 libperl5.32_5.32.1-6 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 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-4 libsasl2-modules-db_2.1.28+dfsg-4 libscalar-list-utils-perl_1:1.62-1 libseccomp2_2.5.3-2+rpi1+b1 libselinux1_3.3-1+b1 libsemanage-common_3.3-1 libsemanage2_3.3-1+b1 libsepol1_3.1-1 libsepol2_3.3-1 libsigsegv2_2.14-1 libsm6_2:1.2.3-1 libsmartcols1_2.38-4 libsqlite3-0_3.38.2-1 libss2_1.46.5-2 libssh2-1_1.10.0-3 libssl1.1_1.1.1n-1 libstdc++-11-dev_11.3.0-1+rpi1 libstdc++6_12.1.0-2+rpi1 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 libsystemd0_250.4-1+rpi1 libtasn1-6_4.18.0-4 libtcl8.6_8.6.12+dfsg-1 libthai-data_0.1.29-1 libthai0_0.1.29-1 libtiff5_4.3.0-8 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 libubsan1_12.1.0-2+rpi1 libuchardet0_0.0.7-1 libudev1_250.4-1+rpi1 libunistring2_1.0-1 liburi-perl_5.10-1 libuuid1_2.38-4 libvariable-magic-perl_0.62-1+b4 libwebp7_1.2.2-2 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 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 libxml2_2.9.14+dfsg-1 libxmuu1_2:1.1.3-3 libxrender1_1:0.9.10-1 libxss1_1:1.2.3-1 libxt6_1:1.2.1-1 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.16.18-1+rpi1 login_1:4.11.1+dfsg1-2 logsave_1.46.5-2 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.10.2-1 mawk_1.3.4.20200120-3 mount_2.38-4 ncurses-base_6.3-2 ncurses-bin_6.3-2 openssl_1.1.1o-1 passwd_1:4.11.1+dfsg1-2 patch_2.7.6-7 perl_5.34.0-4 perl-base_5.34.0-4 perl-modules-5.32_5.32.1-6 perl-modules-5.34_5.34.0-4 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 r-base-core_4.2.0-1 r-base-dev_4.2.0-1 r-bioc-biobase_2.56.0-1 r-bioc-biocgenerics_0.42.0-1 r-bioc-biocparallel_1.30.2-2 r-bioc-biostrings_2.64.0-1 r-bioc-delayedarray_0.22.0+dfsg-1 r-bioc-genomeinfodb_1.32.2-1 r-bioc-genomeinfodbdata_1.2.8-1 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-rhtslib_1.28.0+dfsg-1 r-bioc-rsamtools_2.12.0-1 r-bioc-s4vectors_0.34.0-1 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-bh_1.74.0-2 r-cran-bitops_1.0-7-1 r-cran-codetools_0.2-18-1 r-cran-crayon_1.5.1-1 r-cran-formatr_1.12-1 r-cran-futile.logger_1.4.3-4 r-cran-futile.options_1.0.1-3 r-cran-hwriter_1.3.2.1-1 r-cran-jpeg_0.1-9-1 r-cran-lambda.r_1.2.4-2 r-cran-lattice_0.20-45-3 r-cran-latticeextra_0.6-29-3 r-cran-matrix_1.4-1-1 r-cran-matrixstats_0.62.0-1 r-cran-png_0.1-7-4 r-cran-rcolorbrewer_1.1-3-1 r-cran-rcurl_1.98-1.6-1 r-cran-snow_1:0.4.4-2 raspbian-archive-keyring_20120528.2 readline-common_8.1.2-1.2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.30 sysvinit-utils_3.03-1 tar_1.34+dfsg-1 tzdata_2022a-1 ucf_3.0043 unzip_6.0-26 util-linux_2.37.3-1 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

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

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Hash: SHA512

Format: 3.0 (quilt)
Source: r-bioc-shortread
Binary: r-bioc-shortread
Architecture: any
Version: 1.54.0-1
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: https://bioconductor.org/packages/ShortRead/
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/r-pkg-team/r-bioc-shortread
Vcs-Git: https://salsa.debian.org/r-pkg-team/r-bioc-shortread.git
Testsuite: autopkgtest-pkg-r
Build-Depends: debhelper-compat (= 13), dh-r, r-base-dev, r-bioc-biocgenerics, r-bioc-biocparallel, r-bioc-biostrings, r-bioc-rsamtools, r-bioc-genomicalignments, r-bioc-biobase, r-bioc-s4vectors, r-bioc-iranges, r-bioc-genomeinfodb, r-bioc-genomicranges, r-cran-hwriter, r-bioc-zlibbioc, r-cran-lattice, r-cran-latticeextra, r-bioc-xvector, r-bioc-rhtslib
Package-List:
 r-bioc-shortread deb gnu-r optional arch=any
Checksums-Sha1:
 c76e6c56ceb10760d6c0e46549b0f0e94e450e97 5184736 r-bioc-shortread_1.54.0.orig.tar.gz
 107e59c28ac2c9efca5d4fad0fc607ca25e87440 5636 r-bioc-shortread_1.54.0-1.debian.tar.xz
Checksums-Sha256:
 18ca2c82688c158cdc952436434d4a608000ec4c02b199a0925c6cb2500a030c 5184736 r-bioc-shortread_1.54.0.orig.tar.gz
 1e644288628fd09ba31f99a89a150c2e59bb062bbfb7384b3ffd004e9656c6e8 5636 r-bioc-shortread_1.54.0-1.debian.tar.xz
Files:
 fc2196c41f70001aba4d0f6b4e108e18 5184736 r-bioc-shortread_1.54.0.orig.tar.gz
 39490a1a13a40388f0fb07b5ea6ed663 5636 r-bioc-shortread_1.54.0-1.debian.tar.xz

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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.NETO6mhq/trustedkeys.kbx': General error
gpgv: Signature made Mon May 16 05:39:18 2022 UTC
gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv:                issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./r-bioc-shortread_1.54.0-1.dsc
dpkg-source: info: extracting r-bioc-shortread in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking r-bioc-shortread_1.54.0.orig.tar.gz
dpkg-source: info: unpacking r-bioc-shortread_1.54.0-1.debian.tar.xz

Check disk space
----------------

Sufficient free space for build

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=7b33f05927d544f8acb7289c691791af
JOURNAL_STREAM=8:24067
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-dbb40622-8138-4f77-9f9b-4927412b8fb1
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c16523
XDG_SESSION_TYPE=unspecified

dpkg-buildpackage
-----------------

Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package r-bioc-shortread
dpkg-buildpackage: info: source version 1.54.0-1
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
 debian/rules clean
dh clean --buildsystem R
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
rm -f configure config.log config.status
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   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: 1.54.0
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 07:29:08 +0200
	mkdir -p /<<PKGBUILDDIR>>/debian/r-bioc-shortread/usr/lib/R/site-library
	R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-shortread/usr/lib/R/site-library --clean . "--built-timestamp='Mon, 16 May 2022 07:29:08 +0200'"
* installing *source* package ‘ShortRead’ ...
** using staged installation
checking for gcc... gcc
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 accepts -g... yes
checking for gcc 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... 4
configure: creating ./config.status
config.status: creating src/Makevars
** libs
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -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-2bkVJg/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -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-2bkVJg/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -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-2bkVJg/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -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-2bkVJg/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -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-2bkVJg/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c XVector_stubs.c -o XVector_stubs.o
gcc -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-2bkVJg/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c alphabet.c -o alphabet.o
gcc -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-2bkVJg/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c count.c -o count.o
gcc -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-2bkVJg/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c io.c -o io.o
gcc -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-2bkVJg/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c io_bowtie.c -o io_bowtie.o
gcc -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-2bkVJg/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -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=4 -fpic  -g -O2 -ffile-prefix-map=/build/r-base-2bkVJg/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -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=4 -fpic  -g -O2 -ffile-prefix-map=/build/r-base-2bkVJg/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c read_maq_map.cc -o read_maq_map.o
gcc -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-2bkVJg/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c sampler.c -o sampler.o
gcc -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-2bkVJg/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c trim.c -o trim.o
gcc -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-2bkVJg/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c util.c -o util.o
gcc -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-2bkVJg/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -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 '/<<PKGBUILDDIR>>/src'
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
installing to /<<PKGBUILDDIR>>/debian/r-bioc-shortread/usr/lib/R/site-library/00LOCK-r-bioc-shortread-1.54.0/00new/ShortRead/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ShortRead)
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 substitution (s///) at /usr/share/perl5/Dpkg/Deps.pm line 301.
Use of uninitialized value $dep_line in split at /usr/share/perl5/Dpkg/Deps.pm line 304.
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-3.15
I: Use r-bioc-shortread as Debian binary package for variables substitution
   debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
find debian -name test_readPrb.R -delete
echo "***** DELETED test_readPrb.R ********"
***** DELETED test_readPrb.R ********
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   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_1.54.0-1_armhf.deb'.
dpkg-deb: building package 'r-bioc-shortread-dbgsym' in '../r-bioc-shortread-dbgsym_1.54.0-1_armhf.deb'.
 dpkg-genbuildinfo --build=any -O../r-bioc-shortread_1.54.0-1_armhf.buildinfo
 dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> -O../r-bioc-shortread_1.54.0-1_armhf.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)
--------------------------------------------------------------------------------
Build finished at 2022-05-25T10:57:38Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


r-bioc-shortread_1.54.0-1_armhf.changes:
----------------------------------------

Format: 1.8
Date: Mon, 16 May 2022 07:29:08 +0200
Source: r-bioc-shortread
Binary: r-bioc-shortread r-bioc-shortread-dbgsym
Architecture: armhf
Version: 1.54.0-1
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
 r-bioc-shortread - GNU R classes and methods for high-throughput short-read sequenci
Changes:
 r-bioc-shortread (1.54.0-1) unstable; urgency=medium
 .
   * New upstream version
   * Standards-Version: 4.6.1 (routine-update)
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Files:
 950782c3664212ab8d09a79ab70749bf 154692 debug optional r-bioc-shortread-dbgsym_1.54.0-1_armhf.deb
 c3177a91c57547149742e7b96af3f9e5 10854 gnu-r optional r-bioc-shortread_1.54.0-1_armhf.buildinfo
 975d7e4a3b9e6a52e3f4021a72b2edb1 5139904 gnu-r optional r-bioc-shortread_1.54.0-1_armhf.deb

+------------------------------------------------------------------------------+
| Buildinfo                                                                    |
+------------------------------------------------------------------------------+

Format: 1.0
Source: r-bioc-shortread
Binary: r-bioc-shortread r-bioc-shortread-dbgsym
Architecture: armhf
Version: 1.54.0-1
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 c16a1b5bee3977c5e95da192672fae241d006da1ad07bfd2cf53c859524d9f38 5139904 r-bioc-shortread_1.54.0-1_armhf.deb
Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Wed, 25 May 2022 10:57:36 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
 autoconf (= 2.71-2),
 automake (= 1:1.16.5-1.3),
 autopoint (= 0.21-6),
 autotools-dev (= 20220109.1),
 base-files (= 12.2+rpi1),
 base-passwd (= 3.5.52),
 bash (= 5.1-6),
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 dh-autoreconf (= 20),
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 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),
 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 (= 1.4.0-11),
 libpam-modules-bin (= 1.4.0-11),
 libpam-runtime (= 1.4.0-11),
 libpam0g (= 1.4.0-11),
 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),
 libpaper1 (= 1.1.28),
 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),
 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-4),
 libsasl2-modules-db (= 2.1.28+dfsg-4),
 libscalar-list-utils-perl (= 1:1.62-1),
 libseccomp2 (= 2.5.3-2+rpi1+b1),
 libselinux1 (= 3.3-1+b1),
 libsigsegv2 (= 2.14-1),
 libsm6 (= 2:1.2.3-1),
 libsmartcols1 (= 2.38-4),
 libssh2-1 (= 1.10.0-3),
 libssl1.1 (= 1.1.1n-1),
 libstdc++-11-dev (= 11.3.0-1+rpi1),
 libstdc++6 (= 12.1.0-2+rpi1),
 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),
 libsystemd0 (= 250.4-1+rpi1),
 libtasn1-6 (= 4.18.0-4),
 libtcl8.6 (= 8.6.12+dfsg-1),
 libthai-data (= 0.1.29-1),
 libthai0 (= 0.1.29-1),
 libtiff5 (= 4.3.0-8),
 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),
 libubsan1 (= 12.1.0-2+rpi1),
 libuchardet0 (= 0.0.7-1),
 libudev1 (= 250.4-1+rpi1),
 libunistring2 (= 1.0-1),
 liburi-perl (= 5.10-1),
 libuuid1 (= 2.38-4),
 libvariable-magic-perl (= 0.62-1+b4),
 libwebp7 (= 1.2.2-2),
 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),
 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),
 libxml2 (= 2.9.14+dfsg-1),
 libxmuu1 (= 2:1.1.3-3),
 libxrender1 (= 1:0.9.10-1),
 libxss1 (= 1:1.2.3-1),
 libxt6 (= 1:1.2.1-1),
 libzstd1 (= 1.5.2+dfsg-1),
 linux-libc-dev (= 5.16.18-1+rpi1),
 login (= 1:4.11.1+dfsg1-2),
 lsb-base (= 11.1.0+rpi1),
 m4 (= 1.4.18-5),
 make (= 4.3-4.1),
 man-db (= 2.10.2-1),
 mawk (= 1.3.4.20200120-3),
 ncurses-base (= 6.3-2),
 ncurses-bin (= 6.3-2),
 openssl (= 1.1.1o-1),
 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),
 r-base-dev (= 4.2.0-1),
 r-bioc-biobase (= 2.56.0-1),
 r-bioc-biocgenerics (= 0.42.0-1),
 r-bioc-biocparallel (= 1.30.2-2),
 r-bioc-biostrings (= 2.64.0-1),
 r-bioc-delayedarray (= 0.22.0+dfsg-1),
 r-bioc-genomeinfodb (= 1.32.2-1),
 r-bioc-genomeinfodbdata (= 1.2.8-1),
 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-rhtslib (= 1.28.0+dfsg-1),
 r-bioc-rsamtools (= 2.12.0-1),
 r-bioc-s4vectors (= 0.34.0-1),
 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-bh (= 1.74.0-2),
 r-cran-bitops (= 1.0-7-1),
 r-cran-codetools (= 0.2-18-1),
 r-cran-crayon (= 1.5.1-1),
 r-cran-formatr (= 1.12-1),
 r-cran-futile.logger (= 1.4.3-4),
 r-cran-futile.options (= 1.0.1-3),
 r-cran-hwriter (= 1.3.2.1-1),
 r-cran-jpeg (= 0.1-9-1),
 r-cran-lambda.r (= 1.2.4-2),
 r-cran-lattice (= 0.20-45-3),
 r-cran-latticeextra (= 0.6-29-3),
 r-cran-matrix (= 1.4-1-1),
 r-cran-matrixstats (= 0.62.0-1),
 r-cran-png (= 0.1-7-4),
 r-cran-rcolorbrewer (= 1.1-3-1),
 r-cran-rcurl (= 1.98-1.6-1),
 r-cran-snow (= 1:0.4.4-2),
 readline-common (= 8.1.2-1.2),
 rpcsvc-proto (= 1.4.2-4),
 sed (= 4.8-1),
 sensible-utils (= 0.0.17),
 sgml-base (= 1.30),
 sysvinit-utils (= 3.03-1),
 tar (= 1.34+dfsg-1),
 tzdata (= 2022a-1),
 ucf (= 3.0043),
 unzip (= 6.0-26),
 util-linux (= 2.37.3-1),
 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)
Environment:
 DEB_BUILD_OPTIONS="parallel=4"
 LANG="en_GB.UTF-8"
 LC_ALL="C.UTF-8"
 SOURCE_DATE_EPOCH="1652678948"


+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


r-bioc-shortread-dbgsym_1.54.0-1_armhf.deb
------------------------------------------

 new Debian package, version 2.0.
 size 154692 bytes: control archive=540 bytes.
     402 bytes,    12 lines      control              
     106 bytes,     1 lines      md5sums              
 Package: r-bioc-shortread-dbgsym
 Source: r-bioc-shortread
 Version: 1.54.0-1
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
 Installed-Size: 187
 Depends: r-bioc-shortread (= 1.54.0-1)
 Section: debug
 Priority: optional
 Description: debug symbols for r-bioc-shortread
 Build-Ids: 93e245f660c7f5ad4933792cdfe5517f6664705f

drwxr-xr-x root/root         0 2022-05-16 05:29 ./
drwxr-xr-x root/root         0 2022-05-16 05:29 ./usr/
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drwxr-xr-x root/root         0 2022-05-16 05:29 ./usr/lib/debug/
drwxr-xr-x root/root         0 2022-05-16 05:29 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2022-05-16 05:29 ./usr/lib/debug/.build-id/93/
-rw-r--r-- root/root    180948 2022-05-16 05:29 ./usr/lib/debug/.build-id/93/e245f660c7f5ad4933792cdfe5517f6664705f.debug
drwxr-xr-x root/root         0 2022-05-16 05:29 ./usr/share/
drwxr-xr-x root/root         0 2022-05-16 05:29 ./usr/share/doc/
lrwxrwxrwx root/root         0 2022-05-16 05:29 ./usr/share/doc/r-bioc-shortread-dbgsym -> r-bioc-shortread


r-bioc-shortread_1.54.0-1_armhf.deb
-----------------------------------

 new Debian package, version 2.0.
 size 5139904 bytes: control archive=4088 bytes.
    1319 bytes,    17 lines      control              
   10642 bytes,   111 lines      md5sums              
 Package: r-bioc-shortread
 Version: 1.54.0-1
 Architecture: armhf
 Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
 Installed-Size: 7440
 Depends: r-base-core (>= 4.2.0-1), r-api-4.0, r-api-bioc-3.15, r-bioc-biocgenerics (>= 0.23.3), r-bioc-biocparallel, r-bioc-biostrings (>= 2.47.6), r-bioc-rsamtools (>= 1.31.2), r-bioc-genomicalignments (>= 1.15.6), r-bioc-biobase, r-bioc-s4vectors (>= 0.17.25), r-bioc-iranges (>= 2.13.12), r-bioc-genomeinfodb (>= 1.15.2), r-bioc-genomicranges (>= 1.31.8), r-cran-hwriter, r-bioc-zlibbioc, r-cran-lattice, r-cran-latticeextra, r-bioc-xvector, r-bioc-rhtslib, libc6 (>= 2.7), libgcc-s1 (>= 3.5), libstdc++6 (>= 11), zlib1g (>= 1:1.1.4)
 Suggests: r-bioc-biocstyle, r-cran-runit, r-bioc-biomart, r-bioc-genomicfeatures
 Section: gnu-r
 Priority: optional
 Homepage: https://bioconductor.org/packages/ShortRead/
 Description: GNU R classes and methods for high-throughput short-read sequencing data
  This BioConductor module is a package for input, quality assessment,
  manipulation and output of high-throughput sequencing data. ShortRead is
  provided in the R and Bioconductor environments, allowing ready access
  to additional facilities for advanced statistical analysis, data
  transformation, visualization and integration with diverse genomic
  resources.

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+------------------------------------------------------------------------------+
| Post Build                                                                   |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: armhf
Build Type: any
Build-Space: 21948
Build-Time: 190
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 1191
Job: r-bioc-shortread_1.54.0-1
Machine Architecture: armhf
Package: r-bioc-shortread
Package-Time: 1410
Source-Version: 1.54.0-1
Space: 21948
Status: successful
Version: 1.54.0-1
--------------------------------------------------------------------------------
Finished at 2022-05-25T10:57:38Z
Build needed 00:23:30, 21948k disk space
Raspbian Package Auto-Building

Build log for r-bioc-shortread (1.54.0-1) on armhf
