Raspbian Package Auto-Building

Build log for r-bioc-rsamtools (2.4.0-1) on armhf

r-bioc-rsamtools2.4.0-1armhf → 2020-05-30 20:39:55

sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on test2019

+==============================================================================+
| r-bioc-rsamtools 2.4.0-1 (armhf)             Sat, 30 May 2020 20:18:28 +0000 |
+==============================================================================+

Package: r-bioc-rsamtools
Version: 2.4.0-1
Source Version: 2.4.0-1
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bullseye-staging-armhf-sbuild-07f72cc0-ef14-462a-8a56-330100d7b464' 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 [11.7 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.8 MB]
Fetched 24.5 MB in 22s (1107 kB/s)
Reading package lists...

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


Check APT
---------

Checking available source versions...

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

Reading package lists...
NOTICE: 'r-bioc-rsamtools' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/r-pkg-team/r-bioc-rsamtools.git
Please use:
git clone https://salsa.debian.org/r-pkg-team/r-bioc-rsamtools.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 3043 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main r-bioc-rsamtools 2.4.0-1 (dsc) [2428 B]
Get:2 http://172.17.0.1/private bullseye-staging/main r-bioc-rsamtools 2.4.0-1 (tar) [3034 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main r-bioc-rsamtools 2.4.0-1 (diff) [6420 B]
Fetched 3043 kB in 1s (3028 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/r-bioc-rsamtools-4jnXvp/r-bioc-rsamtools-2.4.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-rsamtools-4jnXvp' 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-gyoZkP/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-gyoZkP/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-gyoZkP/gpg/trustdb.gpg: trustdb created
gpg: key E70254B6505CF8F7: 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 E70254B6505CF8F7: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key E70254B6505CF8F7: 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-gyoZkP/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-gyoZkP/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-gyoZkP/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-gyoZkP/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-gyoZkP/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-gyoZkP/apt_archive ./ Packages [434 B]
Fetched 2110 B in 1s (3572 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-gyoZkP/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-gyoZkP/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY E70254B6505CF8F7
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
  libpam-cap
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 22 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-gyoZkP/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 (30.3 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 14093 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) ...

+------------------------------------------------------------------------------+
| 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-genomeinfodb (>= 1.1.3), r-bioc-genomicranges (>= 1.31.8), r-bioc-biostrings (>= 2.47.6), r-bioc-biocgenerics (>= 0.25.1), r-bioc-s4vectors (>= 0.17.25), r-bioc-iranges (>= 2.13.12), r-bioc-xvector (>= 0.19.7), r-bioc-zlibbioc, r-cran-bitops, r-bioc-biocparallel, r-bioc-rhtslib, libcurl4-openssl-dev
Filtered Build-Depends: debhelper-compat (= 12), dh-r, r-base-dev, r-bioc-genomeinfodb (>= 1.1.3), r-bioc-genomicranges (>= 1.31.8), r-bioc-biostrings (>= 2.47.6), r-bioc-biocgenerics (>= 0.25.1), r-bioc-s4vectors (>= 0.17.25), r-bioc-iranges (>= 2.13.12), r-bioc-xvector (>= 0.19.7), r-bioc-zlibbioc, r-cran-bitops, r-bioc-biocparallel, r-bioc-rhtslib, libcurl4-openssl-dev
dpkg-deb: building package 'sbuild-build-depends-r-bioc-rsamtools-dummy' in '/<<BUILDDIR>>/resolver-gyoZkP/apt_archive/sbuild-build-depends-r-bioc-rsamtools-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-rsamtools-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-gyoZkP/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-gyoZkP/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-gyoZkP/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-gyoZkP/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-gyoZkP/apt_archive ./ Sources [644 B]
Get:5 copy:/<<BUILDDIR>>/resolver-gyoZkP/apt_archive ./ Packages [729 B]
Fetched 2706 B in 1s (4426 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-gyoZkP/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-gyoZkP/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY E70254B6505CF8F7
Reading package lists...

Install r-bioc-rsamtools build dependencies (apt-based resolver)
----------------------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
  libpam-cap
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bsdmainutils ca-certificates cpp-9
  dctrl-tools debhelper dh-autoreconf dh-r dh-strip-nondeterminism dwz file
  fontconfig fontconfig-config fonts-dejavu-core g++-9 gcc-9 gcc-9-base
  gettext gettext-base gfortran gfortran-9 groff-base icu-devtools
  intltool-debian libarchive-zip-perl libasan5 libblas-dev libblas3
  libboost-dev libboost1.67-dev libbrotli1 libbsd0 libbz2-dev libcairo2
  libcroco3 libcurl4 libcurl4-openssl-dev libdatrie1 libdebhelper-perl libelf1
  libexpat1 libfile-stripnondeterminism-perl libfile-which-perl libfontconfig1
  libfreetype6 libfribidi0 libgcc-9-dev 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
  libstdc++-9-dev 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-biocgenerics
  r-bioc-biocparallel r-bioc-biostrings r-bioc-genomeinfodb
  r-bioc-genomeinfodbdata r-bioc-genomicranges r-bioc-iranges r-bioc-rhtslib
  r-bioc-s4vectors r-bioc-xvector r-bioc-zlibbioc r-cran-bh r-cran-bitops
  r-cran-crayon r-cran-formatr r-cran-futile.logger r-cran-futile.options
  r-cran-lambda.r r-cran-rcurl r-cran-snow sensible-utils ucf unzip x11-common
  xauth xdg-utils zip zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
  vacation gcc-9-locales debtags dh-make gcc-9-doc 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
  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
  libstdc++-9-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-biobase
  r-bioc-delayedarray r-bioc-rsamtools r-bioc-annotationdbi r-bioc-affy
  r-bioc-deseq2 r-bioc-annotate r-cran-foreach r-cran-bbmisc
  r-bioc-variantannotation r-bioc-genomicalignments r-bioc-shortread
  r-cran-codetools r-cran-knitr r-cran-data.table r-bioc-bsgenome
  r-bioc-genomicfeatures r-cran-matrix r-bioc-rtracklayer r-bioc-gviz
  r-bioc-annotationhub r-bioc-edger r-bioc-summarizedexperiment r-bioc-graph
  r-cran-rstudioapi r-cran-shiny r-cran-rmarkdown r-cran-jsonlite 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-bioc-rsamtools
  r-cran-batchtools r-cran-rmpi r-cran-digest r-bioc-annotate
  r-bioc-summarizedexperiment r-cran-testthat r-cran-withr r-cran-mockery
  r-cran-testit r-cran-codetools r-cran-survival libfile-mimeinfo-perl
  libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev 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 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-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-biocgenerics r-bioc-biocparallel
  r-bioc-biostrings r-bioc-genomeinfodb r-bioc-genomeinfodbdata
  r-bioc-genomicranges r-bioc-iranges r-bioc-rhtslib r-bioc-s4vectors
  r-bioc-xvector r-bioc-zlibbioc r-cran-bh r-cran-bitops r-cran-crayon
  r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-lambda.r
  r-cran-rcurl r-cran-snow sbuild-build-depends-r-bioc-rsamtools-dummy
  sensible-utils ucf unzip x11-common xauth xdg-utils zip zlib1g-dev
The following packages will be upgraded:
  cpp-9 g++-9 gcc-9 gcc-9-base libasan5 libgcc-9-dev libstdc++-9-dev
7 upgraded, 155 newly installed, 0 to remove and 15 not upgraded.
Need to get 159 MB of archives.
After this operation, 429 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-gyoZkP/apt_archive ./ sbuild-build-depends-r-bioc-rsamtools-dummy 0.invalid.0 [1008 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.2-1 [318 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.1-1 [1262 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf g++-9 armhf 9.3.0-13+rpi1 [8225 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf gcc-9 armhf 9.3.0-13+rpi1 [7731 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf cpp-9 armhf 9.3.0-13+rpi1 [7464 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libasan5 armhf 9.3.0-13+rpi1 [348 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libstdc++-9-dev armhf 9.3.0-13+rpi1 [1713 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libgcc-9-dev armhf 9.3.0-13+rpi1 [639 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf gcc-9-base armhf 9.3.0-13+rpi1 [197 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libswitch-perl all 2.17-2 [20.5 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf ucf all 3.0042 [73.9 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-1 [775 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1g-1 [1272 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf openssl armhf 1.1.1g-1 [811 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf ca-certificates all 20190110 [157 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf dctrl-tools armhf 2.24-3 [94.2 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.1 [187 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.8.1-1 [25.2 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.8.1-1 [14.9 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.64.2-1 [1158 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-3 [7987 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-5 [592 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.1 [1012 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf zip armhf 3.0-11 [212 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf unzip armhf 6.0-25 [152 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libpaper1 armhf 1.1.28 [20.5 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libpaper-utils armhf 1.1.28 [17.7 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf xdg-utils all 1.1.3-2 [74.6 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-2 [108 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libpng16-16 armhf 1.6.37-2 [274 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libfreetype6 armhf 2.10.1-2 [330 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf fonts-dejavu-core all 2.37-1 [1068 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf fontconfig-config all 2.13.1-4.2 [281 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libfontconfig1 armhf 2.13.1-4.2 [328 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libpixman-1-0 armhf 0.36.0-1 [458 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.14-2 [135 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.6.9-2 [298 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.6.9-2 [692 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libxcb-render0 armhf 1.14-2 [110 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libxcb-shm0 armhf 1.14-2 [101 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1+b2 [47.8 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libcairo2 armhf 1.16.0-4 [599 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.7-6.1 [255 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-7+rpi1 [61.5 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-7+rpi1 [112 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6.1-2 [14.5 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-7+rpi1 [318 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-7+rpi1 [135 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.40.0-1+b2 [74.2 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1 [53.9 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b1 [54.3 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libcurl4 armhf 7.68.0-1 [286 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo armhf 1:1.5.2-2+b1 [110 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10.1.0-1+rpi1 [232 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-2 [1602 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf fontconfig armhf 2.13.1-4.2 [416 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libfribidi0 armhf 1.0.8-2 [63.5 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libgraphite2-3 armhf 1.3.14-1 [70.3 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libharfbuzz0b armhf 2.6.4-1+rpi1 [1308 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libthai-data all 0.1.28-3 [170 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libdatrie1 armhf 0.2.12-3+b2 [36.4 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf libthai0 armhf 0.1.28-3 [51.0 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libpango-1.0-0 armhf 1.44.7-4 [165 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libpangoft2-1.0-0 armhf 1.44.7-4 [52.6 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf libpangocairo-1.0-0 armhf 1.44.7-4 [44.9 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf libtcl8.6 armhf 8.6.10+dfsg-1 [886 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf libjbig0 armhf 2.1-3.1+b2 [27.6 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf libwebp6 armhf 0.6.1-2 [228 kB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf libtiff5 armhf 4.1.0+git191117-2 [250 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf libxft2 armhf 2.3.2-2 [49.3 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf x11-common all 1:7.7+20 [252 kB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf libxss1 armhf 1:1.2.3-1 [17.3 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf libtk8.6 armhf 8.6.10-1 [678 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf libice6 armhf 2:1.0.9-2 [51.6 kB]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf libsm6 armhf 2:1.2.3-1 [32.9 kB]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf libxt6 armhf 1:1.1.5-1+b3 [156 kB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf r-base-core armhf 4.0.0-3 [24.6 MB]
Get:109 http://172.17.0.1/private bullseye-staging/main armhf libgfortran-9-dev armhf 9.3.0-13+rpi1 [278 kB]
Get:110 http://172.17.0.1/private bullseye-staging/main armhf gfortran-9 armhf 9.3.0-13+rpi1 [8108 kB]
Get:111 http://172.17.0.1/private bullseye-staging/main armhf gfortran armhf 4:9.2.1-3.1+rpi1 [1440 B]
Get:112 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.9.0-2 [113 kB]
Get:113 http://172.17.0.1/private bullseye-staging/main armhf liblapack-dev armhf 3.9.0-2 [2981 kB]
Get:114 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2-1 [79.5 kB]
Get:115 http://172.17.0.1/private bullseye-staging/main armhf libncurses-dev armhf 6.2-1 [284 kB]
Get:116 http://172.17.0.1/private bullseye-staging/main armhf libncurses5-dev armhf 6.2-1 [932 B]
Get:117 http://172.17.0.1/private bullseye-staging/main armhf libreadline-dev armhf 8.0-4 [116 kB]
Get:118 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.2-2+b1 [179 kB]
Get:119 http://172.17.0.1/private bullseye-staging/main armhf libjpeg-dev all 1:1.5.2-2 [57.5 kB]
Get:120 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-16-0 armhf 10.34-7 [190 kB]
Get:121 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-32-0 armhf 10.34-7 [181 kB]
Get:122 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-posix2 armhf 10.34-7 [44.7 kB]
Get:123 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-dev armhf 10.34-7 [614 kB]
Get:124 http://172.17.0.1/private bullseye-staging/main armhf libpcre16-3 armhf 2:8.39-12 [234 kB]
Get:125 http://172.17.0.1/private bullseye-staging/main armhf libpcre32-3 armhf 2:8.39-12 [227 kB]
Get:126 http://172.17.0.1/private bullseye-staging/main armhf libpcrecpp0v5 armhf 2:8.39-12 [150 kB]
Get:127 http://172.17.0.1/private bullseye-staging/main armhf libpcre3-dev armhf 2:8.39-12 [564 kB]
Get:128 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:129 http://172.17.0.1/private bullseye-staging/main armhf libpng-dev armhf 1.6.37-2 [276 kB]
Get:130 http://172.17.0.1/private bullseye-staging/main armhf libbz2-dev armhf 1.0.8-2 [27.7 kB]
Get:131 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:132 http://172.17.0.1/private bullseye-staging/main armhf icu-devtools armhf 63.2-3 [163 kB]
Get:133 http://172.17.0.1/private bullseye-staging/main armhf libicu-dev armhf 63.2-3 [8860 kB]
Get:134 http://172.17.0.1/private bullseye-staging/main armhf libxmuu1 armhf 2:1.1.2-2+b3 [23.4 kB]
Get:135 http://172.17.0.1/private bullseye-staging/main armhf xauth armhf 1:1.0.10-1 [36.4 kB]
Get:136 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
Get:137 http://172.17.0.1/private bullseye-staging/main armhf r-base-dev all 4.0.0-3 [4480 B]
Get:138 http://172.17.0.1/private bullseye-staging/main armhf libfile-which-perl all 1.23-1 [16.6 kB]
Get:139 http://172.17.0.1/private bullseye-staging/main armhf dh-r all 20200314 [39.1 kB]
Get:140 http://172.17.0.1/private bullseye-staging/main armhf libboost1.67-dev armhf 1.67.0-18 [8389 kB]
Get:141 http://172.17.0.1/private bullseye-staging/main armhf libboost-dev armhf 1.67.0.2+b12 [4464 B]
Get:142 http://172.17.0.1/private bullseye-staging/main armhf libcurl4-openssl-dev armhf 7.68.0-1 [360 kB]
Get:143 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-biocgenerics all 0.34.0-1 [639 kB]
Get:144 http://172.17.0.1/private bullseye-staging/main armhf r-cran-formatr all 1.7-2 [151 kB]
Get:145 http://172.17.0.1/private bullseye-staging/main armhf r-cran-lambda.r all 1.2.4-2 [118 kB]
Get:146 http://172.17.0.1/private bullseye-staging/main armhf r-cran-futile.options all 1.0.1-3 [20.0 kB]
Get:147 http://172.17.0.1/private bullseye-staging/main armhf r-cran-futile.logger all 1.4.3-4 [98.4 kB]
Get:148 http://172.17.0.1/private bullseye-staging/main armhf r-cran-snow all 1:0.4.3-2 [109 kB]
Get:149 http://172.17.0.1/private bullseye-staging/main armhf r-cran-bh all 1.66.0-1 [5072 B]
Get:150 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-biocparallel armhf 1.22.0-1 [1115 kB]
Get:151 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-s4vectors armhf 0.26.1-1 [2007 kB]
Get:152 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-iranges armhf 2.22.2-1 [2280 kB]
Get:153 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-zlibbioc all 1.34.0+dfsg-1 [8788 B]
Get:154 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-xvector armhf 0.28.0-1 [616 kB]
Get:155 http://172.17.0.1/private bullseye-staging/main armhf r-cran-crayon all 1.3.4-5 [750 kB]
Get:156 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-biostrings armhf 2.56.0-1 [14.2 MB]
Get:157 http://172.17.0.1/private bullseye-staging/main armhf r-cran-bitops armhf 1.0-6-4+b1 [23.8 kB]
Get:158 http://172.17.0.1/private bullseye-staging/main armhf r-cran-rcurl armhf 1.98-1.2-1+b1 [788 kB]
Get:159 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-genomeinfodbdata all 1.2.3-1 [10.4 MB]
Get:160 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-genomeinfodb all 1.24.0-1 [3902 kB]
Get:161 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-genomicranges armhf 1.40.0+dfsg-1 [1873 kB]
Get:162 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-rhtslib armhf 1.20.0+dfsg-1 [965 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 159 MB in 48s (3300 kB/s)
Selecting previously unselected package libbsd0:armhf.
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Preparing to unpack .../000-libbsd0_0.10.0-1_armhf.deb ...
Unpacking libbsd0:armhf (0.10.0-1) ...
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Unpacking libtinfo5:armhf (6.2-1) ...
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Unpacking libstdc++-9-dev:armhf (9.3.0-13+rpi1) over (9.3.0-12+rpi1) ...
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Unpacking gcc-9-base:armhf (9.3.0-13+rpi1) over (9.3.0-12+rpi1) ...
Selecting previously unselected package sensible-utils.
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Preparing to unpack .../022-m4_1.4.18-4_armhf.deb ...
Unpacking m4 (1.4.18-4) ...
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Unpacking r-cran-rcurl (1.98-1.2-1+b1) ...
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Unpacking r-bioc-genomeinfodb (1.24.0-1) ...
Selecting previously unselected package r-bioc-genomicranges.
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Unpacking r-bioc-genomicranges (1.40.0+dfsg-1) ...
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Unpacking r-bioc-rhtslib (1.20.0+dfsg-1) ...
Selecting previously unselected package sbuild-build-depends-r-bioc-rsamtools-dummy.
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Unpacking sbuild-build-depends-r-bioc-rsamtools-dummy (0.invalid.0) ...
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 (1.3.14-1) ...
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 (0.21.0-1) ...
Setting up libpcre16-3:armhf (2:8.39-12) ...
Setting up libdatrie1:armhf (0.2.12-3+b2) ...
Setting up libmagic-mgc (1:5.38-5) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.64.2-1) ...
No schema files found: doing nothing.
Setting up libssl1.1:armhf (1.1.1g-1) ...
Setting up unzip (6.0-25) ...
Setting up libdebhelper-perl (13.1) ...
Setting up libbrotli1:armhf (1.0.7-6.1) ...
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
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of start.
Setting up libnghttp2-14:armhf (1.40.0-1+b2) ...
Setting up libmagic1:armhf (1:5.38-5) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.38-5) ...
Setting up libjbig0:armhf (2.1-3.1+b2) ...
Setting up libpcre2-16-0:armhf (10.34-7) ...
Setting up libicu63:armhf (63.2-3) ...
Setting up libkrb5support0:armhf (1.17-7+rpi1) ...
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 (3.9.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libjpeg62-turbo:armhf (1:1.5.2-2+b1) ...
Setting up libswitch-perl (2.17-2) ...
Setting up libx11-data (2:1.6.9-2) ...
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 (6.2-1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libfribidi0:armhf (1.0.8-2) ...
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 (63.2-3) ...
Setting up pkg-config (0.29.2-1) ...
Setting up fonts-dejavu-core (2.37-1) ...
Setting up libpcre2-posix2:armhf (10.34-7) ...
Setting up libk5crypto3:armhf (1.17-7+rpi1) ...
Setting up libgfortran5:armhf (10.1.0-1+rpi1) ...
Setting up liblzma-dev:armhf (5.2.4-1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libthai-data (0.1.28-3) ...
Setting up libssh2-1:armhf (1.8.0-2.1) ...
Setting up libkrb5-3:armhf (1.17-7+rpi1) ...
Setting up libtiff5:armhf (4.1.0+git191117-2) ...
Setting up openssl (1.1.1g-1) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.2-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libicu-dev:armhf (63.2-3) ...
Setting up libxml2:armhf (2.9.10+dfsg-5) ...
Setting up xdg-utils (1.1.3-2) ...
Setting up libblas-dev:armhf (3.9.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up dctrl-tools (2.24-3) ...
Setting up gcc-9-base:armhf (9.3.0-13+rpi1) ...
Setting up libbz2-dev:armhf (1.0.8-2) ...
Setting up libfile-stripnondeterminism-perl (1.8.1-1) ...
Setting up libice6:armhf (2:1.0.9-2) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up liblapack3:armhf (3.9.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libncurses-dev:armhf (6.2-1) ...
Setting up libxcb1:armhf (1.14-2) ...
Setting up libpcre2-dev:armhf (10.34-7) ...
Setting up libtool (2.4.6-14) ...
Setting up libxcb-render0:armhf (1.14-2) ...
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 m4 (1.4.18-4) ...
Setting up libxcb-shm0:armhf (1.14-2) ...
Setting up libreadline-dev:armhf (8.0-4) ...
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 libasan5:armhf (9.3.0-13+rpi1) ...
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 (3.9.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up libgssapi-krb5-2:armhf (1.17-7+rpi1) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up ucf (3.0042) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.8.1-1) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-5) ...
Setting up libncurses5-dev:armhf (6.2-1) ...
Setting up cpp-9 (9.3.0-13+rpi1) ...
Setting up libcurl4:armhf (7.68.0-1) ...
Setting up libx11-6:armhf (2:1.6.9-2) ...
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 (1:1.16.2-1) ...
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 fontconfig-config (2.13.1-4.2) ...
Setting up libxext6:armhf (2:1.3.3-1+b2) ...
Setting up libpaper-utils (1.1.28) ...
Setting up man-db (2.9.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libgcc-9-dev:armhf (9.3.0-13+rpi1) ...
Setting up libcurl4-openssl-dev:armhf (7.68.0-1) ...
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 (2.13.1-4.2) ...
Setting up gcc-9 (9.3.0-13+rpi1) ...
Setting up fontconfig (2.13.1-4.2) ...
Regenerating fonts cache... done.
Setting up libxft2:armhf (2.3.2-2) ...
Setting up libstdc++-9-dev:armhf (9.3.0-13+rpi1) ...
Setting up po-debconf (1.0.21) ...
Setting up libtk8.6:armhf (8.6.10-1) ...
Setting up libpango-1.0-0:armhf (1.44.7-4) ...
Setting up libgfortran-9-dev:armhf (9.3.0-13+rpi1) ...
Setting up libcairo2:armhf (1.16.0-4) ...
Setting up g++-9 (9.3.0-13+rpi1) ...
Setting up libpangoft2-1.0-0:armhf (1.44.7-4) ...
Setting up libpangocairo-1.0-0:armhf (1.44.7-4) ...
Setting up libboost1.67-dev:armhf (1.67.0-18) ...
Setting up gfortran-9 (9.3.0-13+rpi1) ...
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 r-base-core (4.0.0-3) ...

Creating config file /etc/R/Renviron with new version
Setting up r-cran-crayon (1.3.4-5) ...
Setting up r-cran-futile.options (1.0.1-3) ...
Setting up r-cran-formatr (1.7-2) ...
Setting up libboost-dev:armhf (1.67.0.2+b12) ...
Setting up r-bioc-genomeinfodbdata (1.2.3-1) ...
Setting up r-cran-bh (1.66.0-1) ...
Setting up r-bioc-biocgenerics (0.34.0-1) ...
Setting up r-base-dev (4.0.0-3) ...
Setting up r-cran-lambda.r (1.2.4-2) ...
Setting up r-cran-snow (1:0.4.3-2) ...
Setting up r-cran-bitops (1.0-6-4+b1) ...
Setting up r-bioc-zlibbioc (1.34.0+dfsg-1) ...
Setting up r-bioc-s4vectors (0.26.1-1) ...
Setting up r-cran-futile.logger (1.4.3-4) ...
Setting up r-bioc-iranges (2.22.2-1) ...
Setting up r-cran-rcurl (1.98-1.2-1+b1) ...
Setting up r-bioc-biocparallel (1.22.0-1) ...
Setting up r-bioc-rhtslib (1.20.0+dfsg-1) ...
Setting up r-bioc-genomeinfodb (1.24.0-1) ...
Setting up r-bioc-xvector (0.28.0-1) ...
Setting up r-bioc-genomicranges (1.40.0+dfsg-1) ...
Setting up r-bioc-biostrings (2.56.0-1) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (13.1) ...
Setting up dh-r (20200314) ...
Setting up sbuild-build-depends-r-bioc-rsamtools-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.30-8+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.

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

Kernel: Linux 4.19.20-v7+ armhf (armv7l)
Toolchain package versions: binutils_2.34-8+rpi1 dpkg-dev_1.19.7 g++-9_9.3.0-13+rpi1 gcc-9_9.3.0-13+rpi1 libc6-dev_2.30-8+rpi1 libstdc++-9-dev_9.3.0-13+rpi1 libstdc++6_10.1.0-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_2.1.4 autoconf_2.69-11.1 automake_1:1.16.2-1 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-8+rpi1 binutils-arm-linux-gnueabihf_2.34-8+rpi1 binutils-common_2.34-8+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.35.1-5 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_9.3.0-13+rpi1 dash_0.5.10.2-7 dctrl-tools_2.24-3 debconf_1.5.74 debhelper_13.1 debianutils_4.9.1 dh-autoreconf_19 dh-r_20200314 dh-strip-nondeterminism_1.8.1-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.35.1-5 file_1:5.38-5 findutils_4.7.0-1 fontconfig_2.13.1-4.2 fontconfig-config_2.13.1-4.2 fonts-dejavu-core_2.37-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.3.0-13+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10.1.0-1+rpi1 gcc-9_9.3.0-13+rpi1 gcc-9-base_9.3.0-13+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gfortran_4:9.2.1-3.1+rpi1 gfortran-9_9.3.0-13+rpi1 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 icu-devtools_63.2-3 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-3 libacl1_2.2.53-8 libapt-pkg6.0_2.1.4 libarchive-zip-perl_1.68-1 libasan5_9.3.0-13+rpi1 libassuan0_2.5.3-7 libatomic1_10.1.0-1+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.34-8+rpi1 libblas-dev_3.9.0-2 libblas3_3.9.0-2 libblkid1_2.35.1-5 libboost-dev_1.67.0.2+b12 libboost1.67-dev_1.67.0-18 libbrotli1_1.0.7-6.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libbz2-dev_1.0.8-2 libc-bin_2.30-8+rpi1 libc-dev-bin_2.30-8+rpi1 libc6_2.30-8+rpi1 libc6-dev_2.30-8+rpi1 libcairo2_1.16.0-4 libcap-ng0_0.7.9-2.1+b1 libcap2_1:2.34-2 libcap2-bin_1:2.34-2 libcc1-0_10.1.0-1+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.34-8+rpi1 libctf0_2.34-8+rpi1 libcurl4_7.68.0-1 libcurl4-openssl-dev_7.68.0-1 libdatrie1_0.2.12-3+b2 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.252 libdebhelper-perl_13.1 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.35.1-5 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.8.1-1 libfile-which-perl_1.23-1 libfontconfig1_2.13.1-4.2 libfreetype6_2.10.1-2 libfribidi0_1.0.8-2 libgcc-9-dev_9.3.0-13+rpi1 libgcc-s1_10.1.0-1+rpi1 libgcc1_1:10.1.0-1+rpi1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran-9-dev_9.3.0-13+rpi1 libgfortran5_10.1.0-1+rpi1 libglib2.0-0_2.64.2-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-2 libgomp1_10.1.0-1+rpi1 libgpg-error0_1.37-1 libgraphite2-3_1.3.14-1 libgssapi-krb5-2_1.17-7+rpi1 libharfbuzz0b_2.6.4-1+rpi1 libhogweed5_3.5.1+really3.5.1-2 libice6_2:1.0.9-2 libicu-dev_63.2-3 libicu63_63.2-3 libidn2-0_2.3.0-1 libisl22_0.22.1-1 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_1.17-7+rpi1 libkeyutils1_1.6.1-2 libkrb5-3_1.17-7+rpi1 libkrb5support0_1.17-7+rpi1 libksba8_1.3.5-2 liblapack-dev_3.9.0-2 liblapack3_3.9.0-2 libldap-2.4-2_2.4.50+dfsg-1 libldap-common_2.4.50+dfsg-1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.35.1-5 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses-dev_6.2-1 libncurses5-dev_6.2-1 libncurses6_6.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1+b2 libnpth0_1.6-1 libp11-kit0_0.23.20-1 libpam-cap_1:2.34-2 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_1.44.7-4 libpangocairo-1.0-0_1.44.7-4 libpangoft2-1.0-0_1.44.7-4 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 libperl5.28_5.28.1-6 libperl5.30_5.30.0-10 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_0.21.0-1 libreadline-dev_8.0-4 libreadline7_7.0-5 libreadline8_8.0-4 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.0-1+b1 libsemanage-common_3.0-1 libsemanage1_3.0-1+b1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsm6_2:1.2.3-1 libsmartcols1_2.35.1-5 libsqlite3-0_3.31.1-5 libss2_1.45.6-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1g-1 libstdc++-9-dev_9.3.0-13+rpi1 libstdc++6_10.1.0-1+rpi1 libsub-override-perl_0.09-2 libswitch-perl_2.17-2 libsystemd0_245.5-3+rpi1 libtasn1-6_4.16.0-2 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_6.2-1 libtinfo6_6.2-1 libtk8.6_8.6.10-1 libtool_2.4.6-14 libubsan1_10.1.0-1+rpi1 libuchardet0_0.0.6-3 libudev1_245.5-3+rpi1 libunistring2_0.9.10-2 libuuid1_2.35.1-5 libwebp6_0.6.1-2 libx11-6_2:1.6.9-2 libx11-data_2:1.6.9-2 libxau6_1:1.0.8-1+b2 libxcb-render0_1.14-2 libxcb-shm0_1.14-2 libxcb1_1.14-2 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxft2_2.3.2-2 libxml2_2.9.10+dfsg-5 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-3+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-2 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mount_2.35.1-5 ncurses-base_6.2-1 ncurses-bin_6.2-1 openssl_1.1.1g-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-10 perl-base_5.30.0-10 perl-modules-5.28_5.28.1-6 perl-modules-5.30_5.30.0-10 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21 r-base-core_4.0.0-3 r-base-dev_4.0.0-3 r-bioc-biocgenerics_0.34.0-1 r-bioc-biocparallel_1.22.0-1 r-bioc-biostrings_2.56.0-1 r-bioc-genomeinfodb_1.24.0-1 r-bioc-genomeinfodbdata_1.2.3-1 r-bioc-genomicranges_1.40.0+dfsg-1 r-bioc-iranges_2.22.2-1 r-bioc-rhtslib_1.20.0+dfsg-1 r-bioc-s4vectors_0.26.1-1 r-bioc-xvector_0.28.0-1 r-bioc-zlibbioc_1.34.0+dfsg-1 r-cran-bh_1.66.0-1 r-cran-bitops_1.0-6-4+b1 r-cran-crayon_1.3.4-5 r-cran-formatr_1.7-2 r-cran-futile.logger_1.4.3-4 r-cran-futile.options_1.0.1-3 r-cran-lambda.r_1.2.4-2 r-cran-rcurl_1.98-1.2-1+b1 r-cran-snow_1:0.4.3-2 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-rsamtools-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 ucf_3.0042 unzip_6.0-25 util-linux_2.35.1-5 x11-common_1:7.7+20 xauth_1:1.0.10-1 xdg-utils_1.1.3-2 xz-utils_5.2.4-1 zip_3.0-11 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2

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


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

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Tue May 19 09:42:58 2020 UTC
gpgv:                using RSA key 9A3C07BD06DE2F416E813A5D612EF1613E050F54
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./r-bioc-rsamtools_2.4.0-1.dsc
dpkg-source: info: extracting r-bioc-rsamtools in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking r-bioc-rsamtools_2.4.0.orig.tar.gz
dpkg-source: info: unpacking r-bioc-rsamtools_2.4.0-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying skip_test_requiring_network.patch

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

Sufficient free space for build

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

APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=d540cc9aba1e46398de3fa2f71b5e534
JOURNAL_STREAM=8:18935
LANG=en_GB.UTF-8
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=116
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-07f72cc0-ef14-462a-8a56-330100d7b464
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_ID=c21080

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

dpkg-buildpackage: info: source package r-bioc-rsamtools
dpkg-buildpackage: info: source version 2.4.0-1
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
 debian/rules clean
dh clean --buildsystem R
   dh_auto_clean -O--buildsystem=R
   dh_autoreconf_clean -O--buildsystem=R
   dh_clean -O--buildsystem=R
 debian/rules binary-arch
dh binary-arch --buildsystem R
   dh_update_autotools_config -a -O--buildsystem=R
   dh_autoreconf -a -O--buildsystem=R
   dh_auto_configure -a -O--buildsystem=R
   dh_auto_build -a -O--buildsystem=R
   dh_auto_test -a -O--buildsystem=R
   create-stamp debian/debhelper-build-stamp
   dh_testroot -a -O--buildsystem=R
   dh_prep -a -O--buildsystem=R
   dh_auto_install -a -O--buildsystem=R
I: R packages needed for DEP8: runit, shortread
I: R Package: Rsamtools Version: 2.4.0
I: Building using R version 4.0.0-3
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Tue, 19 May 2020 11:32:13 +0200
	mkdir -p /<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library
	R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library --clean . "--built-timestamp='Tue, 19 May 2020 11:32:13 +0200'"
* installing *source* package 'Rsamtools' ...
** 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/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -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/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c IRanges_stubs.c -o IRanges_stubs.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c PileupBuffer.cpp -o PileupBuffer.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c PosCacheColl.cpp -o PosCacheColl.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_Rsamtools.c -o R_init_Rsamtools.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ResultManager.cpp -o ResultManager.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -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 -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -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/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c as_bam.c -o as_bam.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bam.c -o bam.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bam_data.c -o bam_data.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bam_mate_iter.cpp -o bam_mate_iter.o
In file included from /usr/lib/R/site-library/Rhtslib/include/sam.h:29,
                 from Template.h:9,
                 from BamIterator.h:10,
                 from BamRangeIterator.h:7,
                 from bam_mate_iter.cpp:2:
BamRangeIterator.h: In member function 'virtual void BamRangeIterator::finalize_inprogress(bamFile)':
/usr/lib/R/site-library/Rhtslib/include/bam.h:57:41: warning: ignoring return value of 'int64_t bgzf_seek(BGZF*, int64_t, int)', declared with attribute warn_unused_result [-Wunused-result]
   57 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
      |                                ~~~~~~~~~^~~~~~~~~~~~~~
BamRangeIterator.h:138:9: note: in expansion of macro 'bam_seek'
  138 |         bam_seek(bfile, pos, SEEK_SET);
      |         ^~~~~~~~
BamIterator.h: In constructor 'BamIterator::BamIterator(bamFile, const bam_index_t*)':
/usr/lib/R/site-library/Rhtslib/include/bam.h:57:41: warning: ignoring return value of 'int64_t bgzf_seek(BGZF*, int64_t, int)', declared with attribute warn_unused_result [-Wunused-result]
   57 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
      |                                ~~~~~~~~~^~~~~~~~~~~~~~
BamIterator.h:87:9: note: in expansion of macro 'bam_seek'
   87 |         bam_seek(bfile, 0, 0);
      |         ^~~~~~~~
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bam_plbuf.c -o bam_plbuf.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bam_sort.c -o bam_sort.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bambuffer.c -o bambuffer.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bamfile.c -o bamfile.o
bamfile.c: In function 'bamfile_isincomplete':
bamfile.c:168:13: warning: ignoring return value of 'bgzf_seek', declared with attribute warn_unused_result [-Wunused-result]
  168 |             bgzf_seek(bfile->file->x.bam, offset, SEEK_SET);
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bcffile.c -o bcffile.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c encode.c -o encode.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fafile.c -o fafile.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c idxstats.c -o idxstats.o
In file included from /usr/lib/R/site-library/Rhtslib/include/sam.h:29,
                 from bamfile.h:5,
                 from idxstats.c:1:
idxstats.c: In function 'idxstats_bamfile':
/usr/lib/R/site-library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of 'bgzf_seek', declared with attribute warn_unused_result [-Wunused-result]
   57 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
      |                                ^~~~~~~~~~~~~~~~~~~~~~~
idxstats.c:20:5: note: in expansion of macro 'bam_seek'
   20 |     bam_seek(fp, 0, 0);
      |     ^~~~~~~~
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c io_sam.c -o io_sam.o
In file included from /usr/lib/R/site-library/Rhtslib/include/sam.h:29,
                 from io_sam.c:2:
io_sam.c: In function '_scan_bam_all':
/usr/lib/R/site-library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of 'bgzf_seek', declared with attribute warn_unused_result [-Wunused-result]
   57 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
      |                                ^~~~~~~~~~~~~~~~~~~~~~~
io_sam.c:304:5: note: in expansion of macro 'bam_seek'
  304 |     bam_seek(bfile->file->x.bam, bfile->pos0, SEEK_SET);
      |     ^~~~~~~~
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pileup.cpp -o pileup.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pileupbam.c -o pileupbam.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sam.c -o sam.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sam_opts.c -o sam_opts.o
In file included from /usr/include/stdio.h:867,
                 from /usr/lib/R/site-library/Rhtslib/include/sam_opts.c:27,
                 from sam_opts.c:1:
In function 'fprintf',
    inlined from 'parse_sam_global_opt' at /usr/lib/R/site-library/Rhtslib/include/sam_opts.c:85:9:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:100:10: warning: '%s' directive argument is null [-Wformat-overflow=]
  100 |   return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  101 |    __va_arg_pack ());
      |    ~~~~~~~~~~~~~~~~~
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sam_utils.c -o sam_utils.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c samtools_patch.c -o samtools_patch.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c scan_bam_data.c -o scan_bam_data.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c tabixfile.c -o tabixfile.o
tabixfile.c: In function 'index_tabix':
tabixfile.c:190:5: warning: 'bgzf_is_bgzf' is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
  190 |     if (bgzf_is_bgzf(fn) != 1)
      |     ^~
In file included from tabixfile.c:3:
/usr/lib/R/site-library/Rhtslib/include/htslib/bgzf.h:243:9: note: declared here
  243 |     int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
      |         ^~~~~~~~~~~~
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c tagfilter.c -o tagfilter.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -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/Rhtslib/include' -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'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-qUFFBN/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c zip_compression.c -o zip_compression.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-z,relro -o Rsamtools.so Biostrings_stubs.o COMPAT_bcf_hdr_read.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam.o bam_data.o bam_mate_iter.o bam_plbuf.o bam_sort.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o sam.o sam_opts.o sam_utils.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.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-rsamtools/usr/lib/R/site-library/00LOCK-r-bioc-rsamtools-2.4.0/00new/Rsamtools/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rsamtools)
	rm -f /<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/LICENSE
I: Using r-bioc-genomeinfodb for Depends:GenomeInfoDb (>= 1.1.3)
I: Using r-bioc-genomicranges for Depends:GenomicRanges (>= 1.31.8)
I: Using r-bioc-biostrings for Depends:Biostrings (>= 2.47.6)
I: Using r-cran-runit for Recommends:runit
I: Using r-bioc-shortread for Recommends:shortread
I: Using r-bioc-genomicalignments for Suggests:GenomicAlignments
I: Using r-bioc-genomicfeatures for Suggests:GenomicFeatures
W: Cannot find a debian package for Suggests:TxDb.Dmelanogaster.UCSC.dm3.ensGene
W: Cannot find a debian package for Suggests:KEGG.db
W: Cannot find a debian package for Suggests:TxDb.Hsapiens.UCSC.hg18.knownGene
W: Cannot find a debian package for Suggests:RNAseqData.HNRNPC.bam.chr14
W: Cannot find a debian package for Suggests:BSgenome.Hsapiens.UCSC.hg19
W: Cannot find a debian package for Suggests:BiocStyle
I: Using r-bioc-biocgenerics for Imports:BiocGenerics (>= 0.25.1)
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-xvector for Imports:XVector (>= 0.19.7)
I: Using r-bioc-zlibbioc for Imports:zlibbioc
I: Using r-cran-bitops for Imports:bitops
I: Using r-bioc-biocparallel for Imports:BiocParallel
I: Using r-bioc-rhtslib for LinkingTo:Rhtslib (>= 1.17.7)
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-3.11
   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-rsamtools' in '../r-bioc-rsamtools_2.4.0-1_armhf.deb'.
dpkg-deb: building package 'r-bioc-rsamtools-dbgsym' in '../r-bioc-rsamtools-dbgsym_2.4.0-1_armhf.deb'.
 dpkg-genbuildinfo --build=any
 dpkg-genchanges --build=any -mRaspbian 2019 test autobuilder <root@raspbian.org> >../r-bioc-rsamtools_2.4.0-1_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 2020-05-30T20:39:38Z

Finished
--------

I: Built successfully

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


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


r-bioc-rsamtools_2.4.0-1_armhf.changes:
---------------------------------------

Format: 1.8
Date: Tue, 19 May 2020 11:32:13 +0200
Source: r-bioc-rsamtools
Binary: r-bioc-rsamtools r-bioc-rsamtools-dbgsym
Architecture: armhf
Version: 2.4.0-1
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian 2019 test autobuilder <root@raspbian.org>
Changed-By: Dylan Aïssi <daissi@debian.org>
Description:
 r-bioc-rsamtools - GNU R binary alignment (BAM), variant call (BCF), or tabix file i
Changes:
 r-bioc-rsamtools (2.4.0-1) unstable; urgency=medium
 .
   * Team upload.
   * New upstream version
   * Testsuite: autopkgtest-pkg-r (routine-update)
   * Rules-Requires-Root: no (routine-update)
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Files:
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 af2b922fe2ebdd46dd985cb10928f705 8545 gnu-r optional r-bioc-rsamtools_2.4.0-1_armhf.buildinfo
 0992a0ae39f576599e8caba505919c52 3696996 gnu-r optional r-bioc-rsamtools_2.4.0-1_armhf.deb

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

Format: 1.0
Source: r-bioc-rsamtools
Binary: r-bioc-rsamtools
Architecture: armhf
Version: 2.4.0-1
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Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Sat, 30 May 2020 20:39:36 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
 autoconf (= 2.69-11.1),
 automake (= 1:1.16.2-1),
 autopoint (= 0.19.8.1-10),
 autotools-dev (= 20180224.1),
 base-files (= 11+rpi1),
 base-passwd (= 3.5.47),
 bash (= 5.0-6),
 binutils (= 2.34-8+rpi1),
 binutils-arm-linux-gnueabihf (= 2.34-8+rpi1),
 binutils-common (= 2.34-8+rpi1),
 bsdmainutils (= 11.1.2),
 bsdutils (= 1:2.35.1-5),
 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 (= 9.3.0-13+rpi1),
 dash (= 0.5.10.2-7),
 dctrl-tools (= 2.24-3),
 debconf (= 1.5.74),
 debhelper (= 13.1),
 debianutils (= 4.9.1),
 dh-autoreconf (= 19),
 dh-r (= 20200314),
 dh-strip-nondeterminism (= 1.8.1-1),
 diffutils (= 1:3.7-3),
 dpkg (= 1.19.7),
 dpkg-dev (= 1.19.7),
 dwz (= 0.13-5),
 file (= 1:5.38-5),
 findutils (= 4.7.0-1),
 fontconfig (= 2.13.1-4.2),
 fontconfig-config (= 2.13.1-4.2),
 fonts-dejavu-core (= 2.37-1),
 g++ (= 4:9.2.1-3.1+rpi1),
 g++-9 (= 9.3.0-13+rpi1),
 gcc (= 4:9.2.1-3.1+rpi1),
 gcc-10-base (= 10.1.0-1+rpi1),
 gcc-9 (= 9.3.0-13+rpi1),
 gcc-9-base (= 9.3.0-13+rpi1),
 gettext (= 0.19.8.1-10),
 gettext-base (= 0.19.8.1-10),
 gfortran (= 4:9.2.1-3.1+rpi1),
 gfortran-9 (= 9.3.0-13+rpi1),
 grep (= 3.4-1),
 groff-base (= 1.22.4-5),
 gzip (= 1.10-2),
 hostname (= 3.23),
 icu-devtools (= 63.2-3),
 init-system-helpers (= 1.57),
 intltool-debian (= 0.35.0+20060710.5),
 libacl1 (= 2.2.53-8),
 libarchive-zip-perl (= 1.68-1),
 libasan5 (= 9.3.0-13+rpi1),
 libatomic1 (= 10.1.0-1+rpi1),
 libattr1 (= 1:2.4.48-5),
 libaudit-common (= 1:2.8.5-3),
 libaudit1 (= 1:2.8.5-3),
 libbinutils (= 2.34-8+rpi1),
 libblas-dev (= 3.9.0-2),
 libblas3 (= 3.9.0-2),
 libblkid1 (= 2.35.1-5),
 libboost-dev (= 1.67.0.2+b12),
 libboost1.67-dev (= 1.67.0-18),
 libbrotli1 (= 1.0.7-6.1),
 libbsd0 (= 0.10.0-1),
 libbz2-1.0 (= 1.0.8-2),
 libbz2-dev (= 1.0.8-2),
 libc-bin (= 2.30-8+rpi1),
 libc-dev-bin (= 2.30-8+rpi1),
 libc6 (= 2.30-8+rpi1),
 libc6-dev (= 2.30-8+rpi1),
 libcairo2 (= 1.16.0-4),
 libcap-ng0 (= 0.7.9-2.1+b1),
 libcc1-0 (= 10.1.0-1+rpi1),
 libcom-err2 (= 1.45.6-1),
 libcroco3 (= 0.6.13-1),
 libcrypt-dev (= 1:4.4.16-1),
 libcrypt1 (= 1:4.4.16-1),
 libctf-nobfd0 (= 2.34-8+rpi1),
 libctf0 (= 2.34-8+rpi1),
 libcurl4 (= 7.68.0-1),
 libcurl4-openssl-dev (= 7.68.0-1),
 libdatrie1 (= 0.2.12-3+b2),
 libdb5.3 (= 5.3.28+dfsg1-0.6),
 libdebconfclient0 (= 0.252),
 libdebhelper-perl (= 13.1),
 libdpkg-perl (= 1.19.7),
 libelf1 (= 0.176-1.1),
 libexpat1 (= 2.2.9-1),
 libffi7 (= 3.3-4),
 libfile-stripnondeterminism-perl (= 1.8.1-1),
 libfile-which-perl (= 1.23-1),
 libfontconfig1 (= 2.13.1-4.2),
 libfreetype6 (= 2.10.1-2),
 libfribidi0 (= 1.0.8-2),
 libgcc-9-dev (= 9.3.0-13+rpi1),
 libgcc-s1 (= 10.1.0-1+rpi1),
 libgcc1 (= 1:10.1.0-1+rpi1),
 libgcrypt20 (= 1.8.5-5),
 libgdbm-compat4 (= 1.18.1-5),
 libgdbm6 (= 1.18.1-5),
 libgfortran-9-dev (= 9.3.0-13+rpi1),
 libgfortran5 (= 10.1.0-1+rpi1),
 libglib2.0-0 (= 2.64.2-1),
 libgmp10 (= 2:6.2.0+dfsg-4),
 libgnutls30 (= 3.6.13-2),
 libgomp1 (= 10.1.0-1+rpi1),
 libgpg-error0 (= 1.37-1),
 libgraphite2-3 (= 1.3.14-1),
 libgssapi-krb5-2 (= 1.17-7+rpi1),
 libharfbuzz0b (= 2.6.4-1+rpi1),
 libhogweed5 (= 3.5.1+really3.5.1-2),
 libice6 (= 2:1.0.9-2),
 libicu-dev (= 63.2-3),
 libicu63 (= 63.2-3),
 libidn2-0 (= 2.3.0-1),
 libisl22 (= 0.22.1-1),
 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 (= 1.17-7+rpi1),
 libkeyutils1 (= 1.6.1-2),
 libkrb5-3 (= 1.17-7+rpi1),
 libkrb5support0 (= 1.17-7+rpi1),
 liblapack-dev (= 3.9.0-2),
 liblapack3 (= 3.9.0-2),
 libldap-2.4-2 (= 2.4.50+dfsg-1),
 libldap-common (= 2.4.50+dfsg-1),
 liblz4-1 (= 1.9.2-2),
 liblzma-dev (= 5.2.4-1),
 liblzma5 (= 5.2.4-1),
 libmagic-mgc (= 1:5.38-5),
 libmagic1 (= 1:5.38-5),
 libmount1 (= 2.35.1-5),
 libmpc3 (= 1.1.0-1),
 libmpfr6 (= 4.0.2-1),
 libncurses-dev (= 6.2-1),
 libncurses5-dev (= 6.2-1),
 libncurses6 (= 6.2-1),
 libncursesw6 (= 6.2-1),
 libnettle7 (= 3.5.1+really3.5.1-2),
 libnghttp2-14 (= 1.40.0-1+b2),
 libp11-kit0 (= 0.23.20-1),
 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 (= 1.44.7-4),
 libpangocairo-1.0-0 (= 1.44.7-4),
 libpangoft2-1.0-0 (= 1.44.7-4),
 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 (= 5.30.0-10),
 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 (= 0.21.0-1),
 libreadline-dev (= 8.0-4),
 libreadline8 (= 8.0-4),
 librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b1),
 libsasl2-2 (= 2.1.27+dfsg-2),
 libsasl2-modules-db (= 2.1.27+dfsg-2),
 libseccomp2 (= 2.4.3-1+rpi1),
 libselinux1 (= 3.0-1+b1),
 libsigsegv2 (= 2.12-2),
 libsm6 (= 2:1.2.3-1),
 libsmartcols1 (= 2.35.1-5),
 libssh2-1 (= 1.8.0-2.1),
 libssl1.1 (= 1.1.1g-1),
 libstdc++-9-dev (= 9.3.0-13+rpi1),
 libstdc++6 (= 10.1.0-1+rpi1),
 libsub-override-perl (= 0.09-2),
 libswitch-perl (= 2.17-2),
 libsystemd0 (= 245.5-3+rpi1),
 libtasn1-6 (= 4.16.0-2),
 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 (= 6.2-1),
 libtinfo6 (= 6.2-1),
 libtk8.6 (= 8.6.10-1),
 libtool (= 2.4.6-14),
 libubsan1 (= 10.1.0-1+rpi1),
 libuchardet0 (= 0.0.6-3),
 libudev1 (= 245.5-3+rpi1),
 libunistring2 (= 0.9.10-2),
 libuuid1 (= 2.35.1-5),
 libwebp6 (= 0.6.1-2),
 libx11-6 (= 2:1.6.9-2),
 libx11-data (= 2:1.6.9-2),
 libxau6 (= 1:1.0.8-1+b2),
 libxcb-render0 (= 1.14-2),
 libxcb-shm0 (= 1.14-2),
 libxcb1 (= 1.14-2),
 libxdmcp6 (= 1:1.1.2-3),
 libxext6 (= 2:1.3.3-1+b2),
 libxft2 (= 2.3.2-2),
 libxml2 (= 2.9.10+dfsg-5),
 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-3+rpi1),
 linux-libc-dev (= 5.2.17-1+rpi1+b2),
 login (= 1:4.8.1-1),
 lsb-base (= 11.1.0+rpi1),
 m4 (= 1.4.18-4),
 make (= 4.2.1-2),
 man-db (= 2.9.1-1),
 mawk (= 1.3.4.20200120-2),
 ncurses-base (= 6.2-1),
 ncurses-bin (= 6.2-1),
 openssl (= 1.1.1g-1),
 patch (= 2.7.6-6),
 perl (= 5.30.0-10),
 perl-base (= 5.30.0-10),
 perl-modules-5.30 (= 5.30.0-10),
 pkg-config (= 0.29.2-1),
 po-debconf (= 1.0.21),
 r-base-core (= 4.0.0-3),
 r-base-dev (= 4.0.0-3),
 r-bioc-biocgenerics (= 0.34.0-1),
 r-bioc-biocparallel (= 1.22.0-1),
 r-bioc-biostrings (= 2.56.0-1),
 r-bioc-genomeinfodb (= 1.24.0-1),
 r-bioc-genomeinfodbdata (= 1.2.3-1),
 r-bioc-genomicranges (= 1.40.0+dfsg-1),
 r-bioc-iranges (= 2.22.2-1),
 r-bioc-rhtslib (= 1.20.0+dfsg-1),
 r-bioc-s4vectors (= 0.26.1-1),
 r-bioc-xvector (= 0.28.0-1),
 r-bioc-zlibbioc (= 1.34.0+dfsg-1),
 r-cran-bh (= 1.66.0-1),
 r-cran-bitops (= 1.0-6-4+b1),
 r-cran-crayon (= 1.3.4-5),
 r-cran-formatr (= 1.7-2),
 r-cran-futile.logger (= 1.4.3-4),
 r-cran-futile.options (= 1.0.1-3),
 r-cran-lambda.r (= 1.2.4-2),
 r-cran-rcurl (= 1.98-1.2-1+b1),
 r-cran-snow (= 1:0.4.3-2),
 readline-common (= 8.0-4),
 sed (= 4.7-1),
 sensible-utils (= 0.0.12+nmu1),
 sysvinit-utils (= 2.96-3),
 tar (= 1.30+dfsg-7),
 tzdata (= 2020a-1),
 ucf (= 3.0042),
 unzip (= 6.0-25),
 util-linux (= 2.35.1-5),
 x11-common (= 1:7.7+20),
 xauth (= 1:1.0.10-1),
 xdg-utils (= 1.1.3-2),
 xz-utils (= 5.2.4-1),
 zip (= 3.0-11),
 zlib1g (= 1:1.2.11.dfsg-2),
 zlib1g-dev (= 1:1.2.11.dfsg-2)
Environment:
 DEB_BUILD_OPTIONS="parallel=4"
 LANG="en_GB.UTF-8"
 LC_ALL="POSIX"
 SOURCE_DATE_EPOCH="1589880733"


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


r-bioc-rsamtools-dbgsym_2.4.0-1_armhf.deb
-----------------------------------------

 new Debian package, version 2.0.
 size 803064 bytes: control archive=540 bytes.
     400 bytes,    12 lines      control              
     106 bytes,     1 lines      md5sums              
 Package: r-bioc-rsamtools-dbgsym
 Source: r-bioc-rsamtools
 Version: 2.4.0-1
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
 Installed-Size: 881
 Depends: r-bioc-rsamtools (= 2.4.0-1)
 Section: debug
 Priority: optional
 Description: debug symbols for r-bioc-rsamtools
 Build-Ids: 8a2b7d01b18568db766a5af0915973082ba885ff

drwxr-xr-x root/root         0 2020-05-19 09:32 ./
drwxr-xr-x root/root         0 2020-05-19 09:32 ./usr/
drwxr-xr-x root/root         0 2020-05-19 09:32 ./usr/lib/
drwxr-xr-x root/root         0 2020-05-19 09:32 ./usr/lib/debug/
drwxr-xr-x root/root         0 2020-05-19 09:32 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2020-05-19 09:32 ./usr/lib/debug/.build-id/8a/
-rw-r--r-- root/root    891544 2020-05-19 09:32 ./usr/lib/debug/.build-id/8a/2b7d01b18568db766a5af0915973082ba885ff.debug
drwxr-xr-x root/root         0 2020-05-19 09:32 ./usr/share/
drwxr-xr-x root/root         0 2020-05-19 09:32 ./usr/share/doc/
lrwxrwxrwx root/root         0 2020-05-19 09:32 ./usr/share/doc/r-bioc-rsamtools-dbgsym -> r-bioc-rsamtools


r-bioc-rsamtools_2.4.0-1_armhf.deb
----------------------------------

 new Debian package, version 2.0.
 size 3696996 bytes: control archive=3912 bytes.
    1098 bytes,    16 lines      control              
   10256 bytes,   112 lines      md5sums              
 Package: r-bioc-rsamtools
 Version: 2.4.0-1
 Architecture: armhf
 Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
 Installed-Size: 5544
 Depends: r-base-core (>= 4.0.0-3), r-api-4.0, r-api-bioc-3.11, r-bioc-genomeinfodb (>= 1.1.3), r-bioc-genomicranges (>= 1.31.8), r-bioc-biostrings (>= 2.47.6), r-bioc-biocgenerics (>= 0.25.1), r-bioc-s4vectors (>= 0.17.25), r-bioc-iranges (>= 2.13.12), r-bioc-xvector (>= 0.19.7), r-bioc-zlibbioc, r-cran-bitops, r-bioc-biocparallel, r-bioc-rhtslib (>= 1.17.7), libc6 (>= 2.15), libcurl4 (>= 7.18.0), libgcc-s1 (>= 3.5), libstdc++6 (>= 5.2)
 Recommends: r-cran-runit, r-bioc-shortread
 Suggests: r-bioc-genomicalignments, r-bioc-genomicfeatures
 Section: gnu-r
 Priority: optional
 Homepage: https://bioconductor.org/packages/Rsamtools/
 Description: GNU R binary alignment (BAM), variant call (BCF), or tabix file import
  This package provides an interface to the 'samtools', 'bcftools', and
  'tabix' utilities for manipulating SAM (Sequence Alignment / Map),
  binary variant call (BCF) and compressed indexed tab-delimited (tabix)
  files.

drwxr-xr-x root/root         0 2020-05-19 09:32 ./
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drwxr-xr-x root/root         0 2020-05-19 09:32 ./usr/lib/
drwxr-xr-x root/root         0 2020-05-19 09:32 ./usr/lib/R/
drwxr-xr-x root/root         0 2020-05-19 09:32 ./usr/lib/R/site-library/
drwxr-xr-x root/root         0 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/
-rw-r--r-- root/root      1733 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/DESCRIPTION
-rw-r--r-- root/root      2303 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/INDEX
drwxr-xr-x root/root         0 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/Meta/
-rw-r--r-- root/root      3293 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/Meta/Rd.rds
-rw-r--r-- root/root       130 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/Meta/features.rds
-rw-r--r-- root/root      3525 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/Meta/hsearch.rds
-rw-r--r-- root/root      2519 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/Meta/links.rds
-rw-r--r-- root/root       798 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/Meta/nsInfo.rds
-rw-r--r-- root/root      1710 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/Meta/package.rds
-rw-r--r-- root/root       281 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/Meta/vignette.rds
-rw-r--r-- root/root      1431 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/NAMESPACE
-rw-r--r-- root/root     15617 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/NEWS
drwxr-xr-x root/root         0 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/R/
-rw-r--r-- root/root      1056 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/R/Rsamtools
-rw-r--r-- root/root    836900 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/R/Rsamtools.rdb
-rw-r--r-- root/root      6750 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/R/Rsamtools.rdx
drwxr-xr-x root/root         0 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/doc/
-rw-r--r-- root/root      9648 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-Overview.R
-rw-r--r-- root/root     19874 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-Overview.Rnw
-rw-r--r-- root/root    180600 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-Overview.pdf
-rw-r--r-- root/root       221 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-UsingCLibraries.R
-rw-r--r-- root/root      3855 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-UsingCLibraries.Rnw
-rw-r--r-- root/root    125462 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-UsingCLibraries.pdf
-rw-r--r-- root/root      1976 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/doc/index.html
drwxr-xr-x root/root         0 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/
-rw-r--r-- root/root       176 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/ce2dict1.fa
-rw-r--r-- root/root       112 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/ce2dict1.fa.fai
-rw-r--r-- root/root    126539 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bam
-rw-r--r-- root/root       176 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bam.bai
-rw-r--r-- root/root     79176 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bcf.gz
-rw-r--r-- root/root       110 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bcf.gz.csi
-rw-r--r-- root/root    559422 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.sam
-rw-r--r-- root/root     74987 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.vcf.gz
-rw-r--r-- root/root       143 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.vcf.gz.csi
-rw-r--r-- root/root      3778 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/example.gtf.gz
-rw-r--r-- root/root       259 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/example.gtf.gz.tbi
-rw-r--r-- root/root       348 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/example_from_SAM_Spec.bam
-rw-r--r-- root/root        96 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/example_from_SAM_Spec.bam.bai
-rw-r--r-- root/root       368 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/example_from_SAM_Spec.sam
-rw-r--r-- root/root       203 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_buffered_pileup.bam
-rw-r--r-- root/root       176 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_buffered_pileup.bam.bai
-rw-r--r-- root/root       240 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_buffered_pileup.sam
-rw-r--r-- root/root       198 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_whole_file.bam
-rw-r--r-- root/root       176 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_whole_file.bam.bai
-rw-r--r-- root/root       168 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_whole_file.sam
-rw-r--r-- root/root   1663363 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/olaps.Rda
-rw-r--r-- root/root    138598 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/pileup.txt
-rw-r--r-- root/root       181 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/querybins.bam
-rw-r--r-- root/root        96 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/querybins.bam.bai
-rw-r--r-- root/root       117 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/querybins.sam
-rw-r--r-- root/root       381 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/revbins.bam
-rw-r--r-- root/root       416 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/revbins.bam.bai
-rw-r--r-- root/root       770 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/revbins.sam
-rw-r--r-- root/root        31 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/samtools-github.txt
-rw-r--r-- root/root      2808 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/slxMaq09_urls.txt
-rw-r--r-- root/root       333 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/tagfilter.bam
-rw-r--r-- root/root       656 2020-05-19 09:32 ./usr/lib/R/site-library/Rsamtools/extdata/tagfilter.bam.bai
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| Post Build                                                                   |
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| Cleanup                                                                      |
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| Summary                                                                      |
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Build Architecture: armhf
Build Type: any
Build-Space: 15876
Build-Time: 273
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 942
Job: r-bioc-rsamtools_2.4.0-1
Machine Architecture: armhf
Package: r-bioc-rsamtools
Package-Time: 1270
Source-Version: 2.4.0-1
Space: 15876
Status: successful
Version: 2.4.0-1
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Finished at 2020-05-30T20:39:38Z
Build needed 00:21:10, 15876k disk space