r-bioc-bitseq →
1.40.0+dfsg-1+b1 →
armhf → 2022-12-07 02:10:53
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| r-bioc-bitseq 1.40.0+dfsg-1+b1 (armhf) Wed, 07 Dec 2022 01:46:31 +0000 |
+==============================================================================+
Package: r-bioc-bitseq
Version: 1.40.0+dfsg-1+b1
Source Version: 1.40.0+dfsg-1
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-458d230d-bdcb-48f1-af28-7d626acc363a' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-bitseq-frPtN4/resolver-RZF9Ia' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.5 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.3 MB]
Fetched 27.8 MB in 18s (1581 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/bookworm-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-bitseq' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/r-pkg-team/r-bioc-bitseq.git
Please use:
git clone https://salsa.debian.org/r-pkg-team/r-bioc-bitseq.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 758 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main r-bioc-bitseq 1.40.0+dfsg-1 (dsc) [2199 B]
Get:2 http://172.17.4.1/private bookworm-staging/main r-bioc-bitseq 1.40.0+dfsg-1 (tar) [750 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main r-bioc-bitseq 1.40.0+dfsg-1 (diff) [5932 B]
Fetched 758 kB in 0s (3657 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/r-bioc-bitseq-frPtN4/r-bioc-bitseq-1.40.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-bitseq-frPtN4' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), dh-r, r-base-dev, r-bioc-rsamtools (>= 1.99.3), r-bioc-s4vectors, r-bioc-iranges, r-bioc-rhtslib, libboost-dev, libcurl4-openssl-dev, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), dh-r, r-base-dev, r-bioc-rsamtools (>= 1.99.3), r-bioc-s4vectors, r-bioc-iranges, r-bioc-rhtslib, libboost-dev, libcurl4-openssl-dev, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [437 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [521 B]
Fetched 1915 B in 0s (37.2 kB/s)
Reading package lists...
Reading package lists...
Install main 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 libperl5.34 perl-modules-5.34
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils bsdutils
ca-certificates cpp-12 dctrl-tools debhelper dh-autoreconf dh-r
dh-strip-nondeterminism dwz file fontconfig fontconfig-config
fonts-dejavu-core g++-12 gcc-12 gcc-12-base gettext gettext-base gfortran
gfortran-12 groff-base icu-devtools intltool-debian libalgorithm-c3-perl
libarchive-zip-perl libasan8 libatomic1 libb-hooks-endofscope-perl
libb-hooks-op-check-perl libblas-dev libblas3 libblkid1 libboost-dev
libboost1.74-dev libbrotli1 libbsd0 libbz2-dev libcairo2 libcc1-0
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 libgcc-12-dev
libgcc-s1 libgfortran-12-dev libgfortran5 libglib2.0-0 libgomp1
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 liblzma5 libmagic-mgc libmagic1 libmd0
libmodule-implementation-perl libmodule-runtime-conflicts-perl
libmodule-runtime-perl libmoose-perl libmount1 libmro-compat-perl
libnamespace-clean-perl libncurses-dev libncurses5-dev libncurses6
libnghttp2-14 libpackage-deprecationmanager-perl libpackage-stash-perl
libpackage-stash-xs-perl libpango-1.0-0 libpangocairo-1.0-0
libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl
libparams-util-perl libpcre16-3 libpcre2-16-0 libpcre2-32-0 libpcre2-8-0
libpcre2-dev libpcre2-posix3 libpcre3-dev libpcre32-3 libpcrecpp0v5
libpipeline1 libpixman-1-0 libpkgconf3 libpng-dev libpng16-16 libpsl5
libreadline-dev libreadline8 libregexp-ipv6-perl librtmp1 libsm6
libsmartcols1 libssh2-1 libssl3 libstdc++-12-dev libstdc++6
libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl
libsub-install-perl libsub-name-perl libsub-override-perl libswitch-perl
libtcl8.6 libthai-data libthai0 libtiff5 libtimedate-perl libtk8.6 libtool
libtry-tiny-perl libubsan1 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-rsamtools 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
readline-common ucf unzip util-linux util-linux-extra x11-common xauth
xdg-utils xz-utils zip zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc gcc-12-locales cpp-12-doc
debtags dh-make postgresql-client-common gcc-12-doc gettext-doc
libasprintf-dev libgettextpo-dev gfortran-doc gfortran-12-doc
libcoarrays-dev groff liblapack-doc libboost-doc libboost1.74-doc
libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev
libboost-context1.74-dev libboost-contract1.74-dev
libboost-coroutine1.74-dev libboost-date-time1.74-dev
libboost-exception1.74-dev libboost-fiber1.74-dev
libboost-filesystem1.74-dev libboost-graph1.74-dev
libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev
libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev
libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev
libboost-program-options1.74-dev libboost-python1.74-dev
libboost-random1.74-dev libboost-regex1.74-dev
libboost-serialization1.74-dev libboost-stacktrace1.74-dev
libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev
libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev
libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev
libcurl4-doc libidn11-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 libstdc++-12-doc tcl8.6 tk8.6 libtool-doc
gcj-jdk libbusiness-isbn-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-annotationdbi r-bioc-affy
r-bioc-deseq2 r-bioc-annotate r-cran-runit r-cran-foreach r-cran-batchjobs
r-cran-bbmisc r-cran-doparallel r-cran-rmpi 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-bench r-cran-callr
r-cran-cli r-cran-covr r-cran-desc r-cran-ggplot2 r-cran-glue r-cran-lobstr
r-cran-scales r-cran-rcpp r-cran-vctrs r-cran-withr r-cran-rstudioapi
r-cran-shiny r-cran-jsonlite r-cran-xml 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 libdevel-partialdump-perl
libgpm2 libpng-tools publicsuffix libltdl-dev uuid-runtime
libmail-sendmail-perl r-recommended r-doc-html r-cran-testthat
r-cran-mockery r-cran-tibble r-cran-decor r-cran-knitr r-cran-brio
r-cran-progress 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 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 libboost-dev libboost1.74-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 libmd0 libmodule-implementation-perl
libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoose-perl
libmro-compat-perl libnamespace-clean-perl libncurses-dev libncurses5-dev
libncurses6 libnghttp2-14 libpackage-deprecationmanager-perl
libpackage-stash-perl libpackage-stash-xs-perl libpango-1.0-0
libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1
libparams-classify-perl libparams-util-perl libpcre16-3 libpcre2-16-0
libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpcre3-dev libpcre32-3
libpcrecpp0v5 libpipeline1 libpixman-1-0 libpkgconf3 libpng-dev libpng16-16
libpsl5 libreadline-dev libregexp-ipv6-perl librtmp1 libsm6 libssh2-1
libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl
libsub-install-perl libsub-name-perl libsub-override-perl libswitch-perl
libtcl8.6 libthai-data libthai0 libtiff5 libtimedate-perl libtk8.6 libtool
libtry-tiny-perl libuchardet0 liburi-perl libvariable-magic-perl 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-rsamtools 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-main-dummy ucf unzip x11-common xauth
xdg-utils zip zlib1g-dev
The following packages will be upgraded:
bsdutils cpp-12 g++-12 gcc-12 gcc-12-base libasan8 libatomic1 libblkid1
libcc1-0 libgcc-12-dev libgcc-s1 libgomp1 liblzma5 libmount1 libpcre2-8-0
libreadline8 libsmartcols1 libssl3 libstdc++-12-dev libstdc++6 libubsan1
libuuid1 mount readline-common util-linux util-linux-extra xz-utils
27 upgraded, 198 newly installed, 0 to remove and 53 not upgraded.
Need to get 182 MB of archives.
After this operation, 477 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [944 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf bsdutils armhf 1:2.38.1-4 [83.9 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libsmartcols1 armhf 2.38.1-4 [91.6 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf util-linux-extra armhf 2.38.1-4 [98.1 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf util-linux armhf 2.38.1-4 [1062 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf mount armhf 2.38.1-4 [126 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf readline-common all 8.2-1.2 [68.5 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libcc1-0 armhf 12.2.0-9+rpi1 [32.2 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf libgomp1 armhf 12.2.0-9+rpi1 [95.4 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf libatomic1 armhf 12.2.0-9+rpi1 [8224 B]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libasan8 armhf 12.2.0-9+rpi1 [2089 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf libubsan1 armhf 12.2.0-9+rpi1 [861 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf gcc-12-base armhf 12.2.0-9+rpi1 [37.2 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf libstdc++6 armhf 12.2.0-9+rpi1 [504 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf g++-12 armhf 12.2.0-9+rpi1 [7913 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf libstdc++-12-dev armhf 12.2.0-9+rpi1 [2025 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf libgcc-12-dev armhf 12.2.0-9+rpi1 [725 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf gcc-12 armhf 12.2.0-9+rpi1 [14.2 MB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf cpp-12 armhf 12.2.0-9+rpi1 [7156 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf libgcc-s1 armhf 12.2.0-9+rpi1 [36.1 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf libblkid1 armhf 2.38.1-4 [131 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf liblzma5 armhf 5.2.8-0.0 [175 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libmount1 armhf 2.38.1-4 [144 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libpcre2-8-0 armhf 10.40-2 [222 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf libreadline8 armhf 8.2-1.2 [142 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf libuuid1 armhf 2.38.1-4 [27.1 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-9 [774 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-4 [78.8 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.11.1-1 [1341 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf libssl3 armhf 3.0.7-1 [1614 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf openssl armhf 3.0.7-1 [1349 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf ca-certificates all 20211016 [156 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-10 [156 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf xz-utils armhf 5.2.8-0.0 [333 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.19-1 [260 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-10 [495 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf dctrl-tools armhf 2.24-3 [94.2 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.11.1 [80.8 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-5 [517 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-2 [19.4 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-2 [8556 B]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-2+rpi2 [177 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14+20220924-2 [93.1 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf libicu72 armhf 72.1-3 [9009 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.1 [570 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-10 [1203 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.11.1 [941 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf zip armhf 3.0-12 [209 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf unzip armhf 6.0-27 [152 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf libpaper1 armhf 1.1.28 [20.5 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf libpaper-utils armhf 1.1.28 [17.7 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf xdg-utils all 1.1.3-4.1 [75.5 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libblas3 armhf 3.10.1-2 [109 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.5.0-1 [77.2 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf libpng16-16 armhf 1.6.39-2 [258 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf libfreetype6 armhf 2.12.1+dfsg-3 [352 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf fontconfig-config armhf 2.13.1-4.5 [281 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libfontconfig1 armhf 2.13.1-4.5 [330 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libpixman-1-0 armhf 0.42.2-1 [461 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-2 [28.6 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.7-1 [112 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf libxcb1 armhf 1.15-1 [139 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf libx11-data all 2:1.8.1-2 [308 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf libx11-6 armhf 2:1.8.1-2 [704 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf libxcb-render0 armhf 1.15-1 [114 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf libxcb-shm0 armhf 1.15-1 [106 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf libxrender1 armhf 1:0.9.10-1.1 [30.0 kB]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf libcairo2 armhf 1.16.0-6 [496 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.50.0-1 [65.0 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:91 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-3+b1 [161 kB]
Get:92 http://172.17.4.1/private bookworm-staging/main armhf libcurl4 armhf 7.86.0-2 [322 kB]
Get:93 http://172.17.4.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.74.1-2 [1214 kB]
Get:94 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo armhf 1:2.1.2-1 [144 kB]
Get:95 http://172.17.4.1/private bookworm-staging/main armhf libgfortran5 armhf 12.2.0-9+rpi1 [238 kB]
Get:96 http://172.17.4.1/private bookworm-staging/main armhf liblapack3 armhf 3.10.1-2 [1587 kB]
Get:97 http://172.17.4.1/private bookworm-staging/main armhf fontconfig armhf 2.13.1-4.5 [416 kB]
Get:98 http://172.17.4.1/private bookworm-staging/main armhf libfribidi0 armhf 1.0.8-2.1 [63.7 kB]
Get:99 http://172.17.4.1/private bookworm-staging/main armhf libgraphite2-3 armhf 1.3.14-1 [70.3 kB]
Get:100 http://172.17.4.1/private bookworm-staging/main armhf libharfbuzz0b armhf 5.2.0-2+b1 [1832 kB]
Get:101 http://172.17.4.1/private bookworm-staging/main armhf libthai-data all 0.1.29-1 [176 kB]
Get:102 http://172.17.4.1/private bookworm-staging/main armhf libdatrie1 armhf 0.2.13-2+b2 [39.9 kB]
Get:103 http://172.17.4.1/private bookworm-staging/main armhf libthai0 armhf 0.1.29-1 [54.5 kB]
Get:104 http://172.17.4.1/private bookworm-staging/main armhf libpango-1.0-0 armhf 1.50.10+ds-1 [214 kB]
Get:105 http://172.17.4.1/private bookworm-staging/main armhf libpangoft2-1.0-0 armhf 1.50.10+ds-1 [68.6 kB]
Get:106 http://172.17.4.1/private bookworm-staging/main armhf libpangocairo-1.0-0 armhf 1.50.10+ds-1 [58.3 kB]
Get:107 http://172.17.4.1/private bookworm-staging/main armhf libtcl8.6 armhf 8.6.13+dfsg-1 [906 kB]
Get:108 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.14-1 [50.9 kB]
Get:109 http://172.17.4.1/private bookworm-staging/main armhf libjbig0 armhf 2.1-3.1+b2 [27.6 kB]
Get:110 http://172.17.4.1/private bookworm-staging/main armhf liblerc4 armhf 4.0.0+ds-2 [133 kB]
Get:111 http://172.17.4.1/private bookworm-staging/main armhf libwebp7 armhf 1.2.2-2+b1 [237 kB]
Get:112 http://172.17.4.1/private bookworm-staging/main armhf libtiff5 armhf 4.4.0-6 [278 kB]
Get:113 http://172.17.4.1/private bookworm-staging/main armhf libxft2 armhf 2.3.6-1 [53.7 kB]
Get:114 http://172.17.4.1/private bookworm-staging/main armhf x11-common all 1:7.7+23 [252 kB]
Get:115 http://172.17.4.1/private bookworm-staging/main armhf libxss1 armhf 1:1.2.3-1 [17.3 kB]
Get:116 http://172.17.4.1/private bookworm-staging/main armhf libtk8.6 armhf 8.6.13-1 [680 kB]
Get:117 http://172.17.4.1/private bookworm-staging/main armhf libice6 armhf 2:1.0.10-1 [51.7 kB]
Get:118 http://172.17.4.1/private bookworm-staging/main armhf libsm6 armhf 2:1.2.3-1 [32.9 kB]
Get:119 http://172.17.4.1/private bookworm-staging/main armhf libxt6 armhf 1:1.2.1-1 [159 kB]
Get:120 http://172.17.4.1/private bookworm-staging/main armhf r-base-core armhf 4.2.2.20221110-1 [25.6 MB]
Get:121 http://172.17.4.1/private bookworm-staging/main armhf libgfortran-12-dev armhf 12.2.0-9+rpi1 [285 kB]
Get:122 http://172.17.4.1/private bookworm-staging/main armhf gfortran-12 armhf 12.2.0-9+rpi1 [7509 kB]
Get:123 http://172.17.4.1/private bookworm-staging/main armhf gfortran armhf 4:12.2.0-1+rpi1 [1432 B]
Get:124 http://172.17.4.1/private bookworm-staging/main armhf libblas-dev armhf 3.10.1-2 [114 kB]
Get:125 http://172.17.4.1/private bookworm-staging/main armhf liblapack-dev armhf 3.10.1-2 [2847 kB]
Get:126 http://172.17.4.1/private bookworm-staging/main armhf libncurses6 armhf 6.3+20220423-2 [79.6 kB]
Get:127 http://172.17.4.1/private bookworm-staging/main armhf libncurses-dev armhf 6.3+20220423-2 [289 kB]
Get:128 http://172.17.4.1/private bookworm-staging/main armhf libncurses5-dev armhf 6.3+20220423-2 [940 B]
Get:129 http://172.17.4.1/private bookworm-staging/main armhf libreadline-dev armhf 8.2-1.2 [122 kB]
Get:130 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo-dev armhf 1:2.1.2-1 [261 kB]
Get:131 http://172.17.4.1/private bookworm-staging/main armhf libjpeg-dev armhf 1:2.1.2-1 [74.7 kB]
Get:132 http://172.17.4.1/private bookworm-staging/main armhf libpcre2-16-0 armhf 10.40-2 [208 kB]
Get:133 http://172.17.4.1/private bookworm-staging/main armhf libpcre2-32-0 armhf 10.40-2 [199 kB]
Get:134 http://172.17.4.1/private bookworm-staging/main armhf libpcre2-posix3 armhf 10.40-2 [53.2 kB]
Get:135 http://172.17.4.1/private bookworm-staging/main armhf libpcre2-dev armhf 10.40-2 [644 kB]
Get:136 http://172.17.4.1/private bookworm-staging/main armhf libpcre16-3 armhf 2:8.39-14 [239 kB]
Get:137 http://172.17.4.1/private bookworm-staging/main armhf libpcre32-3 armhf 2:8.39-14 [232 kB]
Get:138 http://172.17.4.1/private bookworm-staging/main armhf libpcrecpp0v5 armhf 2:8.39-14 [150 kB]
Get:139 http://172.17.4.1/private bookworm-staging/main armhf libpcre3-dev armhf 2:8.39-14 [569 kB]
Get:140 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-4.1 [183 kB]
Get:141 http://172.17.4.1/private bookworm-staging/main armhf libpng-dev armhf 1.6.39-2 [336 kB]
Get:142 http://172.17.4.1/private bookworm-staging/main armhf libbz2-dev armhf 1.0.8-5+b2 [26.8 kB]
Get:143 http://172.17.4.1/private bookworm-staging/main armhf liblzma-dev armhf 5.2.8-0.0 [232 kB]
Get:144 http://172.17.4.1/private bookworm-staging/main armhf icu-devtools armhf 72.1-3 [175 kB]
Get:145 http://172.17.4.1/private bookworm-staging/main armhf libicu-dev armhf 72.1-3 [9959 kB]
Get:146 http://172.17.4.1/private bookworm-staging/main armhf libxmuu1 armhf 2:1.1.3-3 [23.3 kB]
Get:147 http://172.17.4.1/private bookworm-staging/main armhf xauth armhf 1:1.1.1-1 [36.9 kB]
Get:148 http://172.17.4.1/private bookworm-staging/main armhf libpkgconf3 armhf 1.8.0-11 [30.8 kB]
Get:149 http://172.17.4.1/private bookworm-staging/main armhf pkgconf-bin armhf 1.8.0-11 [27.6 kB]
Get:150 http://172.17.4.1/private bookworm-staging/main armhf pkgconf armhf 1.8.0-11 [25.6 kB]
Get:151 http://172.17.4.1/private bookworm-staging/main armhf pkg-config armhf 1.8.0-11 [13.4 kB]
Get:152 http://172.17.4.1/private bookworm-staging/main armhf r-base-dev all 4.2.2.20221110-1 [4488 B]
Get:153 http://172.17.4.1/private bookworm-staging/main armhf libfile-which-perl all 1.27-2 [15.1 kB]
Get:154 http://172.17.4.1/private bookworm-staging/main armhf libswitch-perl all 2.17-3 [20.3 kB]
Get:155 http://172.17.4.1/private bookworm-staging/main armhf libclone-perl armhf 0.46-1 [13.2 kB]
Get:156 http://172.17.4.1/private bookworm-staging/main armhf libencode-locale-perl all 1.05-3 [12.9 kB]
Get:157 http://172.17.4.1/private bookworm-staging/main armhf libtimedate-perl all 2.3300-2 [39.3 kB]
Get:158 http://172.17.4.1/private bookworm-staging/main armhf libhttp-date-perl all 6.05-2 [10.5 kB]
Get:159 http://172.17.4.1/private bookworm-staging/main armhf libio-html-perl all 1.004-3 [16.2 kB]
Get:160 http://172.17.4.1/private bookworm-staging/main armhf liblwp-mediatypes-perl all 6.04-1 [19.9 kB]
Get:161 http://172.17.4.1/private bookworm-staging/main armhf libregexp-ipv6-perl all 0.03-3 [5212 B]
Get:162 http://172.17.4.1/private bookworm-staging/main armhf liburi-perl all 5.17-1 [90.4 kB]
Get:163 http://172.17.4.1/private bookworm-staging/main armhf libhttp-message-perl all 6.44-1 [81.7 kB]
Get:164 http://172.17.4.1/private bookworm-staging/main armhf libparams-util-perl armhf 1.102-2+b1 [23.9 kB]
Get:165 http://172.17.4.1/private bookworm-staging/main armhf libsub-install-perl all 0.928-3 [9724 B]
Get:166 http://172.17.4.1/private bookworm-staging/main armhf libdata-optlist-perl all 0.112-1 [11.8 kB]
Get:167 http://172.17.4.1/private bookworm-staging/main armhf libb-hooks-op-check-perl armhf 0.22-2+b1 [10.3 kB]
Get:168 http://172.17.4.1/private bookworm-staging/main armhf libdynaloader-functions-perl all 0.003-3 [12.7 kB]
Get:169 http://172.17.4.1/private bookworm-staging/main armhf libdevel-callchecker-perl armhf 0.008-2 [15.8 kB]
Get:170 http://172.17.4.1/private bookworm-staging/main armhf libparams-classify-perl armhf 0.015-2+b1 [22.0 kB]
Get:171 http://172.17.4.1/private bookworm-staging/main armhf libmodule-runtime-perl all 0.016-2 [19.6 kB]
Get:172 http://172.17.4.1/private bookworm-staging/main armhf libtry-tiny-perl all 0.31-2 [22.6 kB]
Get:173 http://172.17.4.1/private bookworm-staging/main armhf libmodule-implementation-perl all 0.09-2 [12.6 kB]
Get:174 http://172.17.4.1/private bookworm-staging/main armhf libpackage-stash-perl all 0.40-1 [22.0 kB]
Get:175 http://172.17.4.1/private bookworm-staging/main armhf libclass-load-perl all 0.25-1 [16.1 kB]
Get:176 http://172.17.4.1/private bookworm-staging/main armhf libclass-load-xs-perl armhf 0.10-2+b1 [13.8 kB]
Get:177 http://172.17.4.1/private bookworm-staging/main armhf libsub-exporter-progressive-perl all 0.001013-3 [7496 B]
Get:178 http://172.17.4.1/private bookworm-staging/main armhf libdevel-globaldestruction-perl all 0.14-4 [7144 B]
Get:179 http://172.17.4.1/private bookworm-staging/main armhf libalgorithm-c3-perl all 0.11-2 [10.8 kB]
Get:180 http://172.17.4.1/private bookworm-staging/main armhf libclass-c3-perl all 0.35-2 [21.0 kB]
Get:181 http://172.17.4.1/private bookworm-staging/main armhf libmro-compat-perl all 0.15-1 [12.6 kB]
Get:182 http://172.17.4.1/private bookworm-staging/main armhf libdevel-overloadinfo-perl all 0.007-1 [7896 B]
Get:183 http://172.17.4.1/private bookworm-staging/main armhf libdevel-stacktrace-perl all 2.0400-2 [26.8 kB]
Get:184 http://172.17.4.1/private bookworm-staging/main armhf libsub-exporter-perl all 0.988-1 [51.9 kB]
Get:185 http://172.17.4.1/private bookworm-staging/main armhf libeval-closure-perl all 0.14-3 [11.2 kB]
Get:186 http://172.17.4.1/private bookworm-staging/main armhf libdist-checkconflicts-perl all 0.11-2 [10.5 kB]
Get:187 http://172.17.4.1/private bookworm-staging/main armhf libmodule-runtime-conflicts-perl all 0.003-2 [7356 B]
Get:188 http://172.17.4.1/private bookworm-staging/main armhf libsub-name-perl armhf 0.26-2+b1 [12.2 kB]
Get:189 http://172.17.4.1/private bookworm-staging/main armhf libpackage-deprecationmanager-perl all 0.17-2 [16.8 kB]
Get:190 http://172.17.4.1/private bookworm-staging/main armhf libpackage-stash-xs-perl armhf 0.30-1+b1 [18.2 kB]
Get:191 http://172.17.4.1/private bookworm-staging/main armhf libmoose-perl armhf 2.2200-1+b2 [794 kB]
Get:192 http://172.17.4.1/private bookworm-staging/main armhf libvariable-magic-perl armhf 0.63-1+b1 [41.6 kB]
Get:193 http://172.17.4.1/private bookworm-staging/main armhf libb-hooks-endofscope-perl all 0.26-1 [19.6 kB]
Get:194 http://172.17.4.1/private bookworm-staging/main armhf libsub-identify-perl armhf 0.14-3 [10.6 kB]
Get:195 http://172.17.4.1/private bookworm-staging/main armhf libnamespace-clean-perl all 0.27-2 [17.8 kB]
Get:196 http://172.17.4.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.86.0-2 [318 kB]
Get:197 http://172.17.4.1/private bookworm-staging/main armhf libwww-curl-perl armhf 4.17-8+b1 [55.9 kB]
Get:198 http://172.17.4.1/private bookworm-staging/main armhf libwww-curl-simple-perl all 0.100191-3 [12.6 kB]
Get:199 http://172.17.4.1/private bookworm-staging/main armhf dh-r all 20210816 [41.6 kB]
Get:200 http://172.17.4.1/private bookworm-staging/main armhf libboost1.74-dev armhf 1.74.0-17+b1 [9508 kB]
Get:201 http://172.17.4.1/private bookworm-staging/main armhf libboost-dev armhf 1.74.0.3+b4 [4824 B]
Get:202 http://172.17.4.1/private bookworm-staging/main armhf libcurl4-openssl-dev armhf 7.86.0-2 [398 kB]
Get:203 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-biocgenerics all 0.44.0-2 [600 kB]
Get:204 http://172.17.4.1/private bookworm-staging/main armhf r-cran-formatr all 1.12-1 [151 kB]
Get:205 http://172.17.4.1/private bookworm-staging/main armhf r-cran-lambda.r all 1.2.4-2 [118 kB]
Get:206 http://172.17.4.1/private bookworm-staging/main armhf r-cran-futile.options all 1.0.1-3 [20.0 kB]
Get:207 http://172.17.4.1/private bookworm-staging/main armhf r-cran-futile.logger all 1.4.3-4 [98.4 kB]
Get:208 http://172.17.4.1/private bookworm-staging/main armhf r-cran-snow all 1:0.4.4-2 [98.9 kB]
Get:209 http://172.17.4.1/private bookworm-staging/main armhf r-cran-codetools all 0.2-18-1 [91.8 kB]
Get:210 http://172.17.4.1/private bookworm-staging/main armhf r-cran-bh all 1.74.0-2 [5524 B]
Get:211 http://172.17.4.1/private bookworm-staging/main armhf r-cran-cpp11 all 0.4.3-1 [223 kB]
Get:212 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-biocparallel armhf 1.32.3-1 [1316 kB]
Get:213 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-s4vectors armhf 0.36.0-1 [2036 kB]
Get:214 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-iranges armhf 2.32.0-1 [2214 kB]
Get:215 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-zlibbioc all 1.44.0+dfsg-1 [9200 B]
Get:216 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-xvector armhf 0.38.0-1 [606 kB]
Get:217 http://172.17.4.1/private bookworm-staging/main armhf r-cran-bitops armhf 1.0-7-1 [30.1 kB]
Get:218 http://172.17.4.1/private bookworm-staging/main armhf r-cran-rcurl armhf 1.98-1.9+dfsg-1 [776 kB]
Get:219 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-genomeinfodbdata all 1.2.9-1 [11.7 MB]
Get:220 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-genomeinfodb all 1.34.3-1 [3920 kB]
Get:221 http://172.17.4.1/private bookworm-staging/main armhf r-cran-crayon all 1.5.2-1 [165 kB]
Get:222 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-biostrings armhf 2.66.0-1 [13.8 MB]
Get:223 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-genomicranges armhf 1.50.1+dfsg-1 [1797 kB]
Get:224 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-rhtslib armhf 2.0.0+dfsg-1 [1189 kB]
Get:225 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-rsamtools armhf 2.14.0-1 [3675 kB]
debconf: delaying package configuration, since apt-utils is not installed
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invoke-rc.d: could not determine current runlevel
All runlevel operations denied by policy
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Setting up libblas3:armhf (3.10.1-2) ...
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 libpkgconf3:armhf (1.8.0-11) ...
Setting up libalgorithm-c3-perl (0.11-2) ...
Setting up libjpeg62-turbo:armhf (1:2.1.2-1) ...
Setting up libswitch-perl (2.17-3) ...
Setting up libx11-data (2:1.8.1-2) ...
Setting up libjpeg62-turbo-dev:armhf (1:2.1.2-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libncurses6:armhf (6.3+20220423-2) ...
Setting up xz-utils (5.2.8-0.0) ...
Setting up libfribidi0:armhf (1.0.8-2.1) ...
Setting up libpng16-16:armhf (1.6.39-2) ...
Setting up libpcre32-3:armhf (2:8.39-14) ...
Setting up libatomic1:armhf (12.2.0-9+rpi1) ...
Setting up libvariable-magic-perl (0.63-1+b1) ...
Setting up libio-html-perl (1.004-3) ...
Setting up libtcl8.6:armhf (8.6.13+dfsg-1) ...
Setting up autopoint (0.21-10) ...
Setting up libb-hooks-op-check-perl:armhf (0.22-2+b1) ...
Setting up icu-devtools (72.1-3) ...
Setting up fonts-dejavu-core (2.37-2) ...
Setting up ucf (3.0043) ...
Setting up pkgconf-bin (1.8.0-11) ...
Setting up libparams-util-perl (1.102-2+b1) ...
Setting up libgfortran5:armhf (12.2.0-9+rpi1) ...
Setting up autoconf (2.71-2) ...
Setting up libsub-exporter-progressive-perl (0.001013-3) ...
Setting up libwebp7:armhf (1.2.2-2+b1) ...
Setting up libtimedate-perl (2.3300-2) ...
Setting up libregexp-ipv6-perl (0.03-3) ...
Setting up liblzma-dev:armhf (5.2.8-0.0) ...
Setting up libubsan1:armhf (12.2.0-9+rpi1) ...
Setting up libsub-name-perl:armhf (0.26-2+b1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-4.1) ...
Setting up libpcre2-posix3:armhf (10.40-2) ...
Setting up libmd0:armhf (1.0.4-2) ...
Setting up mount (2.38.1-4) ...
Setting up libasan8:armhf (12.2.0-9+rpi1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up libthai-data (0.1.29-1) ...
Setting up libdevel-globaldestruction-perl (0.14-4) ...
Setting up libdevel-stacktrace-perl (2.0400-2) ...
Setting up libtiff5:armhf (4.4.0-6) ...
Setting up libbsd0:armhf (0.11.7-1) ...
Setting up libelf1:armhf (0.187-2+rpi2) ...
Setting up libicu-dev:armhf (72.1-3) ...
Setting up libxml2:armhf (2.9.14+dfsg-1.1) ...
Setting up xdg-utils (1.1.3-4.1) ...
update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
Setting up libcc1-0:armhf (12.2.0-9+rpi1) ...
Setting up liburi-perl (5.17-1) ...
Setting up libblas-dev:armhf (3.10.1-2) ...
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 libbz2-dev:armhf (1.0.8-5+b2) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.0-2) ...
Setting up libpaper1:armhf (1.1.28) ...
Creating config file /etc/papersize with new version
Setting up libice6:armhf (2:1.0.10-1) ...
Setting up libhttp-date-perl (6.05-2) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up liblapack3:armhf (3.10.1-2) ...
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 (6.3+20220423-2) ...
Setting up libxcb1:armhf (1.15-1) ...
Setting up gettext (0.21-10) ...
Setting up libpcre2-dev:armhf (10.40-2) ...
Setting up libtool (2.4.7-5) ...
Setting up libxcb-render0:armhf (1.15-1) ...
Setting up libpcre3-dev:armhf (2:8.39-14) ...
Setting up fontconfig-config (2.13.1-4.5) ...
Setting up libpng-dev:armhf (1.6.39-2) ...
Setting up libssl3:armhf (3.0.7-1) ...
Setting up libjpeg-dev:armhf (1:2.1.2-1) ...
Setting up libxcb-shm0:armhf (1.15-1) ...
Setting up libpaper-utils (1.1.28) ...
Setting up libclass-c3-perl (0.35-2) ...
Setting up libreadline-dev:armhf (8.2-1.2) ...
Setting up libdevel-callchecker-perl:armhf (0.008-2) ...
Setting up pkgconf:armhf (1.8.0-11) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up libthai0:armhf (0.1.29-1) ...
Setting up libfreetype6:armhf (2.12.1+dfsg-3) ...
Setting up libgcc-12-dev:armhf (12.2.0-9+rpi1) ...
Setting up liblapack-dev:armhf (3.10.1-2) ...
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 (0.112-1) ...
Setting up pkg-config:armhf (1.8.0-11) ...
Setting up dh-strip-nondeterminism (1.13.0-2) ...
Setting up dwz (0.14+20220924-2) ...
Setting up groff-base (1.22.4-9) ...
Setting up libncurses5-dev:armhf (6.3+20220423-2) ...
Setting up libx11-6:armhf (2:1.8.1-2) ...
Setting up libharfbuzz0b:armhf (5.2.0-2+b1) ...
Setting up libssh2-1:armhf (1.10.0-3+b1) ...
Setting up libmro-compat-perl (0.15-1) ...
Setting up openssl (3.0.7-1) ...
Setting up libsm6:armhf (2:1.2.3-1) ...
Setting up libxmuu1:armhf (2:1.1.3-3) ...
Setting up libsub-exporter-perl (0.988-1) ...
Setting up libhttp-message-perl (6.44-1) ...
Setting up libeval-closure-perl (0.14-3) ...
Setting up libxrender1:armhf (1:0.9.10-1.1) ...
Setting up libstdc++-12-dev:armhf (12.2.0-9+rpi1) ...
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 libcurl3-gnutls:armhf (7.86.0-2) ...
Setting up libgfortran-12-dev:armhf (12.2.0-9+rpi1) ...
Setting up man-db (2.11.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up ca-certificates (20211016) ...
Updating certificates in /etc/ssl/certs...
127 added, 0 removed; done.
Setting up gcc-12 (12.2.0-9+rpi1) ...
Setting up libmodule-runtime-perl (0.016-2) ...
Setting up libdist-checkconflicts-perl (0.11-2) ...
Setting up libxt6:armhf (1:1.2.1-1) ...
Setting up xauth (1:1.1.1-1) ...
Setting up libcurl4:armhf (7.86.0-2) ...
Setting up libxss1:armhf (1:1.2.3-1) ...
Setting up g++-12 (12.2.0-9+rpi1) ...
Setting up libboost1.74-dev:armhf (1.74.0-17+b1) ...
Setting up libmodule-implementation-perl (0.09-2) ...
Setting up libpackage-stash-perl (0.40-1) ...
Setting up libwww-curl-perl:armhf (4.17-8+b1) ...
Setting up debhelper (13.11.1) ...
Setting up libmodule-runtime-conflicts-perl (0.003-2) ...
Setting up libclass-load-perl (0.25-1) ...
Setting up gfortran-12 (12.2.0-9+rpi1) ...
Setting up libcurl4-openssl-dev (7.86.0-2) ...
Setting up libpackage-deprecationmanager-perl (0.17-2) ...
Setting up libdevel-overloadinfo-perl (0.007-1) ...
Setting up libclass-load-xs-perl (0.10-2+b1) ...
Setting up libboost-dev:armhf (1.74.0.3+b4) ...
Setting up libb-hooks-endofscope-perl (0.26-1) ...
Setting up r-cran-bh (1.74.0-2) ...
Setting up libmoose-perl:armhf (2.2200-1+b2) ...
Setting up gfortran (4:12.2.0-1+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 libnamespace-clean-perl (0.27-2) ...
Setting up libwww-curl-simple-perl (0.100191-3) ...
Processing triggers for libc-bin (2.35-2+rpi1) ...
Processing triggers for sgml-base (1.31) ...
Setting up libfontconfig1:armhf (2.13.1-4.5) ...
Setting up fontconfig (2.13.1-4.5) ...
Regenerating fonts cache... done.
Setting up libxft2:armhf (2.3.6-1) ...
Setting up libtk8.6:armhf (8.6.13-1) ...
Setting up libpango-1.0-0:armhf (1.50.10+ds-1) ...
Setting up libcairo2:armhf (1.16.0-6) ...
Setting up libpangoft2-1.0-0:armhf (1.50.10+ds-1) ...
Setting up libpangocairo-1.0-0:armhf (1.50.10+ds-1) ...
Setting up r-base-core (4.2.2.20221110-1) ...
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 (1.12-1) ...
Setting up r-bioc-genomeinfodbdata (1.2.9-1) ...
Setting up r-cran-codetools (0.2-18-1) ...
Setting up r-bioc-biocgenerics (0.44.0-2) ...
Setting up r-base-dev (4.2.2.20221110-1) ...
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 (1.44.0+dfsg-1) ...
Setting up r-cran-cpp11 (0.4.3-1) ...
Setting up r-bioc-s4vectors (0.36.0-1) ...
Setting up r-cran-futile.logger (1.4.3-4) ...
Setting up r-bioc-iranges (2.32.0-1) ...
Setting up dh-r (20210816) ...
Setting up r-cran-rcurl (1.98-1.9+dfsg-1) ...
Setting up r-bioc-biocparallel (1.32.3-1) ...
Setting up r-bioc-rhtslib (2.0.0+dfsg-1) ...
Setting up r-bioc-genomeinfodb (1.34.3-1) ...
Setting up r-bioc-xvector (0.38.0-1) ...
Setting up r-bioc-genomicranges (1.50.1+dfsg-1) ...
Setting up r-bioc-biostrings (2.66.0-1) ...
Setting up r-bioc-rsamtools (2.14.0-1) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for ca-certificates (20211016) ...
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 (2.35-2+rpi1) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.39-6+rpi1 dpkg-dev_1.21.9+rpi1 g++-12_12.2.0-9+rpi1 gcc-12_12.2.0-9+rpi1 libc6-dev_2.35-2+rpi1 libstdc++-12-dev_12.2.0-9+rpi1 libstdc++6_12.2.0-9+rpi1 linux-libc-dev_5.19.6-1+rpi1
Package versions: adduser_3.129 apt_2.5.3 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-10 autotools-dev_20220109.1 base-files_12.3+rpi1 base-passwd_3.6.1 bash_5.2~rc2-2 binutils_2.39-6+rpi1 binutils-arm-linux-gnueabihf_2.39-6+rpi1 binutils-common_2.39-6+rpi1 bsdextrautils_2.38.1-4 bsdutils_1:2.38.1-4 build-essential_12.9 bzip2_1.0.8-5+b2 ca-certificates_20211016 coreutils_9.1-1 cpp_4:12.2.0-1+rpi1 cpp-12_12.2.0-9+rpi1 dash_0.5.11+git20210903+057cd650a4ed-9 dctrl-tools_2.24-3 debconf_1.5.79 debhelper_13.11.1 debianutils_5.7-0.3 dh-autoreconf_20 dh-r_20210816 dh-strip-nondeterminism_1.13.0-2 diffutils_1:3.8-1 dirmngr_2.2.39-1 dpkg_1.21.9+rpi1 dpkg-dev_1.21.9+rpi1 dwz_0.14+20220924-2 e2fsprogs_1.46.6~rc1-1 fakeroot_1.29-1 file_1:5.41-4 findutils_4.9.0-3 fontconfig_2.13.1-4.5 fontconfig-config_2.13.1-4.5 fonts-dejavu-core_2.37-2 g++_4:12.2.0-1+rpi1 g++-12_12.2.0-9+rpi1 gcc_4:12.2.0-1+rpi1 gcc-12_12.2.0-9+rpi1 gcc-12-base_12.2.0-9+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_0.21-10 gettext-base_0.21-10 gfortran_4:12.2.0-1+rpi1 gfortran-12_12.2.0-9+rpi1 gnupg_2.2.39-1 gnupg-l10n_2.2.39-1 gnupg-utils_2.2.39-1 gpg_2.2.39-1 gpg-agent_2.2.39-1 gpg-wks-client_2.2.39-1 gpg-wks-server_2.2.39-1 gpgconf_2.2.39-1 gpgsm_2.2.39-1 gpgv_2.2.39-1 grep_3.7-1 groff-base_1.22.4-9 gzip_1.12-1 hostname_3.23 icu-devtools_72.1-3 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20211215-1 krb5-locales_1.20-1 libacl1_2.3.1-1 libalgorithm-c3-perl_0.11-2 libapt-pkg6.0_2.5.3 libarchive-zip-perl_1.68-1 libasan8_12.2.0-9+rpi1 libassuan0_2.5.5-4 libatomic1_12.2.0-9+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1 libb-hooks-endofscope-perl_0.26-1 libb-hooks-op-check-perl_0.22-2+b1 libbinutils_2.39-6+rpi1 libblas-dev_3.10.1-2 libblas3_3.10.1-2 libblkid1_2.38.1-4 libboost-dev_1.74.0.3+b4 libboost1.74-dev_1.74.0-17+b1 libbrotli1_1.0.9-2+b2 libbsd0_0.11.7-1 libbz2-1.0_1.0.8-5+b2 libbz2-dev_1.0.8-5+b2 libc-bin_2.35-2+rpi1 libc-dev-bin_2.35-2+rpi1 libc6_2.35-2+rpi1 libc6-dev_2.35-2+rpi1 libcairo2_1.16.0-6 libcap-ng0_0.8.3-1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_12.2.0-9+rpi1 libclass-c3-perl_0.35-2 libclass-load-perl_0.25-1 libclass-load-xs-perl_0.10-2+b1 libclone-perl_0.46-1 libcom-err2_1.46.6~rc1-1 libcrypt-dev_1:4.4.28-2 libcrypt1_1:4.4.28-2 libctf-nobfd0_2.39-6+rpi1 libctf0_2.39-6+rpi1 libcurl3-gnutls_7.86.0-2 libcurl4_7.86.0-2 libcurl4-openssl-dev_7.86.0-2 libdata-optlist-perl_0.112-1 libdatrie1_0.2.13-2+b2 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.264 libdebhelper-perl_13.11.1 libdeflate0_1.14-1 libdevel-callchecker-perl_0.008-2 libdevel-globaldestruction-perl_0.14-4 libdevel-overloadinfo-perl_0.007-1 libdevel-stacktrace-perl_2.0400-2 libdist-checkconflicts-perl_0.11-2 libdpkg-perl_1.21.9+rpi1 libdynaloader-functions-perl_0.003-3 libelf1_0.187-2+rpi2 libencode-locale-perl_1.05-3 libeval-closure-perl_0.14-3 libexpat1_2.5.0-1 libext2fs2_1.46.6~rc1-1 libfakeroot_1.29-1 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-2 libfile-which-perl_1.27-2 libfontconfig1_2.13.1-4.5 libfreetype6_2.12.1+dfsg-3 libfribidi0_1.0.8-2.1 libgcc-12-dev_12.2.0-9+rpi1 libgcc-s1_12.2.0-9+rpi1 libgcrypt20_1.10.1-2+b2 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran-12-dev_12.2.0-9+rpi1 libgfortran5_12.2.0-9+rpi1 libglib2.0-0_2.74.1-2 libgmp10_2:6.2.1+dfsg1-1.1 libgnutls30_3.7.8-2 libgomp1_12.2.0-9+rpi1 libgpg-error0_1.45-2 libgraphite2-3_1.3.14-1 libgssapi-krb5-2_1.20-1 libharfbuzz0b_5.2.0-2+b1 libhogweed6_3.8.1-2 libhttp-date-perl_6.05-2 libhttp-message-perl_6.44-1 libice6_2:1.0.10-1 libicu-dev_72.1-3 libicu72_72.1-3 libidn2-0_2.3.3-1 libio-html-perl_1.004-3 libisl23_0.25-1 libjbig0_2.1-3.1+b2 libjpeg-dev_1:2.1.2-1 libjpeg62-turbo_1:2.1.2-1 libjpeg62-turbo-dev_1:2.1.2-1 libk5crypto3_1.20-1 libkeyutils1_1.6.3-1 libkrb5-3_1.20-1 libkrb5support0_1.20-1 libksba8_1.6.0-3 liblapack-dev_3.10.1-2 liblapack3_3.10.1-2 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r-cran-bh_1.74.0-2 r-cran-bitops_1.0-7-1 r-cran-codetools_0.2-18-1 r-cran-cpp11_0.4.3-1 r-cran-crayon_1.5.2-1 r-cran-formatr_1.12-1 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_1.98-1.9+dfsg-1 r-cran-snow_1:0.4.4-2 raspbian-archive-keyring_20120528.2 readline-common_8.2-1.2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.31 sysvinit-utils_3.05-6 tar_1.34+dfsg-1 tzdata_2022d-1 ucf_3.0043 unzip_6.0-27 util-linux_2.38.1-4 util-linux-extra_2.38.1-4 x11-common_1:7.7+23 xauth_1:1.1.1-1 xdg-utils_1.1.3-4.1 xz-utils_5.2.8-0.0 zip_3.0-12 zlib1g_1:1.2.11.dfsg-4.1 zlib1g-dev_1:1.2.11.dfsg-4.1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: r-bioc-bitseq
Binary: r-bioc-bitseq
Architecture: any
Version: 1.40.0+dfsg-1
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: https://bioconductor.org/packages/BitSeq/
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/r-pkg-team/r-bioc-bitseq
Vcs-Git: https://salsa.debian.org/r-pkg-team/r-bioc-bitseq.git
Testsuite: autopkgtest-pkg-r
Build-Depends: debhelper-compat (= 13), dh-r, r-base-dev, r-bioc-rsamtools (>= 1.99.3), r-bioc-s4vectors, r-bioc-iranges, r-bioc-rhtslib, libboost-dev, libcurl4-openssl-dev
Package-List:
r-bioc-bitseq deb gnu-r optional arch=any
Checksums-Sha1:
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Checksums-Sha256:
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Files:
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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.KwFpciOs/trustedkeys.kbx': General error
gpgv: Signature made Sun May 15 18:58:02 2022 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./r-bioc-bitseq_1.40.0+dfsg-1.dsc
dpkg-source: info: extracting r-bioc-bitseq in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking r-bioc-bitseq_1.40.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking r-bioc-bitseq_1.40.0+dfsg-1.debian.tar.xz
Check disk space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 1.40.0+dfsg-1+b1
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=f89ee6850c51463faed427366eb0b008
JOURNAL_STREAM=8:31299
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-458d230d-bdcb-48f1-af28-7d626acc363a
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c42694
XDG_SESSION_TYPE=unspecified
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package r-bioc-bitseq
dpkg-buildpackage: info: source version 1.40.0+dfsg-1+b1
dpkg-buildpackage: info: source distribution bookworm-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-bitseq/ -a -O--buildsystem=R
I: R Package: BitSeq Version: 1.40.0
I: Building using R version 4.2.2.20221110-1
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Wed, 07 Dec 2022 02:09:50 +0000
mkdir -p /<<BUILDDIR>>/r-bioc-bitseq-1.40.0\+dfsg/debian/r-bioc-bitseq/usr/lib/R/site-library
R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-bitseq-1.40.0\+dfsg/debian/r-bioc-bitseq/usr/lib/R/site-library --clean . "--built-timestamp='Wed, 07 Dec 2022 02:09:50 +0000'"
* installing *source* package ‘BitSeq’ ...
** using staged installation
configure: Version def: -DBS_VERSION=\"1.40.0\"
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ -std=gnu++14 accepts -g... yes
checking for g++ -std=gnu++14 option to enable C++11 features... none needed
checking for g++ -std=gnu++14 option to support OpenMP... -fopenmp
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/Makevars.win
** libs
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-S0e7F9/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ArgumentParser.cpp -o ArgumentParser.o
In file included from /usr/include/c++/12/vector:70,
from ArgumentParser.h:6,
from ArgumentParser.cpp:5:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘std::vector<double> tokenizeD(const std::string&, const std::string&)’ at ArgumentParser.cpp:23:26:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘std::vector<double> tokenizeD(const std::string&, const std::string&)’ at ArgumentParser.cpp:28:26:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-S0e7F9/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c CollapsedSampler.cpp -o CollapsedSampler.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-S0e7F9/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c FileHeader.cpp -o FileHeader.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-S0e7F9/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c GibbsParameters.cpp -o GibbsParameters.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-S0e7F9/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c GibbsSampler.cpp -o GibbsSampler.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-S0e7F9/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c MyTimer.cpp -o MyTimer.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-S0e7F9/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c PosteriorSamples.cpp -o PosteriorSamples.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-S0e7F9/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_init_BitSeq.cpp -o R_init_BitSeq.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-S0e7F9/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ReadDistribution.cpp -o ReadDistribution.o
In file included from ReadDistribution.cpp:7:
ReadDistribution.h:13:10: fatal error: bam.h: No such file or directory
13 | #include "bam.h"
| ^~~~~~~
compilation terminated.
make[1]: *** [/usr/lib/R/etc/Makeconf:178: ReadDistribution.o] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
ERROR: compilation failed for package ‘BitSeq’
* removing ‘/<<PKGBUILDDIR>>/debian/r-bioc-bitseq/usr/lib/R/site-library/BitSeq’
dh_auto_install: error: R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-bitseq-1.40.0\+dfsg/debian/r-bioc-bitseq/usr/lib/R/site-library --clean . "--built-timestamp='Wed, 07 Dec 2022 02:09:50 +0000'" returned exit code 1
make: *** [debian/rules:4: binary-arch] Error 25
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2022-12-07T02:10:49Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 6180
Build-Time: 59
Distribution: bookworm-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 1356
Job: r-bioc-bitseq_1.40.0+dfsg-1
Machine Architecture: armhf
Package: r-bioc-bitseq
Package-Time: 1458
Source-Version: 1.40.0+dfsg-1
Space: 6180
Status: attempted
Version: 1.40.0+dfsg-1+b1
--------------------------------------------------------------------------------
Finished at 2022-12-07T02:10:49Z
Build needed 00:24:18, 6180k disk space