r-bioc-variantannotation →
1.32.0-1 →
armhf → 2019-11-18 23:10:29
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| r-bioc-variantannotation 1.32.0-1 (armhf) Mon, 18 Nov 2019 22:52:57 +0000 |
+==============================================================================+
Package: r-bioc-variantannotation
Version: 1.32.0-1
Source Version: 1.32.0-1
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-b154106e-8989-414c-a62d-ef3bbb6a5c4f' 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 [12.9 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-variantannotation' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/r-pkg-team/r-bioc-variantannotation.git
Please use:
git clone https://salsa.debian.org/r-pkg-team/r-bioc-variantannotation.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1738 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main r-bioc-variantannotation 1.32.0-1 (dsc) [2764 B]
Get:2 http://172.17.0.1/private bullseye-staging/main r-bioc-variantannotation 1.32.0-1 (tar) [1728 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main r-bioc-variantannotation 1.32.0-1 (diff) [7928 B]
Fetched 1738 kB in 1s (3295 kB/s)
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I: NOTICE: Log filtering will replace 'build/r-bioc-variantannotation-OiB5KW/r-bioc-variantannotation-1.32.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-variantannotation-OiB5KW' 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-B0J2on/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-B0J2on/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-B0J2on/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-B0J2on/apt_archive ./ InRelease
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Get:3 copy:/<<BUILDDIR>>/resolver-B0J2on/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-B0J2on/apt_archive ./ Sources [349 B]
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Fetched 2107 B in 0s (9449 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:
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 2 not upgraded.
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Get:1 copy:/<<BUILDDIR>>/resolver-B0J2on/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
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(Reading database ... 12227 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 (>= 0.15.3), r-bioc-genomeinfodb (>= 1.15.2), r-bioc-genomicranges (>= 1.37.4), r-bioc-summarizedexperiment (>= 1.9.9), r-bioc-rsamtools (>= 1.99.0), r-cran-dbi, r-bioc-zlibbioc, r-bioc-biobase, r-bioc-s4vectors (>= 0.17.24), r-bioc-iranges (>= 2.13.13), r-bioc-xvector (>= 0.19.7), r-bioc-biostrings (>= 2.47.6), r-bioc-annotationdbi (>= 1.27.9), r-bioc-rtracklayer (>= 1.39.7), r-bioc-bsgenome (>= 1.47.3), r-bioc-genomicfeatures (>= 1.31.3), r-bioc-rhtslib, libcurl4-openssl-dev | libcurl4-dev
Filtered Build-Depends: debhelper-compat (= 12), dh-r, r-base-dev, r-bioc-biocgenerics (>= 0.15.3), r-bioc-genomeinfodb (>= 1.15.2), r-bioc-genomicranges (>= 1.37.4), r-bioc-summarizedexperiment (>= 1.9.9), r-bioc-rsamtools (>= 1.99.0), r-cran-dbi, r-bioc-zlibbioc, r-bioc-biobase, r-bioc-s4vectors (>= 0.17.24), r-bioc-iranges (>= 2.13.13), r-bioc-xvector (>= 0.19.7), r-bioc-biostrings (>= 2.47.6), r-bioc-annotationdbi (>= 1.27.9), r-bioc-rtracklayer (>= 1.39.7), r-bioc-bsgenome (>= 1.47.3), r-bioc-genomicfeatures (>= 1.31.3), r-bioc-rhtslib, libcurl4-openssl-dev
dpkg-deb: building package 'sbuild-build-depends-r-bioc-variantannotation-dummy' in '/<<BUILDDIR>>/resolver-B0J2on/apt_archive/sbuild-build-depends-r-bioc-variantannotation-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-variantannotation-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-B0J2on/apt_archive ./ InRelease
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Get:4 copy:/<<BUILDDIR>>/resolver-B0J2on/apt_archive ./ Sources [727 B]
Get:5 copy:/<<BUILDDIR>>/resolver-B0J2on/apt_archive ./ Packages [800 B]
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Reading package lists...
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Reading package lists...
Install r-bioc-variantannotation 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 libbrotli1 libbsd0 libbz2-dev libcairo2 libcroco3
libcurl4 libcurl4-openssl-dev 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-posix0 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 littler m4 man-db openssl pkg-config po-debconf r-base-core
r-base-dev r-bioc-annotationdbi r-bioc-biobase r-bioc-biocfilecache
r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biomart r-bioc-biostrings
r-bioc-bsgenome r-bioc-delayedarray r-bioc-genomeinfodb
r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures
r-bioc-genomicranges r-bioc-iranges r-bioc-rhtslib r-bioc-rsamtools
r-bioc-rtracklayer r-bioc-s4vectors r-bioc-summarizedexperiment
r-bioc-xvector r-bioc-zlibbioc r-cran-askpass r-cran-assertthat
r-cran-backports r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob
r-cran-cli r-cran-crayon r-cran-curl r-cran-dbi r-cran-dbplyr r-cran-digest
r-cran-dplyr r-cran-ellipsis r-cran-fansi r-cran-formatr
r-cran-futile.logger r-cran-futile.options r-cran-glue r-cran-hms
r-cran-httr r-cran-jsonlite r-cran-lambda.r r-cran-lattice r-cran-littler
r-cran-magrittr r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mime
r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten
r-cran-prettyunits r-cran-progress r-cran-purrr r-cran-r6 r-cran-rappdirs
r-cran-rcpp r-cran-rcurl r-cran-rlang r-cran-rsqlite r-cran-snow
r-cran-stringi r-cran-stringr r-cran-sys r-cran-tibble r-cran-tidyselect
r-cran-utf8 r-cran-vctrs r-cran-xml r-cran-zeallot sensible-utils ucf unzip
x11-common xauth xdg-utils zip 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 libgfortran5-dbg libcoarrays-dev groff
liblapack-doc libcurl4-doc libidn11-dev libkrb5-dev libldap2-dev librtmp-dev
libssh2-1-dev libssl-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-graph
r-cran-knitr r-bioc-all r-cran-rmarkdown 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-data.table r-cran-testthat
r-cran-biocmanager r-cran-runit r-bioc-edger r-bioc-ensembldb r-bioc-gviz
r-bioc-annotationhub r-bioc-genefilter r-bioc-limma r-bioc-rhdf5
r-cran-webshot r-cran-rstudioapi r-cran-rmysql r-cran-withr r-cran-callr
r-cran-ggplot2 r-cran-lubridate r-cran-mgcv r-cran-rpostgresql r-cran-broom
r-cran-readr r-cran-shiny r-cran-r.utils r-cran-forcats r-cran-httpuv
r-cran-jpeg r-cran-png r-cran-xml2 r-cran-plyr r-cran-getopt
r-cran-base64enc libgdal-dev r-cran-covr r-cran-scales r-cran-inline
r-cran-rmpi r-cran-rsprng r-cran-rlecuyer r-cran-htmltools r-cran-generics
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-bioc-go.db r-cran-runit r-cran-testthat r-cran-batchjobs r-cran-doparallel
r-cran-batchtools r-cran-rmpi r-bioc-biovizbase r-bioc-genefilter
r-bioc-shortread r-bioc-annotate r-cran-withr r-cran-mockery r-cran-httpuv
r-cran-webutils r-cran-rmysql r-cran-rpostgresql r-cran-data.table
r-cran-mass r-cran-testit r-cran-codetools r-cran-survival r-cran-sp
r-cran-lubridate r-cran-rmarkdown r-cran-dbitest r-cran-htmltools
r-cran-htmlwidgets r-cran-knitr r-cran-mockr 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 libbrotli1 libbsd0 libbz2-dev libcairo2 libcroco3
libcurl4 libcurl4-openssl-dev 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-posix0 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 littler m4 man-db openssl pkg-config po-debconf r-base-core
r-base-dev r-bioc-annotationdbi r-bioc-biobase r-bioc-biocfilecache
r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biomart r-bioc-biostrings
r-bioc-bsgenome r-bioc-delayedarray r-bioc-genomeinfodb
r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures
r-bioc-genomicranges r-bioc-iranges r-bioc-rhtslib r-bioc-rsamtools
r-bioc-rtracklayer r-bioc-s4vectors r-bioc-summarizedexperiment
r-bioc-xvector r-bioc-zlibbioc r-cran-askpass r-cran-assertthat
r-cran-backports r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob
r-cran-cli r-cran-crayon r-cran-curl r-cran-dbi r-cran-dbplyr r-cran-digest
r-cran-dplyr r-cran-ellipsis r-cran-fansi r-cran-formatr
r-cran-futile.logger r-cran-futile.options r-cran-glue r-cran-hms
r-cran-httr r-cran-jsonlite r-cran-lambda.r r-cran-lattice r-cran-littler
r-cran-magrittr r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mime
r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten
r-cran-prettyunits r-cran-progress r-cran-purrr r-cran-r6 r-cran-rappdirs
r-cran-rcpp r-cran-rcurl r-cran-rlang r-cran-rsqlite r-cran-snow
r-cran-stringi r-cran-stringr r-cran-sys r-cran-tibble r-cran-tidyselect
r-cran-utf8 r-cran-vctrs r-cran-xml r-cran-zeallot
sbuild-build-depends-r-bioc-variantannotation-dummy sensible-utils ucf unzip
x11-common xauth xdg-utils zip zlib1g-dev
0 upgraded, 210 newly installed, 0 to remove and 2 not upgraded.
Need to get 172 MB of archives.
After this operation, 390 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-B0J2on/apt_archive ./ sbuild-build-depends-r-bioc-variantannotation-dummy 0.invalid.0 [1084 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
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Get:12 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.37-6 [66.2 kB]
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Get:14 http://172.17.0.1/private bullseye-staging/main armhf libswitch-perl all 2.17-2 [20.5 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf ucf all 3.0038+nmu1 [69.0 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
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Get:18 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
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Get:34 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.7.1 [173 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.2-3 [1137 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b2 [571 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.1+20191019-1 [79.5 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-9 [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 12.7.1 [997 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 3.8.0-8 [107 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 1.6.37-1 [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 1.0.7-5 [257 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6-6 [14.0 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 1.39.2-1 [71.3 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 7.66.0-1+b1 [297 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 9.2.1-17+rpi1 [231 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.8.0-8 [1568 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 8.6.9+dfsg-2 [878 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 4.1.0-1 [249 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 8.6.9-2 [664 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 3.6.1-7 [24.3 MB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf libgfortran-9-dev armhf 9.2.1-17+rpi1 [279 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf gfortran-9 armhf 9.2.1-17+rpi1 [7451 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf gfortran armhf 4:9.2.1-3+rpi1 [1432 B]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.8.0-8 [112 kB]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf liblapack-dev armhf 3.8.0-8 [2839 kB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf libncurses-dev armhf 6.1+20191019-1 [284 kB]
Get:109 http://172.17.0.1/private bullseye-staging/main armhf libncurses5-dev armhf 6.1+20191019-1 [940 B]
Get:110 http://172.17.0.1/private bullseye-staging/main armhf libreadline-dev armhf 8.0-3 [114 kB]
Get:111 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.2-2+b1 [179 kB]
Get:112 http://172.17.0.1/private bullseye-staging/main armhf libjpeg-dev all 1:1.5.2-2 [57.5 kB]
Get:113 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-16-0 armhf 10.32-5 [175 kB]
Get:114 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-32-0 armhf 10.32-5 [168 kB]
Get:115 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-posix0 armhf 10.32-5 [38.3 kB]
Get:116 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-dev armhf 10.32-5 [572 kB]
Get:117 http://172.17.0.1/private bullseye-staging/main armhf libpcre16-3 armhf 2:8.39-12 [234 kB]
Get:118 http://172.17.0.1/private bullseye-staging/main armhf libpcre32-3 armhf 2:8.39-12 [227 kB]
Get:119 http://172.17.0.1/private bullseye-staging/main armhf libpcrecpp0v5 armhf 2:8.39-12 [150 kB]
Get:120 http://172.17.0.1/private bullseye-staging/main armhf libpcre3-dev armhf 2:8.39-12 [564 kB]
Get:121 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:122 http://172.17.0.1/private bullseye-staging/main armhf libpng-dev armhf 1.6.37-1 [275 kB]
Get:123 http://172.17.0.1/private bullseye-staging/main armhf libbz2-dev armhf 1.0.8-2 [27.7 kB]
Get:124 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:125 http://172.17.0.1/private bullseye-staging/main armhf icu-devtools armhf 63.2-2 [163 kB]
Get:126 http://172.17.0.1/private bullseye-staging/main armhf libicu-dev armhf 63.2-2 [8846 kB]
Get:127 http://172.17.0.1/private bullseye-staging/main armhf libxmuu1 armhf 2:1.1.2-2+b3 [23.4 kB]
Get:128 http://172.17.0.1/private bullseye-staging/main armhf xauth armhf 1:1.0.10-1 [36.4 kB]
Get:129 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29-6 [59.8 kB]
Get:130 http://172.17.0.1/private bullseye-staging/main armhf r-base-dev all 3.6.1-7 [4488 B]
Get:131 http://172.17.0.1/private bullseye-staging/main armhf libfile-which-perl all 1.23-1 [16.6 kB]
Get:132 http://172.17.0.1/private bullseye-staging/main armhf dh-r all 20190917 [36.2 kB]
Get:133 http://172.17.0.1/private bullseye-staging/main armhf libcurl4-openssl-dev armhf 7.66.0-1+b1 [370 kB]
Get:134 http://172.17.0.1/private bullseye-staging/main armhf r-cran-littler armhf 0.3.9-1 [308 kB]
Get:135 http://172.17.0.1/private bullseye-staging/main armhf littler all 0.3.9-1 [14.6 kB]
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-bioc-s4vectors armhf 0.24.0-1 [1944 kB]
Get:139 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-iranges armhf 2.20.0-1 [2217 kB]
Get:140 http://172.17.0.1/private bullseye-staging/main armhf r-cran-dbi all 1.0.0-2 [789 kB]
Get:141 http://172.17.0.1/private bullseye-staging/main armhf r-cran-bit armhf 1.1-14-1 [218 kB]
Get:142 http://172.17.0.1/private bullseye-staging/main armhf r-cran-bit64 armhf 0.9-7-3 [433 kB]
Get:143 http://172.17.0.1/private bullseye-staging/main armhf r-cran-magrittr all 1.5-5 [152 kB]
Get:144 http://172.17.0.1/private bullseye-staging/main armhf r-cran-assertthat all 0.2.1-1 [56.7 kB]
Get:145 http://172.17.0.1/private bullseye-staging/main armhf r-cran-prettyunits all 1.0.2-3 [32.4 kB]
Get:146 http://172.17.0.1/private bullseye-staging/main armhf r-cran-rlang armhf 0.4.1-1 [1102 kB]
Get:147 http://172.17.0.1/private bullseye-staging/main armhf r-cran-backports armhf 1.1.5-1 [57.9 kB]
Get:148 http://172.17.0.1/private bullseye-staging/main armhf r-cran-ellipsis armhf 0.3.0-1 [30.3 kB]
Get:149 http://172.17.0.1/private bullseye-staging/main armhf r-cran-digest armhf 0.6.22-1 [171 kB]
Get:150 http://172.17.0.1/private bullseye-staging/main armhf r-cran-glue armhf 1.3.1-1 [156 kB]
Get:151 http://172.17.0.1/private bullseye-staging/main armhf r-cran-zeallot all 0.1.0-2 [59.9 kB]
Get:152 http://172.17.0.1/private bullseye-staging/main armhf r-cran-vctrs armhf 0.2.0-1 [735 kB]
Get:153 http://172.17.0.1/private bullseye-staging/main armhf r-cran-blob all 1.2.0-1 [46.0 kB]
Get:154 http://172.17.0.1/private bullseye-staging/main armhf r-cran-memoise all 1.1.0-2 [38.6 kB]
Get:155 http://172.17.0.1/private bullseye-staging/main armhf r-cran-pkgconfig all 2.0.3-1 [19.7 kB]
Get:156 http://172.17.0.1/private bullseye-staging/main armhf r-cran-pkgkitten all 0.1.5-1 [23.8 kB]
Get:157 http://172.17.0.1/private bullseye-staging/main armhf r-cran-rcpp armhf 1.0.3-1 [1928 kB]
Get:158 http://172.17.0.1/private bullseye-staging/main armhf r-cran-rsqlite armhf 2.1.2-1 [804 kB]
Get:159 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-annotationdbi all 1.48.0-1 [4629 kB]
Get:160 http://172.17.0.1/private bullseye-staging/main armhf r-cran-r6 all 2.4.1-1 [79.4 kB]
Get:161 http://172.17.0.1/private bullseye-staging/main armhf r-cran-crayon all 1.3.4-4 [750 kB]
Get:162 http://172.17.0.1/private bullseye-staging/main armhf r-cran-cli all 1.1.0-1 [175 kB]
Get:163 http://172.17.0.1/private bullseye-staging/main armhf r-cran-fansi armhf 0.4.0-1 [330 kB]
Get:164 http://172.17.0.1/private bullseye-staging/main armhf r-cran-utf8 armhf 1.1.4-1+b1 [126 kB]
Get:165 http://172.17.0.1/private bullseye-staging/main armhf r-cran-pillar all 1.3.1-1 [203 kB]
Get:166 http://172.17.0.1/private bullseye-staging/main armhf r-cran-tibble armhf 2.0.1-1 [656 kB]
Get:167 http://172.17.0.1/private bullseye-staging/main armhf r-cran-purrr armhf 0.3.3-1 [399 kB]
Get:168 http://172.17.0.1/private bullseye-staging/main armhf r-cran-tidyselect armhf 0.2.5-1 [113 kB]
Get:169 http://172.17.0.1/private bullseye-staging/main armhf r-cran-dplyr armhf 0.8.3-1 [1735 kB]
Get:170 http://172.17.0.1/private bullseye-staging/main armhf r-cran-dbplyr all 1.4.2-1 [586 kB]
Get:171 http://172.17.0.1/private bullseye-staging/main armhf r-cran-rappdirs armhf 0.3.1-1 [94.8 kB]
Get:172 http://172.17.0.1/private bullseye-staging/main armhf r-cran-curl armhf 4.2+dfsg-1 [147 kB]
Get:173 http://172.17.0.1/private bullseye-staging/main armhf r-cran-jsonlite armhf 1.6+dfsg-1 [432 kB]
Get:174 http://172.17.0.1/private bullseye-staging/main armhf r-cran-mime armhf 0.7-1 [35.4 kB]
Get:175 http://172.17.0.1/private bullseye-staging/main armhf r-cran-sys armhf 3.3-1 [42.6 kB]
Get:176 http://172.17.0.1/private bullseye-staging/main armhf r-cran-askpass armhf 1.1-1 [21.8 kB]
Get:177 http://172.17.0.1/private bullseye-staging/main armhf r-cran-openssl armhf 1.4.1+dfsg-2 [370 kB]
Get:178 http://172.17.0.1/private bullseye-staging/main armhf r-cran-httr all 1.4.1-1 [480 kB]
Get:179 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-biocfilecache all 1.10.2+dfsg-1 [248 kB]
Get:180 http://172.17.0.1/private bullseye-staging/main armhf r-cran-formatr all 1.7-1 [152 kB]
Get:181 http://172.17.0.1/private bullseye-staging/main armhf r-cran-lambda.r all 1.2.4-1 [119 kB]
Get:182 http://172.17.0.1/private bullseye-staging/main armhf r-cran-futile.options all 1.0.1-2 [19.8 kB]
Get:183 http://172.17.0.1/private bullseye-staging/main armhf r-cran-futile.logger all 1.4.3-3 [102 kB]
Get:184 http://172.17.0.1/private bullseye-staging/main armhf r-cran-snow all 1:0.4.3-1 [108 kB]
Get:185 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-biocparallel armhf 1.20.0-1 [1070 kB]
Get:186 http://172.17.0.1/private bullseye-staging/main armhf r-cran-xml armhf 3.98-1.20-2 [1957 kB]
Get:187 http://172.17.0.1/private bullseye-staging/main armhf r-cran-hms all 0.5.2-1 [111 kB]
Get:188 http://172.17.0.1/private bullseye-staging/main armhf r-cran-progress all 1.2.2-1 [89.6 kB]
Get:189 http://172.17.0.1/private bullseye-staging/main armhf r-cran-stringi armhf 1.4.3-1 [679 kB]
Get:190 http://172.17.0.1/private bullseye-staging/main armhf r-cran-stringr all 1.4.0-1 [198 kB]
Get:191 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-biomart all 2.42.0+dfsg-1 [330 kB]
Get:192 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-zlibbioc all 1.32.0+dfsg-1 [8780 B]
Get:193 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-xvector armhf 0.26.0-1 [610 kB]
Get:194 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-biostrings armhf 2.54.0-1 [14.1 MB]
Get:195 http://172.17.0.1/private bullseye-staging/main armhf r-cran-bitops armhf 1.0-6-4 [23.9 kB]
Get:196 http://172.17.0.1/private bullseye-staging/main armhf r-cran-rcurl armhf 1.95-4.12-1 [722 kB]
Get:197 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-genomeinfodbdata all 1.2.2-1 [10.2 MB]
Get:198 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-genomeinfodb all 1.22.0-1 [3687 kB]
Get:199 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-genomicranges armhf 1.38.0+dfsg-1 [1828 kB]
Get:200 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-rsamtools armhf 2.2.1-1 [3657 kB]
Get:201 http://172.17.0.1/private bullseye-staging/main armhf r-cran-matrixstats armhf 0.55.0-1 [576 kB]
Get:202 http://172.17.0.1/private bullseye-staging/main armhf r-cran-lattice armhf 0.20-38-1 [1120 kB]
Get:203 http://172.17.0.1/private bullseye-staging/main armhf r-cran-matrix armhf 1.2-17-2 [3458 kB]
Get:204 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-delayedarray armhf 0.12.0+dfsg-1 [1666 kB]
Get:205 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-summarizedexperiment all 1.16.0+dfsg-1 [1893 kB]
Get:206 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-genomicalignments armhf 1.22.0-1 [2124 kB]
Get:207 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-rtracklayer armhf 1.46.0-1 [2603 kB]
Get:208 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-bsgenome all 1.54.0-1 [6987 kB]
Get:209 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-genomicfeatures all 1.38.0+dfsg-1 [1561 kB]
Get:210 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-rhtslib armhf 1.18.0+dfsg-1 [964 kB]
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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+dfsg1-7+b2) ...
Setting up xdg-utils (1.1.3-1) ...
Setting up libblas-dev:armhf (3.8.0-8) ...
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 (1.6.1-1) ...
Setting up libice6:armhf (2:1.0.9-2) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up liblapack3:armhf (3.8.0-8) ...
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 (10.32-5) ...
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 (1.6.37-1) ...
Setting up libjpeg-dev (1:1.5.2-2) ...
Setting up libgfortran-9-dev:armhf (9.2.1-17+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 (3.8.0-8) ...
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) ...
Setting up dwz (0.13-2) ...
Setting up groff-base (1.22.4-3) ...
Setting up libncurses5-dev:armhf (6.1+20191019-1) ...
Setting up libcurl4:armhf (7.66.0-1+b1) ...
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 (0.19.8.1-9) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up gfortran-9 (9.2.1-17+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 (2.9.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up gfortran (4:9.2.1-3+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 libcurl4-openssl-dev:armhf (7.66.0-1+b1) ...
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 (8.6.9-2) ...
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 (3.6.1-7) ...
Creating config file /etc/R/Renviron with new version
Setting up r-cran-crayon (1.3.4-4) ...
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-xml (3.98-1.20-2) ...
Setting up r-cran-r6 (2.4.1-1) ...
Setting up r-cran-pkgkitten (0.1.5-1) ...
Setting up r-cran-magrittr (1.5-5) ...
Setting up r-cran-rappdirs (0.3.1-1) ...
Setting up r-bioc-genomeinfodbdata (1.2.2-1) ...
Setting up r-cran-littler (0.3.9-1) ...
Setting up r-cran-rcpp (1.0.3-1) ...
Setting up r-cran-curl (4.2+dfsg-1) ...
Setting up r-bioc-biocgenerics (0.32.0-1) ...
Setting up r-cran-rlang (0.4.1-1) ...
Setting up r-cran-matrixstats (0.55.0-1) ...
Setting up r-base-dev (3.6.1-7) ...
Setting up r-cran-assertthat (0.2.1-1) ...
Setting up littler (0.3.9-1) ...
Setting up r-cran-sys (3.3-1) ...
Setting up r-cran-backports (1.1.5-1) ...
Setting up r-cran-mime (0.7-1) ...
Setting up r-cran-digest (0.6.22-1) ...
Setting up r-cran-lambda.r (1.2.4-1) ...
Setting up r-cran-dbi (1.0.0-2) ...
Setting up r-cran-prettyunits (1.0.2-3) ...
Setting up r-cran-fansi (0.4.0-1) ...
Setting up r-cran-snow (1:0.4.3-1) ...
Setting up r-cran-glue (1.3.1-1) ...
Setting up r-cran-bit (1.1-14-1) ...
Setting up r-cran-zeallot (0.1.0-2) ...
Setting up r-cran-cli (1.1.0-1) ...
Setting up r-cran-bitops (1.0-6-4) ...
Setting up r-cran-bit64 (0.9-7-3) ...
Setting up r-bioc-zlibbioc (1.32.0+dfsg-1) ...
Setting up r-cran-askpass (1.1-1) ...
Setting up r-bioc-biobase (2.46.0-1) ...
Setting up r-cran-jsonlite (1.6+dfsg-1) ...
Setting up r-cran-pkgconfig (2.0.3-1) ...
Setting up r-cran-utf8 (1.1.4-1+b1) ...
Setting up r-cran-stringi (1.4.3-1) ...
Setting up r-bioc-s4vectors (0.24.0-1) ...
Setting up r-cran-futile.logger (1.4.3-3) ...
Setting up r-cran-memoise (1.1.0-2) ...
Setting up r-cran-purrr (0.3.3-1) ...
Setting up r-cran-matrix (1.2-17-2) ...
Setting up r-bioc-iranges (2.20.0-1) ...
Setting up r-cran-rcurl (1.95-4.12-1) ...
Setting up r-cran-pillar (1.3.1-1) ...
Setting up r-cran-ellipsis (0.3.0-1) ...
Setting up r-cran-openssl (1.4.1+dfsg-2) ...
Setting up r-cran-stringr (1.4.0-1) ...
Setting up r-bioc-biocparallel (1.20.0-1) ...
Setting up r-bioc-rhtslib (1.18.0+dfsg-1) ...
Setting up r-cran-tibble (2.0.1-1) ...
Setting up r-cran-tidyselect (0.2.5-1) ...
Setting up r-bioc-genomeinfodb (1.22.0-1) ...
Setting up r-cran-httr (1.4.1-1) ...
Setting up r-bioc-xvector (0.26.0-1) ...
Setting up r-cran-dplyr (0.8.3-1) ...
Setting up r-cran-dbplyr (1.4.2-1) ...
Setting up r-cran-vctrs (0.2.0-1) ...
Setting up r-bioc-delayedarray (0.12.0+dfsg-1) ...
Setting up r-bioc-genomicranges (1.38.0+dfsg-1) ...
Setting up r-bioc-biostrings (2.54.0-1) ...
Setting up r-cran-hms (0.5.2-1) ...
Setting up r-cran-blob (1.2.0-1) ...
Setting up r-bioc-rsamtools (2.2.1-1) ...
Setting up r-cran-rsqlite (2.1.2-1) ...
Setting up r-cran-progress (1.2.2-1) ...
Setting up r-bioc-summarizedexperiment (1.16.0+dfsg-1) ...
Setting up r-bioc-biocfilecache (1.10.2+dfsg-1) ...
Setting up r-bioc-annotationdbi (1.48.0-1) ...
Setting up r-bioc-biomart (2.42.0+dfsg-1) ...
Setting up r-bioc-genomicalignments (1.22.0-1) ...
Setting up r-bioc-rtracklayer (1.46.0-1) ...
Setting up r-bioc-genomicfeatures (1.38.0+dfsg-1) ...
Setting up r-bioc-bsgenome (1.54.0-1) ...
Setting up dh-autoreconf (19) ...
Setting up dh-strip-nondeterminism (1.6.1-1) ...
Setting up debhelper (12.7.1) ...
Setting up dh-r (20190917) ...
Setting up sbuild-build-depends-r-bioc-variantannotation-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.29-2+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 4.15.0-58-generic armhf (armv8l)
Toolchain package versions: binutils_2.33.1-2+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-17+rpi1 gcc-9_9.2.1-17+rpi1 libc6-dev_2.29-2+rpi1 libstdc++-9-dev_9.2.1-17+rpi1 libstdc++6_9.2.1-17+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.46 bash_5.0-5 binutils_2.33.1-2+rpi1 binutils-arm-linux-gnueabihf_2.33.1-2+rpi1 binutils-common_2.33.1-2+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+rpi1 cpp-9_9.2.1-17+rpi1 dash_0.5.10.2-6 dctrl-tools_2.24-3 debconf_1.5.73 debhelper_12.7.1 debianutils_4.9 dh-autoreconf_19 dh-r_20190917 dh-strip-nondeterminism_1.6.1-1 diffutils_1:3.7-3 dirmngr_2.2.17-3+b1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-2 e2fsprogs_1.45.4-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.37-6 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+rpi1 g++-9_9.2.1-17+rpi1 gcc_4:9.2.1-3+rpi1 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-6-base_6.5.0-1+rpi1+b3 gcc-9_9.2.1-17+rpi1 gcc-9-base_9.2.1-17+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gfortran_4:9.2.1-3+rpi1 gfortran-9_9.2.1-17+rpi1 gnupg_2.2.17-3 gnupg-l10n_2.2.17-3 gnupg-utils_2.2.17-3+b1 gpg_2.2.17-3+b1 gpg-agent_2.2.17-3+b1 gpg-wks-client_2.2.17-3+b1 gpg-wks-server_2.2.17-3+b1 gpgconf_2.2.17-3+b1 gpgsm_2.2.17-3+b1 gpgv_2.2.17-3+b1 grep_3.3-1 groff-base_1.22.4-3 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_3:20190709-2 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-17+rpi1 libassuan0_2.5.3-7 libatomic1_9.2.1-17+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2 libbinutils_2.33.1-2+rpi1 libblas-dev_3.8.0-8 libblas3_3.8.0-8 libblkid1_2.34-0.1 libbrotli1_1.0.7-5 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libbz2-dev_1.0.8-2 libc-bin_2.29-2+rpi1 libc-dev-bin_2.29-2+rpi1 libc6_2.29-2+rpi1 libc6-dev_2.29-2+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_9.2.1-17+rpi1 libcom-err2_1.45.4-1 libcroco3_0.6.13-1 libcurl4_7.66.0-1+b1 libcurl4-openssl-dev_7.66.0-1+b1 libdatrie1_0.2.12-3+b1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.250 libdebhelper-perl_12.7.1 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.4-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.1-1 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_9.2.1-17+rpi1 libgcc1_1:9.2.1-17+rpi1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran-9-dev_9.2.1-17+rpi1 libgfortran5_9.2.1-17+rpi1 libglib2.0-0_2.62.2-3 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.10-4 libgomp1_9.2.1-17+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 libisl19_0.20-2 libisl21_0.21-2 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_1.6-6 libkrb5-3_1.17-6+b1 libkrb5support0_1.17-6+b1 libksba8_1.3.5-2 liblapack-dev_3.8.0-8 liblapack3_3.8.0-8 libldap-2.4-2_2.4.48+dfsg-1+b2 libldap-common_2.4.48+dfsg-1 liblz4-1_1.9.2-1 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-6 libmagic1_1:5.37-6 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_1.39.2-1 libnpth0_1.6-1 libp11-kit0_0.23.18.1-2 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_10.32-5 libpcre2-32-0_10.32-5 libpcre2-8-0_10.32-5 libpcre2-dev_10.32-5 libpcre2-posix0_10.32-5 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_1.5.1-2 libpixman-1-0_0.36.0-1 libpng-dev_1.6.37-1 libpng16-16_1.6.37-1 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-1+b1 libsasl2-modules-db_2.1.27+dfsg-1+b1 libseccomp2_2.4.1-2+rpi1 libselinux1_2.9-2 libsemanage-common_2.9-3 libsemanage1_2.9-3 libsepol1_2.9-2 libsigsegv2_2.12-2 libsm6_2:1.2.3-1 libsmartcols1_2.34-0.1 libsqlite3-0_3.30.1-1 libss2_1.45.4-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-17+rpi1 libstdc++6_9.2.1-17+rpi1 libsub-override-perl_0.09-2 libswitch-perl_2.17-2 libsystemd0_242-7+rpi1 libtasn1-6_4.14-3 libtcl8.6_8.6.9+dfsg-2 libthai-data_0.1.28-3 libthai0_0.1.28-3 libtiff5_4.1.0-1 libtinfo5_6.1+20191019-1 libtinfo6_6.1+20191019-1 libtk8.6_8.6.9-2 libtool_2.4.6-11 libubsan1_9.2.1-17+rpi1 libuchardet0_0.0.6-3 libudev1_242-7+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+dfsg1-7+b2 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_1.4.3+dfsg-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 littler_0.3.9-1 login_1:4.7-2 logsave_1.45.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-1 mawk_1.3.3-17 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 netbase_5.6 openssl_1.1.1d-2 passwd_1:4.7-2 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_3.6.1-7 r-base-dev_3.6.1-7 r-bioc-annotationdbi_1.48.0-1 r-bioc-biobase_2.46.0-1 r-bioc-biocfilecache_1.10.2+dfsg-1 r-bioc-biocgenerics_0.32.0-1 r-bioc-biocparallel_1.20.0-1 r-bioc-biomart_2.42.0+dfsg-1 r-bioc-biostrings_2.54.0-1 r-bioc-bsgenome_1.54.0-1 r-bioc-delayedarray_0.12.0+dfsg-1 r-bioc-genomeinfodb_1.22.0-1 r-bioc-genomeinfodbdata_1.2.2-1 r-bioc-genomicalignments_1.22.0-1 r-bioc-genomicfeatures_1.38.0+dfsg-1 r-bioc-genomicranges_1.38.0+dfsg-1 r-bioc-iranges_2.20.0-1 r-bioc-rhtslib_1.18.0+dfsg-1 r-bioc-rsamtools_2.2.1-1 r-bioc-rtracklayer_1.46.0-1 r-bioc-s4vectors_0.24.0-1 r-bioc-summarizedexperiment_1.16.0+dfsg-1 r-bioc-xvector_0.26.0-1 r-bioc-zlibbioc_1.32.0+dfsg-1 r-cran-askpass_1.1-1 r-cran-assertthat_0.2.1-1 r-cran-backports_1.1.5-1 r-cran-bit_1.1-14-1 r-cran-bit64_0.9-7-3 r-cran-bitops_1.0-6-4 r-cran-blob_1.2.0-1 r-cran-cli_1.1.0-1 r-cran-crayon_1.3.4-4 r-cran-curl_4.2+dfsg-1 r-cran-dbi_1.0.0-2 r-cran-dbplyr_1.4.2-1 r-cran-digest_0.6.22-1 r-cran-dplyr_0.8.3-1 r-cran-ellipsis_0.3.0-1 r-cran-fansi_0.4.0-1 r-cran-formatr_1.7-1 r-cran-futile.logger_1.4.3-3 r-cran-futile.options_1.0.1-2 r-cran-glue_1.3.1-1 r-cran-hms_0.5.2-1 r-cran-httr_1.4.1-1 r-cran-jsonlite_1.6+dfsg-1 r-cran-lambda.r_1.2.4-1 r-cran-lattice_0.20-38-1 r-cran-littler_0.3.9-1 r-cran-magrittr_1.5-5 r-cran-matrix_1.2-17-2 r-cran-matrixstats_0.55.0-1 r-cran-memoise_1.1.0-2 r-cran-mime_0.7-1 r-cran-openssl_1.4.1+dfsg-2 r-cran-pillar_1.3.1-1 r-cran-pkgconfig_2.0.3-1 r-cran-pkgkitten_0.1.5-1 r-cran-prettyunits_1.0.2-3 r-cran-progress_1.2.2-1 r-cran-purrr_0.3.3-1 r-cran-r6_2.4.1-1 r-cran-rappdirs_0.3.1-1 r-cran-rcpp_1.0.3-1 r-cran-rcurl_1.95-4.12-1 r-cran-rlang_0.4.1-1 r-cran-rsqlite_2.1.2-1 r-cran-snow_1:0.4.3-1 r-cran-stringi_1.4.3-1 r-cran-stringr_1.4.0-1 r-cran-sys_3.3-1 r-cran-tibble_2.0.1-1 r-cran-tidyselect_0.2.5-1 r-cran-utf8_1.1.4-1+b1 r-cran-vctrs_0.2.0-1 r-cran-xml_3.98-1.20-2 r-cran-zeallot_0.1.0-2 raspbian-archive-keyring_20120528.2 readline-common_8.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-variantannotation-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.96-1 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 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Tue Nov 12 15:45:32 2019 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-variantannotation_1.32.0-1.dsc
dpkg-source: info: extracting r-bioc-variantannotation in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking r-bioc-variantannotation_1.32.0.orig.tar.gz
dpkg-source: info: unpacking r-bioc-variantannotation_1.32.0-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying drop_tests_requiring_large_data_sets.patch
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-b154106e-8989-414c-a62d-ef3bbb6a5c4f
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package r-bioc-variantannotation
dpkg-buildpackage: info: source version 1.32.0-1
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, snpstats
I: R Package: VariantAnnotation Version: 1.32.0
I: Building using R version 3.6.1-7
I: R API version: r-api-3.5
I: Using built-time from d/changelog: Tue, 12 Nov 2019 16:34:32 +0100
mkdir -p /<<PKGBUILDDIR>>/debian/r-bioc-variantannotation/usr/lib/R/site-library
R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-variantannotation/usr/lib/R/site-library --clean . "--built-timestamp='Tue, 12 Nov 2019 16:34:32 +0100'"
* installing *source* package 'VariantAnnotation' ...
** using staged installation
** libs
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -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 -D_FILE_OFFSET_BITS=64 -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" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -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 -D_FILE_OFFSET_BITS=64 -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" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -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 -D_FILE_OFFSET_BITS=64 -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" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dna_hash.c -o dna_hash.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rle.c -o rle.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c strhash.c -o strhash.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utilities.c -o utilities.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c vcffile.c -o vcffile.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c vcftype.c -o vcftype.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c writevcf.c -o writevcf.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o VariantAnnotation.so Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o writevcf.o /usr/lib/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -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-variantannotation/usr/lib/R/site-library/00LOCK-r-bioc-variantannotation-1.32.0/00new/VariantAnnotation/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'tabulate' in package 'VariantAnnotation'
** 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 (VariantAnnotation)
W: Ignoring specified R dependency: R (>= 2.8.0)
I: Using r-bioc-biocgenerics for Depends:BiocGenerics (>= 0.15.3)
I: Using r-bioc-genomeinfodb for Depends:GenomeInfoDb (>= 1.15.2)
I: Using r-bioc-genomicranges for Depends:GenomicRanges (>= 1.37.4)
I: Using r-bioc-summarizedexperiment for Depends:SummarizedExperiment (>= 1.9.9)
I: Using r-bioc-rsamtools for Depends:Rsamtools (>= 1.99.0)
I: Using r-cran-runit for Recommends:runit
I: Using r-bioc-snpstats for Recommends:snpstats
I: Using r-bioc-annotationhub for Suggests:AnnotationHub
W: Cannot find a debian package for Suggests:BSgenome.Hsapiens.UCSC.hg19
W: Cannot find a debian package for Suggests:TxDb.Hsapiens.UCSC.hg19.knownGene
W: Cannot find a debian package for Suggests:SNPlocs.Hsapiens.dbSNP.20101109
W: Cannot find a debian package for Suggests:SIFT.Hsapiens.dbSNP132
W: Cannot find a debian package for Suggests:SIFT.Hsapiens.dbSNP137
W: Cannot find a debian package for Suggests:PolyPhen.Hsapiens.dbSNP131
I: Using r-cran-ggplot2 for Suggests:ggplot2
W: Cannot find a debian package for Suggests:BiocStyle
I: Using r-cran-dbi for Imports:DBI
I: Using r-bioc-zlibbioc for Imports:zlibbioc
I: Using r-bioc-biobase for Imports:Biobase
I: Using r-bioc-s4vectors for Imports:S4Vectors (>= 0.17.24)
I: Using r-bioc-iranges for Imports:IRanges (>= 2.13.13)
I: Using r-bioc-xvector for Imports:XVector (>= 0.19.7)
I: Using r-bioc-biostrings for Imports:Biostrings (>= 2.47.6)
I: Using r-bioc-annotationdbi for Imports:AnnotationDbi (>= 1.27.9)
I: Using r-bioc-rtracklayer for Imports:rtracklayer (>= 1.39.7)
I: Using r-bioc-bsgenome for Imports:BSgenome (>= 1.47.3)
I: Using r-bioc-genomicfeatures for Imports:GenomicFeatures (>= 1.31.3)
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-variantannotation-dbgsym' in '../r-bioc-variantannotation-dbgsym_1.32.0-1_armhf.deb'.
dpkg-deb: building package 'r-bioc-variantannotation' in '../r-bioc-variantannotation_1.32.0-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../r-bioc-variantannotation_1.32.0-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2019-11-18T23:10:24Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
r-bioc-variantannotation_1.32.0-1_armhf.changes:
------------------------------------------------
Format: 1.8
Date: Tue, 12 Nov 2019 16:34:32 +0100
Source: r-bioc-variantannotation
Binary: r-bioc-variantannotation r-bioc-variantannotation-dbgsym
Architecture: armhf
Version: 1.32.0-1
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
r-bioc-variantannotation - BioConductor annotation of genetic variants
Changes:
r-bioc-variantannotation (1.32.0-1) unstable; urgency=medium
.
* New upstream version
* Fixed debian/watch for BioConductor
* debhelper-compat 12
* Standards-Version: 4.4.1
* debian/copyright: Use spaces rather than tabs in continuation lines.
* Remove obsolete fields Name, Contact from debian/upstream/metadata.
* Build-Depends: libcurl4-openssl-dev | libcurl4-dev
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r-bioc-variantannotation-dbgsym_1.32.0-1_armhf.deb
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new Debian package, version 2.0.
size 83288 bytes: control archive=544 bytes.
434 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: r-bioc-variantannotation-dbgsym
Source: r-bioc-variantannotation
Version: 1.32.0-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Installed-Size: 140
Depends: r-bioc-variantannotation (= 1.32.0-1)
Section: debug
Priority: optional
Description: debug symbols for r-bioc-variantannotation
Build-Ids: 0cf259002b9e5f1715e97642a520b96d677d2a66
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lrwxrwxrwx root/root 0 2019-11-12 15:34 ./usr/share/doc/r-bioc-variantannotation-dbgsym -> r-bioc-variantannotation
r-bioc-variantannotation_1.32.0-1_armhf.deb
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new Debian package, version 2.0.
size 3128116 bytes: control archive=3024 bytes.
1119 bytes, 14 lines control
7508 bytes, 75 lines md5sums
Package: r-bioc-variantannotation
Version: 1.32.0-1
Architecture: armhf
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Installed-Size: 4386
Depends: r-base-core (>= 3.6.1-7), r-api-3.5, r-api-bioc-3.10, r-bioc-biocgenerics (>= 0.15.3), r-bioc-genomeinfodb (>= 1.15.2), r-bioc-genomicranges (>= 1.37.4), r-bioc-summarizedexperiment (>= 1.9.9), r-bioc-rsamtools (>= 1.99.0), r-cran-dbi, r-bioc-zlibbioc, r-bioc-biobase, r-bioc-s4vectors (>= 0.17.24), r-bioc-iranges (>= 2.13.13), r-bioc-xvector (>= 0.19.7), r-bioc-biostrings (>= 2.47.6), r-bioc-annotationdbi (>= 1.27.9), r-bioc-rtracklayer (>= 1.39.7), r-bioc-bsgenome (>= 1.47.3), r-bioc-genomicfeatures (>= 1.31.3), libc6 (>= 2.15), libcurl4 (>= 7.18.0)
Recommends: r-cran-runit, r-bioc-snpstats
Suggests: r-bioc-annotationhub, r-cran-ggplot2
Section: gnu-r
Priority: optional
Homepage: https://bioconductor.org/packages/VariantAnnotation/
Description: BioConductor annotation of genetic variants
This BioConductor package provides R functions to annotate variants,
compute amino acid coding changess and to predict coding outcomes.
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Build Architecture: armhf
Build-Space: 10404
Build-Time: 203
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 826
Job: r-bioc-variantannotation_1.32.0-1
Machine Architecture: armhf
Package: r-bioc-variantannotation
Package-Time: 1047
Source-Version: 1.32.0-1
Space: 10404
Status: successful
Version: 1.32.0-1
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Finished at 2019-11-18T23:10:24Z
Build needed 00:17:27, 10404k disk space