r-bioc-shortread →
1.44.3-1 →
armhf → 2020-02-16 06:17:10
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| r-bioc-shortread 1.44.3-1 (armhf) Sun, 16 Feb 2020 06:01:04 +0000 |
+==============================================================================+
Package: r-bioc-shortread
Version: 1.44.3-1
Source Version: 1.44.3-1
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-be11c592-5319-4406-9667-aefa049e463a' 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 [11.5 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.7 MB]
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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 5192 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main r-bioc-shortread 1.44.3-1 (dsc) [2496 B]
Get:2 http://172.17.0.1/private bullseye-staging/main r-bioc-shortread 1.44.3-1 (tar) [5184 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main r-bioc-shortread 1.44.3-1 (diff) [5184 B]
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Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/r-bioc-shortread-oWru5E/r-bioc-shortread-1.44.3' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-shortread-oWru5E' 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-VFWU7J/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-VFWU7J/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-VFWU7J/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-VFWU7J/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-VFWU7J/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-VFWU7J/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-VFWU7J/apt_archive ./ Sources [349 B]
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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:
libpam-cap netbase
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 7 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-VFWU7J/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12214 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 (= 12), 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
Filtered Build-Depends: debhelper-compat (= 12), 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
dpkg-deb: building package 'sbuild-build-depends-r-bioc-shortread-dummy' in '/<<BUILDDIR>>/resolver-VFWU7J/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-VFWU7J/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-VFWU7J/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-VFWU7J/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-VFWU7J/apt_archive ./ Sources [661 B]
Get:5 copy:/<<BUILDDIR>>/resolver-VFWU7J/apt_archive ./ Packages [746 B]
Fetched 2740 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:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils 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-9 groff-base icu-devtools intltool-debian libarchive-zip-perl
libblas-dev libblas3 libboost-dev libboost1.67-dev libbrotli1 libbsd0
libbz2-dev libcairo2 libcroco3 libcurl4 libdatrie1 libdebhelper-perl libelf1
libexpat1 libfile-stripnondeterminism-perl libfile-which-perl libfontconfig1
libfreetype6 libfribidi0 libgfortran-9-dev libgfortran5 libglib2.0-0
libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu-dev libicu63
libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 liblzma-dev
libmagic-mgc libmagic1 libncurses-dev libncurses5-dev libncurses6
libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
libpaper-utils libpaper1 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 libssl1.1 libsub-override-perl
libswitch-perl libtcl8.6 libthai-data libthai0 libtiff5 libtinfo5 libtk8.6
libtool libuchardet0 libwebp6 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-rsamtools r-bioc-s4vectors r-bioc-summarizedexperiment
r-bioc-xvector r-bioc-zlibbioc r-cran-bh r-cran-bitops 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
sensible-utils ucf unzip x11-common xauth xdg-utils zip zlib1g zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation debtags dh-make gettext-doc libasprintf-dev libgettextpo-dev
gfortran-doc gfortran-9-doc libcoarrays-dev groff liblapack-doc libboost-doc
libboost1.67-doc libboost-atomic1.67-dev libboost-chrono1.67-dev
libboost-container1.67-dev libboost-context1.67-dev
libboost-contract1.67-dev libboost-coroutine1.67-dev
libboost-date-time1.67-dev libboost-exception1.67-dev libboost-fiber1.67-dev
libboost-filesystem1.67-dev libboost-graph1.67-dev
libboost-graph-parallel1.67-dev libboost-iostreams1.67-dev
libboost-locale1.67-dev libboost-log1.67-dev libboost-math1.67-dev
libboost-mpi1.67-dev libboost-mpi-python1.67-dev libboost-numpy1.67-dev
libboost-program-options1.67-dev libboost-python1.67-dev
libboost-random1.67-dev libboost-regex1.67-dev
libboost-serialization1.67-dev libboost-signals1.67-dev
libboost-stacktrace1.67-dev libboost-system1.67-dev libboost-test1.67-dev
libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev
libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev
krb5-doc krb5-user icu-doc liblzma-doc ncurses-doc readline-doc tcl8.6 tk8.6
libtool-doc gcj-jdk 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-rtracklayer
r-bioc-edger r-bioc-gviz r-bioc-annotationhub r-bioc-graph r-cran-rmarkdown
r-cran-jsonlite r-bioc-rhdf5 r-cran-testthat 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 libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs krb5-locales 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-genefilter r-bioc-shortread r-cran-digest r-bioc-annotate
r-cran-testit r-cran-codetools r-cran-survival r-cran-testthat
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 bsdmainutils 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-9 groff-base icu-devtools intltool-debian libarchive-zip-perl
libblas-dev libblas3 libboost-dev libboost1.67-dev libbrotli1 libbsd0
libbz2-dev libcairo2 libcroco3 libcurl4 libdatrie1 libdebhelper-perl libelf1
libexpat1 libfile-stripnondeterminism-perl libfile-which-perl libfontconfig1
libfreetype6 libfribidi0 libgfortran-9-dev libgfortran5 libglib2.0-0
libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu-dev libicu63
libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 liblzma-dev
libmagic-mgc libmagic1 libncurses-dev libncurses5-dev libncurses6
libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
libpaper-utils libpaper1 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 libssl1.1 libsub-override-perl
libswitch-perl libtcl8.6 libthai-data libthai0 libtiff5 libtinfo5 libtk8.6
libtool libuchardet0 libwebp6 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-rsamtools r-bioc-s4vectors r-bioc-summarizedexperiment
r-bioc-xvector r-bioc-zlibbioc r-cran-bh r-cran-bitops 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 sensible-utils ucf unzip
x11-common xauth xdg-utils zip zlib1g-dev
The following packages will be upgraded:
zlib1g
1 upgraded, 165 newly installed, 0 to remove and 6 not upgraded.
Need to get 149 MB of archives.
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Get:13 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-4 [66.9 kB]
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Get:15 http://172.17.0.1/private bullseye-staging/main armhf libswitch-perl all 2.17-2 [20.5 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf ucf all 3.0038+nmu1 [69.0 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
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Get:34 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
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Get:36 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.4-1+rpi1 [1137 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-8 [593 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.9 [994 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf zip armhf 3.0-11 [212 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf unzip armhf 6.0-25 [152 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libpaper1 armhf 1.1.28 [20.5 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libpaper-utils armhf 1.1.28 [17.7 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf xdg-utils all 1.1.3-1 [73.3 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-1 [108 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libpng16-16 armhf 1.6.37-2 [274 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libfreetype6 armhf 2.10.1-2 [330 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf fonts-dejavu-core all 2.37-1 [1068 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf fontconfig-config all 2.13.1-2 [280 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libfontconfig1 armhf 2.13.1-2 [327 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libpixman-1-0 armhf 0.36.0-1 [458 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.13.1-2 [132 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.6.8-1 [298 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.6.8-1 [691 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libxcb-render0 armhf 1.13.1-2 [108 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libxcb-shm0 armhf 1.13.1-2 [99.3 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1+b2 [47.8 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libcairo2 armhf 1.16.0-4 [599 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.7-6 [261 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6.1-2 [14.5 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-6+b1 [61.5 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-6+b1 [112 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-6+b1 [316 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-6+b1 [134 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.40.0-1+b2 [74.2 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b1 [54.3 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libcurl4 armhf 7.67.0-2 [286 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo armhf 1:1.5.2-2+b1 [110 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 9.2.1-25+rpi1 [231 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-1 [1597 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf fontconfig armhf 2.13.1-2 [404 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libfribidi0 armhf 1.0.7-1.1 [62.8 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libthai-data all 0.1.28-3 [170 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libdatrie1 armhf 0.2.12-3+b1 [36.4 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libthai0 armhf 0.1.28-3 [51.0 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libpango-1.0-0 armhf 1.42.4-7+b1 [168 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libgraphite2-3 armhf 1.3.13-11 [70.1 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libharfbuzz0b armhf 2.6.4-1+rpi1 [1308 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libpangoft2-1.0-0 armhf 1.42.4-7+b1 [62.2 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libpangocairo-1.0-0 armhf 1.42.4-7+b1 [51.9 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libtcl8.6 armhf 8.6.10+dfsg-1 [886 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libjbig0 armhf 2.1-3.1+b2 [27.6 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf libwebp6 armhf 0.6.1-2 [228 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libtiff5 armhf 4.1.0+git191117-2 [250 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libxft2 armhf 2.3.2-2 [49.3 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf x11-common all 1:7.7+20 [252 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf libxss1 armhf 1:1.2.3-1 [17.3 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf libtk8.6 armhf 8.6.10-1 [678 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf libice6 armhf 2:1.0.9-2 [51.6 kB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf libsm6 armhf 2:1.2.3-1 [32.9 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf libxt6 armhf 1:1.1.5-1+b3 [156 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf r-base-core armhf 3.6.2-2 [24.3 MB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf libgfortran-9-dev armhf 9.2.1-25+rpi1 [279 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf gfortran-9 armhf 9.2.1-25+rpi1 [8095 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf gfortran armhf 4:9.2.1-3.1+rpi1 [1440 B]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.9.0-1 [113 kB]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf liblapack-dev armhf 3.9.0-1 [2981 kB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.1+20191019-1 [79.5 kB]
Get:109 http://172.17.0.1/private bullseye-staging/main armhf libncurses-dev armhf 6.1+20191019-1 [284 kB]
Get:110 http://172.17.0.1/private bullseye-staging/main armhf libncurses5-dev armhf 6.1+20191019-1 [940 B]
Get:111 http://172.17.0.1/private bullseye-staging/main armhf libreadline-dev armhf 8.0-3 [114 kB]
Get:112 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.2-2+b1 [179 kB]
Get:113 http://172.17.0.1/private bullseye-staging/main armhf libjpeg-dev all 1:1.5.2-2 [57.5 kB]
Get:114 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-16-0 armhf 10.34-7 [190 kB]
Get:115 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-32-0 armhf 10.34-7 [181 kB]
Get:116 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-posix2 armhf 10.34-7 [44.7 kB]
Get:117 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-dev armhf 10.34-7 [614 kB]
Get:118 http://172.17.0.1/private bullseye-staging/main armhf libpcre16-3 armhf 2:8.39-12 [234 kB]
Get:119 http://172.17.0.1/private bullseye-staging/main armhf libpcre32-3 armhf 2:8.39-12 [227 kB]
Get:120 http://172.17.0.1/private bullseye-staging/main armhf libpcrecpp0v5 armhf 2:8.39-12 [150 kB]
Get:121 http://172.17.0.1/private bullseye-staging/main armhf libpcre3-dev armhf 2:8.39-12 [564 kB]
Get:122 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1.2 [203 kB]
Get:123 http://172.17.0.1/private bullseye-staging/main armhf libpng-dev armhf 1.6.37-2 [276 kB]
Get:124 http://172.17.0.1/private bullseye-staging/main armhf libbz2-dev armhf 1.0.8-2 [27.7 kB]
Get:125 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:126 http://172.17.0.1/private bullseye-staging/main armhf icu-devtools armhf 63.2-2 [163 kB]
Get:127 http://172.17.0.1/private bullseye-staging/main armhf libicu-dev armhf 63.2-2 [8846 kB]
Get:128 http://172.17.0.1/private bullseye-staging/main armhf libxmuu1 armhf 2:1.1.2-2+b3 [23.4 kB]
Get:129 http://172.17.0.1/private bullseye-staging/main armhf xauth armhf 1:1.0.10-1 [36.4 kB]
Get:130 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29-6 [59.8 kB]
Get:131 http://172.17.0.1/private bullseye-staging/main armhf r-base-dev all 3.6.2-2 [4488 B]
Get:132 http://172.17.0.1/private bullseye-staging/main armhf libfile-which-perl all 1.23-1 [16.6 kB]
Get:133 http://172.17.0.1/private bullseye-staging/main armhf dh-r all 20200104 [38.2 kB]
Get:134 http://172.17.0.1/private bullseye-staging/main armhf libboost1.67-dev armhf 1.67.0-17 [8389 kB]
Get:135 http://172.17.0.1/private bullseye-staging/main armhf libboost-dev armhf 1.67.0.2+b11 [4464 B]
Get:136 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-biocgenerics all 0.32.0-1 [639 kB]
Get:137 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-biobase armhf 2.46.0-1 [2229 kB]
Get:138 http://172.17.0.1/private bullseye-staging/main armhf r-cran-formatr all 1.7-1 [152 kB]
Get:139 http://172.17.0.1/private bullseye-staging/main armhf r-cran-lambda.r all 1.2.4-1 [119 kB]
Get:140 http://172.17.0.1/private bullseye-staging/main armhf r-cran-futile.options all 1.0.1-2 [19.8 kB]
Get:141 http://172.17.0.1/private bullseye-staging/main armhf r-cran-futile.logger all 1.4.3-3 [102 kB]
Get:142 http://172.17.0.1/private bullseye-staging/main armhf r-cran-snow all 1:0.4.3-1 [108 kB]
Get:143 http://172.17.0.1/private bullseye-staging/main armhf r-cran-bh all 1.66.0-1 [5072 B]
Get:144 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-biocparallel armhf 1.20.1-1 [1070 kB]
Get:145 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-s4vectors armhf 0.24.3-1 [1940 kB]
Get:146 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-iranges armhf 2.20.2-1 [2215 kB]
Get:147 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-zlibbioc all 1.32.0+dfsg-1 [8780 B]
Get:148 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-xvector armhf 0.26.0-1 [610 kB]
Get:149 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-biostrings armhf 2.54.0-1 [14.1 MB]
Get:150 http://172.17.0.1/private bullseye-staging/main armhf r-cran-matrixstats armhf 0.55.0-1 [576 kB]
Get:151 http://172.17.0.1/private bullseye-staging/main armhf r-cran-lattice armhf 0.20-38-1 [1120 kB]
Get:152 http://172.17.0.1/private bullseye-staging/main armhf r-cran-matrix armhf 1.2-18-1 [3468 kB]
Get:153 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-delayedarray armhf 0.12.2+dfsg-1 [1672 kB]
Get:154 http://172.17.0.1/private bullseye-staging/main armhf r-cran-bitops armhf 1.0-6-4 [23.9 kB]
Get:155 http://172.17.0.1/private bullseye-staging/main armhf r-cran-rcurl armhf 1.98-1.1-1 [733 kB]
Get:156 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-genomeinfodbdata all 1.2.2-1 [10.2 MB]
Get:157 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-genomeinfodb all 1.22.0-1 [3687 kB]
Get:158 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-genomicranges armhf 1.38.0+dfsg-1 [1828 kB]
Get:159 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-summarizedexperiment all 1.16.1+dfsg-1 [1899 kB]
Get:160 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-rsamtools armhf 2.2.1-1 [3657 kB]
Get:161 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-genomicalignments armhf 1.22.1-1 [2124 kB]
Get:162 http://172.17.0.1/private bullseye-staging/main armhf r-cran-hwriter all 1.3.2-3 [162 kB]
Get:163 http://172.17.0.1/private bullseye-staging/main armhf r-cran-jpeg armhf 0.1-8.1-1 [29.3 kB]
Get:164 http://172.17.0.1/private bullseye-staging/main armhf r-cran-png armhf 0.1-7-3 [39.3 kB]
Get:165 http://172.17.0.1/private bullseye-staging/main armhf r-cran-rcolorbrewer all 1.1-2-2 [54.3 kB]
Get:166 http://172.17.0.1/private bullseye-staging/main armhf r-cran-latticeextra all 0.6-29-2 [2192 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package libbsd0:armhf.
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Unpacking zlib1g:armhf (1:1.2.11.dfsg-1.2) over (1:1.2.11.dfsg-1) ...
Setting up zlib1g:armhf (1:1.2.11.dfsg-1.2) ...
Selecting previously unselected package man-db.
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Unpacking man-db (2.9.0-2) ...
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Unpacking sensible-utils (0.0.12+nmu1) ...
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Unpacking libmagic-mgc (1:5.38-4) ...
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Unpacking libmagic1:armhf (1:5.38-4) ...
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Unpacking file (1:5.38-4) ...
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Preparing to unpack .../005-gettext-base_0.19.8.1-10_armhf.deb ...
Unpacking gettext-base (0.19.8.1-10) ...
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Preparing to unpack .../006-libswitch-perl_2.17-2_all.deb ...
Unpacking libswitch-perl (2.17-2) ...
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Preparing to unpack .../007-ucf_3.0038+nmu1_all.deb ...
Moving old data out of the way
Unpacking ucf (3.0038+nmu1) ...
Selecting previously unselected package libsigsegv2:armhf.
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Unpacking libsigsegv2:armhf (2.12-2) ...
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Preparing to unpack .../009-m4_1.4.18-4_armhf.deb ...
Unpacking m4 (1.4.18-4) ...
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Unpacking autoconf (2.69-11.1) ...
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Unpacking autopoint (0.19.8.1-10) ...
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Unpacking libssl1.1:armhf (1.1.1d-2) ...
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Unpacking openssl (1.1.1d-2) ...
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Unpacking dctrl-tools (2.24-3) ...
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Unpacking sbuild-build-depends-r-bioc-shortread-dummy (0.invalid.0) ...
Setting up libboost1.67-dev:armhf (1.67.0-17) ...
Setting up libexpat1:armhf (2.2.9-1) ...
Setting up libpcrecpp0v5:armhf (2:8.39-12) ...
Setting up libpipeline1:armhf (1.5.2-2) ...
Setting up libgraphite2-3:armhf (1.3.13-11) ...
Setting up libpixman-1-0:armhf (0.36.0-1) ...
Setting up libfile-which-perl (1.23-1) ...
Setting up libxau6:armhf (1:1.0.8-1+b2) ...
Setting up libkeyutils1:armhf (1.6.1-2) ...
Setting up libpsl5:armhf (0.20.2-2) ...
Setting up libpcre16-3:armhf (2:8.39-12) ...
Setting up libdatrie1:armhf (0.2.12-3+b1) ...
Setting up libmagic-mgc (1:5.38-4) ...
Setting up libarchive-zip-perl (1.67-1) ...
Setting up libglib2.0-0:armhf (2.62.4-1+rpi1) ...
No schema files found: doing nothing.
Setting up libssl1.1:armhf (1.1.1d-2) ...
Setting up unzip (6.0-25) ...
Setting up libdebhelper-perl (12.9) ...
Setting up libbrotli1:armhf (1.0.7-6) ...
Setting up x11-common (1:7.7+20) ...
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
invoke-rc.d: could not determine current runlevel
invoke-rc.d: policy-rc.d denied execution of start.
Setting up libnghttp2-14:armhf (1.40.0-1+b2) ...
Setting up libmagic1:armhf (1:5.38-4) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.38-4) ...
Setting up libjbig0:armhf (2.1-3.1+b2) ...
Setting up libpcre2-16-0:armhf (10.34-7) ...
Setting up libicu63:armhf (63.2-2) ...
Setting up libkrb5support0:armhf (1.17-6+b1) ...
Setting up zip (3.0-11) ...
Setting up autotools-dev (20180224.1) ...
Setting up libpcre2-32-0:armhf (10.34-7) ...
Setting up libblas3:armhf (3.9.0-1) ...
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 libjpeg62-turbo:armhf (1:1.5.2-2+b1) ...
Setting up libswitch-perl (2.17-2) ...
Setting up libx11-data (2:1.6.8-1) ...
Setting up libjpeg62-turbo-dev:armhf (1:1.5.2-2+b1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b1) ...
Setting up libncurses6:armhf (6.1+20191019-1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libfribidi0:armhf (1.0.7-1.1) ...
Setting up libpng16-16:armhf (1.6.37-2) ...
Setting up libpcre32-3:armhf (2:8.39-12) ...
Setting up libtcl8.6:armhf (8.6.10+dfsg-1) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up libwebp6:armhf (0.6.1-2) ...
Setting up icu-devtools (63.2-2) ...
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Setting up fonts-dejavu-core (2.37-1) ...
Setting up libpcre2-posix2:armhf (10.34-7) ...
Setting up libk5crypto3:armhf (1.17-6+b1) ...
Setting up libgfortran5:armhf (9.2.1-25+rpi1) ...
Setting up liblzma-dev:armhf (5.2.4-1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1.2) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
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Setting up libssh2-1:armhf (1.8.0-2.1) ...
Setting up libkrb5-3:armhf (1.17-6+b1) ...
Setting up libboost-dev:armhf (1.67.0.2+b11) ...
Setting up libtiff5:armhf (4.1.0+git191117-2) ...
Setting up openssl (1.1.1d-2) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.1+20191019-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libicu-dev:armhf (63.2-2) ...
Setting up libxml2:armhf (2.9.4+dfsg1-8) ...
Setting up xdg-utils (1.1.3-1) ...
Setting up libblas-dev:armhf (3.9.0-1) ...
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 dctrl-tools (2.24-3) ...
Setting up libbz2-dev:armhf (1.0.8-2) ...
Setting up libfile-stripnondeterminism-perl (1.6.3-2) ...
Setting up r-cran-bh (1.66.0-1) ...
Setting up libice6:armhf (2:1.0.9-2) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up liblapack3:armhf (3.9.0-1) ...
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 libncurses-dev:armhf (6.1+20191019-1) ...
Setting up libxcb1:armhf (1.13.1-2) ...
Setting up libpcre2-dev:armhf (10.34-7) ...
Setting up libtool (2.4.6-11) ...
Setting up libxcb-render0:armhf (1.13.1-2) ...
Setting up libpcre3-dev:armhf (2:8.39-12) ...
Setting up libpng-dev:armhf (1.6.37-2) ...
Setting up libjpeg-dev (1:1.5.2-2) ...
Setting up libgfortran-9-dev:armhf (9.2.1-25+rpi1) ...
Setting up m4 (1.4.18-4) ...
Setting up libxcb-shm0:armhf (1.13.1-2) ...
Setting up libreadline-dev:armhf (8.0-3) ...
Setting up libthai0:armhf (0.1.28-3) ...
Setting up ca-certificates (20190110) ...
Updating certificates in /etc/ssl/certs...
128 added, 0 removed; done.
Setting up libfreetype6:armhf (2.10.1-2) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up liblapack-dev:armhf (3.9.0-1) ...
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 libgssapi-krb5-2:armhf (1.17-6+b1) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up ucf (3.0038+nmu1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.6.3-2) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-4) ...
Setting up libncurses5-dev:armhf (6.1+20191019-1) ...
Setting up libcurl4:armhf (7.67.0-2) ...
Setting up libx11-6:armhf (2:1.6.8-1) ...
Setting up libharfbuzz0b:armhf (2.6.4-1+rpi1) ...
Setting up libsm6:armhf (2:1.2.3-1) ...
Setting up libxmuu1:armhf (2:1.1.2-2+b3) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libpaper1:armhf (1.1.28) ...
Creating config file /etc/papersize with new version
Setting up gettext (0.19.8.1-10) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up gfortran-9 (9.2.1-25+rpi1) ...
Setting up fontconfig-config (2.13.1-2) ...
Setting up libxext6:armhf (2:1.3.3-1+b2) ...
Setting up libpaper-utils (1.1.28) ...
Setting up man-db (2.9.0-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up gfortran (4:9.2.1-3.1+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 intltool-debian (0.35.0+20060710.5) ...
Setting up libxt6:armhf (1:1.1.5-1+b3) ...
Setting up xauth (1:1.0.10-1) ...
Setting up libxss1:armhf (1:1.2.3-1) ...
Setting up libfontconfig1:armhf (2.13.1-2) ...
Setting up fontconfig (2.13.1-2) ...
Regenerating fonts cache... done.
Setting up libxft2:armhf (2.3.2-2) ...
Setting up po-debconf (1.0.21) ...
Setting up libtk8.6:armhf (8.6.10-1) ...
Setting up libpango-1.0-0:armhf (1.42.4-7+b1) ...
Setting up libcairo2:armhf (1.16.0-4) ...
Setting up libpangoft2-1.0-0:armhf (1.42.4-7+b1) ...
Setting up libpangocairo-1.0-0:armhf (1.42.4-7+b1) ...
Setting up r-base-core (3.6.2-2) ...
Creating config file /etc/R/Renviron with new version
Setting up r-cran-futile.options (1.0.1-2) ...
Setting up r-cran-lattice (0.20-38-1) ...
Setting up r-cran-formatr (1.7-1) ...
Setting up r-cran-jpeg (0.1-8.1-1) ...
Setting up r-bioc-genomeinfodbdata (1.2.2-1) ...
Setting up r-bioc-biocgenerics (0.32.0-1) ...
Setting up r-cran-matrixstats (0.55.0-1) ...
Setting up r-base-dev (3.6.2-2) ...
Setting up r-cran-lambda.r (1.2.4-1) ...
Setting up r-cran-snow (1:0.4.3-1) ...
Setting up r-cran-bitops (1.0-6-4) ...
Setting up r-bioc-zlibbioc (1.32.0+dfsg-1) ...
Setting up r-cran-png (0.1-7-3) ...
Setting up r-bioc-biobase (2.46.0-1) ...
Setting up r-cran-hwriter (1.3.2-3) ...
Setting up r-cran-rcolorbrewer (1.1-2-2) ...
Setting up r-bioc-s4vectors (0.24.3-1) ...
Setting up r-cran-futile.logger (1.4.3-3) ...
Setting up r-cran-matrix (1.2-18-1) ...
Setting up r-bioc-iranges (2.20.2-1) ...
Setting up r-cran-rcurl (1.98-1.1-1) ...
Setting up r-bioc-biocparallel (1.20.1-1) ...
Setting up r-cran-latticeextra (0.6-29-2) ...
Setting up r-bioc-genomeinfodb (1.22.0-1) ...
Setting up r-bioc-xvector (0.26.0-1) ...
Setting up r-bioc-delayedarray (0.12.2+dfsg-1) ...
Setting up r-bioc-genomicranges (1.38.0+dfsg-1) ...
Setting up r-bioc-biostrings (2.54.0-1) ...
Setting up r-bioc-rsamtools (2.2.1-1) ...
Setting up r-bioc-summarizedexperiment (1.16.1+dfsg-1) ...
Setting up r-bioc-genomicalignments (1.22.1-1) ...
Setting up debhelper (12.9) ...
Setting up dh-autoreconf (19) ...
Setting up dh-r (20200104) ...
Setting up sbuild-build-depends-r-bioc-shortread-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.29-9+rpi1) ...
Processing triggers for ca-certificates (20190110) ...
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_2.33.90.20200122-2+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-25+rpi1 gcc-9_9.2.1-25+rpi1 libc6-dev_2.29-9+rpi1 libstdc++-9-dev_9.2.1-25+rpi1 libstdc++6_9.2.1-25+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11.1 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-5 binutils_2.33.90.20200122-2+rpi1 binutils-arm-linux-gnueabihf_2.33.90.20200122-2+rpi1 binutils-common_2.33.90.20200122-2+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 ca-certificates_20190110 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.2.1-25+rpi1 dash_0.5.10.2-6 dctrl-tools_2.24-3 debconf_1.5.73 debhelper_12.9 debianutils_4.9.1 dh-autoreconf_19 dh-r_20200104 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dirmngr_2.2.19-1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.5-2 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 fontconfig_2.13.1-2 fontconfig-config_2.13.1-2 fonts-dejavu-core_2.37-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.2.1-25+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-9_9.2.1-25+rpi1 gcc-9-base_9.2.1-25+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gfortran_4:9.2.1-3.1+rpi1 gfortran-9_9.2.1-25+rpi1 gnupg_2.2.19-1 gnupg-l10n_2.2.19-1 gnupg-utils_2.2.19-1 gpg_2.2.19-1 gpg-agent_2.2.19-1 gpg-wks-client_2.2.19-1 gpg-wks-server_2.2.19-1 gpgconf_2.2.19-1 gpgsm_2.2.19-1 gpgv_2.2.19-1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.9-3 hostname_3.23 icu-devtools_63.2-2 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-3 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-25+rpi1 libassuan0_2.5.3-7 libatomic1_9.2.1-25+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbinutils_2.33.90.20200122-2+rpi1 libblas-dev_3.9.0-1 libblas3_3.9.0-1 libblkid1_2.34-0.1 libboost-dev_1.67.0.2+b11 libboost1.67-dev_1.67.0-17 libbrotli1_1.0.7-6 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libbz2-dev_1.0.8-2 libc-bin_2.29-9+rpi1 libc-dev-bin_2.29-9+rpi1 libc6_2.29-9+rpi1 libc6-dev_2.29-9+rpi1 libcairo2_1.16.0-4 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcap2-bin_1:2.27-1 libcc1-0_9.2.1-25+rpi1 libcom-err2_1.45.5-2 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.10-10+b5 libcrypt1_1:4.4.10-10+b5 libctf-nobfd0_2.33.90.20200122-2+rpi1 libctf0_2.33.90.20200122-2+rpi1 libcurl4_7.67.0-2 libdatrie1_0.2.12-3+b1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.250 libdebhelper-perl_12.9 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.5-2 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi7_3.3-3 libfile-stripnondeterminism-perl_1.6.3-2 libfile-which-perl_1.23-1 libfontconfig1_2.13.1-2 libfreetype6_2.10.1-2 libfribidi0_1.0.7-1.1 libgcc-9-dev_9.2.1-25+rpi1 libgcc1_1:9.2.1-25+rpi1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran-9-dev_9.2.1-25+rpi1 libgfortran5_9.2.1-25+rpi1 libglib2.0-0_2.62.4-1+rpi1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.11.1-2 libgomp1_9.2.1-25+rpi1 libgpg-error0_1.36-7 libgraphite2-3_1.3.13-11 libgssapi-krb5-2_1.17-6+b1 libharfbuzz0b_2.6.4-1+rpi1 libhogweed5_3.5.1+really3.5.1-2 libice6_2:1.0.9-2 libicu-dev_63.2-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl22_0.22-2 libjbig0_2.1-3.1+b2 libjpeg-dev_1:1.5.2-2 libjpeg62-turbo_1:1.5.2-2+b1 libjpeg62-turbo-dev_1:1.5.2-2+b1 libk5crypto3_1.17-6+b1 libkeyutils1_1.6.1-2 libkrb5-3_1.17-6+b1 libkrb5support0_1.17-6+b1 libksba8_1.3.5-2 liblapack-dev_3.9.0-1 liblapack3_3.9.0-1 libldap-2.4-2_2.4.48+dfsg-1+b2 libldap-common_2.4.48+dfsg-1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses-dev_6.1+20191019-1 libncurses5-dev_6.1+20191019-1 libncurses6_6.1+20191019-1 libncursesw6_6.1+20191019-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1+b2 libnpth0_1.6-1 libp11-kit0_0.23.18.1-2+b1 libpam-cap_1:2.27-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpango-1.0-0_1.42.4-7+b1 libpangocairo-1.0-0_1.42.4-7+b1 libpangoft2-1.0-0_1.42.4-7+b1 libpaper-utils_1.1.28 libpaper1_1.1.28 libpcre16-3_2:8.39-12 libpcre2-16-0_10.34-7 libpcre2-32-0_10.34-7 libpcre2-8-0_10.34-7 libpcre2-dev_10.34-7 libpcre2-posix2_10.34-7 libpcre3_2:8.39-12 libpcre3-dev_2:8.39-12 libpcre32-3_2:8.39-12 libpcrecpp0v5_2:8.39-12 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2 libpixman-1-0_0.36.0-1 libpng-dev_1.6.37-2 libpng16-16_1.6.37-2 libpsl5_0.20.2-2 libreadline-dev_8.0-3 libreadline7_7.0-5 libreadline8_8.0-3 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.2-2+rpi1 libselinux1_3.0-1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsm6_2:1.2.3-1 libsmartcols1_2.34-0.1 libsqlite3-0_3.31.0+really3.30.1+fossil191229-1 libss2_1.45.5-2 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-25+rpi1 libstdc++6_9.2.1-25+rpi1 libsub-override-perl_0.09-2 libswitch-perl_2.17-2 libsystemd0_244.1-1+rpi1 libtasn1-6_4.15.0-2 libtcl8.6_8.6.10+dfsg-1 libthai-data_0.1.28-3 libthai0_0.1.28-3 libtiff5_4.1.0+git191117-2 libtinfo5_6.1+20191019-1 libtinfo6_6.1+20191019-1 libtk8.6_8.6.10-1 libtool_2.4.6-11 libubsan1_9.2.1-25+rpi1 libuchardet0_0.0.6-3 libudev1_244.1-1+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libwebp6_0.6.1-2 libx11-6_2:1.6.8-1 libx11-data_2:1.6.8-1 libxau6_1:1.0.8-1+b2 libxcb-render0_1.13.1-2 libxcb-shm0_1.13.1-2 libxcb1_1.13.1-2 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxft2_2.3.2-2 libxml2_2.9.4+dfsg1-8 libxmuu1_2:1.1.2-2+b3 libxrender1_1:0.9.10-1 libxss1_1:1.2.3-1 libxt6_1:1.1.5-1+b3 libzstd1_1.4.4+dfsg-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8-1 logsave_1.45.5-2 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.4.20200120-1 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 netbase_6.0 openssl_1.1.1d-2 passwd_1:4.8-1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 pkg-config_0.29-6 po-debconf_1.0.21 r-base-core_3.6.2-2 r-base-dev_3.6.2-2 r-bioc-biobase_2.46.0-1 r-bioc-biocgenerics_0.32.0-1 r-bioc-biocparallel_1.20.1-1 r-bioc-biostrings_2.54.0-1 r-bioc-delayedarray_0.12.2+dfsg-1 r-bioc-genomeinfodb_1.22.0-1 r-bioc-genomeinfodbdata_1.2.2-1 r-bioc-genomicalignments_1.22.1-1 r-bioc-genomicranges_1.38.0+dfsg-1 r-bioc-iranges_2.20.2-1 r-bioc-rsamtools_2.2.1-1 r-bioc-s4vectors_0.24.3-1 r-bioc-summarizedexperiment_1.16.1+dfsg-1 r-bioc-xvector_0.26.0-1 r-bioc-zlibbioc_1.32.0+dfsg-1 r-cran-bh_1.66.0-1 r-cran-bitops_1.0-6-4 r-cran-formatr_1.7-1 r-cran-futile.logger_1.4.3-3 r-cran-futile.options_1.0.1-2 r-cran-hwriter_1.3.2-3 r-cran-jpeg_0.1-8.1-1 r-cran-lambda.r_1.2.4-1 r-cran-lattice_0.20-38-1 r-cran-latticeextra_0.6-29-2 r-cran-matrix_1.2-18-1 r-cran-matrixstats_0.55.0-1 r-cran-png_0.1-7-3 r-cran-rcolorbrewer_1.1-2-2 r-cran-rcurl_1.98-1.1-1 r-cran-snow_1:0.4.3-1 raspbian-archive-keyring_20120528.2 readline-common_8.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-shortread-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-2.1 tar_1.30+dfsg-6 tzdata_2019c-3 ucf_3.0038+nmu1 unzip_6.0-25 util-linux_2.34-0.1 x11-common_1:7.7+20 xauth_1:1.0.10-1 xdg-utils_1.1.3-1 xz-utils_5.2.4-1 zip_3.0-11 zlib1g_1:1.2.11.dfsg-1.2 zlib1g-dev_1:1.2.11.dfsg-1.2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Fri Feb 7 20:00:15 2020 UTC
gpgv: using RSA key 9A3C07BD06DE2F416E813A5D612EF1613E050F54
gpgv: issuer "daissi@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./r-bioc-shortread_1.44.3-1.dsc
dpkg-source: info: extracting r-bioc-shortread in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking r-bioc-shortread_1.44.3.orig.tar.gz
dpkg-source: info: unpacking r-bioc-shortread_1.44.3-1.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-be11c592-5319-4406-9667-aefa049e463a
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 1.44.3-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot 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 build-arch
dh build-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
fakeroot debian/rules binary-arch
dh binary-arch --buildsystem R
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: 1.44.3
I: Building using R version 3.6.2-2
I: R API version: r-api-3.5
I: Using built-time from d/changelog: Fri, 07 Feb 2020 20:50:24 +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='Fri, 07 Feb 2020 20:50:24 +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" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-BI9Pjj/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -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" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-BI9Pjj/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -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" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-BI9Pjj/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -std=gnu99 -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" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-BI9Pjj/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -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" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-BI9Pjj/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -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" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-BI9Pjj/r-base-3.6.2=. -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" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-BI9Pjj/r-base-3.6.2=. -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" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-BI9Pjj/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c io_bowtie.c -o io_bowtie.o
gcc -std=gnu99 -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" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-BI9Pjj/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c io_soap.c -o io_soap.o
g++ -std=gnu++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" -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-BI9Pjj/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c readBfaToc.cc -o readBfaToc.o
readBfaToc.cc: In function 'SEXPREC* readBfaToc(SEXP)':
readBfaToc.cc:35:19: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
35 | (void) fread( seq_name, sizeof(char), name_len, fp );
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readBfaToc.cc:36:19: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
36 | (void) fread( &seq_ori_len, sizeof(int), 1, fp );
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readBfaToc.cc:37:19: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
37 | (void) fread( &seq_len, sizeof(int), 1, fp );
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++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" -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-BI9Pjj/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c read_maq_map.cc -o read_maq_map.o
gcc -std=gnu99 -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" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-BI9Pjj/r-base-3.6.2=. -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" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-BI9Pjj/r-base-3.6.2=. -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" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-BI9Pjj/r-base-3.6.2=. -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" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-BI9Pjj/r-base-3.6.2=. -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 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-1.44.3/00new/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
W: Cannot find a debian package 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: BioConductor API version: r-api-bioc-3.10
dh_installdocs -a -O--buildsystem=R
dh_installchangelogs -a -O--buildsystem=R
dh_installinit -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_1.44.3-1_armhf.deb'.
dpkg-deb: building package 'r-bioc-shortread-dbgsym' in '../r-bioc-shortread-dbgsym_1.44.3-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../r-bioc-shortread_1.44.3-1_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 2020-02-16T06:17:06Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
r-bioc-shortread_1.44.3-1_armhf.changes:
----------------------------------------
Format: 1.8
Date: Fri, 07 Feb 2020 20:50:24 +0100
Source: r-bioc-shortread
Binary: r-bioc-shortread r-bioc-shortread-dbgsym
Architecture: armhf
Version: 1.44.3-1
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Dylan Aïssi <daissi@debian.org>
Description:
r-bioc-shortread - GNU R classes and methods for high-throughput short-read sequenci
Changes:
r-bioc-shortread (1.44.3-1) unstable; urgency=medium
.
* Team upload.
* New upstream version
* Standards-Version: 4.5.0
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Files:
908e971b681ad8e931816503ff9e1c99 151792 debug optional r-bioc-shortread-dbgsym_1.44.3-1_armhf.deb
841aa98983369f6add94d4d0a7283c90 9014 gnu-r optional r-bioc-shortread_1.44.3-1_armhf.buildinfo
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
r-bioc-shortread-dbgsym_1.44.3-1_armhf.deb
------------------------------------------
new Debian package, version 2.0.
size 151792 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: 1.44.3-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Installed-Size: 185
Depends: r-bioc-shortread (= 1.44.3-1)
Section: debug
Priority: optional
Description: debug symbols for r-bioc-shortread
Build-Ids: f5190e7374affc8d02b8b1fda7f36ccf909c53ce
drwxr-xr-x root/root 0 2020-02-07 19:50 ./
drwxr-xr-x root/root 0 2020-02-07 19:50 ./usr/
drwxr-xr-x root/root 0 2020-02-07 19:50 ./usr/lib/
drwxr-xr-x root/root 0 2020-02-07 19:50 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-02-07 19:50 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-02-07 19:50 ./usr/lib/debug/.build-id/f5/
-rw-r--r-- root/root 178580 2020-02-07 19:50 ./usr/lib/debug/.build-id/f5/190e7374affc8d02b8b1fda7f36ccf909c53ce.debug
drwxr-xr-x root/root 0 2020-02-07 19:50 ./usr/share/
drwxr-xr-x root/root 0 2020-02-07 19:50 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-02-07 19:50 ./usr/share/doc/r-bioc-shortread-dbgsym -> r-bioc-shortread
r-bioc-shortread_1.44.3-1_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 5011556 bytes: control archive=4132 bytes.
1297 bytes, 18 lines control
10811 bytes, 113 lines md5sums
Package: r-bioc-shortread
Version: 1.44.3-1
Architecture: armhf
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Installed-Size: 7318
Depends: r-base-core (>= 3.6.2-2), r-api-3.5, r-api-bioc-3.10, 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, libc6 (>= 2.7), libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4)
Recommends: r-cran-runit
Suggests: 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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-rw-r--r-- root/root 1158 2020-02-07 19:50 ./usr/lib/R/site-library/ShortRead/CITATION
-rw-r--r-- root/root 1504 2020-02-07 19:50 ./usr/lib/R/site-library/ShortRead/DESCRIPTION
-rw-r--r-- root/root 5917 2020-02-07 19:50 ./usr/lib/R/site-library/ShortRead/INDEX
drwxr-xr-x root/root 0 2020-02-07 19:50 ./usr/lib/R/site-library/ShortRead/Meta/
-rw-r--r-- root/root 5616 2020-02-07 19:50 ./usr/lib/R/site-library/ShortRead/Meta/Rd.rds
-rw-r--r-- root/root 132 2020-02-07 19:50 ./usr/lib/R/site-library/ShortRead/Meta/features.rds
-rw-r--r-- root/root 5866 2020-02-07 19:50 ./usr/lib/R/site-library/ShortRead/Meta/hsearch.rds
-rw-r--r-- root/root 4231 2020-02-07 19:50 ./usr/lib/R/site-library/ShortRead/Meta/links.rds
-rw-r--r-- root/root 880 2020-02-07 19:50 ./usr/lib/R/site-library/ShortRead/Meta/nsInfo.rds
-rw-r--r-- root/root 1521 2020-02-07 19:50 ./usr/lib/R/site-library/ShortRead/Meta/package.rds
-rw-r--r-- root/root 262 2020-02-07 19:50 ./usr/lib/R/site-library/ShortRead/Meta/vignette.rds
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-rw-r--r-- root/root 12652 2020-02-07 19:50 ./usr/lib/R/site-library/ShortRead/NEWS
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drwxr-xr-x root/root 0 2020-02-07 19:50 ./usr/lib/R/site-library/ShortRead/extdata/Data/
drwxr-xr-x root/root 0 2020-02-07 19:50 ./usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/
drwxr-xr-x root/root 0 2020-02-07 19:50 ./usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/
drwxr-xr-x root/root 0 2020-02-07 19:50 ./usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/
-rw-r--r-- root/root 31740 2020-02-07 19:50 ./usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt
-rw-r--r-- root/root 121368 2020-02-07 19:50 ./usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_2_export.txt
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-rw-r--r-- root/root 12452 2020-02-07 19:50 ./usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/s_1_0001_seq.txt
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Purging /<<BUILDDIR>>
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| Summary |
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Build Architecture: armhf
Build-Space: 21556
Build-Time: 164
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 777
Job: r-bioc-shortread_1.44.3-1
Machine Architecture: armhf
Package: r-bioc-shortread
Package-Time: 962
Source-Version: 1.44.3-1
Space: 21556
Status: successful
Version: 1.44.3-1
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Finished at 2020-02-16T06:17:06Z
Build needed 00:16:02, 21556k disk space