r-bioc-rsamtools →
2.14.0-1+b2 →
armhf → 2023-10-04 06:08:22
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| r-bioc-rsamtools 2.14.0-1+b2 (armhf) Wed, 04 Oct 2023 05:56:02 +0000 |
+==============================================================================+
Package: r-bioc-rsamtools
Version: 2.14.0-1+b2
Source Version: 2.14.0-1
Distribution: trixie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/trixie-staging-armhf-sbuild-47d77ea9-7976-4872-8d8d-0a800fd9db1b' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.1 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [14.8 MB]
Fetched 28.9 MB in 10s (2867 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http://172.17.4.1/private/dists/trixie-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'r-bioc-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 2882 kB of source archives.
Get:1 http://172.17.4.1/private trixie-staging/main r-bioc-rsamtools 2.14.0-1 (dsc) [2319 B]
Get:2 http://172.17.4.1/private trixie-staging/main r-bioc-rsamtools 2.14.0-1 (tar) [2874 kB]
Get:3 http://172.17.4.1/private trixie-staging/main r-bioc-rsamtools 2.14.0-1 (diff) [6368 B]
Fetched 2882 kB in 0s (8116 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/r-bioc-rsamtools-z7MeOH/r-bioc-rsamtools-2.14.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-rsamtools-z7MeOH' 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-bMsdCK/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-bMsdCK/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-bMsdCK/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-bMsdCK/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-bMsdCK/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-bMsdCK/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-bMsdCK/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-bMsdCK/apt_archive ./ Packages [430 B]
Fetched 2106 B in 0s (8957 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales libpam-cap netbase sensible-utils sgml-base util-linux-extra
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 32 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-bMsdCK/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (60.8 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 11775 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), dh-r, r-base-dev, r-bioc-genomeinfodb, r-bioc-genomicranges, r-bioc-biostrings, r-bioc-biocgenerics, r-bioc-s4vectors, r-bioc-iranges, r-bioc-xvector, r-bioc-zlibbioc, r-cran-bitops, r-bioc-biocparallel, r-bioc-rhtslib (>= 1.99.3), libcurl4-openssl-dev
Filtered Build-Depends: debhelper-compat (= 13), dh-r, r-base-dev, r-bioc-genomeinfodb, r-bioc-genomicranges, r-bioc-biostrings, r-bioc-biocgenerics, r-bioc-s4vectors, r-bioc-iranges, r-bioc-xvector, r-bioc-zlibbioc, r-cran-bitops, r-bioc-biocparallel, r-bioc-rhtslib (>= 1.99.3), libcurl4-openssl-dev
dpkg-deb: building package 'sbuild-build-depends-r-bioc-rsamtools-dummy' in '/<<BUILDDIR>>/resolver-bMsdCK/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-bMsdCK/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-bMsdCK/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-bMsdCK/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-bMsdCK/apt_archive ./ Sources [610 B]
Get:5 copy:/<<BUILDDIR>>/resolver-bMsdCK/apt_archive ./ Packages [689 B]
Fetched 2632 B in 0s (10.8 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
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 packages were automatically installed and are no longer required:
krb5-locales libpam-cap netbase sgml-base util-linux-extra
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils bsdutils
ca-certificates dctrl-tools debhelper dh-autoreconf dh-r
dh-strip-nondeterminism dwz file fontconfig fontconfig-config
fonts-dejavu-core fonts-dejavu-mono gettext gettext-base gfortran
gfortran-12 groff-base icu-devtools intltool-debian libalgorithm-c3-perl
libarchive-zip-perl libb-hooks-endofscope-perl libb-hooks-op-check-perl
libblas-dev libblas3 libblkid1 libboost1.81-dev libbrotli1 libbsd0
libbz2-dev libcairo2 libclass-c3-perl libclass-load-perl
libclass-load-xs-perl libclone-perl libcurl3-gnutls libcurl4
libcurl4-openssl-dev libdata-optlist-perl libdatrie1 libdebhelper-perl
libdeflate0 libdevel-callchecker-perl libdevel-globaldestruction-perl
libdevel-overloadinfo-perl libdevel-stacktrace-perl
libdist-checkconflicts-perl libdynaloader-functions-perl libelf1
libencode-locale-perl libeval-closure-perl libexpat1
libfile-stripnondeterminism-perl libfile-which-perl libfontconfig1
libfreetype6 libfribidi0 libgfortran-12-dev libgfortran5 libglib2.0-0
libgraphite2-3 libharfbuzz0b libhttp-date-perl libhttp-message-perl libice6
libicu-dev libicu72 libio-html-perl libjbig0 libjpeg-dev libjpeg62-turbo
libjpeg62-turbo-dev liblapack-dev liblapack3 liblerc4 liblwp-mediatypes-perl
liblzma-dev libmagic-mgc libmagic1 libmodule-implementation-perl
libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoose-perl
libmount1 libmro-compat-perl libnamespace-clean-perl libncurses-dev
libncurses6 libnghttp2-14 libpackage-deprecationmanager-perl
libpackage-stash-perl libpackage-stash-xs-perl libpango-1.0-0
libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1
libparams-classify-perl libparams-util-perl libpcre2-16-0 libpcre2-32-0
libpcre2-dev libpcre2-posix3 libpipeline1 libpixman-1-0 libpkgconf3
libpng-dev libpng16-16 libpsl5 libreadline-dev librtmp1 libsharpyuv0 libsm6
libsmartcols1 libssh2-1 libssl3 libsub-exporter-perl
libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl
libsub-name-perl libsub-override-perl libswitch-perl libtcl8.6 libthai-data
libthai0 libtiff6 libtimedate-perl libtk8.6 libtool libtry-tiny-perl
libuchardet0 liburi-perl libuuid1 libvariable-magic-perl libwebp7
libwww-curl-perl libwww-curl-simple-perl libx11-6 libx11-data libxau6
libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2
libxmuu1 libxrender1 libxss1 libxt6 m4 man-db mount openssl pkg-config
pkgconf pkgconf-bin 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-codetools r-cran-cpp11 r-cran-crayon r-cran-formatr
r-cran-futile.logger r-cran-futile.options r-cran-lambda.r r-cran-rcurl
r-cran-snow ucf unzip util-linux util-linux-extra x11-common xauth xdg-utils
zip zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc debtags dh-make
postgresql-client-common gettext-doc libasprintf-dev libgettextpo-dev
gfortran-doc gfortran-12-doc libcoarrays-dev groff liblapack-doc
libboost1.81-doc libboost-atomic1.81-dev libboost-chrono1.81-dev
libboost-container1.81-dev libboost-context1.81-dev
libboost-contract1.81-dev libboost-coroutine1.81-dev
libboost-date-time1.81-dev libboost-exception1.81-dev libboost-fiber1.81-dev
libboost-filesystem1.81-dev libboost-graph1.81-dev
libboost-graph-parallel1.81-dev libboost-iostreams1.81-dev
libboost-locale1.81-dev libboost-log1.81-dev libboost-math1.81-dev
libboost-mpi1.81-dev libboost-mpi-python1.81-dev libboost-numpy1.81-dev
libboost-program-options1.81-dev libboost-python1.81-dev
libboost-random1.81-dev libboost-regex1.81-dev
libboost-serialization1.81-dev libboost-stacktrace1.81-dev
libboost-system1.81-dev libboost-test1.81-dev libboost-thread1.81-dev
libboost-timer1.81-dev libboost-type-erasure1.81-dev libboost-wave1.81-dev
libboost1.81-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.81-dev
libcurl4-doc libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev
libssl-dev low-memory-monitor icu-doc liblzma-doc cryptsetup-bin ncurses-doc
libscalar-number-perl readline-doc tcl8.6 tk8.6 libtool-doc gcj-jdk
libbusiness-isbn-perl libregexp-ipv6-perl libwww-perl libcurl4-gnutls-dev
m4-doc apparmor less www-browser nfs-common 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-runit r-cran-foreach
r-cran-bbmisc r-cran-doparallel r-bioc-variantannotation
r-bioc-genomicalignments r-bioc-shortread r-bioc-biocstyle r-cran-knitr
r-cran-batchtools r-cran-data.table r-bioc-bsgenome r-bioc-genomicfeatures
r-cran-matrix r-bioc-summarizedexperiment r-bioc-rtracklayer r-bioc-gviz
r-bioc-annotationhub r-bioc-dexseq r-bioc-edger r-bioc-keggrest
r-cran-digest r-cran-rmarkdown r-bioc-graph r-cran-rstudioapi r-cran-shiny
r-cran-jsonlite r-cran-xml r-cran-rmpi r-cran-rlecuyer dosfstools kbd
util-linux-locales
Recommended packages:
devscripts cme git-buildpackage curl | wget | lynx bzip2-doc
libclass-c3-xs-perl libdevel-lexalias-perl libarchive-cpio-perl
libglib2.0-data shared-mime-info xdg-user-dirs libio-compress-brotli-perl
libdevel-partialdump-perl libgpm2 libpng-tools publicsuffix libltdl-dev
uuid-runtime libmail-sendmail-perl r-recommended r-doc-html r-cran-bench
r-cran-brio r-cran-callr r-cran-cli r-cran-covr r-cran-decor r-cran-desc
r-cran-ggplot2 r-cran-glue r-cran-knitr r-cran-lobstr r-cran-mockery
r-cran-progress r-cran-rmarkdown r-cran-scales r-cran-rcpp r-cran-testthat
r-cran-tibble r-cran-vctrs r-cran-withr r-cran-testit r-cran-survival
libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils
x11-xserver-utils
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils ca-certificates
dctrl-tools debhelper dh-autoreconf dh-r dh-strip-nondeterminism dwz file
fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono gettext
gettext-base gfortran gfortran-12 groff-base icu-devtools intltool-debian
libalgorithm-c3-perl libarchive-zip-perl libb-hooks-endofscope-perl
libb-hooks-op-check-perl libblas-dev libblas3 libboost1.81-dev libbrotli1
libbsd0 libbz2-dev libcairo2 libclass-c3-perl libclass-load-perl
libclass-load-xs-perl libclone-perl libcurl3-gnutls libcurl4
libcurl4-openssl-dev libdata-optlist-perl libdatrie1 libdebhelper-perl
libdeflate0 libdevel-callchecker-perl libdevel-globaldestruction-perl
libdevel-overloadinfo-perl libdevel-stacktrace-perl
libdist-checkconflicts-perl libdynaloader-functions-perl libelf1
libencode-locale-perl libeval-closure-perl libexpat1
libfile-stripnondeterminism-perl libfile-which-perl libfontconfig1
libfreetype6 libfribidi0 libgfortran-12-dev libgfortran5 libglib2.0-0
libgraphite2-3 libharfbuzz0b libhttp-date-perl libhttp-message-perl libice6
libicu-dev libicu72 libio-html-perl libjbig0 libjpeg-dev libjpeg62-turbo
libjpeg62-turbo-dev liblapack-dev liblapack3 liblerc4 liblwp-mediatypes-perl
liblzma-dev libmagic-mgc libmagic1 libmodule-implementation-perl
libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoose-perl
libmro-compat-perl libnamespace-clean-perl libncurses-dev libncurses6
libnghttp2-14 libpackage-deprecationmanager-perl libpackage-stash-perl
libpackage-stash-xs-perl libpango-1.0-0 libpangocairo-1.0-0
libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl
libparams-util-perl libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3
libpipeline1 libpixman-1-0 libpkgconf3 libpng-dev libpng16-16 libpsl5
libreadline-dev librtmp1 libsharpyuv0 libsm6 libssh2-1 libsub-exporter-perl
libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl
libsub-name-perl libsub-override-perl libswitch-perl libtcl8.6 libthai-data
libthai0 libtiff6 libtimedate-perl libtk8.6 libtool libtry-tiny-perl
libuchardet0 liburi-perl libvariable-magic-perl libwebp7 libwww-curl-perl
libwww-curl-simple-perl libx11-6 libx11-data libxau6 libxcb-render0
libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxmuu1 libxrender1
libxss1 libxt6 m4 man-db openssl pkg-config pkgconf pkgconf-bin 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-codetools
r-cran-cpp11 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 ucf unzip x11-common xauth
xdg-utils zip zlib1g-dev
The following packages will be upgraded:
bsdutils libblkid1 libmount1 libsmartcols1 libssl3 libuuid1 mount util-linux
util-linux-extra
9 upgraded, 191 newly installed, 0 to remove and 23 not upgraded.
Need to get 145 MB of archives.
After this operation, 485 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-bMsdCK/apt_archive ./ sbuild-build-depends-r-bioc-rsamtools-dummy 0.invalid.0 [980 B]
Get:2 http://172.17.4.1/private trixie-staging/main armhf bsdutils armhf 1:2.39.2-2 [85.9 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf libsmartcols1 armhf 2.39.2-2 [101 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf util-linux-extra armhf 2.39.2-2 [136 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf util-linux armhf 2.39.2-2 [1106 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf mount armhf 2.39.2-2 [132 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf libblkid1 armhf 2.39.2-2 [143 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf libmount1 armhf 2.39.2-2 [166 kB]
Get:9 http://172.17.4.1/private trixie-staging/main armhf libssl3 armhf 3.0.11-1 [1620 kB]
Get:10 http://172.17.4.1/private trixie-staging/main armhf libuuid1 armhf 2.39.2-2 [27.8 kB]
Get:11 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:12 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.23.0-2 [1033 kB]
Get:13 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.2-2 [80.6 kB]
Get:14 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:15 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.11.2-3 [1342 kB]
Get:16 http://172.17.4.1/private trixie-staging/main armhf openssl armhf 3.0.11-1 [1367 kB]
Get:17 http://172.17.4.1/private trixie-staging/main armhf ca-certificates all 20230311 [153 kB]
Get:18 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.45-2 [314 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf libmagic1 armhf 1:5.45-2 [96.1 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-13 [156 kB]
Get:22 http://172.17.4.1/private trixie-staging/main armhf ucf all 3.0043+nmu1 [55.2 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf m4 armhf 1.4.19-4 [256 kB]
Get:24 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-13 [496 kB]
Get:28 http://172.17.4.1/private trixie-staging/main armhf dctrl-tools armhf 2.24-3 [94.2 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.11.6 [81.9 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:34 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:36 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-3 [9009 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-13 [1201 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:42 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:43 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.11.6 [952 kB]
Get:44 http://172.17.4.1/private trixie-staging/main armhf zip armhf 3.0-13 [207 kB]
Get:45 http://172.17.4.1/private trixie-staging/main armhf unzip armhf 6.0-28 [147 kB]
Get:46 http://172.17.4.1/private trixie-staging/main armhf libpaper1 armhf 1.1.29 [11.9 kB]
Get:47 http://172.17.4.1/private trixie-staging/main armhf libpaper-utils armhf 1.1.29 [8416 B]
Get:48 http://172.17.4.1/private trixie-staging/main armhf xdg-utils all 1.1.3-4.1 [75.5 kB]
Get:49 http://172.17.4.1/private trixie-staging/main armhf libblas3 armhf 3.11.0-2 [100.0 kB]
Get:50 http://172.17.4.1/private trixie-staging/main armhf libexpat1 armhf 2.5.0-2 [76.8 kB]
Get:51 http://172.17.4.1/private trixie-staging/main armhf libbrotli1 armhf 1.0.9-2+b3 [258 kB]
Get:52 http://172.17.4.1/private trixie-staging/main armhf libpng16-16 armhf 1.6.40-1 [258 kB]
Get:53 http://172.17.4.1/private trixie-staging/main armhf libfreetype6 armhf 2.13.2+dfsg-1 [366 kB]
Get:54 http://172.17.4.1/private trixie-staging/main armhf fonts-dejavu-mono all 2.37-8 [489 kB]
Get:55 http://172.17.4.1/private trixie-staging/main armhf fonts-dejavu-core all 2.37-8 [840 kB]
Get:56 http://172.17.4.1/private trixie-staging/main armhf fontconfig-config armhf 2.14.2-6 [316 kB]
Get:57 http://172.17.4.1/private trixie-staging/main armhf libfontconfig1 armhf 2.14.2-6 [367 kB]
Get:58 http://172.17.4.1/private trixie-staging/main armhf libpixman-1-0 armhf 0.42.2-1 [461 kB]
Get:59 http://172.17.4.1/private trixie-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:60 http://172.17.4.1/private trixie-staging/main armhf libbsd0 armhf 0.11.7-4 [111 kB]
Get:61 http://172.17.4.1/private trixie-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:62 http://172.17.4.1/private trixie-staging/main armhf libxcb1 armhf 1.15-1 [139 kB]
Get:63 http://172.17.4.1/private trixie-staging/main armhf libx11-data all 2:1.8.6-1 [323 kB]
Get:64 http://172.17.4.1/private trixie-staging/main armhf libx11-6 armhf 2:1.8.6-1 [726 kB]
Get:65 http://172.17.4.1/private trixie-staging/main armhf libxcb-render0 armhf 1.15-1 [114 kB]
Get:66 http://172.17.4.1/private trixie-staging/main armhf libxcb-shm0 armhf 1.15-1 [106 kB]
Get:67 http://172.17.4.1/private trixie-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:68 http://172.17.4.1/private trixie-staging/main armhf libxrender1 armhf 1:0.9.10-1.1 [30.0 kB]
Get:69 http://172.17.4.1/private trixie-staging/main armhf libcairo2 armhf 1.18.0-1 [425 kB]
Get:70 http://172.17.4.1/private trixie-staging/main armhf libnghttp2-14 armhf 1.56.0-1 [60.5 kB]
Get:71 http://172.17.4.1/private trixie-staging/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB]
Get:72 http://172.17.4.1/private trixie-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:73 http://172.17.4.1/private trixie-staging/main armhf libssh2-1 armhf 1.11.0-2 [195 kB]
Get:74 http://172.17.4.1/private trixie-staging/main armhf libcurl4 armhf 8.2.1-2+rpi1 [343 kB]
Get:75 http://172.17.4.1/private trixie-staging/main armhf libglib2.0-0 armhf 2.78.0-2+rpi1 [1249 kB]
Get:76 http://172.17.4.1/private trixie-staging/main armhf libjpeg62-turbo armhf 1:2.1.5-2 [143 kB]
Get:77 http://172.17.4.1/private trixie-staging/main armhf libgfortran5 armhf 12.2.0-14+rpi1 [238 kB]
Get:78 http://172.17.4.1/private trixie-staging/main armhf liblapack3 armhf 3.11.0-2 [1624 kB]
Get:79 http://172.17.4.1/private trixie-staging/main armhf fontconfig armhf 2.14.2-6 [461 kB]
Get:80 http://172.17.4.1/private trixie-staging/main armhf libfribidi0 armhf 1.0.13-3 [69.9 kB]
Get:81 http://172.17.4.1/private trixie-staging/main armhf libgraphite2-3 armhf 1.3.14-1 [70.3 kB]
Get:82 http://172.17.4.1/private trixie-staging/main armhf libharfbuzz0b armhf 8.0.1-1 [2098 kB]
Get:83 http://172.17.4.1/private trixie-staging/main armhf libthai-data all 0.1.29-1 [176 kB]
Get:84 http://172.17.4.1/private trixie-staging/main armhf libdatrie1 armhf 0.2.13-2+b2 [39.9 kB]
Get:85 http://172.17.4.1/private trixie-staging/main armhf libthai0 armhf 0.1.29-1 [54.5 kB]
Get:86 http://172.17.4.1/private trixie-staging/main armhf libpango-1.0-0 armhf 1.51.0+ds-2 [187 kB]
Get:87 http://172.17.4.1/private trixie-staging/main armhf libpangoft2-1.0-0 armhf 1.51.0+ds-2 [40.4 kB]
Get:88 http://172.17.4.1/private trixie-staging/main armhf libpangocairo-1.0-0 armhf 1.51.0+ds-2 [30.0 kB]
Get:89 http://172.17.4.1/private trixie-staging/main armhf libtcl8.6 armhf 8.6.13+dfsg-2 [904 kB]
Get:90 http://172.17.4.1/private trixie-staging/main armhf libdeflate0 armhf 1.18-1 [38.3 kB]
Get:91 http://172.17.4.1/private trixie-staging/main armhf libjbig0 armhf 2.1-6.1 [27.0 kB]
Get:92 http://172.17.4.1/private trixie-staging/main armhf liblerc4 armhf 4.0.0+ds-3 [133 kB]
Get:93 http://172.17.4.1/private trixie-staging/main armhf libsharpyuv0 armhf 1.3.2-0.3 [106 kB]
Get:94 http://172.17.4.1/private trixie-staging/main armhf libwebp7 armhf 1.3.2-0.3 [261 kB]
Get:95 http://172.17.4.1/private trixie-staging/main armhf libtiff6 armhf 4.5.1+git230720-1 [298 kB]
Get:96 http://172.17.4.1/private trixie-staging/main armhf libxft2 armhf 2.3.6-1 [53.7 kB]
Get:97 http://172.17.4.1/private trixie-staging/main armhf x11-common all 1:7.7+23 [252 kB]
Get:98 http://172.17.4.1/private trixie-staging/main armhf libxss1 armhf 1:1.2.3-1 [17.3 kB]
Get:99 http://172.17.4.1/private trixie-staging/main armhf libtk8.6 armhf 8.6.13-2 [680 kB]
Get:100 http://172.17.4.1/private trixie-staging/main armhf libice6 armhf 2:1.0.10-1 [51.7 kB]
Get:101 http://172.17.4.1/private trixie-staging/main armhf libsm6 armhf 2:1.2.3-1 [32.9 kB]
Get:102 http://172.17.4.1/private trixie-staging/main armhf libxt6 armhf 1:1.2.1-1.1 [155 kB]
Get:103 http://172.17.4.1/private trixie-staging/main armhf r-base-core armhf 4.3.1-4 [26.3 MB]
Get:104 http://172.17.4.1/private trixie-staging/main armhf libgfortran-12-dev armhf 12.2.0-14+rpi1 [285 kB]
Get:105 http://172.17.4.1/private trixie-staging/main armhf gfortran-12 armhf 12.2.0-14+rpi1 [7509 kB]
Get:106 http://172.17.4.1/private trixie-staging/main armhf gfortran armhf 4:12.2.0-3+rpi1 [1424 B]
Get:107 http://172.17.4.1/private trixie-staging/main armhf libblas-dev armhf 3.11.0-2 [106 kB]
Get:108 http://172.17.4.1/private trixie-staging/main armhf liblapack-dev armhf 3.11.0-2 [3007 kB]
Get:109 http://172.17.4.1/private trixie-staging/main armhf libncurses6 armhf 6.4+20230625-2 [79.6 kB]
Get:110 http://172.17.4.1/private trixie-staging/main armhf libncurses-dev armhf 6.4+20230625-2 [290 kB]
Get:111 http://172.17.4.1/private trixie-staging/main armhf libreadline-dev armhf 8.2-1.3 [123 kB]
Get:112 http://172.17.4.1/private trixie-staging/main armhf libjpeg62-turbo-dev armhf 1:2.1.5-2 [258 kB]
Get:113 http://172.17.4.1/private trixie-staging/main armhf libjpeg-dev armhf 1:2.1.5-2 [71.8 kB]
Get:114 http://172.17.4.1/private trixie-staging/main armhf libpcre2-16-0 armhf 10.42-4 [211 kB]
Get:115 http://172.17.4.1/private trixie-staging/main armhf libpcre2-32-0 armhf 10.42-4 [201 kB]
Get:116 http://172.17.4.1/private trixie-staging/main armhf libpcre2-posix3 armhf 10.42-4 [55.1 kB]
Get:117 http://172.17.4.1/private trixie-staging/main armhf libpcre2-dev armhf 10.42-4 [648 kB]
Get:118 http://172.17.4.1/private trixie-staging/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-3 [901 kB]
Get:119 http://172.17.4.1/private trixie-staging/main armhf libpng-dev armhf 1.6.40-1 [336 kB]
Get:120 http://172.17.4.1/private trixie-staging/main armhf libbz2-dev armhf 1.0.8-5+b2 [26.8 kB]
Get:121 http://172.17.4.1/private trixie-staging/main armhf liblzma-dev armhf 5.4.4-0.1 [269 kB]
Get:122 http://172.17.4.1/private trixie-staging/main armhf icu-devtools armhf 72.1-3 [175 kB]
Get:123 http://172.17.4.1/private trixie-staging/main armhf libicu-dev armhf 72.1-3 [9959 kB]
Get:124 http://172.17.4.1/private trixie-staging/main armhf libxmuu1 armhf 2:1.1.3-3 [23.3 kB]
Get:125 http://172.17.4.1/private trixie-staging/main armhf xauth armhf 1:1.1.2-1 [32.4 kB]
Get:126 http://172.17.4.1/private trixie-staging/main armhf libpkgconf3 armhf 1.8.1-1 [31.3 kB]
Get:127 http://172.17.4.1/private trixie-staging/main armhf pkgconf-bin armhf 1.8.1-1 [27.8 kB]
Get:128 http://172.17.4.1/private trixie-staging/main armhf pkgconf armhf 1.8.1-1 [25.9 kB]
Get:129 http://172.17.4.1/private trixie-staging/main armhf pkg-config armhf 1.8.1-1 [13.7 kB]
Get:130 http://172.17.4.1/private trixie-staging/main armhf r-base-dev all 4.3.1-4 [4512 B]
Get:131 http://172.17.4.1/private trixie-staging/main armhf libfile-which-perl all 1.27-2 [15.1 kB]
Get:132 http://172.17.4.1/private trixie-staging/main armhf libswitch-perl all 2.17-3 [20.3 kB]
Get:133 http://172.17.4.1/private trixie-staging/main armhf libclone-perl armhf 0.46-1 [13.2 kB]
Get:134 http://172.17.4.1/private trixie-staging/main armhf libencode-locale-perl all 1.05-3 [12.9 kB]
Get:135 http://172.17.4.1/private trixie-staging/main armhf libtimedate-perl all 2.3300-2 [39.3 kB]
Get:136 http://172.17.4.1/private trixie-staging/main armhf libhttp-date-perl all 6.05-2 [10.5 kB]
Get:137 http://172.17.4.1/private trixie-staging/main armhf libio-html-perl all 1.004-3 [16.2 kB]
Get:138 http://172.17.4.1/private trixie-staging/main armhf liblwp-mediatypes-perl all 6.04-2 [20.2 kB]
Get:139 http://172.17.4.1/private trixie-staging/main armhf liburi-perl all 5.21-1 [95.6 kB]
Get:140 http://172.17.4.1/private trixie-staging/main armhf libhttp-message-perl all 6.44-2 [81.8 kB]
Get:141 http://172.17.4.1/private trixie-staging/main armhf libparams-util-perl armhf 1.102-2+b1 [23.9 kB]
Get:142 http://172.17.4.1/private trixie-staging/main armhf libsub-install-perl all 0.929-1 [10.5 kB]
Get:143 http://172.17.4.1/private trixie-staging/main armhf libdata-optlist-perl all 0.114-1 [10.6 kB]
Get:144 http://172.17.4.1/private trixie-staging/main armhf libb-hooks-op-check-perl armhf 0.22-2+b1 [10.3 kB]
Get:145 http://172.17.4.1/private trixie-staging/main armhf libdynaloader-functions-perl all 0.003-3 [12.7 kB]
Get:146 http://172.17.4.1/private trixie-staging/main armhf libdevel-callchecker-perl armhf 0.008-2 [15.8 kB]
Get:147 http://172.17.4.1/private trixie-staging/main armhf libparams-classify-perl armhf 0.015-2+b1 [22.0 kB]
Get:148 http://172.17.4.1/private trixie-staging/main armhf libmodule-runtime-perl all 0.016-2 [19.6 kB]
Get:149 http://172.17.4.1/private trixie-staging/main armhf libtry-tiny-perl all 0.31-2 [22.6 kB]
Get:150 http://172.17.4.1/private trixie-staging/main armhf libmodule-implementation-perl all 0.09-2 [12.6 kB]
Get:151 http://172.17.4.1/private trixie-staging/main armhf libpackage-stash-perl all 0.40-1 [22.0 kB]
Get:152 http://172.17.4.1/private trixie-staging/main armhf libclass-load-perl all 0.25-2 [15.3 kB]
Get:153 http://172.17.4.1/private trixie-staging/main armhf libclass-load-xs-perl armhf 0.10-2+b1 [13.8 kB]
Get:154 http://172.17.4.1/private trixie-staging/main armhf libsub-exporter-progressive-perl all 0.001013-3 [7496 B]
Get:155 http://172.17.4.1/private trixie-staging/main armhf libdevel-globaldestruction-perl all 0.14-4 [7144 B]
Get:156 http://172.17.4.1/private trixie-staging/main armhf libalgorithm-c3-perl all 0.11-2 [10.8 kB]
Get:157 http://172.17.4.1/private trixie-staging/main armhf libclass-c3-perl all 0.35-2 [21.0 kB]
Get:158 http://172.17.4.1/private trixie-staging/main armhf libmro-compat-perl all 0.15-2 [11.8 kB]
Get:159 http://172.17.4.1/private trixie-staging/main armhf libdevel-overloadinfo-perl all 0.007-1 [7896 B]
Get:160 http://172.17.4.1/private trixie-staging/main armhf libdevel-stacktrace-perl all 2.0400-2 [26.8 kB]
Get:161 http://172.17.4.1/private trixie-staging/main armhf libsub-exporter-perl all 0.990-1 [50.6 kB]
Get:162 http://172.17.4.1/private trixie-staging/main armhf libeval-closure-perl all 0.14-3 [11.2 kB]
Get:163 http://172.17.4.1/private trixie-staging/main armhf libdist-checkconflicts-perl all 0.11-2 [10.5 kB]
Get:164 http://172.17.4.1/private trixie-staging/main armhf libmodule-runtime-conflicts-perl all 0.003-2 [7356 B]
Get:165 http://172.17.4.1/private trixie-staging/main armhf libpackage-deprecationmanager-perl all 0.18-1 [17.6 kB]
Get:166 http://172.17.4.1/private trixie-staging/main armhf libpackage-stash-xs-perl armhf 0.30-1+b1 [18.2 kB]
Get:167 http://172.17.4.1/private trixie-staging/main armhf libmoose-perl armhf 2.2206-1 [795 kB]
Get:168 http://172.17.4.1/private trixie-staging/main armhf libvariable-magic-perl armhf 0.63-1+b1 [41.6 kB]
Get:169 http://172.17.4.1/private trixie-staging/main armhf libb-hooks-endofscope-perl all 0.26-1 [19.6 kB]
Get:170 http://172.17.4.1/private trixie-staging/main armhf libsub-identify-perl armhf 0.14-3 [10.6 kB]
Get:171 http://172.17.4.1/private trixie-staging/main armhf libsub-name-perl armhf 0.27-1 [12.0 kB]
Get:172 http://172.17.4.1/private trixie-staging/main armhf libnamespace-clean-perl all 0.27-2 [17.8 kB]
Get:173 http://172.17.4.1/private trixie-staging/main armhf libcurl3-gnutls armhf 8.2.1-2+rpi1 [338 kB]
Get:174 http://172.17.4.1/private trixie-staging/main armhf libwww-curl-perl armhf 4.17-10 [55.8 kB]
Get:175 http://172.17.4.1/private trixie-staging/main armhf libwww-curl-simple-perl all 0.100191-3 [12.6 kB]
Get:176 http://172.17.4.1/private trixie-staging/main armhf dh-r all 20230912 [40.8 kB]
Get:177 http://172.17.4.1/private trixie-staging/main armhf libboost1.81-dev armhf 1.81.0-6 [10.4 MB]
Get:178 http://172.17.4.1/private trixie-staging/main armhf libcurl4-openssl-dev armhf 8.2.1-2+rpi1 [425 kB]
Get:179 http://172.17.4.1/private trixie-staging/main armhf r-bioc-biocgenerics all 0.46.0-1 [594 kB]
Get:180 http://172.17.4.1/private trixie-staging/main armhf r-cran-formatr all 1.14-1 [152 kB]
Get:181 http://172.17.4.1/private trixie-staging/main armhf r-cran-lambda.r all 1.2.4-2 [118 kB]
Get:182 http://172.17.4.1/private trixie-staging/main armhf r-cran-futile.options all 1.0.1-3 [20.0 kB]
Get:183 http://172.17.4.1/private trixie-staging/main armhf r-cran-futile.logger all 1.4.3-4 [98.4 kB]
Get:184 http://172.17.4.1/private trixie-staging/main armhf r-cran-snow all 1:0.4.4-2 [98.9 kB]
Get:185 http://172.17.4.1/private trixie-staging/main armhf r-cran-codetools all 0.2-19-1 [90.9 kB]
Get:186 http://172.17.4.1/private trixie-staging/main armhf r-cran-bh all 1.81.0-1 [5776 B]
Get:187 http://172.17.4.1/private trixie-staging/main armhf r-cran-cpp11 all 0.4.6-1 [219 kB]
Get:188 http://172.17.4.1/private trixie-staging/main armhf r-bioc-biocparallel armhf 1.34.2-1 [1337 kB]
Get:189 http://172.17.4.1/private trixie-staging/main armhf r-bioc-s4vectors armhf 0.38.2+dfsg-1 [2047 kB]
Get:190 http://172.17.4.1/private trixie-staging/main armhf r-bioc-iranges armhf 2.34.1-1 [2247 kB]
Get:191 http://172.17.4.1/private trixie-staging/main armhf r-bioc-zlibbioc all 1.46.0+dfsg-1 [9336 B]
Get:192 http://172.17.4.1/private trixie-staging/main armhf r-bioc-xvector armhf 0.40.0-1 [617 kB]
Get:193 http://172.17.4.1/private trixie-staging/main armhf r-cran-bitops armhf 1.0-7-1 [30.1 kB]
Get:194 http://172.17.4.1/private trixie-staging/main armhf r-cran-rcurl armhf 1.98-1.12+dfsg-1 [787 kB]
Get:195 http://172.17.4.1/private trixie-staging/main armhf r-bioc-genomeinfodbdata all 1.2.10-1 [12.0 MB]
Get:196 http://172.17.4.1/private trixie-staging/main armhf r-bioc-genomeinfodb all 1.36.3+dfsg-1 [3840 kB]
Get:197 http://172.17.4.1/private trixie-staging/main armhf r-cran-crayon all 1.5.2-1 [165 kB]
Get:198 http://172.17.4.1/private trixie-staging/main armhf r-bioc-biostrings armhf 2.68.1-1 [13.8 MB]
Get:199 http://172.17.4.1/private trixie-staging/main armhf r-bioc-genomicranges armhf 1.52.0+dfsg-1 [1831 kB]
Get:200 http://172.17.4.1/private trixie-staging/main armhf r-bioc-rhtslib armhf 2.2.0+dfsg-1 [1188 kB]
debconf: delaying package configuration, since apt-utils is not installed
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No schema files found: doing nothing.
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invoke-rc.d: could not determine current runlevel
invoke-rc.d: policy-rc.d denied execution of restart.
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Setting up libnghttp2-14:armhf (1.56.0-1) ...
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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
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update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
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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) ...
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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
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Setting up intltool-debian (0.35.0+20060710.6) ...
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Setting up ca-certificates (20230311) ...
Updating certificates in /etc/ssl/certs...
140 added, 0 removed; done.
Setting up gfortran-12 (12.2.0-14+rpi1) ...
Setting up libfreetype6:armhf (2.13.2+dfsg-1) ...
Setting up liblapack-dev:armhf (3.11.0-2) ...
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 libdata-optlist-perl (0.114-1) ...
Setting up pkg-config:armhf (1.8.1-1) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.23.0-2) ...
Setting up libcurl4:armhf (8.2.1-2+rpi1) ...
Setting up libx11-6:armhf (2:1.8.6-1) ...
Setting up libharfbuzz0b:armhf (8.0.1-1) ...
Setting up libmro-compat-perl (0.15-2) ...
Setting up libsm6:armhf (2:1.2.3-1) ...
Setting up libxmuu1:armhf (2:1.1.3-3) ...
Setting up libsub-exporter-perl (0.990-1) ...
Setting up libhttp-message-perl (6.44-2) ...
Setting up libeval-closure-perl (0.14-3) ...
Setting up libxrender1:armhf (1:0.9.10-1.1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libparams-classify-perl:armhf (0.015-2+b1) ...
Setting up libxext6:armhf (2:1.3.4-1) ...
Setting up libwww-curl-perl:armhf (4.17-10) ...
Setting up man-db (2.11.2-3) ...
Not building database; man-db/auto-update is not 'true'.
Setting up gfortran (4:12.2.0-3+rpi1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up libmodule-runtime-perl (0.016-2) ...
Setting up libcurl4-openssl-dev:armhf (8.2.1-2+rpi1) ...
Setting up libdist-checkconflicts-perl (0.11-2) ...
Setting up libxt6:armhf (1:1.2.1-1.1) ...
Setting up xauth (1:1.1.2-1) ...
Setting up libxss1:armhf (1:1.2.3-1) ...
Setting up libmodule-implementation-perl (0.09-2) ...
Setting up libpackage-stash-perl (0.40-1) ...
Setting up debhelper (13.11.6) ...
Setting up libmodule-runtime-conflicts-perl (0.003-2) ...
Setting up libclass-load-perl (0.25-2) ...
Setting up libpackage-deprecationmanager-perl (0.18-1) ...
Setting up libdevel-overloadinfo-perl (0.007-1) ...
Setting up libclass-load-xs-perl (0.10-2+b1) ...
Setting up libb-hooks-endofscope-perl (0.26-1) ...
Setting up libmoose-perl:armhf (2.2206-1) ...
Setting up libnamespace-clean-perl (0.27-2) ...
Setting up libwww-curl-simple-perl (0.100191-3) ...
Processing triggers for sgml-base (1.31) ...
Setting up libfontconfig1:armhf (2.14.2-6) ...
Setting up fontconfig (2.14.2-6) ...
Regenerating fonts cache... done.
Setting up libxft2:armhf (2.3.6-1) ...
Setting up libtk8.6:armhf (8.6.13-2) ...
Processing triggers for libc-bin (2.36-9+rpi1+deb12u1) ...
Setting up libpango-1.0-0:armhf (1.51.0+ds-2) ...
Setting up libcairo2:armhf (1.18.0-1) ...
Setting up libpangoft2-1.0-0:armhf (1.51.0+ds-2) ...
Setting up libpangocairo-1.0-0:armhf (1.51.0+ds-2) ...
Setting up r-base-core (4.3.1-4) ...
Creating config file /etc/R/Renviron with new version
Setting up r-cran-crayon (1.5.2-1) ...
Setting up r-cran-futile.options (1.0.1-3) ...
Setting up r-cran-formatr (1.14-1) ...
Setting up r-bioc-genomeinfodbdata (1.2.10-1) ...
Setting up r-cran-codetools (0.2-19-1) ...
Setting up r-bioc-biocgenerics (0.46.0-1) ...
Setting up r-base-dev (4.3.1-4) ...
Setting up r-cran-lambda.r (1.2.4-2) ...
Setting up r-cran-snow (1:0.4.4-2) ...
Setting up r-cran-bitops (1.0-7-1) ...
Setting up r-bioc-zlibbioc (1.46.0+dfsg-1) ...
Setting up r-cran-cpp11 (0.4.6-1) ...
Setting up r-bioc-s4vectors (0.38.2+dfsg-1) ...
Setting up r-cran-futile.logger (1.4.3-4) ...
Setting up r-bioc-iranges (2.34.1-1) ...
Setting up dh-r (20230912) ...
Setting up r-cran-rcurl (1.98-1.12+dfsg-1) ...
Setting up r-bioc-biocparallel (1.34.2-1) ...
Setting up r-bioc-rhtslib (2.2.0+dfsg-1) ...
Setting up r-bioc-genomeinfodb (1.36.3+dfsg-1) ...
Setting up r-bioc-xvector (0.40.0-1) ...
Setting up r-bioc-genomicranges (1.52.0+dfsg-1) ...
Setting up r-bioc-biostrings (2.68.1-1) ...
Setting up sbuild-build-depends-r-bioc-rsamtools-dummy (0.invalid.0) ...
Processing triggers for ca-certificates (20230311) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Processing triggers for libc-bin (2.36-9+rpi1+deb12u1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-187-generic armhf (armv8l)
Toolchain package versions: binutils_2.40-2+rpi2 dpkg-dev_1.21.22+rpi1 g++-12_12.2.0-14+rpi1 gcc-12_12.2.0-14+rpi1 libc6-dev_2.36-9+rpi1+deb12u1 libstdc++-12-dev_12.2.0-14+rpi1 libstdc++6_12.2.0-14+rpi1 linux-libc-dev_6.1.38-1+rpi1
Package versions: adduser_3.137 apt_2.7.3 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-13 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.1 bash_5.2.15-2 binutils_2.40-2+rpi2 binutils-arm-linux-gnueabihf_2.40-2+rpi2 binutils-common_2.40-2+rpi2 bsdextrautils_2.39.2-2 bsdutils_1:2.39.2-2 build-essential_12.9 bzip2_1.0.8-5+b2 ca-certificates_20230311 coreutils_9.1-1 cpp_4:12.2.0-3+rpi1 cpp-12_12.2.0-14+rpi1 dash_0.5.12-6 dctrl-tools_2.24-3 debconf_1.5.82 debhelper_13.11.6 debianutils_5.13 dh-autoreconf_20 dh-r_20230912 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 dirmngr_2.2.40-1.1 dpkg_1.21.22+rpi1 dpkg-dev_1.21.22+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.32.1-1 file_1:5.45-2 findutils_4.9.0-4 fontconfig_2.14.2-6 fontconfig-config_2.14.2-6 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 g++_4:12.2.0-3+rpi1 g++-12_12.2.0-14+rpi1 gcc_4:12.2.0-3+rpi1 gcc-12_12.2.0-14+rpi1 gcc-12-base_12.2.0-14+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-13 gettext-base_0.21-13 gfortran_4:12.2.0-3+rpi1 gfortran-12_12.2.0-14+rpi1 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 gpg_2.2.40-1.1 gpg-agent_2.2.40-1.1 gpg-wks-client_2.2.40-1.1 gpg-wks-server_2.2.40-1.1 gpgconf_2.2.40-1.1 gpgsm_2.2.40-1.1 gpgv_2.2.40-1.1 grep_3.8-5 groff-base_1.23.0-2 gzip_1.12-1 hostname_3.23+nmu1 icu-devtools_72.1-3 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20221126-1 krb5-locales_1.20.1-3 libacl1_2.3.1-3 libalgorithm-c3-perl_0.11-2 libapt-pkg6.0_2.7.3 libarchive-zip-perl_1.68-1 libasan8_12.2.0-14+rpi1 libassuan0_2.5.6-1 libatomic1_12.2.0-14+rpi1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1 libaudit1_1:3.1.1-1 libb-hooks-endofscope-perl_0.26-1 libb-hooks-op-check-perl_0.22-2+b1 libbinutils_2.40-2+rpi2 libblas-dev_3.11.0-2 libblas3_3.11.0-2 libblkid1_2.39.2-2 libboost1.81-dev_1.81.0-6 libbrotli1_1.0.9-2+b3 libbsd0_0.11.7-4 libbz2-1.0_1.0.8-5+b2 libbz2-dev_1.0.8-5+b2 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libxss1_1:1.2.3-1 libxt6_1:1.2.1-1.1 libxxhash0_0.8.1-1 libzstd1_1.5.5+dfsg2-1 linux-libc-dev_6.1.38-1+rpi1 login_1:4.13+dfsg1-1 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-4 make_4.3-4.1 man-db_2.11.2-3 mawk_1.3.4.20230808-1 mount_2.39.2-2 nano_7.2-1 ncurses-base_6.4+20230625-2 ncurses-bin_6.4+20230625-2 netbase_6.4 openssl_3.0.11-1 passwd_1:4.13+dfsg1-1 patch_2.7.6-7 perl_5.36.0-7 perl-base_5.36.0-7 perl-modules-5.36_5.36.0-9 pinentry-curses_1.2.1-1 pkg-config_1.8.1-1 pkgconf_1.8.1-1 pkgconf-bin_1.8.1-1 po-debconf_1.0.21+nmu1 r-base-core_4.3.1-4 r-base-dev_4.3.1-4 r-bioc-biocgenerics_0.46.0-1 r-bioc-biocparallel_1.34.2-1 r-bioc-biostrings_2.68.1-1 r-bioc-genomeinfodb_1.36.3+dfsg-1 r-bioc-genomeinfodbdata_1.2.10-1 r-bioc-genomicranges_1.52.0+dfsg-1 r-bioc-iranges_2.34.1-1 r-bioc-rhtslib_2.2.0+dfsg-1 r-bioc-s4vectors_0.38.2+dfsg-1 r-bioc-xvector_0.40.0-1 r-bioc-zlibbioc_1.46.0+dfsg-1 r-cran-bh_1.81.0-1 r-cran-bitops_1.0-7-1 r-cran-codetools_0.2-19-1 r-cran-cpp11_0.4.6-1 r-cran-crayon_1.5.2-1 r-cran-formatr_1.14-1 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_1.98-1.12+dfsg-1 r-cran-snow_1:0.4.4-2 raspbian-archive-keyring_20120528.2 readline-common_8.2-1.3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-rsamtools-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 sgml-base_1.31 sysvinit-utils_3.07-1 tar_1.34+dfsg-1.2 tzdata_2023c-10 ucf_3.0043+nmu1 unzip_6.0-28 usrmerge_37 util-linux_2.39.2-2 util-linux-extra_2.39.2-2 x11-common_1:7.7+23 xauth_1:1.1.2-1 xdg-utils_1.1.3-4.1 xz-utils_5.4.4-0.1 zip_3.0-13 zlib1g_1:1.2.13.dfsg-3 zlib1g-dev_1:1.2.13.dfsg-3
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: Signature made Mon Nov 21 10:23:34 2022 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tillea@rki.de"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./r-bioc-rsamtools_2.14.0-1.dsc: no acceptable signature found
dpkg-source: info: extracting r-bioc-rsamtools in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking r-bioc-rsamtools_2.14.0.orig.tar.gz
dpkg-source: info: unpacking r-bioc-rsamtools_2.14.0-1.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
Hack binNMU version
-------------------
Created changelog entry for binNMU version 2.14.0-1+b2
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-47d77ea9-7976-4872-8d8d-0a800fd9db1b
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package r-bioc-rsamtools
dpkg-buildpackage: info: source version 2.14.0-1+b2
dpkg-buildpackage: info: source distribution trixie-staging
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 --destdir=debian/r-bioc-rsamtools/ -a -O--buildsystem=R
I: R Package: Rsamtools Version: 2.14.0
I: Building using R version 4.3.1-4
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Mon, 21 Nov 2022 11:21:24 +0100
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='Mon, 21 Nov 2022 11:21:24 +0100'"
* installing *source* package 'Rsamtools' ...
** using staged installation
** libs
using C compiler: 'gcc (Raspbian 12.2.0-14+rpi1) 12.2.0'
using C++ compiler: 'g++ (Raspbian 12.2.0-14+rpi1) 12.2.0'
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o
gcc -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c IRanges_stubs.c -o IRanges_stubs.o
g++ -std=gnu++17 -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c PileupBuffer.cpp -o PileupBuffer.o
g++ -std=gnu++17 -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c PosCacheColl.cpp -o PosCacheColl.o
gcc -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c R_init_Rsamtools.c -o R_init_Rsamtools.o
g++ -std=gnu++17 -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c ResultManager.cpp -o ResultManager.o
gcc -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c XVector_stubs.c -o XVector_stubs.o
gcc -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c as_bam.c -o as_bam.o
gcc -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c bam_data.c -o bam_data.o
g++ -std=gnu++17 -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c bam_mate_iter.cpp -o bam_mate_iter.o
In file included 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/samtools-1.7-compat.h:14:41: warning: ignoring return value of 'int64_t bgzf_seek(BGZF*, int64_t, int)' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
| ~~~~~~~~~^~~~~~~~~~~~~~
BamRangeIterator.h:138:16: note: in expansion of macro 'bam_seek'
138 | (void) bam_seek(bfile, pos, SEEK_SET);
| ^~~~~~~~
BamIterator.h: In constructor 'BamIterator::BamIterator(bamFile, const bam_index_t*)':
/usr/lib/R/site-library/Rhtslib/include/samtools-1.7-compat.h:14:41: warning: ignoring return value of 'int64_t bgzf_seek(BGZF*, int64_t, int)' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
| ~~~~~~~~~^~~~~~~~~~~~~~
BamIterator.h:87:16: note: in expansion of macro 'bam_seek'
87 | (void) bam_seek(bfile, 0, 0);
| ^~~~~~~~
gcc -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c bam_plbuf.c -o bam_plbuf.o
gcc -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c bam_sort.c -o bam_sort.o
gcc -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c bambuffer.c -o bambuffer.o
gcc -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c bamfile.c -o bamfile.o
bamfile.c: In function 'bamfile_isincomplete':
bamfile.c:168:20: warning: ignoring return value of 'bgzf_seek' declared with attribute 'warn_unused_result' [-Wunused-result]
168 | (void) bgzf_seek(bfile->file->x.bam, offset, SEEK_SET);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c bcffile.c -o bcffile.o
gcc -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c bedidx.c -o bedidx.o
gcc -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c encode.c -o encode.o
gcc -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c fafile.c -o fafile.o
gcc -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c idxstats.c -o idxstats.o
In file included from bamfile.h:5,
from idxstats.c:1:
idxstats.c: In function 'idxstats_bamfile':
/usr/lib/R/site-library/Rhtslib/include/samtools-1.7-compat.h:14:32: warning: ignoring return value of 'bgzf_seek' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
| ^~~~~~~~~~~~~~~~~~~~~~~
idxstats.c:20:12: note: in expansion of macro 'bam_seek'
20 | (void) bam_seek(fp, 0, 0);
| ^~~~~~~~
gcc -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c io_sam.c -o io_sam.o
In file included from io_sam.c:2:
io_sam.c: In function '_scan_bam_all':
/usr/lib/R/site-library/Rhtslib/include/samtools-1.7-compat.h:14:32: warning: ignoring return value of 'bgzf_seek' declared with attribute 'warn_unused_result' [-Wunused-result]
14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
| ^~~~~~~~~~~~~~~~~~~~~~~
io_sam.c:304:12: note: in expansion of macro 'bam_seek'
304 | (void) bam_seek(bfile->file->x.bam, bfile->pos0, SEEK_SET);
| ^~~~~~~~
g++ -std=gnu++17 -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
g++ -std=gnu++17 -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c pileup.cpp -o pileup.o
gcc -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c pileupbam.c -o pileupbam.o
gcc -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c sam_opts.c -o sam_opts.o
gcc -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c sam_utils.c -o sam_utils.o
gcc -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c samtools_patch.c -o samtools_patch.o
gcc -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c scan_bam_data.c -o scan_bam_data.o
gcc -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -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:270:9: note: declared here
270 | int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
| ^~~~~~~~~~~~
gcc -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c tagfilter.c -o tagfilter.o
gcc -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c utilities.c -o utilities.o
gcc -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 -ffile-prefix-map=/build/r-base-zZwmPk/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g1 -Wdate-time -D_FORTIFY_SOURCE=2 -c zip_compression.c -o zip_compression.o
g++ -std=gnu++17 -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_data.o bam_mate_iter.o bam_plbuf.o bam_sort.o bambuffer.o bamfile.o bcffile.o bedidx.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.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-2.14.0/00new/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
Use of uninitialized value $dep_line in substitution (s///) at /usr/share/perl5/Dpkg/Deps.pm line 300.
Use of uninitialized value $dep_line in substitution (s///) at /usr/share/perl5/Dpkg/Deps.pm line 302.
Use of uninitialized value $dep_line in substitution (s///) at /usr/share/perl5/Dpkg/Deps.pm line 303.
Use of uninitialized value $dep_line in split at /usr/share/perl5/Dpkg/Deps.pm line 306.
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)
W: Ignoring specified R dependency: R (>= 3.5.0)
I: Using r-bioc-genomicalignments for Suggests:GenomicAlignments
I: Using r-bioc-shortread for Suggests:ShortRead (>= 1.19.10)
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: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
I: Using r-cran-runit for Suggests:RUnit
I: Using r-bioc-biocstyle 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 (>= 1.99.3)
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-3.16
I: Use r-bioc-rsamtools as Debian binary package for variables substitution
dh_installdocs -a -O--buildsystem=R
dh_installchangelogs -a -O--buildsystem=R
dh_installsystemduser -a -O--buildsystem=R
dh_perl -a -O--buildsystem=R
dh_link -a -O--buildsystem=R
dh_strip_nondeterminism -a -O--buildsystem=R
dh_compress -a -O--buildsystem=R
dh_fixperms -a -O--buildsystem=R
dh_missing -a -O--buildsystem=R
dh_dwz -a -O--buildsystem=R
dh_strip -a -O--buildsystem=R
dh_makeshlibs -a -O--buildsystem=R
dh_shlibdeps -a -O--buildsystem=R
dh_installdeb -a -O--buildsystem=R
dh_gencontrol -a -O--buildsystem=R
dh_md5sums -a -O--buildsystem=R
dh_builddeb -a -O--buildsystem=R
dpkg-deb: building package 'r-bioc-rsamtools' in '../r-bioc-rsamtools_2.14.0-1+b2_armhf.deb'.
dpkg-deb: building package 'r-bioc-rsamtools-dbgsym' in '../r-bioc-rsamtools-dbgsym_2.14.0-1+b2_armhf.deb'.
dpkg-genbuildinfo --build=any -O../r-bioc-rsamtools_2.14.0-1+b2_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> -O../r-bioc-rsamtools_2.14.0-1+b2_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 2023-10-04T06:08:19Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
r-bioc-rsamtools_2.14.0-1+b2_armhf.changes:
-------------------------------------------
Format: 1.8
Date: Mon, 21 Nov 2022 11:21:24 +0100
Source: r-bioc-rsamtools (2.14.0-1)
Binary: r-bioc-rsamtools r-bioc-rsamtools-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 2.14.0-1+b2
Distribution: trixie-staging
Urgency: low
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Description:
r-bioc-rsamtools - GNU R binary alignment (BAM), variant call (BCF), or tabix file i
Changes:
r-bioc-rsamtools (2.14.0-1+b2) trixie-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
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Checksums-Sha256:
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366e6994a851ac666248fa5874e7cae63df5500444236d5b8f3e97d92d6c6f3c 10890 r-bioc-rsamtools_2.14.0-1+b2_armhf.buildinfo
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Files:
0f52e4a8a7cf0639aa9f8319cd3544eb 189232 debug optional r-bioc-rsamtools-dbgsym_2.14.0-1+b2_armhf.deb
e916b9bdf790ad971f8cbe578ecf6c30 10890 gnu-r optional r-bioc-rsamtools_2.14.0-1+b2_armhf.buildinfo
743cbf452f6963fdebba6dd1f5133e10 3677988 gnu-r optional r-bioc-rsamtools_2.14.0-1+b2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
r-bioc-rsamtools-dbgsym_2.14.0-1+b2_armhf.deb
---------------------------------------------
new Debian package, version 2.0.
size 189232 bytes: control archive=544 bytes.
419 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: r-bioc-rsamtools-dbgsym
Source: r-bioc-rsamtools (2.14.0-1)
Version: 2.14.0-1+b2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Installed-Size: 292
Depends: r-bioc-rsamtools (= 2.14.0-1+b2)
Section: debug
Priority: optional
Description: debug symbols for r-bioc-rsamtools
Build-Ids: 0414f90179e42ef67ee77b6a38dea91c26545100
drwxr-xr-x root/root 0 2022-11-21 10:21 ./
drwxr-xr-x root/root 0 2022-11-21 10:21 ./usr/
drwxr-xr-x root/root 0 2022-11-21 10:21 ./usr/lib/
drwxr-xr-x root/root 0 2022-11-21 10:21 ./usr/lib/debug/
drwxr-xr-x root/root 0 2022-11-21 10:21 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2022-11-21 10:21 ./usr/lib/debug/.build-id/04/
-rw-r--r-- root/root 288564 2022-11-21 10:21 ./usr/lib/debug/.build-id/04/14f90179e42ef67ee77b6a38dea91c26545100.debug
drwxr-xr-x root/root 0 2022-11-21 10:21 ./usr/share/
drwxr-xr-x root/root 0 2022-11-21 10:21 ./usr/share/doc/
lrwxrwxrwx root/root 0 2022-11-21 10:21 ./usr/share/doc/r-bioc-rsamtools-dbgsym -> r-bioc-rsamtools
r-bioc-rsamtools_2.14.0-1+b2_armhf.deb
--------------------------------------
new Debian package, version 2.0.
size 3677988 bytes: control archive=3836 bytes.
1131 bytes, 16 lines control
9969 bytes, 109 lines md5sums
Package: r-bioc-rsamtools
Source: r-bioc-rsamtools (2.14.0-1)
Version: 2.14.0-1+b2
Architecture: armhf
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Installed-Size: 5607
Depends: r-api-4.0, r-api-bioc-3.16, 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 (>= 1.99.3), libc6 (>= 2.34), libcurl4 (>= 7.18.0), libgcc-s1 (>= 3.5), libstdc++6 (>= 11)
Suggests: r-bioc-genomicalignments, r-bioc-shortread (>= 1.19.10), r-bioc-genomicfeatures, r-cran-runit, r-bioc-biocstyle
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 2022-11-21 10:21 ./
drwxr-xr-x root/root 0 2022-11-21 10:21 ./usr/
drwxr-xr-x root/root 0 2022-11-21 10:21 ./usr/lib/
drwxr-xr-x root/root 0 2022-11-21 10:21 ./usr/lib/R/
drwxr-xr-x root/root 0 2022-11-21 10:21 ./usr/lib/R/site-library/
drwxr-xr-x root/root 0 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/
-rw-r--r-- root/root 1815 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/DESCRIPTION
-rw-r--r-- root/root 2303 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/INDEX
drwxr-xr-x root/root 0 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/Meta/
-rw-r--r-- root/root 3297 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/Meta/Rd.rds
-rw-r--r-- root/root 132 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/Meta/features.rds
-rw-r--r-- root/root 3438 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/Meta/hsearch.rds
-rw-r--r-- root/root 2478 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/Meta/links.rds
-rw-r--r-- root/root 800 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/Meta/nsInfo.rds
-rw-r--r-- root/root 1770 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/Meta/package.rds
-rw-r--r-- root/root 247 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/Meta/vignette.rds
-rw-r--r-- root/root 1431 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/NAMESPACE
-rw-r--r-- root/root 15994 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/NEWS
drwxr-xr-x root/root 0 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/R/
-rw-r--r-- root/root 1058 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/R/Rsamtools
-rw-r--r-- root/root 856233 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/R/Rsamtools.rdb
-rw-r--r-- root/root 6757 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/R/Rsamtools.rdx
drwxr-xr-x root/root 0 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/doc/
-rw-r--r-- root/root 10341 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-Overview.R
-rw-r--r-- root/root 20661 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-Overview.Rnw
-rw-r--r-- root/root 185080 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-Overview.pdf
-rw-r--r-- root/root 1459 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/doc/index.html
drwxr-xr-x root/root 0 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/
-rw-r--r-- root/root 176 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/ce2dict1.fa
-rw-r--r-- root/root 112 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/ce2dict1.fa.fai
-rw-r--r-- root/root 126539 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bam
-rw-r--r-- root/root 176 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bam.bai
-rw-r--r-- root/root 79176 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bcf.gz
-rw-r--r-- root/root 110 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bcf.gz.csi
-rw-r--r-- root/root 559422 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.sam
-rw-r--r-- root/root 74987 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.vcf.gz
-rw-r--r-- root/root 143 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.vcf.gz.csi
-rw-r--r-- root/root 3778 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/example.gtf.gz
-rw-r--r-- root/root 259 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/example.gtf.gz.tbi
-rw-r--r-- root/root 348 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/example_from_SAM_Spec.bam
-rw-r--r-- root/root 96 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/example_from_SAM_Spec.bam.bai
-rw-r--r-- root/root 368 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/example_from_SAM_Spec.sam
-rw-r--r-- root/root 203 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_buffered_pileup.bam
-rw-r--r-- root/root 176 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_buffered_pileup.bam.bai
-rw-r--r-- root/root 240 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_buffered_pileup.sam
-rw-r--r-- root/root 198 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_whole_file.bam
-rw-r--r-- root/root 176 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_whole_file.bam.bai
-rw-r--r-- root/root 168 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_whole_file.sam
-rw-r--r-- root/root 1626553 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/olaps.Rda
-rw-r--r-- root/root 138598 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/pileup.txt
-rw-r--r-- root/root 181 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/querybins.bam
-rw-r--r-- root/root 96 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/querybins.bam.bai
-rw-r--r-- root/root 117 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/querybins.sam
-rw-r--r-- root/root 381 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/revbins.bam
-rw-r--r-- root/root 416 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/revbins.bam.bai
-rw-r--r-- root/root 770 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/revbins.sam
-rw-r--r-- root/root 31 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/samtools-github.txt
-rw-r--r-- root/root 2808 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/slxMaq09_urls.txt
-rw-r--r-- root/root 333 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/tagfilter.bam
-rw-r--r-- root/root 656 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/tagfilter.bam.bai
-rw-r--r-- root/root 804 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/tagfilter.sam
-rw-r--r-- root/root 1167 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/tiny.bam
-rw-r--r-- root/root 2336 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/tiny.bam.bai
-rw-r--r-- root/root 4102 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/tiny.sam
drwxr-xr-x root/root 0 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/
-rw-r--r-- root/root 36 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/README
-rw-r--r-- root/root 36039 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/accepted_hits.sam
-rw-r--r-- root/root 4381 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/coverage.wig
-rw-r--r-- root/root 196 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/junctions.bed
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-rw-r--r-- root/root 11579 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/help/AnIndex
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-rw-r--r-- root/root 389 2022-11-21 10:21 ./usr/lib/R/site-library/Rsamtools/help/paths.rds
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+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 14560
Build-Time: 159
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 557
Job: r-bioc-rsamtools_2.14.0-1
Machine Architecture: armhf
Package: r-bioc-rsamtools
Package-Time: 737
Source-Version: 2.14.0-1
Space: 14560
Status: successful
Version: 2.14.0-1+b2
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Finished at 2023-10-04T06:08:19Z
Build needed 00:12:17, 14560k disk space