r-bioc-shortread →
1.48.0-2 →
armhf → 2021-02-09 05:38:55
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| r-bioc-shortread 1.48.0-2 (armhf) Tue, 09 Feb 2021 05:27:36 +0000 |
+==============================================================================+
Package: r-bioc-shortread
Version: 1.48.0-2
Source Version: 1.48.0-2
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-72726a01-c970-42c6-9f3c-16870f23760c' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [12.2 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [13.2 MB]
Fetched 25.4 MB in 9s (2776 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| 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://172.17.0.1/private bullseye-staging/main r-bioc-shortread 1.48.0-2 (dsc) [2531 B]
Get:2 http://172.17.0.1/private bullseye-staging/main r-bioc-shortread 1.48.0-2 (tar) [5185 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main r-bioc-shortread 1.48.0-2 (diff) [5548 B]
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Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/r-bioc-shortread-vH2SZk/r-bioc-shortread-1.48.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-shortread-vH2SZk' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-51gW2w/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-51gW2w/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-51gW2w/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-51gW2w/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-51gW2w/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-51gW2w/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-51gW2w/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-51gW2w/apt_archive ./ Packages [433 B]
Fetched 2109 B in 0s (9922 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
bsdextrautils krb5-locales libnss-nis libnss-nisplus libpam-cap netbase
sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 2 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-51gW2w/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (63.6 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12563 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), dh-r, r-base-dev, 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
Filtered Build-Depends: debhelper-compat (= 13), dh-r, r-base-dev, 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
dpkg-deb: building package 'sbuild-build-depends-r-bioc-shortread-dummy' in '/<<BUILDDIR>>/resolver-51gW2w/apt_archive/sbuild-build-depends-r-bioc-shortread-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-r-bioc-shortread-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-51gW2w/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-51gW2w/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-51gW2w/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-51gW2w/apt_archive ./ Sources [667 B]
Get:5 copy:/<<BUILDDIR>>/resolver-51gW2w/apt_archive ./ Packages [748 B]
Fetched 2748 B in 0s (12.9 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install r-bioc-shortread build dependencies (apt-based resolver)
----------------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales libnss-nis libnss-nisplus libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev 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-10 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-10-dev libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b
libhttp-date-perl libhttp-message-perl libice6 libicu-dev libicu67
libio-html-perl libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev
liblapack-dev liblapack3 liblwp-mediatypes-perl liblzma-dev libmagic-mgc
libmagic1 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-posix2 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1
libpixman-1-0 libpng-dev libpng16-16 libpsl5 libreadline-dev librtmp1
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 libwebp6 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-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 ucf unzip x11-common
xauth xdg-utils zip zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc debtags dh-make gettext-doc
libasprintf-dev libgettextpo-dev gfortran-doc gfortran-10-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 tcl8.6
tk8.6 libtool-doc gcj-jdk 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-cran-codetools r-cran-knitr r-cran-data.table r-bioc-bsgenome
r-bioc-genomicfeatures r-bioc-hdf5array r-bioc-genefilter
r-bioc-delayedmatrixstats r-bioc-biocstyle r-cran-runit r-bioc-rtracklayer
r-bioc-edger r-bioc-gviz r-bioc-annotationhub r-bioc-dexseq r-bioc-graph
r-cran-jsonlite r-bioc-rhdf5 r-cran-rmarkdown r-cran-testthat
r-cran-rstudioapi r-cran-shiny r-cran-base64enc r-cran-ggplot2 r-cran-xml
r-cran-rmpi r-cran-rsprng r-cran-rlecuyer
Recommended packages:
devscripts 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-bioc-shortread r-cran-digest r-bioc-annotate r-cran-testthat
r-cran-withr r-cran-mockery r-cran-testit r-cran-codetools 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 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-10 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-10-dev libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b
libhttp-date-perl libhttp-message-perl libice6 libicu-dev libicu67
libio-html-perl libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev
liblapack-dev liblapack3 liblwp-mediatypes-perl liblzma-dev libmagic-mgc
libmagic1 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-posix2 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1
libpixman-1-0 libpng-dev libpng16-16 libpsl5 libreadline-dev librtmp1
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 libwebp6 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-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-r-bioc-shortread-dummy ucf unzip x11-common xauth
xdg-utils zip zlib1g-dev
0 upgraded, 201 newly installed, 0 to remove and 2 not upgraded.
Need to get 153 MB of archives.
After this operation, 472 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-51gW2w/apt_archive ./ sbuild-build-depends-r-bioc-shortread-dummy 0.invalid.0 [1032 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-6 [793 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
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Get:6 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-14 [313 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.3-2 [814 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf openssl armhf 1.1.1i-3 [814 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf ca-certificates all 20210119 [158 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf dctrl-tools armhf 2.24-3 [94.2 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-15 [513 kB]
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Get:22 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.3.3 [189 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB]
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Get:29 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-6 [8289 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.3 [580 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.3.3 [1011 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf zip armhf 3.0-12 [209 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf unzip armhf 6.0-26 [151 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libpaper1 armhf 1.1.28 [20.5 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libpaper-utils armhf 1.1.28 [17.7 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf xdg-utils all 1.1.3-2 [74.6 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-3 [108 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.10-1 [73.3 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libpng16-16 armhf 1.6.37-3 [276 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libfreetype6 armhf 2.10.4+dfsg-1 [353 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf fontconfig-config all 2.13.1-4.2 [281 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libfontconfig1 armhf 2.13.1-4.2 [328 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libpixman-1-0 armhf 0.40.0-1 [463 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.14-3 [136 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.7.0-2 [310 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.7.0-2 [706 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libxcb-render0 armhf 1.14-3 [110 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libxcb-shm0 armhf 1.14-3 [101 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1.1 [47.8 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libcairo2 armhf 1.16.0-5 [602 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.42.0-1 [66.7 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.9.0-2 [141 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libcurl4 armhf 7.74.0-1 [305 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.6-1 [1186 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo armhf 1:2.0.5-2 [120 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10.2.1-6+rpi1 [232 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-3 [1597 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf fontconfig armhf 2.13.1-4.2 [416 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libfribidi0 armhf 1.0.8-2 [63.5 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libgraphite2-3 armhf 1.3.14-1 [70.3 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libharfbuzz0b armhf 2.7.4-1 [1422 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libthai-data all 0.1.28-3 [170 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libdatrie1 armhf 0.2.13-1+b1 [39.7 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libthai0 armhf 0.1.28-3 [51.0 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libpango-1.0-0 armhf 1.46.2-3 [172 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libpangoft2-1.0-0 armhf 1.46.2-3 [55.7 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libpangocairo-1.0-0 armhf 1.46.2-3 [46.7 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libtcl8.6 armhf 8.6.11+dfsg-1 [894 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.7-1 [44.0 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libjbig0 armhf 2.1-3.1+b2 [27.6 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libwebp6 armhf 0.6.1-2 [228 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libtiff5 armhf 4.2.0-1 [268 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libxft2 armhf 2.3.2-2 [49.3 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf x11-common all 1:7.7+21 [252 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libxss1 armhf 1:1.2.3-1 [17.3 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libtk8.6 armhf 8.6.11-2 [681 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libice6 armhf 2:1.0.10-1 [51.7 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libsm6 armhf 2:1.2.3-1 [32.9 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libxt6 armhf 1:1.2.0-1 [159 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf r-base-core armhf 4.0.3-1 [24.7 MB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libgfortran-10-dev armhf 10.2.1-6+rpi1 [278 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf gfortran-10 armhf 10.2.1-6+rpi1 [7195 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf gfortran armhf 4:10.2.1-1+rpi1 [1428 B]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.9.0-3 [113 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf liblapack-dev armhf 3.9.0-3 [2980 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2+20201114-2 [79.9 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf libncurses-dev armhf 6.2+20201114-2 [288 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf libncurses5-dev armhf 6.2+20201114-2 [936 B]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf libreadline-dev armhf 8.1-1 [121 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo-dev armhf 1:2.0.5-2 [239 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf libjpeg-dev armhf 1:2.0.5-2 [66.2 kB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-16-0 armhf 10.36-2 [197 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-32-0 armhf 10.36-2 [187 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-posix2 armhf 10.36-2 [48.7 kB]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-dev armhf 10.36-2 [626 kB]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf libpcre16-3 armhf 2:8.39-13 [235 kB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf libpcre32-3 armhf 2:8.39-13 [228 kB]
Get:109 http://172.17.0.1/private bullseye-staging/main armhf libpcrecpp0v5 armhf 2:8.39-13 [150 kB]
Get:110 http://172.17.0.1/private bullseye-staging/main armhf libpcre3-dev armhf 2:8.39-13 [566 kB]
Get:111 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:112 http://172.17.0.1/private bullseye-staging/main armhf libpng-dev armhf 1.6.37-3 [277 kB]
Get:113 http://172.17.0.1/private bullseye-staging/main armhf libbz2-dev armhf 1.0.8-4 [28.0 kB]
Get:114 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.5-1.0 [219 kB]
Get:115 http://172.17.0.1/private bullseye-staging/main armhf icu-devtools armhf 67.1-6 [172 kB]
Get:116 http://172.17.0.1/private bullseye-staging/main armhf libicu-dev armhf 67.1-6 [9229 kB]
Get:117 http://172.17.0.1/private bullseye-staging/main armhf libxmuu1 armhf 2:1.1.2-2+b3 [23.4 kB]
Get:118 http://172.17.0.1/private bullseye-staging/main armhf xauth armhf 1:1.1-1 [36.6 kB]
Get:119 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
Get:120 http://172.17.0.1/private bullseye-staging/main armhf r-base-dev all 4.0.3-1 [4484 B]
Get:121 http://172.17.0.1/private bullseye-staging/main armhf libfile-which-perl all 1.23-1 [16.6 kB]
Get:122 http://172.17.0.1/private bullseye-staging/main armhf libswitch-perl all 2.17-2.1 [20.0 kB]
Get:123 http://172.17.0.1/private bullseye-staging/main armhf libencode-locale-perl all 1.05-1.1 [13.2 kB]
Get:124 http://172.17.0.1/private bullseye-staging/main armhf libtimedate-perl all 2.3300-1 [39.2 kB]
Get:125 http://172.17.0.1/private bullseye-staging/main armhf libhttp-date-perl all 6.05-1 [10.4 kB]
Get:126 http://172.17.0.1/private bullseye-staging/main armhf libio-html-perl all 1.001-1.1 [18.6 kB]
Get:127 http://172.17.0.1/private bullseye-staging/main armhf liblwp-mediatypes-perl all 6.04-1 [19.9 kB]
Get:128 http://172.17.0.1/private bullseye-staging/main armhf liburi-perl all 5.07-1 [90.4 kB]
Get:129 http://172.17.0.1/private bullseye-staging/main armhf libhttp-message-perl all 6.27-1 [79.5 kB]
Get:130 http://172.17.0.1/private bullseye-staging/main armhf libparams-util-perl armhf 1.102-1+b1 [24.6 kB]
Get:131 http://172.17.0.1/private bullseye-staging/main armhf libsub-install-perl all 0.928-1.1 [10.8 kB]
Get:132 http://172.17.0.1/private bullseye-staging/main armhf libdata-optlist-perl all 0.110-1.1 [10.8 kB]
Get:133 http://172.17.0.1/private bullseye-staging/main armhf libb-hooks-op-check-perl armhf 0.22-1+b4 [11.0 kB]
Get:134 http://172.17.0.1/private bullseye-staging/main armhf libdynaloader-functions-perl all 0.003-1.1 [12.7 kB]
Get:135 http://172.17.0.1/private bullseye-staging/main armhf libdevel-callchecker-perl armhf 0.008-1+b2 [15.7 kB]
Get:136 http://172.17.0.1/private bullseye-staging/main armhf libparams-classify-perl armhf 0.015-1+b3 [24.6 kB]
Get:137 http://172.17.0.1/private bullseye-staging/main armhf libmodule-runtime-perl all 0.016-1 [19.4 kB]
Get:138 http://172.17.0.1/private bullseye-staging/main armhf libtry-tiny-perl all 0.30-1 [23.3 kB]
Get:139 http://172.17.0.1/private bullseye-staging/main armhf libmodule-implementation-perl all 0.09-1.1 [12.4 kB]
Get:140 http://172.17.0.1/private bullseye-staging/main armhf libpackage-stash-perl all 0.39-1 [21.9 kB]
Get:141 http://172.17.0.1/private bullseye-staging/main armhf libclass-load-perl all 0.25-1 [16.1 kB]
Get:142 http://172.17.0.1/private bullseye-staging/main armhf libclass-load-xs-perl armhf 0.10-1+b4 [14.3 kB]
Get:143 http://172.17.0.1/private bullseye-staging/main armhf libsub-exporter-progressive-perl all 0.001013-1 [7588 B]
Get:144 http://172.17.0.1/private bullseye-staging/main armhf libdevel-globaldestruction-perl all 0.14-1.1 [8312 B]
Get:145 http://172.17.0.1/private bullseye-staging/main armhf libalgorithm-c3-perl all 0.11-1 [11.7 kB]
Get:146 http://172.17.0.1/private bullseye-staging/main armhf libclass-c3-perl all 0.35-1 [22.9 kB]
Get:147 http://172.17.0.1/private bullseye-staging/main armhf libmro-compat-perl all 0.13-1 [12.2 kB]
Get:148 http://172.17.0.1/private bullseye-staging/main armhf libsub-identify-perl armhf 0.14-1+b3 [11.6 kB]
Get:149 http://172.17.0.1/private bullseye-staging/main armhf libdevel-overloadinfo-perl all 0.005-1 [7212 B]
Get:150 http://172.17.0.1/private bullseye-staging/main armhf libdevel-stacktrace-perl all 2.0400-1 [28.6 kB]
Get:151 http://172.17.0.1/private bullseye-staging/main armhf libsub-exporter-perl all 0.987-1 [47.2 kB]
Get:152 http://172.17.0.1/private bullseye-staging/main armhf libeval-closure-perl all 0.14-1 [11.5 kB]
Get:153 http://172.17.0.1/private bullseye-staging/main armhf libdist-checkconflicts-perl all 0.11-1.1 [10.2 kB]
Get:154 http://172.17.0.1/private bullseye-staging/main armhf libmodule-runtime-conflicts-perl all 0.003-1.1 [7156 B]
Get:155 http://172.17.0.1/private bullseye-staging/main armhf libsub-name-perl armhf 0.26-1+b1 [13.2 kB]
Get:156 http://172.17.0.1/private bullseye-staging/main armhf libpackage-deprecationmanager-perl all 0.17-1.1 [16.6 kB]
Get:157 http://172.17.0.1/private bullseye-staging/main armhf libpackage-stash-xs-perl armhf 0.29-1+b2 [18.5 kB]
Get:158 http://172.17.0.1/private bullseye-staging/main armhf libmoose-perl armhf 2.2014-2 [802 kB]
Get:159 http://172.17.0.1/private bullseye-staging/main armhf libvariable-magic-perl armhf 0.62-1+b3 [43.0 kB]
Get:160 http://172.17.0.1/private bullseye-staging/main armhf libb-hooks-endofscope-perl all 0.24-1.1 [18.9 kB]
Get:161 http://172.17.0.1/private bullseye-staging/main armhf libnamespace-clean-perl all 0.27-1 [17.3 kB]
Get:162 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.74.0-1 [301 kB]
Get:163 http://172.17.0.1/private bullseye-staging/main armhf libwww-curl-perl armhf 4.17-7+b1 [58.9 kB]
Get:164 http://172.17.0.1/private bullseye-staging/main armhf libwww-curl-simple-perl all 0.100191-2 [12.5 kB]
Get:165 http://172.17.0.1/private bullseye-staging/main armhf dh-r all 20201129 [41.0 kB]
Get:166 http://172.17.0.1/private bullseye-staging/main armhf libboost1.74-dev armhf 1.74.0-8 [9534 kB]
Get:167 http://172.17.0.1/private bullseye-staging/main armhf libboost-dev armhf 1.74.0.3+b1 [4820 B]
Get:168 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-biocgenerics all 0.36.0-1 [648 kB]
Get:169 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-biobase armhf 2.50.0-1 [2228 kB]
Get:170 http://172.17.0.1/private bullseye-staging/main armhf r-cran-formatr all 1.7-2 [151 kB]
Get:171 http://172.17.0.1/private bullseye-staging/main armhf r-cran-lambda.r all 1.2.4-2 [118 kB]
Get:172 http://172.17.0.1/private bullseye-staging/main armhf r-cran-futile.options all 1.0.1-3 [20.0 kB]
Get:173 http://172.17.0.1/private bullseye-staging/main armhf r-cran-futile.logger all 1.4.3-4 [98.4 kB]
Get:174 http://172.17.0.1/private bullseye-staging/main armhf r-cran-snow all 1:0.4.3-2 [109 kB]
Get:175 http://172.17.0.1/private bullseye-staging/main armhf r-cran-bh all 1.74.0-1 [5196 B]
Get:176 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-biocparallel armhf 1.24.1-1 [1136 kB]
Get:177 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-s4vectors armhf 0.28.1-1 [2038 kB]
Get:178 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-iranges armhf 2.24.1-1 [2205 kB]
Get:179 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-zlibbioc all 1.36.0+dfsg-1 [8824 B]
Get:180 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-xvector armhf 0.30.0-1 [611 kB]
Get:181 http://172.17.0.1/private bullseye-staging/main armhf r-cran-crayon all 1.4.0-1 [143 kB]
Get:182 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-biostrings armhf 2.58.0-1 [14.2 MB]
Get:183 http://172.17.0.1/private bullseye-staging/main armhf r-cran-lattice armhf 0.20-41-1+b1 [1167 kB]
Get:184 http://172.17.0.1/private bullseye-staging/main armhf r-cran-matrix armhf 1.3-2-1 [3565 kB]
Get:185 http://172.17.0.1/private bullseye-staging/main armhf r-cran-matrixstats armhf 0.57.0-1 [574 kB]
Get:186 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-matrixgenerics all 1.2.0-2 [285 kB]
Get:187 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-delayedarray armhf 0.16.1+dfsg-1 [1800 kB]
Get:188 http://172.17.0.1/private bullseye-staging/main armhf r-cran-bitops armhf 1.0-6-5 [23.6 kB]
Get:189 http://172.17.0.1/private bullseye-staging/main armhf r-cran-rcurl armhf 1.98-1.2-1+b1 [788 kB]
Get:190 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-genomeinfodbdata all 1.2.4-1 [10.7 MB]
Get:191 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-genomeinfodb all 1.26.2-1 [3914 kB]
Get:192 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-genomicranges armhf 1.42.0+dfsg-1 [1864 kB]
Get:193 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-summarizedexperiment all 1.20.0+dfsg-1 [1955 kB]
Get:194 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-rhtslib armhf 1.22.0+dfsg-1 [948 kB]
Get:195 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-rsamtools armhf 2.6.0-1 [3572 kB]
Get:196 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-genomicalignments armhf 1.26.0-1 [2214 kB]
Get:197 http://172.17.0.1/private bullseye-staging/main armhf r-cran-hwriter all 1.3.2-4 [162 kB]
Get:198 http://172.17.0.1/private bullseye-staging/main armhf r-cran-jpeg armhf 0.1-8.1-1+b1 [29.5 kB]
Get:199 http://172.17.0.1/private bullseye-staging/main armhf r-cran-png armhf 0.1-7-4 [39.9 kB]
Get:200 http://172.17.0.1/private bullseye-staging/main armhf r-cran-rcolorbrewer all 1.1-2-3 [54.4 kB]
Get:201 http://172.17.0.1/private bullseye-staging/main armhf r-cran-latticeextra all 0.6-29-3 [2192 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 153 MB in 23s (6570 kB/s)
Selecting previously unselected package libuchardet0:armhf.
(Reading database ... 12563 files and directories currently installed.)
Preparing to unpack .../000-libuchardet0_0.0.7-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../001-groff-base_1.22.4-6_armhf.deb ...
Unpacking groff-base (1.22.4-6) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../002-libpipeline1_1.5.3-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.3-1) ...
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invoke-rc.d: could not determine current runlevel
invoke-rc.d: policy-rc.d denied execution of start.
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Setting up libfreetype6:armhf (2.10.4+dfsg-1) ...
Setting up liblapack-dev:armhf (3.9.0-3) ...
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 gfortran-10 (10.2.1-6+rpi1) ...
Setting up libdata-optlist-perl (0.110-1.1) ...
Setting up autoconf (2.69-14) ...
Setting up dh-strip-nondeterminism (1.11.0-1) ...
Setting up dwz (0.13+20210126-1) ...
Setting up groff-base (1.22.4-6) ...
Setting up libncurses5-dev:armhf (6.2+20201114-2) ...
Setting up libcurl4:armhf (7.74.0-1) ...
Setting up libx11-6:armhf (2:1.7.0-2) ...
Setting up libharfbuzz0b:armhf (2.7.4-1) ...
Setting up libfontconfig1:armhf (2.13.1-4.2) ...
Setting up libmro-compat-perl (0.13-1) ...
Setting up libsm6:armhf (2:1.2.3-1) ...
Setting up libxmuu1:armhf (2:1.1.2-2+b3) ...
Setting up libsub-exporter-perl (0.987-1) ...
Setting up libhttp-message-perl (6.27-1) ...
Setting up libeval-closure-perl (0.14-1) ...
Setting up automake (1:1.16.3-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up fontconfig (2.13.1-4.2) ...
Regenerating fonts cache... done.
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libparams-classify-perl (0.015-1+b3) ...
Setting up libpango-1.0-0:armhf (1.46.2-3) ...
Setting up libxext6:armhf (2:1.3.3-1.1) ...
Setting up libwww-curl-perl (4.17-7+b1) ...
Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up gfortran (4:10.2.1-1+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 libcairo2:armhf (1.16.0-5) ...
Setting up libmodule-runtime-perl (0.016-1) ...
Setting up libdist-checkconflicts-perl (0.11-1.1) ...
Setting up libxt6:armhf (1:1.2.0-1) ...
Setting up xauth (1:1.1-1) ...
Setting up libxss1:armhf (1:1.2.3-1) ...
Setting up libpangoft2-1.0-0:armhf (1.46.2-3) ...
Setting up libpangocairo-1.0-0:armhf (1.46.2-3) ...
Setting up libxft2:armhf (2.3.2-2) ...
Setting up libmodule-implementation-perl (0.09-1.1) ...
Setting up libpackage-stash-perl (0.39-1) ...
Setting up libtk8.6:armhf (8.6.11-2) ...
Setting up libmodule-runtime-conflicts-perl (0.003-1.1) ...
Setting up libclass-load-perl (0.25-1) ...
Setting up r-base-core (4.0.3-1) ...
Creating config file /etc/R/Renviron with new version
Setting up r-cran-crayon (1.4.0-1) ...
Setting up r-cran-futile.options (1.0.1-3) ...
Setting up r-cran-lattice (0.20-41-1+b1) ...
Setting up r-cran-formatr (1.7-2) ...
Setting up libpackage-deprecationmanager-perl (0.17-1.1) ...
Setting up libdevel-overloadinfo-perl (0.005-1) ...
Setting up libclass-load-xs-perl (0.10-1+b4) ...
Setting up r-cran-jpeg (0.1-8.1-1+b1) ...
Setting up libb-hooks-endofscope-perl (0.24-1.1) ...
Setting up r-bioc-genomeinfodbdata (1.2.4-1) ...
Setting up r-bioc-biocgenerics (0.36.0-1) ...
Setting up r-cran-matrixstats (0.57.0-1) ...
Setting up r-base-dev (4.0.3-1) ...
Setting up r-bioc-matrixgenerics (1.2.0-2) ...
Setting up libmoose-perl (2.2014-2) ...
Setting up r-cran-lambda.r (1.2.4-2) ...
Setting up r-cran-snow (1:0.4.3-2) ...
Setting up r-cran-bitops (1.0-6-5) ...
Setting up r-bioc-zlibbioc (1.36.0+dfsg-1) ...
Setting up r-cran-png (0.1-7-4) ...
Setting up r-bioc-biobase (2.50.0-1) ...
Setting up r-cran-hwriter (1.3.2-4) ...
Setting up r-cran-rcolorbrewer (1.1-2-3) ...
Setting up r-bioc-s4vectors (0.28.1-1) ...
Setting up r-cran-futile.logger (1.4.3-4) ...
Setting up libnamespace-clean-perl (0.27-1) ...
Setting up r-cran-matrix (1.3-2-1) ...
Setting up r-bioc-iranges (2.24.1-1) ...
Setting up r-cran-rcurl (1.98-1.2-1+b1) ...
Setting up r-bioc-delayedarray (0.16.1+dfsg-1) ...
Setting up r-bioc-biocparallel (1.24.1-1) ...
Setting up libwww-curl-simple-perl (0.100191-2) ...
Setting up r-bioc-rhtslib (1.22.0+dfsg-1) ...
Setting up r-cran-latticeextra (0.6-29-3) ...
Setting up r-bioc-genomeinfodb (1.26.2-1) ...
Setting up r-bioc-xvector (0.30.0-1) ...
Setting up r-bioc-genomicranges (1.42.0+dfsg-1) ...
Setting up r-bioc-biostrings (2.58.0-1) ...
Setting up r-bioc-rsamtools (2.6.0-1) ...
Setting up r-bioc-summarizedexperiment (1.20.0+dfsg-1) ...
Setting up r-bioc-genomicalignments (1.26.0-1) ...
Setting up debhelper (13.3.3) ...
Setting up dh-autoreconf (19) ...
Setting up dh-r (20201129) ...
Setting up sbuild-build-depends-r-bioc-shortread-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-9+rpi1) ...
Processing triggers for ca-certificates (20210119) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.35.1-7+rpi1 dpkg-dev_1.20.7.1+rpi1 g++-10_10.2.1-6+rpi1 gcc-10_10.2.1-6+rpi1 libc6-dev_2.31-9+rpi1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 linux-libc-dev_5.10.9-1+rpi1
Package versions: adduser_3.118 apt_2.1.18 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_11+rpi1 base-passwd_3.5.48 bash_5.1-2 binutils_2.35.1-7+rpi1 binutils-arm-linux-gnueabihf_2.35.1-7+rpi1 binutils-common_2.35.1-7+rpi1 bsdextrautils_2.36.1-6 bsdutils_1:2.36.1-6 build-essential_12.9 bzip2_1.0.8-4 ca-certificates_20210119 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.2.1-6+rpi1 dash_0.5.11+git20200708+dd9ef66-5 dctrl-tools_2.24-3 debconf_1.5.74 debhelper_13.3.3 debianutils_4.11.2 dh-autoreconf_19 dh-r_20201129 dh-strip-nondeterminism_1.11.0-1 diffutils_1:3.7-5 dirmngr_2.2.20-1 dpkg_1.20.7.1+rpi1 dpkg-dev_1.20.7.1+rpi1 dwz_0.13+20210126-1 e2fsprogs_1.45.7-1 fakeroot_1.25.3-1.1 fdisk_2.36.1-6 file_1:5.39-3 findutils_4.8.0-1 fontconfig_2.13.1-4.2 fontconfig-config_2.13.1-4.2 fonts-dejavu-core_2.37-2 g++_4:10.2.1-1+rpi1 g++-10_10.2.1-6+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.2.1-6+rpi1 gcc-10-base_10.2.1-6+rpi1 gettext_0.21-4 gettext-base_0.21-4 gfortran_4:10.2.1-1+rpi1 gfortran-10_10.2.1-6+rpi1 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.6-1 groff-base_1.22.4-6 gzip_1.10-2 hostname_3.23 icu-devtools_67.1-6 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20200821-2 krb5-locales_1.18.3-4 libacl1_2.2.53-10 libalgorithm-c3-perl_0.11-1 libapt-pkg6.0_2.1.18 libarchive-zip-perl_1.68-1 libasan6_10.2.1-6+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.1-6+rpi1 libattr1_1:2.4.48-6 libaudit-common_1:3.0-2 libaudit1_1:3.0-2 libb-hooks-endofscope-perl_0.24-1.1 libb-hooks-op-check-perl_0.22-1+b4 libbinutils_2.35.1-7+rpi1 libblas-dev_3.9.0-3 libblas3_3.9.0-3 libblkid1_2.36.1-6 libboost-dev_1.74.0.3+b1 libboost1.74-dev_1.74.0-8 libbrotli1_1.0.9-2+b1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-4 libbz2-dev_1.0.8-4 libc-bin_2.31-9+rpi1 libc-dev-bin_2.31-9+rpi1 libc6_2.31-9+rpi1 libc6-dev_2.31-9+rpi1 libcairo2_1.16.0-5 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_10.2.1-6+rpi1 libclass-c3-perl_0.35-1 libclass-load-perl_0.25-1 libclass-load-xs-perl_0.10-1+b4 libcom-err2_1.45.7-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-7+rpi1 libctf0_2.35.1-7+rpi1 libcurl3-gnutls_7.74.0-1 libcurl4_7.74.0-1 libdata-optlist-perl_0.110-1.1 libdatrie1_0.2.13-1+b1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.256 libdebhelper-perl_13.3.3 libdeflate0_1.7-1 libdevel-callchecker-perl_0.008-1+b2 libdevel-globaldestruction-perl_0.14-1.1 libdevel-overloadinfo-perl_0.005-1 libdevel-stacktrace-perl_2.0400-1 libdist-checkconflicts-perl_0.11-1.1 libdpkg-perl_1.20.7.1+rpi1 libdynaloader-functions-perl_0.003-1.1 libelf1_0.182+20210205-1 libencode-locale-perl_1.05-1.1 libeval-closure-perl_0.14-1 libexpat1_2.2.10-1 libext2fs2_1.45.7-1 libfakeroot_1.25.3-1.1 libfdisk1_2.36.1-6 libffi7_3.3-5 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liblwp-mediatypes-perl_6.04-1 liblz4-1_1.9.3-1+rpi1 liblzma-dev_5.2.5-1.0 liblzma5_5.2.5-1.0 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmodule-implementation-perl_0.09-1.1 libmodule-runtime-conflicts-perl_0.003-1.1 libmodule-runtime-perl_0.016-1 libmoose-perl_2.2014-2 libmount1_2.36.1-6 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libmro-compat-perl_0.13-1 libnamespace-clean-perl_0.27-1 libncurses-dev_6.2+20201114-2 libncurses5-dev_6.2+20201114-2 libncurses6_6.2+20201114-2 libncursesw6_6.2+20201114-2 libnettle8_3.6-2 libnghttp2-14_1.42.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnss-nis_3.1-4 libnss-nisplus_1.3-4 libp11-kit0_0.23.22-1 libpackage-deprecationmanager-perl_0.17-1.1 libpackage-stash-perl_0.39-1 libpackage-stash-xs-perl_0.29-1+b2 libpam-cap_1:2.44-1 libpam-modules_1.4.0-2 libpam-modules-bin_1.4.0-2 libpam-runtime_1.4.0-2 libpam0g_1.4.0-2 libpango-1.0-0_1.46.2-3 libpangocairo-1.0-0_1.46.2-3 libpangoft2-1.0-0_1.46.2-3 libpaper-utils_1.1.28 libpaper1_1.1.28 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libsub-name-perl_0.26-1+b1 libsub-override-perl_0.09-2 libswitch-perl_2.17-2.1 libsystemd0_247.2-5+rpi1 libtasn1-6_4.16.0-2 libtcl8.6_8.6.11+dfsg-1 libthai-data_0.1.28-3 libthai0_0.1.28-3 libtiff5_4.2.0-1 libtimedate-perl_2.3300-1 libtinfo6_6.2+20201114-2 libtirpc-common_1.3.1-1 libtirpc-dev_1.3.1-1 libtirpc3_1.3.1-1 libtk8.6_8.6.11-2 libtool_2.4.6-15 libtry-tiny-perl_0.30-1 libubsan1_10.2.1-6+rpi1 libuchardet0_0.0.7-1 libudev1_247.2-5+rpi1 libunistring2_0.9.10-4 liburi-perl_5.07-1 libuuid1_2.36.1-6 libvariable-magic-perl_0.62-1+b3 libwebp6_0.6.1-2 libwww-curl-perl_4.17-7+b1 libwww-curl-simple-perl_0.100191-2 libx11-6_2:1.7.0-2 libx11-data_2:1.7.0-2 libxau6_1:1.0.9-1 libxcb-render0_1.14-3 libxcb-shm0_1.14-3 libxcb1_1.14-3 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1.1 libxft2_2.3.2-2 libxml2_2.9.10+dfsg-6.3 libxmuu1_2:1.1.2-2+b3 libxrender1_1:0.9.10-1 libxss1_1:1.2.3-1 libxt6_1:1.2.0-1 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-1 linux-libc-dev_5.10.9-1+rpi1 login_1:4.8.1-1 logsave_1.45.7-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.36.1-6 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 netbase_6.2 openssl_1.1.1i-3 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-2 perl-base_5.32.1-2 perl-modules-5.32_5.32.1-2 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 r-base-core_4.0.3-1 r-base-dev_4.0.3-1 r-bioc-biobase_2.50.0-1 r-bioc-biocgenerics_0.36.0-1 r-bioc-biocparallel_1.24.1-1 r-bioc-biostrings_2.58.0-1 r-bioc-delayedarray_0.16.1+dfsg-1 r-bioc-genomeinfodb_1.26.2-1 r-bioc-genomeinfodbdata_1.2.4-1 r-bioc-genomicalignments_1.26.0-1 r-bioc-genomicranges_1.42.0+dfsg-1 r-bioc-iranges_2.24.1-1 r-bioc-matrixgenerics_1.2.0-2 r-bioc-rhtslib_1.22.0+dfsg-1 r-bioc-rsamtools_2.6.0-1 r-bioc-s4vectors_0.28.1-1 r-bioc-summarizedexperiment_1.20.0+dfsg-1 r-bioc-xvector_0.30.0-1 r-bioc-zlibbioc_1.36.0+dfsg-1 r-cran-bh_1.74.0-1 r-cran-bitops_1.0-6-5 r-cran-crayon_1.4.0-1 r-cran-formatr_1.7-2 r-cran-futile.logger_1.4.3-4 r-cran-futile.options_1.0.1-3 r-cran-hwriter_1.3.2-4 r-cran-jpeg_0.1-8.1-1+b1 r-cran-lambda.r_1.2.4-2 r-cran-lattice_0.20-41-1+b1 r-cran-latticeextra_0.6-29-3 r-cran-matrix_1.3-2-1 r-cran-matrixstats_0.57.0-1 r-cran-png_0.1-7-4 r-cran-rcolorbrewer_1.1-2-3 r-cran-rcurl_1.98-1.2-1+b1 r-cran-snow_1:0.4.3-2 raspbian-archive-keyring_20120528.2 readline-common_8.1-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-shortread-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.14 sysvinit-utils_2.96-5 tar_1.32+dfsg-1+rpi1 tzdata_2021a-1 ucf_3.0043 unzip_6.0-26 util-linux_2.36.1-6 x11-common_1:7.7+21 xauth_1:1.1-1 xdg-utils_1.1.3-2 xz-utils_5.2.5-1.0 zip_3.0-12 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.b9KR_eKI/trustedkeys.kbx': General error
gpgv: Signature made Sun Feb 7 11:37:30 2021 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./r-bioc-shortread_1.48.0-2.dsc
dpkg-source: info: extracting r-bioc-shortread in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking r-bioc-shortread_1.48.0.orig.tar.gz
dpkg-source: info: unpacking r-bioc-shortread_1.48.0-2.debian.tar.xz
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-72726a01-c970-42c6-9f3c-16870f23760c
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package r-bioc-shortread
dpkg-buildpackage: info: source version 1.48.0-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean --buildsystem R
dh_auto_clean -O--buildsystem=R
dh_autoreconf_clean -O--buildsystem=R
dh_clean -O--buildsystem=R
debian/rules binary-arch
dh binary-arch --buildsystem R
dh_update_autotools_config -a -O--buildsystem=R
dh_autoreconf -a -O--buildsystem=R
dh_auto_configure -a -O--buildsystem=R
dh_auto_build -a -O--buildsystem=R
dh_auto_test -a -O--buildsystem=R
create-stamp debian/debhelper-build-stamp
dh_testroot -a -O--buildsystem=R
dh_prep -a -O--buildsystem=R
dh_auto_install -a -O--buildsystem=R
I: R packages needed for DEP8: runit
I: R Package: ShortRead Version: 1.48.0
I: Building using R version 4.0.3-1
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Sun, 07 Feb 2021 12:28:32 +0100
mkdir -p /<<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='Sun, 07 Feb 2021 12:28:32 +0100'"
* installing *source* package 'ShortRead' ...
** using staged installation
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking for gzeof in -lz... yes
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking size of unsigned long... 4
configure: creating ./config.status
config.status: creating src/Makevars
** libs
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-sMz9ls/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-sMz9ls/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-sMz9ls/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-sMz9ls/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-sMz9ls/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-sMz9ls/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c alphabet.c -o alphabet.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-sMz9ls/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c count.c -o count.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-sMz9ls/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c io.c -o io.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-sMz9ls/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c io_bowtie.c -o io_bowtie.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-sMz9ls/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c io_soap.c -o io_soap.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=4 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-sMz9ls/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c readBfaToc.cc -o readBfaToc.o
readBfaToc.cc: In function 'SEXPREC* readBfaToc(SEXP)':
readBfaToc.cc:35:19: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
35 | (void) fread( seq_name, sizeof(char), name_len, fp );
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readBfaToc.cc:36:19: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
36 | (void) fread( &seq_ori_len, sizeof(int), 1, fp );
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readBfaToc.cc:37:19: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
37 | (void) fread( &seq_len, sizeof(int), 1, fp );
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=4 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-sMz9ls/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c read_maq_map.cc -o read_maq_map.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-sMz9ls/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sampler.c -o sampler.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-sMz9ls/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c trim.c -o trim.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-sMz9ls/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c util.c -o util.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include' -I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-sMz9ls/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xsnap.c -o xsnap.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-z,relro -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o count.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -lz -fopenmp -L/usr/lib/R/lib -lR
make[1]: Leaving directory '/<<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-1.48.0/00new/ShortRead/libs
** R
** inst
** byte-compile and prepare package for lazy loading
code for methods in class "ShortReadFile" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
code for methods in class "FastqFileReader" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
code for methods in class "QAData" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
code for methods in class "Snapshot" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
code for methods in class "SpTrellis" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
code for methods in class "FastqSampler" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
code for methods in class "FastqStreamer" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ShortRead)
I: Using r-bioc-biocgenerics for Depends:BiocGenerics (>= 0.23.3)
I: Using r-bioc-biocparallel for Depends:BiocParallel
I: Using r-bioc-biostrings for Depends:Biostrings (>= 2.47.6)
I: Using r-bioc-rsamtools for Depends:Rsamtools (>= 1.31.2)
I: Using r-bioc-genomicalignments for Depends:GenomicAlignments (>= 1.15.6)
I: Using r-cran-runit for Recommends:runit
I: Using r-bioc-biocstyle for Suggests:BiocStyle
I: Using r-bioc-biomart for Suggests:biomaRt
I: Using r-bioc-genomicfeatures for Suggests:GenomicFeatures
W: Cannot find a debian package for Suggests:yeastNagalakshmi
I: Using r-bioc-biobase for Imports:Biobase
I: Using r-bioc-s4vectors for Imports:S4Vectors (>= 0.17.25)
I: Using r-bioc-iranges for Imports:IRanges (>= 2.13.12)
I: Using r-bioc-genomeinfodb for Imports:GenomeInfoDb (>= 1.15.2)
I: Using r-bioc-genomicranges for Imports:GenomicRanges (>= 1.31.8)
I: Using r-cran-hwriter for Imports:hwriter
I: Using r-bioc-zlibbioc for Imports:zlibbioc
I: Using r-cran-lattice for Imports:lattice
I: Using r-cran-latticeextra for Imports:latticeExtra
I: Using r-bioc-s4vectors for LinkingTo:S4Vectors
I: Using r-bioc-iranges for LinkingTo:IRanges
I: Using r-bioc-xvector for LinkingTo:XVector
I: Using r-bioc-biostrings for LinkingTo:Biostrings
I: Using r-bioc-rhtslib for LinkingTo:Rhtslib
I: Using r-bioc-zlibbioc for LinkingTo:zlibbioc
I: BioConductor API version: r-api-bioc-3.12
I: Use r-bioc-shortread as Debian binary package for variables substitution
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 -a -O--buildsystem=R
dh_strip -a -a -O--buildsystem=R
dh_makeshlibs -a -a -O--buildsystem=R
dh_shlibdeps -a -a -O--buildsystem=R
dh_installdeb -a -O--buildsystem=R
dh_gencontrol -a -O--buildsystem=R
dh_md5sums -a -O--buildsystem=R
dh_builddeb -a -O--buildsystem=R
dpkg-deb: building package 'r-bioc-shortread-dbgsym' in '../r-bioc-shortread-dbgsym_1.48.0-2_armhf.deb'.
dpkg-deb: building package 'r-bioc-shortread' in '../r-bioc-shortread_1.48.0-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../r-bioc-shortread_1.48.0-2_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 2021-02-09T05:38:49Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
r-bioc-shortread_1.48.0-2_armhf.changes:
----------------------------------------
Format: 1.8
Date: Sun, 07 Feb 2021 12:28:32 +0100
Source: r-bioc-shortread
Binary: r-bioc-shortread r-bioc-shortread-dbgsym
Architecture: armhf
Version: 1.48.0-2
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <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
Closes: 980082
Changes:
r-bioc-shortread (1.48.0-2) unstable; urgency=medium
.
* Exclude failing test on non-Intel architectures
Closes: #980082
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Checksums-Sha256:
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Files:
151824a5b95e5b0406cb723479779519 153504 debug optional r-bioc-shortread-dbgsym_1.48.0-2_armhf.deb
e92deed61b1923d643fddf476faac76a 10633 gnu-r optional r-bioc-shortread_1.48.0-2_armhf.buildinfo
f034d69dc853418be05bf20b418c8700 5058952 gnu-r optional r-bioc-shortread_1.48.0-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
r-bioc-shortread-dbgsym_1.48.0-2_armhf.deb
------------------------------------------
new Debian package, version 2.0.
size 153504 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: 1.48.0-2
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 (= 1.48.0-2)
Section: debug
Priority: optional
Description: debug symbols for r-bioc-shortread
Build-Ids: 5a6476e47f0e92fecfadb2aeeff1200e0143dc03
drwxr-xr-x root/root 0 2021-02-07 11:28 ./
drwxr-xr-x root/root 0 2021-02-07 11:28 ./usr/
drwxr-xr-x root/root 0 2021-02-07 11:28 ./usr/lib/
drwxr-xr-x root/root 0 2021-02-07 11:28 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-02-07 11:28 ./usr/lib/debug/.build-id/
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r-bioc-shortread_1.48.0-2_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 5058952 bytes: control archive=4128 bytes.
1331 bytes, 18 lines control
10719 bytes, 112 lines md5sums
Package: r-bioc-shortread
Version: 1.48.0-2
Architecture: armhf
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Installed-Size: 7373
Depends: r-base-core (>= 4.0.3-1), r-api-4.0, r-api-bioc-3.12, 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 (>= 5.2), zlib1g (>= 1:1.1.4)
Recommends: r-cran-runit
Suggests: r-bioc-biocstyle, 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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Build Architecture: armhf
Build-Space: 21676
Build-Time: 162
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 493
Job: r-bioc-shortread_1.48.0-2
Machine Architecture: armhf
Package: r-bioc-shortread
Package-Time: 673
Source-Version: 1.48.0-2
Space: 21676
Status: successful
Version: 1.48.0-2
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Finished at 2021-02-09T05:38:49Z
Build needed 00:11:13, 21676k disk space