r-bioc-biostrings →
2.52.0-1 →
armhf → 2019-08-22 17:13:16
sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on test2019
+==============================================================================+
| r-bioc-biostrings 2.52.0-1 (armhf) Thu, 22 Aug 2019 16:55:05 +0000 |
+==============================================================================+
Package: r-bioc-biostrings
Version: 2.52.0-1
Source Version: 2.52.0-1
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bullseye-staging-armhf-sbuild-61cb6af8-39df-4ddf-8bf5-fa5b82334f50' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.5 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [13.0 MB]
Fetched 24.5 MB in 24s (1036 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'r-bioc-biostrings' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/r-pkg-team/r-bioc-biostrings.git
Please use:
git clone https://salsa.debian.org/r-pkg-team/r-bioc-biostrings.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 12.7 MB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main r-bioc-biostrings 2.52.0-1 (dsc) [2220 B]
Get:2 http://172.17.0.1/private bullseye-staging/main r-bioc-biostrings 2.52.0-1 (tar) [12.7 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main r-bioc-biostrings 2.52.0-1 (diff) [4644 B]
Fetched 12.7 MB in 5s (2724 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/r-bioc-biostrings-ZawX6U/r-bioc-biostrings-2.52.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-biostrings-ZawX6U' 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-tELySV/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-tELySV/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-tELySV/gpg/trustdb.gpg: trustdb created
gpg: key E70254B6505CF8F7: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key E70254B6505CF8F7: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key E70254B6505CF8F7: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-tELySV/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-tELySV/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-tELySV/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-tELySV/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-tELySV/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-tELySV/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2966 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-tELySV/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-tELySV/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY E70254B6505CF8F7
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 87 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-tELySV/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12044 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 12~), dh-r, r-base-dev, r-bioc-biocgenerics, r-bioc-s4vectors (>= 0.21.13), r-bioc-iranges, r-bioc-xvector (>= 0.23.2)
Filtered Build-Depends: debhelper (>= 12~), dh-r, r-base-dev, r-bioc-biocgenerics, r-bioc-s4vectors (>= 0.21.13), r-bioc-iranges, r-bioc-xvector (>= 0.23.2)
dpkg-deb: building package 'sbuild-build-depends-r-bioc-biostrings-dummy' in '/<<BUILDDIR>>/resolver-tELySV/apt_archive/sbuild-build-depends-r-bioc-biostrings-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-biostrings-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-tELySV/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-tELySV/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-tELySV/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-tELySV/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-tELySV/apt_archive ./ Sources [549 B]
Get:5 copy:/<<BUILDDIR>>/resolver-tELySV/apt_archive ./ Packages [632 B]
Fetched 2514 B in 1s (3640 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-tELySV/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-tELySV/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY E70254B6505CF8F7
Reading package lists...
Install r-bioc-biostrings build dependencies (apt-based resolver)
-----------------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils bzip2 ca-certificates
cpp-8 dctrl-tools debhelper dh-autoreconf dh-r dh-strip-nondeterminism dwz
file fontconfig fontconfig-config fonts-dejavu-core g++-8 gcc-8 gcc-8-base
gcc-9-base gettext gettext-base gfortran gfortran-8 groff-base icu-devtools
intltool-debian libarchive-zip-perl libasan5 libatomic1 libblas-dev libblas3
libbsd0 libbz2-1.0 libbz2-dev libcairo2 libcc1-0 libcroco3 libcurl4
libdatrie1 libelf1 libexpat1 libfile-stripnondeterminism-perl
libfile-which-perl libfontconfig1 libfreetype6 libfribidi0 libgcc-8-dev
libgcc1 libgfortran-8-dev libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3
libgssapi-krb5-2 libharfbuzz0b libice6 libicu-dev libicu63 libjbig0
libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3 libkeyutils1
libkrb5-3 libkrb5support0 liblapack-dev liblapack3 liblzma-dev libmagic-mgc
libmagic1 libncurses-dev libncurses5-dev libncurses6 libncursesw6
libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
libpaper-utils libpaper1 libpcre16-3 libpcre2-16-0 libpcre2-32-0
libpcre2-8-0 libpcre2-dev libpcre2-posix0 libpcre3-dev libpcre32-3
libpcrecpp0v5 libpipeline1 libpixman-1-0 libpng-dev libpng16-16 libpsl5
libreadline-dev libreadline8 librtmp1 libsigsegv2 libsm6 libssh2-1 libssl1.1
libstdc++-8-dev libstdc++6 libsub-override-perl libswitch-perl libtcl8.6
libthai-data libthai0 libtiff5 libtinfo5 libtinfo6 libtk8.6 libtool
libubsan1 libuchardet0 libwebp6 libx11-6 libx11-data libxau6 libxcb-render0
libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxmuu1 libxrender1
libxss1 libxt6 m4 man-db openssl pkg-config po-debconf r-base-core
r-base-dev r-bioc-biocgenerics r-bioc-iranges r-bioc-s4vectors
r-bioc-xvector r-bioc-zlibbioc sensible-utils ucf unzip x11-common xauth
xdg-utils zip zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation bzip2-doc gcc-8-locales debtags dh-make gcc-8-doc libstdc++6-8-dbg
libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg libasan5-dbg
liblsan0-dbg libtsan0-dbg libubsan1-dbg libmpx2-dbg libquadmath0-dbg
gettext-doc libasprintf-dev libgettextpo-dev gfortran-doc gfortran-8-doc
libgfortran5-dbg libcoarrays-dev groff liblapack-doc krb5-doc krb5-user
icu-doc liblzma-doc ncurses-doc readline-doc libstdc++-8-doc tcl8.6 tk8.6
libtool-doc gcj-jdk m4-doc apparmor less www-browser libmail-box-perl
elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html texlive-base
texlive-latex-base texlive-plain-generic texlive-fonts-recommended
texlive-fonts-extra texlive-extra-utils texlive-latex-recommended
texlive-latex-extra texinfo r-bioc-biobase r-bioc-genomicranges
r-bioc-rsamtools r-bioc-annotationdbi r-bioc-affy r-bioc-deseq2
r-bioc-annotate r-bioc-genomicalignments r-bioc-genomicfeatures
r-bioc-summarizedexperiment r-cran-matrix r-bioc-delayedarray
r-bioc-shortread r-bioc-graph r-cran-data.table r-bioc-biostrings
Recommended packages:
devscripts curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs krb5-locales libgpm2 libpng-tools
publicsuffix libltdl-dev libmail-sendmail-perl r-recommended r-doc-html
r-cran-runit r-bioc-genomicranges libfile-mimeinfo-perl libnet-dbus-perl
libx11-protocol-perl x11-utils x11-xserver-utils
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils ca-certificates
dctrl-tools debhelper dh-autoreconf dh-r dh-strip-nondeterminism dwz file
fontconfig fontconfig-config fonts-dejavu-core gcc-9-base gettext
gettext-base gfortran gfortran-8 groff-base icu-devtools intltool-debian
libarchive-zip-perl libblas-dev libblas3 libbsd0 libbz2-dev libcairo2
libcroco3 libcurl4 libdatrie1 libelf1 libexpat1
libfile-stripnondeterminism-perl libfile-which-perl libfontconfig1
libfreetype6 libfribidi0 libgfortran-8-dev libgfortran5 libglib2.0-0
libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu-dev libicu63
libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 liblzma-dev
libmagic-mgc libmagic1 libncurses-dev libncurses5-dev libncurses6
libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
libpaper-utils libpaper1 libpcre16-3 libpcre2-16-0 libpcre2-32-0
libpcre2-8-0 libpcre2-dev libpcre2-posix0 libpcre3-dev libpcre32-3
libpcrecpp0v5 libpipeline1 libpixman-1-0 libpng-dev libpng16-16 libpsl5
libreadline-dev libreadline8 librtmp1 libsigsegv2 libsm6 libssh2-1 libssl1.1
libsub-override-perl libswitch-perl libtcl8.6 libthai-data libthai0 libtiff5
libtinfo5 libtk8.6 libtool libuchardet0 libwebp6 libx11-6 libx11-data
libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2
libxml2 libxmuu1 libxrender1 libxss1 libxt6 m4 man-db openssl pkg-config
po-debconf r-base-core r-base-dev r-bioc-biocgenerics r-bioc-iranges
r-bioc-s4vectors r-bioc-xvector r-bioc-zlibbioc
sbuild-build-depends-r-bioc-biostrings-dummy sensible-utils ucf unzip
x11-common xauth xdg-utils zip zlib1g-dev
The following packages will be upgraded:
bzip2 cpp-8 g++-8 gcc-8 gcc-8-base libasan5 libatomic1 libbz2-1.0 libcc1-0
libgcc-8-dev libgcc1 libgomp1 libncursesw6 libstdc++-8-dev libstdc++6
libtinfo6 libubsan1
17 upgraded, 138 newly installed, 0 to remove and 70 not upgraded.
Need to get 110 MB of archives.
After this operation, 231 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-tELySV/apt_archive ./ sbuild-build-depends-r-bioc-biostrings-dummy 0.invalid.0 [916 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20190803-1 [314 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf gcc-9-base armhf 9.1.0-10+rpi1 [190 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libgcc1 armhf 1:9.1.0-10+rpi1 [37.0 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libstdc++6 armhf 9.1.0-10+rpi1 [413 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-3 [782 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.1-2 [26.6 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.8.6.1-1 [1248 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf bzip2 armhf 1.0.6-9.2 [46.2 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libbz2-1.0 armhf 1.0.6-9.2 [43.1 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libtinfo6 armhf 6.1+20190803-1 [318 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libncursesw6 armhf 6.1+20190803-1 [104 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libubsan1 armhf 9.1.0-10+rpi1 [112 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf g++-8 armhf 8.3.0-19+rpi1 [7184 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf gcc-8 armhf 8.3.0-19+rpi1 [6893 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf cpp-8 armhf 8.3.0-19+rpi1 [6487 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libcc1-0 armhf 9.1.0-10+rpi1 [38.0 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libgomp1 armhf 9.1.0-10+rpi1 [73.8 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libatomic1 armhf 9.1.0-10+rpi1 [8164 B]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libasan5 armhf 9.1.0-10+rpi1 [347 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libstdc++-8-dev armhf 8.3.0-19+rpi1 [1551 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libgcc-8-dev armhf 8.3.0-19+rpi1 [595 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf gcc-8-base armhf 8.3.0-19+rpi1 [192 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libreadline8 armhf 8.0-2 [137 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12 [15.8 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.37-5 [253 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.37-5 [111 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.37-5 [66.2 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libswitch-perl all 2.17-2 [20.5 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf ucf all 3.0038+nmu1 [69.0 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1c-1 [1259 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf openssl armhf 1.1.1c-1 [804 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf ca-certificates all 20190110 [157 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf dctrl-tools armhf 2.24-3 [94.2 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-9 [547 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.5.0-1 [22.8 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.5.0-1 [14.1 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-1 [69.7 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.60.6-2 [1109 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b2 [571 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.1+20190803-1 [79.3 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.5.3 [1036 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf zip armhf 3.0-11 [212 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf unzip armhf 6.0-25 [152 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libpaper1 armhf 1.1.28 [20.5 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libpaper-utils armhf 1.1.28 [17.7 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf xdg-utils all 1.1.3-1 [73.3 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 9.1.0-10+rpi1 [230 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.8.0-2 [103 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.7-1 [77.2 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libpng16-16 armhf 1.6.37-1 [274 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libfreetype6 armhf 2.9.1-4 [317 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf fonts-dejavu-core all 2.37-1 [1068 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf fontconfig-config all 2.13.1-2 [280 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libfontconfig1 armhf 2.13.1-2 [327 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libpixman-1-0 armhf 0.36.0-1 [458 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.13.1-2 [132 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.6.7-1 [298 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.6.7-1 [689 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libxcb-render0 armhf 1.13.1-2 [108 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libxcb-shm0 armhf 1.13.1-2 [99.3 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1+b2 [47.8 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libcairo2 armhf 1.16.0-4 [599 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6-6 [14.0 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-6+b1 [61.5 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-6+b1 [112 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-6+b1 [316 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-6+b1 [134 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.39.2-1 [71.3 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libcurl4 armhf 7.65.3-1 [300 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf x11-common all 1:7.7+19 [251 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf libice6 armhf 2:1.0.9-2 [51.6 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo armhf 1:1.5.2-2+b1 [110 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.8.0-2 [1493 kB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf fontconfig armhf 2.13.1-2 [404 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf libfribidi0 armhf 1.0.5-3.1 [62.1 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf libthai-data all 0.1.28-2 [170 kB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf libdatrie1 armhf 0.2.12-2 [35.9 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf libthai0 armhf 0.1.28-2 [50.9 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf libpango-1.0-0 armhf 1.42.4-7 [168 kB]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf libgraphite2-3 armhf 1.3.13-8 [70.5 kB]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf libharfbuzz0b armhf 2.6.0-1 [1268 kB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf libpangoft2-1.0-0 armhf 1.42.4-7 [61.9 kB]
Get:109 http://172.17.0.1/private bullseye-staging/main armhf libpangocairo-1.0-0 armhf 1.42.4-7 [51.6 kB]
Get:110 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-8-0 armhf 10.32-5 [184 kB]
Get:111 http://172.17.0.1/private bullseye-staging/main armhf libsm6 armhf 2:1.2.3-1 [32.9 kB]
Get:112 http://172.17.0.1/private bullseye-staging/main armhf libtcl8.6 armhf 8.6.9+dfsg-2 [878 kB]
Get:113 http://172.17.0.1/private bullseye-staging/main armhf libjbig0 armhf 2.1-3.1+b2 [27.6 kB]
Get:114 http://172.17.0.1/private bullseye-staging/main armhf libwebp6 armhf 0.6.1-2 [228 kB]
Get:115 http://172.17.0.1/private bullseye-staging/main armhf libtiff5 armhf 4.0.10+git190818-1 [240 kB]
Get:116 http://172.17.0.1/private bullseye-staging/main armhf libxft2 armhf 2.3.2-2 [49.3 kB]
Get:117 http://172.17.0.1/private bullseye-staging/main armhf libxss1 armhf 1:1.2.3-1 [17.3 kB]
Get:118 http://172.17.0.1/private bullseye-staging/main armhf libtk8.6 armhf 8.6.9-2 [664 kB]
Get:119 http://172.17.0.1/private bullseye-staging/main armhf libxt6 armhf 1:1.1.5-1 [155 kB]
Get:120 http://172.17.0.1/private bullseye-staging/main armhf r-base-core armhf 3.6.1-4 [24.3 MB]
Get:121 http://172.17.0.1/private bullseye-staging/main armhf libgfortran-8-dev armhf 8.3.0-19+rpi1 [249 kB]
Get:122 http://172.17.0.1/private bullseye-staging/main armhf gfortran-8 armhf 8.3.0-19+rpi1 [6855 kB]
Get:123 http://172.17.0.1/private bullseye-staging/main armhf gfortran armhf 4:8.3.0-1+rpi2 [1428 B]
Get:124 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.8.0-2 [113 kB]
Get:125 http://172.17.0.1/private bullseye-staging/main armhf liblapack-dev armhf 3.8.0-2 [1551 kB]
Get:126 http://172.17.0.1/private bullseye-staging/main armhf libncurses-dev armhf 6.1+20190803-1 [281 kB]
Get:127 http://172.17.0.1/private bullseye-staging/main armhf libncurses5-dev armhf 6.1+20190803-1 [940 B]
Get:128 http://172.17.0.1/private bullseye-staging/main armhf libreadline-dev armhf 8.0-2 [114 kB]
Get:129 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.2-2+b1 [179 kB]
Get:130 http://172.17.0.1/private bullseye-staging/main armhf libjpeg-dev all 1:1.5.2-2 [57.5 kB]
Get:131 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-16-0 armhf 10.32-5 [175 kB]
Get:132 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-32-0 armhf 10.32-5 [168 kB]
Get:133 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-posix0 armhf 10.32-5 [38.3 kB]
Get:134 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-dev armhf 10.32-5 [572 kB]
Get:135 http://172.17.0.1/private bullseye-staging/main armhf libpcre16-3 armhf 2:8.39-12 [234 kB]
Get:136 http://172.17.0.1/private bullseye-staging/main armhf libpcre32-3 armhf 2:8.39-12 [227 kB]
Get:137 http://172.17.0.1/private bullseye-staging/main armhf libpcrecpp0v5 armhf 2:8.39-12 [150 kB]
Get:138 http://172.17.0.1/private bullseye-staging/main armhf libpcre3-dev armhf 2:8.39-12 [564 kB]
Get:139 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:140 http://172.17.0.1/private bullseye-staging/main armhf libpng-dev armhf 1.6.37-1 [275 kB]
Get:141 http://172.17.0.1/private bullseye-staging/main armhf libbz2-dev armhf 1.0.6-9.2 [27.7 kB]
Get:142 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:143 http://172.17.0.1/private bullseye-staging/main armhf icu-devtools armhf 63.2-2 [163 kB]
Get:144 http://172.17.0.1/private bullseye-staging/main armhf libicu-dev armhf 63.2-2 [8846 kB]
Get:145 http://172.17.0.1/private bullseye-staging/main armhf libxmuu1 armhf 2:1.1.2-2 [23.0 kB]
Get:146 http://172.17.0.1/private bullseye-staging/main armhf xauth armhf 1:1.0.10-1 [36.4 kB]
Get:147 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29-6 [59.8 kB]
Get:148 http://172.17.0.1/private bullseye-staging/main armhf r-base-dev all 3.6.1-4 [4484 B]
Get:149 http://172.17.0.1/private bullseye-staging/main armhf libfile-which-perl all 1.23-1 [16.6 kB]
Get:150 http://172.17.0.1/private bullseye-staging/main armhf dh-r all 20190807 [35.9 kB]
Get:151 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-biocgenerics all 0.30.0-3 [634 kB]
Get:152 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-s4vectors armhf 0.22.0-1 [1846 kB]
Get:153 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-iranges armhf 2.18.1-1 [2162 kB]
Get:154 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-zlibbioc all 1.30.0+dfsg-1 [8712 B]
Get:155 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-xvector armhf 0.24.0-1 [608 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libgcc1:armhf (1:9.1.0-10+rpi1) ...
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Setting up libbz2-1.0:armhf (1.0.6-9.2) ...
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Preparing to unpack .../libtinfo6_6.1+20190803-1_armhf.deb ...
Unpacking libtinfo6:armhf (6.1+20190803-1) over (6.1+20181013-2) ...
Setting up libtinfo6:armhf (6.1+20190803-1) ...
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Preparing to unpack .../libncursesw6_6.1+20190803-1_armhf.deb ...
Unpacking libncursesw6:armhf (6.1+20190803-1) over (6.1+20181013-2) ...
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Preparing to unpack .../000-libubsan1_9.1.0-10+rpi1_armhf.deb ...
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Unpacking g++-8 (8.3.0-19+rpi1) over (8.3.0-6+rpi1) ...
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Setting up libsub-override-perl (0.09-2) ...
Setting up libthai-data (0.1.28-2) ...
Setting up libssh2-1:armhf (1.8.0-2.1) ...
Setting up libkrb5-3:armhf (1.17-6+b1) ...
Setting up libtiff5:armhf (4.0.10+git190818-1) ...
Setting up cpp-8 (8.3.0-19+rpi1) ...
Setting up openssl (1.1.1c-1) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.1+20190803-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libicu-dev:armhf (63.2-2) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7+b2) ...
Setting up xdg-utils (1.1.3-1) ...
Setting up libcc1-0:armhf (9.1.0-10+rpi1) ...
Setting up dctrl-tools (2.24-3) ...
Setting up libbz2-dev:armhf (1.0.6-9.2) ...
Setting up libfile-stripnondeterminism-perl (1.5.0-1) ...
Setting up libice6:armhf (2:1.0.9-2) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up libncurses-dev:armhf (6.1+20190803-1) ...
Setting up libxcb1:armhf (1.13.1-2) ...
Setting up libtool (2.4.6-9) ...
Setting up libxcb-render0:armhf (1.13.1-2) ...
Setting up libpcre3-dev:armhf (2:8.39-12) ...
Setting up libpng-dev:armhf (1.6.37-1) ...
Setting up libjpeg-dev (1:1.5.2-2) ...
Setting up m4 (1.4.18-2) ...
Setting up libxcb-shm0:armhf (1.13.1-2) ...
Setting up libreadline-dev:armhf (8.0-2) ...
Setting up libthai0:armhf (0.1.28-2) ...
Setting up ca-certificates (20190110) ...
Updating certificates in /etc/ssl/certs...
128 added, 0 removed; done.
Setting up libblas3:armhf (3.8.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libpcre2-posix0:armhf (10.32-5) ...
Setting up libfreetype6:armhf (2.9.1-4) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libgssapi-krb5-2:armhf (1.17-6+b1) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up ucf (3.0038+nmu1) ...
Setting up libgcc-8-dev:armhf (8.3.0-19+rpi1) ...
Setting up autoconf (2.69-11) ...
Setting up dwz (0.13-1) ...
Setting up groff-base (1.22.4-3) ...
Setting up libncurses5-dev:armhf (6.1+20190803-1) ...
Setting up libcurl4:armhf (7.65.3-1) ...
Setting up libx11-6:armhf (2:1.6.7-1) ...
Setting up libharfbuzz0b:armhf (2.6.0-1) ...
Setting up libsm6:armhf (2:1.2.3-1) ...
Setting up libxmuu1:armhf (2:1.1.2-2) ...
Setting up libblas-dev:armhf (3.8.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up libstdc++-8-dev:armhf (8.3.0-19+rpi1) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libgfortran-8-dev:armhf (8.3.0-19+rpi1) ...
Setting up libpaper1:armhf (1.1.28) ...
Creating config file /etc/papersize with new version
Setting up liblapack3:armhf (3.8.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up gettext (0.19.8.1-9) ...
Setting up gcc-8 (8.3.0-19+rpi1) ...
Setting up libpcre2-dev:armhf (10.32-5) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up fontconfig-config (2.13.1-2) ...
Setting up gfortran-8 (8.3.0-19+rpi1) ...
Setting up libxext6:armhf (2:1.3.3-1+b2) ...
Setting up libpaper-utils (1.1.28) ...
Setting up man-db (2.8.6.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up gfortran (4:8.3.0-1+rpi2) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up liblapack-dev:armhf (3.8.0-2) ...
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 libxt6:armhf (1:1.1.5-1) ...
Setting up g++-8 (8.3.0-19+rpi1) ...
Setting up xauth (1:1.0.10-1) ...
Setting up libxss1:armhf (1:1.2.3-1) ...
Setting up libfontconfig1:armhf (2.13.1-2) ...
Setting up fontconfig (2.13.1-2) ...
Regenerating fonts cache... done.
Setting up libxft2:armhf (2.3.2-2) ...
Setting up po-debconf (1.0.21) ...
Setting up libtk8.6:armhf (8.6.9-2) ...
Setting up libpango-1.0-0:armhf (1.42.4-7) ...
Setting up libcairo2:armhf (1.16.0-4) ...
Setting up libpangoft2-1.0-0:armhf (1.42.4-7) ...
Setting up libpangocairo-1.0-0:armhf (1.42.4-7) ...
Setting up r-base-core (3.6.1-4) ...
Creating config file /etc/R/Renviron with new version
Setting up r-bioc-biocgenerics (0.30.0-3) ...
Setting up r-base-dev (3.6.1-4) ...
Setting up r-bioc-zlibbioc (1.30.0+dfsg-1) ...
Setting up r-bioc-s4vectors (0.22.0-1) ...
Setting up r-bioc-iranges (2.18.1-1) ...
Setting up r-bioc-xvector (0.24.0-1) ...
Setting up dh-autoreconf (19) ...
Setting up dh-strip-nondeterminism (1.5.0-1) ...
Setting up debhelper (12.5.3) ...
Setting up dh-r (20190807) ...
Setting up sbuild-build-depends-r-bioc-biostrings-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.28-10+rpi1) ...
Processing triggers for ca-certificates (20190110) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ armhf (armv7l)
Toolchain package versions: binutils_2.31.1-16+rpi1 dpkg-dev_1.19.7 g++-8_8.3.0-19+rpi1 gcc-8_8.3.0-19+rpi1 libc6-dev_2.28-10+rpi1 libstdc++-8-dev_8.3.0-19+rpi1 libstdc++6_9.1.0-10+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.2 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.3+rpi1 base-passwd_3.5.46 bash_5.0-4 binutils_2.31.1-16+rpi1 binutils-arm-linux-gnueabihf_2.31.1-16+rpi1 binutils-common_2.31.1-16+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33.1-0.1 build-essential_12.6 bzip2_1.0.6-9.2 ca-certificates_20190110 coreutils_8.30-3 cpp_4:8.3.0-1+rpi2 cpp-8_8.3.0-19+rpi1 dash_0.5.10.2-5 dctrl-tools_2.24-3 debconf_1.5.71 debhelper_12.5.3 debianutils_4.8.6.1 dh-autoreconf_19 dh-r_20190807 dh-strip-nondeterminism_1.5.0-1 diffutils_1:3.7-3 dirmngr_2.2.12-1+rpi1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-1 e2fsprogs_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.37-5 findutils_4.6.0+git+20190209-2 fontconfig_2.13.1-2 fontconfig-config_2.13.1-2 fonts-dejavu-core_2.37-1 g++_4:8.3.0-1+rpi2 g++-8_8.3.0-19+rpi1 gcc_4:8.3.0-1+rpi2 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-6-base_6.5.0-1+rpi1+b1 gcc-7-base_7.3.0-19 gcc-8_8.3.0-19+rpi1 gcc-8-base_8.3.0-19+rpi1 gcc-9-base_9.1.0-10+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gfortran_4:8.3.0-1+rpi2 gfortran-8_8.3.0-19+rpi1 gnupg_2.2.12-1+rpi1 gnupg-l10n_2.2.12-1+rpi1 gnupg-utils_2.2.12-1+rpi1 gpg_2.2.12-1+rpi1 gpg-agent_2.2.12-1+rpi1 gpg-wks-client_2.2.12-1+rpi1 gpg-wks-server_2.2.12-1+rpi1 gpgconf_2.2.12-1+rpi1 gpgsm_2.2.12-1+rpi1 gpgv_2.2.12-1+rpi1 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hostname_3.21 icu-devtools_63.2-2 init-system-helpers_1.56+nmu1 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-4 libapt-pkg5.0_1.8.2 libarchive-zip-perl_1.64-1 libasan5_9.1.0-10+rpi1 libassuan0_2.5.2-1 libatomic1_9.1.0-10+rpi1 libattr1_1:2.4.48-4 libaudit-common_1:2.8.4-3 libaudit1_1:2.8.4-3 libbinutils_2.31.1-16+rpi1 libblas-dev_3.8.0-2 libblas3_3.8.0-2 libblkid1_2.33.1-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.6-9.2 libbz2-dev_1.0.6-9.2 libc-bin_2.28-10+rpi1 libc-dev-bin_2.28-10+rpi1 libc6_2.28-10+rpi1 libc6-dev_2.28-10+rpi1 libcairo2_1.16.0-4 libcap-ng0_0.7.9-2 libcc1-0_9.1.0-10+rpi1 libcom-err2_1.44.5-1 libcroco3_0.6.13-1 libcurl4_7.65.3-1 libdatrie1_0.2.12-2 libdb5.3_5.3.28+dfsg1-0.5 libdebconfclient0_0.249 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.7-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.5.0-1 libfile-which-perl_1.23-1 libfontconfig1_2.13.1-2 libfreetype6_2.9.1-4 libfribidi0_1.0.5-3.1 libgcc-8-dev_8.3.0-19+rpi1 libgcc1_1:9.1.0-10+rpi1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-4 libgdbm6_1.18.1-4 libgfortran-8-dev_8.3.0-19+rpi1 libgfortran5_9.1.0-10+rpi1 libglib2.0-0_2.60.6-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.7-4 libgomp1_9.1.0-10+rpi1 libgpg-error0_1.35-1 libgraphite2-3_1.3.13-8 libgssapi-krb5-2_1.17-6+b1 libharfbuzz0b_2.6.0-1 libhogweed4_3.4.1-1 libice6_2:1.0.9-2 libicu-dev_63.2-2 libicu63_63.2-2 libidn2-0_2.0.5-1 libisl19_0.20-2 libjbig0_2.1-3.1+b2 libjpeg-dev_1:1.5.2-2 libjpeg62-turbo_1:1.5.2-2+b1 libjpeg62-turbo-dev_1:1.5.2-2+b1 libk5crypto3_1.17-6+b1 libkeyutils1_1.6-6 libkrb5-3_1.17-6+b1 libkrb5support0_1.17-6+b1 libksba8_1.3.5-2 liblapack-dev_3.8.0-2 liblapack3_3.8.0-2 libldap-2.4-2_2.4.47+dfsg-3+rpi1 libldap-common_2.4.47+dfsg-3+rpi1 liblocale-gettext-perl_1.07-3+b3 liblz4-1_1.8.3-1 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-5 libmagic1_1:5.37-5 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses-dev_6.1+20190803-1 libncurses5-dev_6.1+20190803-1 libncurses6_6.1+20190803-1 libncursesw6_6.1+20190803-1 libnettle6_3.4.1-1 libnghttp2-14_1.39.2-1 libnpth0_1.6-1 libp11-kit0_0.23.15-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpango-1.0-0_1.42.4-7 libpangocairo-1.0-0_1.42.4-7 libpangoft2-1.0-0_1.42.4-7 libpaper-utils_1.1.28 libpaper1_1.1.28 libpcre16-3_2:8.39-12 libpcre2-16-0_10.32-5 libpcre2-32-0_10.32-5 libpcre2-8-0_10.32-5 libpcre2-dev_10.32-5 libpcre2-posix0_10.32-5 libpcre3_2:8.39-12 libpcre3-dev_2:8.39-12 libpcre32-3_2:8.39-12 libpcrecpp0v5_2:8.39-12 libperl5.28_5.28.1-6 libpipeline1_1.5.1-2 libpixman-1-0_0.36.0-1 libpng-dev_1.6.37-1 libpng16-16_1.6.37-1 libpsl5_0.20.2-2 libreadline-dev_8.0-2 libreadline7_7.0-5 libreadline8_8.0-2 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27+dfsg-1+b1 libsasl2-modules-db_2.1.27+dfsg-1+b1 libseccomp2_2.3.3-4 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsm6_2:1.2.3-1 libsmartcols1_2.33.1-0.1 libsqlite3-0_3.27.2-3 libss2_1.44.5-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1c-1 libstdc++-8-dev_8.3.0-19+rpi1 libstdc++6_9.1.0-10+rpi1 libsub-override-perl_0.09-2 libswitch-perl_2.17-2 libsystemd0_241-5+rpi1 libtasn1-6_4.13-3 libtcl8.6_8.6.9+dfsg-2 libtext-charwidth-perl_0.04-7.1+b1 libtext-iconv-perl_1.7-5+b10 libtext-wrapi18n-perl_0.06-7.1 libthai-data_0.1.28-2 libthai0_0.1.28-2 libtiff5_4.0.10+git190818-1 libtinfo5_6.1+20190803-1 libtinfo6_6.1+20190803-1 libtk8.6_8.6.9-2 libtool_2.4.6-9 libubsan1_9.1.0-10+rpi1 libuchardet0_0.0.6-3 libudev1_241-5+rpi1 libunistring2_0.9.10-1 libuuid1_2.33.1-0.1 libwebp6_0.6.1-2 libx11-6_2:1.6.7-1 libx11-data_2:1.6.7-1 libxau6_1:1.0.8-1+b2 libxcb-render0_1.13.1-2 libxcb-shm0_1.13.1-2 libxcb1_1.13.1-2 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxft2_2.3.2-2 libxml2_2.9.4+dfsg1-7+b2 libxmuu1_2:1.1.2-2 libxrender1_1:0.9.10-1 libxss1_1:1.2.3-1 libxt6_1:1.1.5-1 libzstd1_1.3.8+dfsg-3+rpi1 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2019051400+rpi1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.6.1-1 mawk_1.3.3-17 mount_2.33.1-0.1 ncurses-base_6.1+20181013-2 ncurses-bin_6.1+20181013-2 openssl_1.1.1c-1 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6 pinentry-curses_1.1.0-2 pkg-config_0.29-6 po-debconf_1.0.21 r-base-core_3.6.1-4 r-base-dev_3.6.1-4 r-bioc-biocgenerics_0.30.0-3 r-bioc-iranges_2.18.1-1 r-bioc-s4vectors_0.22.0-1 r-bioc-xvector_0.24.0-1 r-bioc-zlibbioc_1.30.0+dfsg-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-biostrings-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.93-8 tar_1.30+dfsg-6 tzdata_2019a-1 ucf_3.0038+nmu1 unzip_6.0-25 util-linux_2.33.1-0.1 x11-common_1:7.7+19 xauth_1:1.0.10-1 xdg-utils_1.1.3-1 xz-utils_5.2.4-1 zip_3.0-11 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed Jul 3 15:03:06 2019 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./r-bioc-biostrings_2.52.0-1.dsc
dpkg-source: info: extracting r-bioc-biostrings in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking r-bioc-biostrings_2.52.0.orig.tar.gz
dpkg-source: info: unpacking r-bioc-biostrings_2.52.0-1.debian.tar.xz
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/build/buildd
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=116
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-61cb6af8-39df-4ddf-8bf5-fa5b82334f50
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_ID=c35613
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package r-bioc-biostrings
dpkg-buildpackage: info: source version 2.52.0-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --buildsystem R
dh_auto_clean -O--buildsystem=R
dh_autoreconf_clean -O--buildsystem=R
dh_clean -O--buildsystem=R
debian/rules build-arch
dh build-arch --buildsystem R
dh_update_autotools_config -a -O--buildsystem=R
dh_autoreconf -a -O--buildsystem=R
dh_auto_configure -a -O--buildsystem=R
dh_auto_build -a -O--buildsystem=R
dh_auto_test -a -O--buildsystem=R
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --buildsystem R
dh_testroot -a -O--buildsystem=R
dh_prep -a -O--buildsystem=R
dh_auto_install -a -O--buildsystem=R
I: R packages needed for DEP8: runit
I: R Package: Biostrings Version: 2.52.0
I: Building using R version 3.6.1-4
I: R API version: r-api-3.5
I: Using built-time from d/changelog: Wed, 03 Jul 2019 16:54:03 +0200
mkdir -p /<<PKGBUILDDIR>>/debian/r-bioc-biostrings/usr/lib/R/site-library
R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-biostrings/usr/lib/R/site-library --clean . "--built-timestamp='Wed, 03 Jul 2019 16:54:03 +0200'"
* installing *source* package 'Biostrings' ...
** using staged installation
** libs
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c BAB_class.c -o BAB_class.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c BitMatrix.c -o BitMatrix.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c MIndex_class.c -o MIndex_class.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SparseList_utils.c -o SparseList_utils.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c XStringSetList_class.c -o XStringSetList_class.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c XStringSet_class.c -o XStringSet_class.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c XString_class.c -o XString_class.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c align_needwunsQS.c -o align_needwunsQS.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c align_utils.c -o align_utils.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c find_palindromes.c -o find_palindromes.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gtestsim.c -o gtestsim.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c inject_code.c -o inject_code.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c letter_frequency.c -o letter_frequency.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lowlevel_matching.c -o lowlevel_matching.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c match_PWM.c -o match_PWM.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c match_pattern.c -o match_pattern.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c match_pattern_indels.c -o match_pattern_indels.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c match_pdict.c -o match_pdict.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c match_pdict_Twobit.c -o match_pdict_Twobit.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c match_pdict_utils.c -o match_pdict_utils.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c match_reporting.c -o match_reporting.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c matchprobes.c -o matchprobes.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pmatchPattern.c -o pmatchPattern.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c read_fasta_files.c -o read_fasta_files.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c read_fastq_files.c -o read_fastq_files.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c replaceAt.c -o replaceAt.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c replace_letter_at.c -o replace_letter_at.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c strutils.c -o strutils.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c translate.c -o translate.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-IRhjso/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xscat.c -o xscat.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o read_fasta_files.o read_fastq_files.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -L/usr/lib/R/lib -lR
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
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installing to /<<PKGBUILDDIR>>/debian/r-bioc-biostrings/usr/lib/R/site-library/00LOCK-r-bioc-biostrings-2.52.0/00new/Biostrings/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for 'twoWayAlphabetFrequencyByQuality' with signature '"QualityScaledXStringSet"': no definition for class "QualityScaledXStringSet"
Creating a new generic function for 'strsplit' in package 'Biostrings'
Creating a generic function for 'ls' from package 'base' in package 'Biostrings'
Creating a new generic function for 'offset' in package 'Biostrings'
** 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 (Biostrings)
W: Ignoring specified R dependency: R (>= 3.5.0)
I: Using r-bioc-biocgenerics for Depends:BiocGenerics
I: Using r-bioc-s4vectors for Depends:S4Vectors (>= 0.21.13)
I: Using r-bioc-iranges for Depends:IRanges
I: Using r-bioc-xvector for Depends:XVector (>= 0.23.2)
I: Using r-cran-runit for Recommends:runit
I: Using r-bioc-bsgenome for Suggests:BSgenome (>= 1.13.14)
W: Cannot find a debian package for Suggests:BSgenome.Celegans.UCSC.ce2 (>= 1.3.11)
W: Cannot find a debian package for Suggests:BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11)
W: Cannot find a debian package for Suggests:BSgenome.Hsapiens.UCSC.hg18
W: Cannot find a debian package for Suggests:drosophila2probe
W: Cannot find a debian package for Suggests:hgu95av2probe
W: Cannot find a debian package for Suggests:hgu133aprobe
I: Using r-bioc-genomicfeatures for Suggests:GenomicFeatures (>= 1.3.14)
W: Cannot find a debian package for Suggests:hgu95av2cdf
I: Using r-bioc-affy for Suggests:affy (>= 1.41.3)
W: Cannot find a debian package for Suggests:affydata (>= 1.11.5)
I: BioConductor API version: r-api-bioc-3.9
dh_installdocs -a -O--buildsystem=R
dh_installchangelogs -a -O--buildsystem=R
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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-biostrings' in '../r-bioc-biostrings_2.52.0-1_armhf.deb'.
dpkg-deb: building package 'r-bioc-biostrings-dbgsym' in '../r-bioc-biostrings-dbgsym_2.52.0-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian 2019 test autobuilder <root@raspbian.org> >../r-bioc-biostrings_2.52.0-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2019-08-22T17:12:48Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
r-bioc-biostrings_2.52.0-1_armhf.changes:
-----------------------------------------
Format: 1.8
Date: Wed, 03 Jul 2019 16:54:03 +0200
Source: r-bioc-biostrings
Binary: r-bioc-biostrings r-bioc-biostrings-dbgsym
Architecture: armhf
Version: 2.52.0-1
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian 2019 test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
r-bioc-biostrings - GNU R string objects representing biological sequences
Changes:
r-bioc-biostrings (2.52.0-1) unstable; urgency=medium
.
* New upstream version
* debhelper 12
* dh-update-R to update Build-Depends
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Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Thu, 22 Aug 2019 17:12:45 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
autoconf (= 2.69-11),
automake (= 1:1.16.1-4),
autopoint (= 0.19.8.1-9),
autotools-dev (= 20180224.1),
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bash (= 5.0-4),
binutils (= 2.31.1-16+rpi1),
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binutils-common (= 2.31.1-16+rpi1),
bsdmainutils (= 11.1.2),
bsdutils (= 1:2.33.1-0.1),
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coreutils (= 8.30-3),
cpp (= 4:8.3.0-1+rpi2),
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dash (= 0.5.10.2-5),
dctrl-tools (= 2.24-3),
debconf (= 1.5.71),
debhelper (= 12.5.3),
debianutils (= 4.8.6.1),
dh-autoreconf (= 19),
dh-r (= 20190807),
dh-strip-nondeterminism (= 1.5.0-1),
diffutils (= 1:3.7-3),
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libc6-dev (= 2.28-10+rpi1),
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Environment:
DEB_BUILD_OPTIONS="parallel=4"
LC_ALL="POSIX"
SOURCE_DATE_EPOCH="1562165643"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
r-bioc-biostrings-dbgsym_2.52.0-1_armhf.deb
-------------------------------------------
new Debian package, version 2.0.
size 221072 bytes: control archive=544 bytes.
406 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: r-bioc-biostrings-dbgsym
Source: r-bioc-biostrings
Version: 2.52.0-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Installed-Size: 260
Depends: r-bioc-biostrings (= 2.52.0-1)
Section: debug
Priority: optional
Description: debug symbols for r-bioc-biostrings
Build-Ids: c61a0fb6a18ad12a802fd0633738dd33e9340c2c
drwxr-xr-x root/root 0 2019-07-03 14:54 ./
drwxr-xr-x root/root 0 2019-07-03 14:54 ./usr/
drwxr-xr-x root/root 0 2019-07-03 14:54 ./usr/lib/
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drwxr-xr-x root/root 0 2019-07-03 14:54 ./usr/share/
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lrwxrwxrwx root/root 0 2019-07-03 14:54 ./usr/share/doc/r-bioc-biostrings-dbgsym -> r-bioc-biostrings
r-bioc-biostrings_2.52.0-1_armhf.deb
------------------------------------
new Debian package, version 2.0.
size 14144904 bytes: control archive=2992 bytes.
783 bytes, 15 lines control
7165 bytes, 81 lines md5sums
Package: r-bioc-biostrings
Version: 2.52.0-1
Architecture: armhf
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Installed-Size: 15193
Depends: r-base-core (>= 3.6.1-4), r-api-3.5, r-api-bioc-3.9, r-bioc-biocgenerics, r-bioc-s4vectors (>= 0.21.13), r-bioc-iranges, r-bioc-xvector (>= 0.23.2), libc6 (>= 2.7)
Recommends: r-cran-runit
Suggests: r-bioc-bsgenome (>= 1.13.14), r-bioc-genomicfeatures (>= 1.3.14), r-bioc-affy (>= 1.41.3)
Section: gnu-r
Priority: optional
Homepage: https://bioconductor.org/packages/Biostrings/
Description: GNU R string objects representing biological sequences
Memory efficient string containers, string matching algorithms, and other
utilities, for fast manipulation of large biological sequences or set of
sequences.
drwxr-xr-x root/root 0 2019-07-03 14:54 ./
drwxr-xr-x root/root 0 2019-07-03 14:54 ./usr/
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| Summary |
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Build Architecture: armhf
Build Type: any
Build-Space: 44300
Build-Time: 242
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 758
Job: r-bioc-biostrings_2.52.0-1
Machine Architecture: armhf
Package: r-bioc-biostrings
Package-Time: 1063
Source-Version: 2.52.0-1
Space: 44300
Status: successful
Version: 2.52.0-1
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Finished at 2019-08-22T17:12:48Z
Build needed 00:17:43, 44300k disk space