r-bioc-rsubread →
2.2.5-1 →
armhf → 2020-07-30 12:52:37
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| r-bioc-rsubread 2.2.5-1 (armhf) Thu, 30 Jul 2020 12:36:27 +0000 |
+==============================================================================+
Package: r-bioc-rsubread
Version: 2.2.5-1
Source Version: 2.2.5-1
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-4c0e92c2-0a93-4146-97f1-1021bfe00641' 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 [11.8 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.9 MB]
Fetched 24.7 MB in 26s (967 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'r-bioc-rsubread' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/r-pkg-team/r-bioc-rsubread.git
Please use:
git clone https://salsa.debian.org/r-pkg-team/r-bioc-rsubread.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 10.8 MB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main r-bioc-rsubread 2.2.5-1 (dsc) [2090 B]
Get:2 http://172.17.0.1/private bullseye-staging/main r-bioc-rsubread 2.2.5-1 (tar) [10.8 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main r-bioc-rsubread 2.2.5-1 (diff) [3432 B]
Fetched 10.8 MB in 1s (11.3 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/r-bioc-rsubread-NsfbYs/r-bioc-rsubread-2.2.5' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-rsubread-NsfbYs' 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-mNymlI/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-mNymlI/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-mNymlI/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: 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 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: 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-mNymlI/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-mNymlI/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-mNymlI/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-mNymlI/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-mNymlI/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2828 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
bsdextrautils dmsetup libargon2-1 libcryptsetup12 libdevmapper1.02.1
libjson-c4 libpam-cap libssl1.1 netbase
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 19 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-mNymlI/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (23.3 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12373 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), dh-r, r-base-dev, r-cran-matrix
Filtered Build-Depends: debhelper-compat (= 13), dh-r, r-base-dev, r-cran-matrix
dpkg-deb: building package 'sbuild-build-depends-r-bioc-rsubread-dummy' in '/<<BUILDDIR>>/resolver-mNymlI/apt_archive/sbuild-build-depends-r-bioc-rsubread-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-rsubread-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-mNymlI/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-mNymlI/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-mNymlI/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-mNymlI/apt_archive ./ Sources [515 B]
Get:5 copy:/<<BUILDDIR>>/resolver-mNymlI/apt_archive ./ Packages [600 B]
Fetched 2448 B in 1s (3047 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install r-bioc-rsubread 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:
dmsetup libargon2-1 libcryptsetup12 libdevmapper1.02.1 libjson-c4 libpam-cap
netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bzip2 ca-certificates cpp-9
dctrl-tools debhelper dh-autoreconf dh-r dh-strip-nondeterminism dwz file
fontconfig fontconfig-config fonts-dejavu-core g++-9 gcc-9 gcc-9-base
gettext gettext-base gfortran gfortran-9 groff-base icu-devtools
intltool-debian libarchive-zip-perl libasan5 libblas-dev libblas3 libbrotli1
libbsd0 libbz2-1.0 libbz2-dev libcairo2 libcroco3 libcurl4 libdatrie1
libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl
libfile-which-perl libfontconfig1 libfreetype6 libfribidi0 libgcc-9-dev
libgfortran-9-dev libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2
libharfbuzz0b libice6 libicu-dev libicu67 libjbig0 libjpeg-dev
libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblapack-dev liblapack3 liblzma-dev libmagic-mgc libmagic1
libncurses-dev libncurses5-dev libncurses6 libnghttp2-14 libpango-1.0-0
libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre16-3
libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix2 libpcre3-dev
libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0 libpng-dev libpng16-16
libpsl5 libreadline-dev librtmp1 libsigsegv2 libsm6 libssh2-1
libstdc++-9-dev libsub-override-perl libswitch-perl libtcl8.6 libthai-data
libthai0 libtiff5 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-cran-lattice r-cran-matrix
sensible-utils ucf unzip x11-common xauth xdg-utils zip zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc bzip2-doc gcc-9-locales debtags
dh-make gcc-9-doc gettext-doc libasprintf-dev libgettextpo-dev gfortran-doc
gfortran-9-doc libcoarrays-dev groff liblapack-doc krb5-doc krb5-user
icu-doc liblzma-doc ncurses-doc readline-doc libstdc++-9-doc tcl8.6 tk8.6
libtool-doc gcj-jdk m4-doc apparmor less www-browser libmail-box-perl
elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html texlive-base
texlive-latex-base texlive-plain-generic texlive-fonts-recommended
texlive-fonts-extra texlive-extra-utils texlive-latex-recommended
texlive-latex-extra texinfo
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
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 ca-certificates dctrl-tools
debhelper dh-autoreconf dh-r dh-strip-nondeterminism dwz file fontconfig
fontconfig-config fonts-dejavu-core gettext gettext-base gfortran gfortran-9
groff-base icu-devtools intltool-debian libarchive-zip-perl libblas-dev
libblas3 libbrotli1 libbsd0 libbz2-dev libcairo2 libcroco3 libcurl4
libdatrie1 libdebhelper-perl libelf1 libexpat1
libfile-stripnondeterminism-perl libfile-which-perl libfontconfig1
libfreetype6 libfribidi0 libgfortran-9-dev libgfortran5 libglib2.0-0
libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu-dev libicu67
libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 liblzma-dev
libmagic-mgc libmagic1 libncurses-dev libncurses5-dev libncurses6
libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
libpaper-utils libpaper1 libpcre16-3 libpcre2-16-0 libpcre2-32-0
libpcre2-dev libpcre2-posix2 libpcre3-dev libpcre32-3 libpcrecpp0v5
libpipeline1 libpixman-1-0 libpng-dev libpng16-16 libpsl5 libreadline-dev
librtmp1 libsigsegv2 libsm6 libssh2-1 libsub-override-perl libswitch-perl
libtcl8.6 libthai-data libthai0 libtiff5 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-cran-lattice
r-cran-matrix sbuild-build-depends-r-bioc-rsubread-dummy sensible-utils ucf
unzip x11-common xauth xdg-utils zip zlib1g-dev
The following packages will be upgraded:
bzip2 cpp-9 g++-9 gcc-9 gcc-9-base libasan5 libbz2-1.0 libgcc-9-dev
libstdc++-9-dev
9 upgraded, 131 newly installed, 0 to remove and 10 not upgraded.
Need to get 114 MB of archives.
After this operation, 249 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-mNymlI/apt_archive ./ sbuild-build-depends-r-bioc-rsubread-dummy 0.invalid.0 [888 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf bzip2 armhf 1.0.8-4 [47.0 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libbz2-1.0 armhf 1.0.8-4 [44.1 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libasan5 armhf 9.3.0-15+rpi1 [348 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf g++-9 armhf 9.3.0-15+rpi1 [8227 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libstdc++-9-dev armhf 9.3.0-15+rpi1 [1713 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf gcc-9 armhf 9.3.0-15+rpi1 [7735 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libgcc-9-dev armhf 9.3.0-15+rpi1 [640 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf cpp-9 armhf 9.3.0-15+rpi1 [7461 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf gcc-9-base armhf 9.3.0-15+rpi1 [197 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libswitch-perl all 2.17-2 [20.5 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-3 [801 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf openssl armhf 1.1.1g-1 [811 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf ca-certificates all 20200601 [158 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf dctrl-tools armhf 2.24-3 [94.2 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2 [187 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.64.4-1 [1159 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-3 [8287 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-5+b1 [593 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2 [1007 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf zip armhf 3.0-11 [212 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf unzip armhf 6.0-25 [152 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libpaper1 armhf 1.1.28 [20.5 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libpaper-utils armhf 1.1.28 [17.7 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf xdg-utils all 1.1.3-2 [74.6 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-2 [108 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.7-7 [258 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libpng16-16 armhf 1.6.37-2 [274 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libfreetype6 armhf 2.10.2+dfsg-3 [347 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf fontconfig-config all 2.13.1-4.2 [281 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libfontconfig1 armhf 2.13.1-4.2 [328 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libpixman-1-0 armhf 0.36.0-1 [458 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.14-2 [135 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.6.9-2 [298 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.6.9-2 [692 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libxcb-render0 armhf 1.14-2 [110 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libxcb-shm0 armhf 1.14-2 [101 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1+b2 [47.8 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libcairo2 armhf 1.16.0-4 [599 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-10 [61.7 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-10 [112 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6.1-2 [14.5 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-10 [320 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-10 [135 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.41.0-2 [61.2 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1.1 [54.2 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libcurl4 armhf 7.68.0-1+b1 [286 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo armhf 1:1.5.2-2+b1 [110 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10.1.0-4+rpi1 [231 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-2 [1602 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf fontconfig armhf 2.13.1-4.2 [416 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libfribidi0 armhf 1.0.8-2 [63.5 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libgraphite2-3 armhf 1.3.14-1 [70.3 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libharfbuzz0b armhf 2.6.4-1+rpi1+b1 [1309 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libthai-data all 0.1.28-3 [170 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libdatrie1 armhf 0.2.12-3+b3 [36.4 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libthai0 armhf 0.1.28-3 [51.0 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf libpango-1.0-0 armhf 1.44.7-4 [165 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libpangoft2-1.0-0 armhf 1.44.7-4 [52.6 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libpangocairo-1.0-0 armhf 1.44.7-4 [44.9 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf libtcl8.6 armhf 8.6.10+dfsg-1 [886 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf libjbig0 armhf 2.1-3.1+b2 [27.6 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf libwebp6 armhf 0.6.1-2 [228 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf libtiff5 armhf 4.1.0+git191117-2 [250 kB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf libxft2 armhf 2.3.2-2 [49.3 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf x11-common all 1:7.7+20 [252 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf libxss1 armhf 1:1.2.3-1 [17.3 kB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf libtk8.6 armhf 8.6.10-1 [678 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf libice6 armhf 2:1.0.9-2 [51.6 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf libsm6 armhf 2:1.2.3-1 [32.9 kB]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf libxt6 armhf 1:1.1.5-1+b3 [156 kB]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf r-base-core armhf 4.0.2-1 [24.7 MB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf libgfortran-9-dev armhf 9.3.0-15+rpi1 [278 kB]
Get:109 http://172.17.0.1/private bullseye-staging/main armhf gfortran-9 armhf 9.3.0-15+rpi1 [8107 kB]
Get:110 http://172.17.0.1/private bullseye-staging/main armhf gfortran armhf 4:9.2.1-3.1+rpi1 [1440 B]
Get:111 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.9.0-2 [113 kB]
Get:112 http://172.17.0.1/private bullseye-staging/main armhf liblapack-dev armhf 3.9.0-2 [2981 kB]
Get:113 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2-1 [79.5 kB]
Get:114 http://172.17.0.1/private bullseye-staging/main armhf libncurses-dev armhf 6.2-1 [284 kB]
Get:115 http://172.17.0.1/private bullseye-staging/main armhf libncurses5-dev armhf 6.2-1 [932 B]
Get:116 http://172.17.0.1/private bullseye-staging/main armhf libreadline-dev armhf 8.0-4 [116 kB]
Get:117 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.2-2+b1 [179 kB]
Get:118 http://172.17.0.1/private bullseye-staging/main armhf libjpeg-dev all 1:1.5.2-2 [57.5 kB]
Get:119 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-16-0 armhf 10.34-7 [190 kB]
Get:120 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-32-0 armhf 10.34-7 [181 kB]
Get:121 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-posix2 armhf 10.34-7 [44.7 kB]
Get:122 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-dev armhf 10.34-7 [614 kB]
Get:123 http://172.17.0.1/private bullseye-staging/main armhf libpcre16-3 armhf 2:8.39-13 [235 kB]
Get:124 http://172.17.0.1/private bullseye-staging/main armhf libpcre32-3 armhf 2:8.39-13 [228 kB]
Get:125 http://172.17.0.1/private bullseye-staging/main armhf libpcrecpp0v5 armhf 2:8.39-13 [150 kB]
Get:126 http://172.17.0.1/private bullseye-staging/main armhf libpcre3-dev armhf 2:8.39-13 [566 kB]
Get:127 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:128 http://172.17.0.1/private bullseye-staging/main armhf libpng-dev armhf 1.6.37-2 [276 kB]
Get:129 http://172.17.0.1/private bullseye-staging/main armhf libbz2-dev armhf 1.0.8-4 [28.0 kB]
Get:130 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:131 http://172.17.0.1/private bullseye-staging/main armhf icu-devtools armhf 67.1-3 [170 kB]
Get:132 http://172.17.0.1/private bullseye-staging/main armhf libicu-dev armhf 67.1-3 [9213 kB]
Get:133 http://172.17.0.1/private bullseye-staging/main armhf libxmuu1 armhf 2:1.1.2-2+b3 [23.4 kB]
Get:134 http://172.17.0.1/private bullseye-staging/main armhf xauth armhf 1:1.0.10-1 [36.4 kB]
Get:135 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
Get:136 http://172.17.0.1/private bullseye-staging/main armhf r-base-dev all 4.0.2-1 [4484 B]
Get:137 http://172.17.0.1/private bullseye-staging/main armhf libfile-which-perl all 1.23-1 [16.6 kB]
Get:138 http://172.17.0.1/private bullseye-staging/main armhf dh-r all 20200710 [39.3 kB]
Get:139 http://172.17.0.1/private bullseye-staging/main armhf r-cran-lattice armhf 0.20-41-1+b1 [1167 kB]
Get:140 http://172.17.0.1/private bullseye-staging/main armhf r-cran-matrix armhf 1.2-18-1+b1 [3451 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libexpat1:armhf (2.2.9-1) ...
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Setting up libpipeline1:armhf (1.5.2-2) ...
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Setting up libkeyutils1:armhf (1.6.1-2) ...
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Setting up libicu67:armhf (67.1-3) ...
Setting up libdatrie1:armhf (0.2.12-3+b3) ...
Setting up libmagic-mgc (1:5.38-5) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.64.4-1) ...
No schema files found: doing nothing.
Setting up unzip (6.0-25) ...
Setting up libdebhelper-perl (13.2) ...
Setting up libbrotli1:armhf (1.0.7-7) ...
Setting up x11-common (1:7.7+20) ...
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
invoke-rc.d: could not determine current runlevel
invoke-rc.d: WARNING: No init system and policy-rc.d missing! Defaulting to block.
Setting up libnghttp2-14:armhf (1.41.0-2) ...
Setting up libmagic1:armhf (1:5.38-5) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.38-5) ...
Setting up bzip2 (1.0.8-4) ...
Setting up libjbig0:armhf (2.1-3.1+b2) ...
Setting up libpcre2-16-0:armhf (10.34-7) ...
Setting up libkrb5support0:armhf (1.17-10) ...
Setting up zip (3.0-11) ...
Setting up autotools-dev (20180224.1) ...
Setting up libpcre2-32-0:armhf (10.34-7) ...
Setting up libblas3:armhf (3.9.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libjpeg62-turbo:armhf (1:1.5.2-2+b1) ...
Setting up libswitch-perl (2.17-2) ...
Setting up libx11-data (2:1.6.9-2) ...
Setting up libjpeg62-turbo-dev:armhf (1:1.5.2-2+b1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libncurses6:armhf (6.2-1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libfribidi0:armhf (1.0.8-2) ...
Setting up libpng16-16:armhf (1.6.37-2) ...
Setting up libpcre32-3:armhf (2:8.39-13) ...
Setting up libtcl8.6:armhf (8.6.10+dfsg-1) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up libwebp6:armhf (0.6.1-2) ...
Setting up icu-devtools (67.1-3) ...
Setting up pkg-config (0.29.2-1) ...
Setting up fonts-dejavu-core (2.37-2) ...
Setting up libpcre2-posix2:armhf (10.34-7) ...
Setting up libk5crypto3:armhf (1.17-10) ...
Setting up libgfortran5:armhf (10.1.0-4+rpi1) ...
Setting up liblzma-dev:armhf (5.2.4-1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
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Setting up libssh2-1:armhf (1.8.0-2.1) ...
Setting up libkrb5-3:armhf (1.17-10) ...
Setting up libtiff5:armhf (4.1.0+git191117-2) ...
Setting up openssl (1.1.1g-1) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libicu-dev:armhf (67.1-3) ...
Setting up libxml2:armhf (2.9.10+dfsg-5+b1) ...
Setting up xdg-utils (1.1.3-2) ...
Setting up libblas-dev:armhf (3.9.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up dctrl-tools (2.24-3) ...
Setting up gcc-9-base:armhf (9.3.0-15+rpi1) ...
Setting up libbz2-dev:armhf (1.0.8-4) ...
Setting up libfile-stripnondeterminism-perl (1.9.0-1) ...
Setting up libice6:armhf (2:1.0.9-2) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up liblapack3:armhf (3.9.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libncurses-dev:armhf (6.2-1) ...
Setting up libxcb1:armhf (1.14-2) ...
Setting up libpcre2-dev:armhf (10.34-7) ...
Setting up libtool (2.4.6-14) ...
Setting up libxcb-render0:armhf (1.14-2) ...
Setting up libpcre3-dev:armhf (2:8.39-13) ...
Setting up libpng-dev:armhf (1.6.37-2) ...
Setting up libjpeg-dev (1:1.5.2-2) ...
Setting up m4 (1.4.18-4) ...
Setting up libxcb-shm0:armhf (1.14-2) ...
Setting up libreadline-dev:armhf (8.0-4) ...
Setting up libthai0:armhf (0.1.28-3) ...
Setting up ca-certificates (20200601) ...
Updating certificates in /etc/ssl/certs...
126 added, 0 removed; done.
Setting up libasan5:armhf (9.3.0-15+rpi1) ...
Setting up libfreetype6:armhf (2.10.2+dfsg-3) ...
Setting up liblapack-dev:armhf (3.9.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up libgssapi-krb5-2:armhf (1.17-10) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up ucf (3.0043) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.9.0-1) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-5) ...
Setting up libncurses5-dev:armhf (6.2-1) ...
Setting up cpp-9 (9.3.0-15+rpi1) ...
Setting up libcurl4:armhf (7.68.0-1+b1) ...
Setting up libx11-6:armhf (2:1.6.9-2) ...
Setting up libharfbuzz0b:armhf (2.6.4-1+rpi1+b1) ...
Setting up libsm6:armhf (2:1.2.3-1) ...
Setting up libxmuu1:armhf (2:1.1.2-2+b3) ...
Setting up automake (1:1.16.2-3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libpaper1:armhf (1.1.28) ...
Creating config file /etc/papersize with new version
Setting up gettext (0.19.8.1-10) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up fontconfig-config (2.13.1-4.2) ...
Setting up libxext6:armhf (2:1.3.3-1+b2) ...
Setting up libpaper-utils (1.1.28) ...
Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libgcc-9-dev:armhf (9.3.0-15+rpi1) ...
Setting up libxt6:armhf (1:1.1.5-1+b3) ...
Setting up xauth (1:1.0.10-1) ...
Setting up libxss1:armhf (1:1.2.3-1) ...
Setting up libfontconfig1:armhf (2.13.1-4.2) ...
Setting up gcc-9 (9.3.0-15+rpi1) ...
Setting up fontconfig (2.13.1-4.2) ...
Regenerating fonts cache... done.
Setting up libxft2:armhf (2.3.2-2) ...
Setting up libstdc++-9-dev:armhf (9.3.0-15+rpi1) ...
Setting up po-debconf (1.0.21) ...
Setting up libtk8.6:armhf (8.6.10-1) ...
Setting up libpango-1.0-0:armhf (1.44.7-4) ...
Setting up libgfortran-9-dev:armhf (9.3.0-15+rpi1) ...
Setting up libcairo2:armhf (1.16.0-4) ...
Setting up g++-9 (9.3.0-15+rpi1) ...
Setting up libpangoft2-1.0-0:armhf (1.44.7-4) ...
Setting up libpangocairo-1.0-0:armhf (1.44.7-4) ...
Setting up gfortran-9 (9.3.0-15+rpi1) ...
Setting up gfortran (4:9.2.1-3.1+rpi1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up r-base-core (4.0.2-1) ...
Creating config file /etc/R/Renviron with new version
Setting up r-cran-lattice (0.20-41-1+b1) ...
Setting up r-base-dev (4.0.2-1) ...
Setting up r-cran-matrix (1.2-18-1+b1) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (13.2) ...
Setting up dh-r (20200710) ...
Setting up sbuild-build-depends-r-bioc-rsubread-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-1+rpi1) ...
Processing triggers for ca-certificates (20200601) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.34.90.20200706-1+rpi1 dpkg-dev_1.19.7 g++-9_9.3.0-15+rpi1 gcc-9_9.3.0-15+rpi1 libc6-dev_2.31-1+rpi1 libstdc++-9-dev_9.3.0-15+rpi1 libstdc++6_10.1.0-4+rpi1 linux-libc-dev_5.7.6-1+rpi1
Package versions: adduser_3.118 apt_2.1.7 autoconf_2.69-11.1 automake_1:1.16.2-3 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-6 binutils_2.34.90.20200706-1+rpi1 binutils-arm-linux-gnueabihf_2.34.90.20200706-1+rpi1 binutils-common_2.34.90.20200706-1+rpi1 bsdextrautils_2.35.2-7 bsdutils_1:2.35.2-7 build-essential_12.8 bzip2_1.0.8-4 ca-certificates_20200601 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.3.0-15+rpi1 dash_0.5.10.2-7 dctrl-tools_2.24-3 debconf_1.5.74 debhelper_13.2 debianutils_4.9.1 dh-autoreconf_19 dh-r_20200710 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dmsetup_2:1.02.167-1+b2 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.35.2-7 file_1:5.38-5 findutils_4.7.0-1 fontconfig_2.13.1-4.2 fontconfig-config_2.13.1-4.2 fonts-dejavu-core_2.37-2 g++_4:9.2.1-3.1+rpi1 g++-9_9.3.0-15+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10.1.0-4+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-6+rpi1 gcc-8-base_8.4.0-4+rpi1 gcc-9_9.3.0-15+rpi1 gcc-9-base_9.3.0-15+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gfortran_4:9.2.1-3.1+rpi1 gfortran-9_9.3.0-15+rpi1 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 icu-devtools_67.1-3 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-3 libacl1_2.2.53-8 libapt-pkg6.0_2.1.7 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2 libasan5_9.3.0-15+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.1.0-4+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.34.90.20200706-1+rpi1 libblas-dev_3.9.0-2 libblas3_3.9.0-2 libblkid1_2.35.2-7 libbrotli1_1.0.7-7 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-4 libbz2-dev_1.0.8-4 libc-bin_2.31-1+rpi1 libc-dev-bin_2.31-1+rpi1 libc6_2.31-1+rpi1 libc6-dev_2.31-1+rpi1 libcairo2_1.16.0-4 libcap-ng0_0.7.9-2.2 libcap2_1:2.36-1 libcap2-bin_1:2.36-1 libcc1-0_10.1.0-4+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libcryptsetup12_2:2.3.3-1 libctf-nobfd0_2.34.90.20200706-1+rpi1 libctf0_2.34.90.20200706-1+rpi1 libcurl4_7.68.0-1+b1 libdatrie1_0.2.12-3+b3 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.253 libdebhelper-perl_13.2 libdevmapper1.02.1_2:1.02.167-1+b2 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.35.2-7 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libfile-which-perl_1.23-1 libfontconfig1_2.13.1-4.2 libfreetype6_2.10.2+dfsg-3 libfribidi0_1.0.8-2 libgcc-9-dev_9.3.0-15+rpi1 libgcc-s1_10.1.0-4+rpi1 libgcrypt20_1.8.6-2 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran-9-dev_9.3.0-15+rpi1 libgfortran5_10.1.0-4+rpi1 libglib2.0-0_2.64.4-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.14-2+b1 libgomp1_10.1.0-4+rpi1 libgpg-error0_1.38-2 libgraphite2-3_1.3.14-1 libgssapi-krb5-2_1.17-10 libharfbuzz0b_2.6.4-1+rpi1+b1 libhogweed6_3.6-2 libice6_2:1.0.9-2 libicu-dev_67.1-3 libicu67_67.1-3 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libjbig0_2.1-3.1+b2 libjpeg-dev_1:1.5.2-2 libjpeg62-turbo_1:1.5.2-2+b1 libjpeg62-turbo-dev_1:1.5.2-2+b1 libjson-c4_0.13.1+dfsg-9 libk5crypto3_1.17-10 libkeyutils1_1.6.1-2 libkrb5-3_1.17-10 libkrb5support0_1.17-10 libksba8_1.4.0-2 liblapack-dev_3.9.0-2 liblapack3_3.9.0-2 libldap-2.4-2_2.4.50+dfsg-1+b1 libldap-common_2.4.50+dfsg-1 liblocale-gettext-perl_1.07-4 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.35.2-7 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses-dev_6.2-1 libncurses5-dev_6.2-1 libncurses6_6.2-1 libncursesw6_6.2-1 libnettle8_3.6-2 libnghttp2-14_1.41.0-2 libnpth0_1.6-2 libp11-kit0_0.23.20-1 libpam-cap_1:2.36-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpango-1.0-0_1.44.7-4 libpangocairo-1.0-0_1.44.7-4 libpangoft2-1.0-0_1.44.7-4 libpaper-utils_1.1.28 libpaper1_1.1.28 libpcre16-3_2:8.39-13 libpcre2-16-0_10.34-7 libpcre2-32-0_10.34-7 libpcre2-8-0_10.34-7 libpcre2-dev_10.34-7 libpcre2-posix2_10.34-7 libpcre3_2:8.39-13 libpcre3-dev_2:8.39-13 libpcre32-3_2:8.39-13 libpcrecpp0v5_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.2-2 libpixman-1-0_0.36.0-1 libpng-dev_1.6.37-2 libpng16-16_1.6.37-2 libpsl5_0.21.0-1.1 libreadline-dev_8.0-4 libreadline8_8.0-4 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigsegv2_2.12-2 libsm6_2:1.2.3-1 libsmartcols1_2.35.2-7 libsqlite3-0_3.32.3-1 libss2_1.45.6-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1g-1 libstdc++-9-dev_9.3.0-15+rpi1 libstdc++6_10.1.0-4+rpi1 libsub-override-perl_0.09-2 libswitch-perl_2.17-2 libsystemd0_245.6-2+rpi1+b1 libtasn1-6_4.16.0-2 libtcl8.6_8.6.10+dfsg-1 libtext-charwidth-perl_0.04-10 libtext-iconv-perl_1.7-7 libthai-data_0.1.28-3 libthai0_0.1.28-3 libtiff5_4.1.0+git191117-2 libtinfo6_6.2-1 libtk8.6_8.6.10-1 libtool_2.4.6-14 libubsan1_10.1.0-4+rpi1 libuchardet0_0.0.7-1 libudev1_245.6-2+rpi1+b1 libunistring2_0.9.10-4 libuuid1_2.35.2-7 libwebp6_0.6.1-2 libx11-6_2:1.6.9-2 libx11-data_2:1.6.9-2 libxau6_1:1.0.8-1+b2 libxcb-render0_1.14-2 libxcb-shm0_1.14-2 libxcb1_1.14-2 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxft2_2.3.2-2 libxml2_2.9.10+dfsg-5+b1 libxmuu1_2:1.1.2-2+b3 libxrender1_1:0.9.10-1 libxss1_1:1.2.3-1 libxt6_1:1.1.5-1+b3 libzstd1_1.4.5+dfsg-3+rpi1 linux-libc-dev_5.7.6-1+rpi1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-2 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.35.2-7 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 openssl_1.1.1g-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21 r-base-core_4.0.2-1 r-base-dev_4.0.2-1 r-cran-lattice_0.20-41-1+b1 r-cran-matrix_1.2-18-1+b1 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-rsubread-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 ucf_3.0043 unzip_6.0-25 util-linux_2.35.2-7 x11-common_1:7.7+20 xauth_1:1.0.10-1 xdg-utils_1.1.3-2 xz-utils_5.2.4-1 zip_3.0-11 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Tue Jul 28 06:36:06 2020 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-rsubread_2.2.5-1.dsc
dpkg-source: info: extracting r-bioc-rsubread in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking r-bioc-rsubread_2.2.5.orig.tar.gz
dpkg-source: info: unpacking r-bioc-rsubread_2.2.5-1.debian.tar.xz
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-4c0e92c2-0a93-4146-97f1-1021bfe00641
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package r-bioc-rsubread
dpkg-buildpackage: info: source version 2.2.5-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean --buildsystem R
dh_auto_clean -O--buildsystem=R
dh_autoreconf_clean -O--buildsystem=R
dh_clean -O--buildsystem=R
debian/rules binary-arch
dh binary-arch --buildsystem R
dh_update_autotools_config -a -O--buildsystem=R
dh_autoreconf -a -O--buildsystem=R
dh_auto_configure -a -O--buildsystem=R
dh_auto_build -a -O--buildsystem=R
dh_auto_test -a -O--buildsystem=R
create-stamp debian/debhelper-build-stamp
dh_testroot -a -O--buildsystem=R
dh_prep -a -O--buildsystem=R
dh_auto_install -a -O--buildsystem=R
I: R Package: Rsubread Version: 2.2.5
I: Building using R version 4.0.2-1
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Mon, 27 Jul 2020 11:44:20 +0200
mkdir -p /<<PKGBUILDDIR>>/debian/r-bioc-rsubread/usr/lib/R/site-library
R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-rsubread/usr/lib/R/site-library --clean . "--built-timestamp='Mon, 27 Jul 2020 11:44:20 +0200'"
* installing *source* package 'Rsubread' ...
** using staged installation
@@@@@ The operating system is Linux.
** libs
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.5\"" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-nKXijO/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c HelperFunctions.c -o HelperFunctions.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.5\"" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-nKXijO/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c LRMbase-index.c -o LRMbase-index.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.5\"" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-nKXijO/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c LRMchro-event.c -o LRMchro-event.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.5\"" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-nKXijO/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c LRMfile-io.c -o LRMfile-io.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.5\"" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-nKXijO/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c LRMhashtable.c -o LRMhashtable.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.5\"" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-nKXijO/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c LRMhelper.c -o LRMhelper.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.5\"" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-nKXijO/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c LRMseek-zlib.c -o LRMseek-zlib.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.5\"" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-nKXijO/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.5\"" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-nKXijO/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_wrapper.c -o R_wrapper.o
In file included from /usr/lib/gcc/arm-linux-gnueabihf/9/include/stdint.h:9,
from HelperFunctions.h:139,
from R_wrapper.c:35:
/usr/include/stdint.h:96:23: error: conflicting types for 'uintptr_t'
96 | typedef unsigned int uintptr_t;
| ^~~~~~~~~
In file included from R_wrapper.c:30:
/usr/share/R/include/Rinterface.h:110:24: note: previous declaration of 'uintptr_t' was here
110 | typedef unsigned long uintptr_t;
| ^~~~~~~~~
make[1]: *** [/usr/lib/R/etc/Makeconf:167: R_wrapper.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 'Rsubread'
* removing '/<<PKGBUILDDIR>>/debian/r-bioc-rsubread/usr/lib/R/site-library/Rsubread'
dh_auto_install: error: R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-rsubread/usr/lib/R/site-library --clean . "--built-timestamp='Mon, 27 Jul 2020 11:44:20 +0200'" 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 2020-07-30T12:52:33Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 0
Build-Time: 40
Distribution: bullseye-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 874
Job: r-bioc-rsubread_2.2.5-1
Machine Architecture: armhf
Package: r-bioc-rsubread
Package-Time: 966
Source-Version: 2.2.5-1
Space: 0
Status: failed
Version: 2.2.5-1
--------------------------------------------------------------------------------
Finished at 2020-07-30T12:52:33Z
Build needed 00:00:00, 0k disc space