r-bioc-rsamtools →
1.26.1-1 →
armhf → 2016-11-01 13:22:47
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01
+==============================================================================+
| r-bioc-rsamtools 1.26.1-1 (armhf) Tue, 01 Nov 2016 12:58:11 +0000 |
+==============================================================================+
Package: r-bioc-rsamtools
Version: 1.26.1-1
Source Version: 1.26.1-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/stretch-staging-armhf-sbuild-a6082793-3aa4-4b51-83b0-f31592c1935f' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [9422 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.4 MB]
Fetched 20.8 MB in 24s (850 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'r-bioc-rsamtools' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-rsamtools/trunk/
Need to get 2993 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main r-bioc-rsamtools 1.26.1-1 (dsc) [2258 B]
Get:2 http://172.17.0.1/private stretch-staging/main r-bioc-rsamtools 1.26.1-1 (tar) [2984 kB]
Get:3 http://172.17.0.1/private stretch-staging/main r-bioc-rsamtools 1.26.1-1 (diff) [6872 B]
Fetched 2993 kB in 0s (8778 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/r-bioc-rsamtools-TavqD4/r-bioc-rsamtools-1.26.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-rsamtools-TavqD4' 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-1woqyx/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-1woqyx/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-1woqyx/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-1woqyx/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-1woqyx/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-1woqyx/apt_archive ./ Release.gpg [342 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-1woqyx/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-1woqyx/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-1woqyx/apt_archive ./ Packages [433 B]
Fetched 2081 B in 0s (3146 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-1woqyx/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 'root' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-1woqyx/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
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:
dirmngr fuse2fs gnupg-l10n libffi6 libfuse2 libgnutls30 libhogweed4
libldap-2.4-2 libnettle6 libp11-kit0 libsasl2-2 libsasl2-modules
libsasl2-modules-db libssl1.0.2 libtasn1-6 manpages
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 5 not upgraded.
Need to get 762 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-1woqyx/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [762 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 762 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13152 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 (>= 9), dh-r, r-base-dev, r-cran-bitops, r-bioc-biostrings (>= 2.40.0), r-bioc-genomicranges (>= 1.24.0), r-bioc-biocparallel, libbam-dev
Filtered Build-Depends: debhelper (>= 9), dh-r, r-base-dev, r-cran-bitops, r-bioc-biostrings (>= 2.40.0), r-bioc-genomicranges (>= 1.24.0), r-bioc-biocparallel, libbam-dev
dpkg-deb: building package 'sbuild-build-depends-r-bioc-rsamtools-dummy' in '/<<BUILDDIR>>/resolver-1woqyx/apt_archive/sbuild-build-depends-r-bioc-rsamtools-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-r-bioc-rsamtools-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-1woqyx/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-1woqyx/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-1woqyx/apt_archive ./ Release.gpg [342 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-1woqyx/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-1woqyx/apt_archive ./ Sources [562 B]
Get:5 copy:/<<BUILDDIR>>/resolver-1woqyx/apt_archive ./ Packages [643 B]
Fetched 2510 B in 0s (3847 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-1woqyx/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 'root' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-1woqyx/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install r-bioc-rsamtools build dependencies (apt-based resolver)
----------------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
dirmngr fuse2fs gnupg-l10n libfuse2 libsasl2-modules manpages
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils ca-certificates cdbs
dctrl-tools debhelper dh-autoreconf dh-r dh-strip-nondeterminism file
fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base gfortran
gfortran-6 groff-base icu-devtools intltool-debian libarchive-zip-perl
libbam-dev libblas-common libblas-dev libblas3 libbsd0 libbz2-dev libcairo2
libcroco3 libcurl3 libdatrie1 libexpat1 libfile-stripnondeterminism-perl
libfontconfig1 libfreetype6 libgfortran-6-dev libgfortran3 libglib2.0-0
libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu-dev libicu57
libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 liblzma-dev
libmagic-mgc libmagic1 libncurses5-dev libnghttp2-14 libpango-1.0-0
libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre16-3
libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0 libpng-dev
libpng16-16 libreadline-dev librtmp1 libsigsegv2 libsm6 libssh2-1 libtcl8.6
libthai-data libthai0 libtiff5 libtimedate-perl libtinfo-dev libtk8.6
libtool libunistring0 libx11-6 libx11-data libxau6 libxcb-render0
libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxmuu1 libxrender1
libxss1 libxt6 m4 man-db openssl po-debconf r-base-core r-base-dev
r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biostrings
r-bioc-genomeinfodb r-bioc-genomicranges r-bioc-iranges r-bioc-s4vectors
r-bioc-xvector r-cran-bitops r-cran-futile.logger r-cran-futile.options
r-cran-lambda.r r-cran-snow ucf unzip x11-common xauth xdg-utils zip
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation devscripts debtags dh-make gettext-doc libasprintf-dev
libgettextpo-dev gfortran-doc gfortran-6-doc libgfortran3-dbg
libcoarrays-dev groff liblapack-doc-man liblapack-doc krb5-doc krb5-user
icu-doc liblzma-doc ncurses-doc readline-doc tcl8.6 tk8.6 libtool-doc
gcj-jdk less www-browser libmail-box-perl ess r-doc-info | r-doc-pdf
r-mathlib r-base-html texlive-base texlive-latex-base
texlive-generic-recommended texlive-fonts-recommended texlive-fonts-extra
texlive-extra-utils texlive-latex-recommended texlive-latex-extra texinfo
r-cran-foreach r-cran-batchjobs r-cran-bbmisc r-cran-doparallel r-cran-rmpi
r-bioc-rsamtools r-bioc-genomicalignments r-bioc-shortread r-cran-codetools
r-cran-runit r-cran-knitr r-bioc-bsgenome r-bioc-genomicfeatures
r-cran-rsprng r-cran-rlecuyer gvfs-bin
Recommended packages:
curl | wget | lynx-cur bzip2-doc libglib2.0-data shared-mime-info
xdg-user-dirs krb5-locales libpng-tools libltdl-dev xml-core
libmail-sendmail-perl r-recommended r-doc-html r-cran-digest
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 cdbs
dctrl-tools debhelper dh-autoreconf dh-r dh-strip-nondeterminism file
fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base gfortran
gfortran-6 groff-base icu-devtools intltool-debian libarchive-zip-perl
libbam-dev libblas-common libblas-dev libblas3 libbsd0 libbz2-dev libcairo2
libcroco3 libcurl3 libdatrie1 libexpat1 libfile-stripnondeterminism-perl
libfontconfig1 libfreetype6 libgfortran-6-dev libgfortran3 libglib2.0-0
libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu-dev libicu57
libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 liblzma-dev
libmagic-mgc libmagic1 libncurses5-dev libnghttp2-14 libpango-1.0-0
libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre16-3
libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0 libpng-dev
libpng16-16 libreadline-dev librtmp1 libsigsegv2 libsm6 libssh2-1 libtcl8.6
libthai-data libthai0 libtiff5 libtimedate-perl libtinfo-dev libtk8.6
libtool libunistring0 libx11-6 libx11-data libxau6 libxcb-render0
libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxmuu1 libxrender1
libxss1 libxt6 m4 man-db openssl po-debconf r-base-core r-base-dev
r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biostrings
r-bioc-genomeinfodb r-bioc-genomicranges r-bioc-iranges r-bioc-s4vectors
r-bioc-xvector r-cran-bitops r-cran-futile.logger r-cran-futile.options
r-cran-lambda.r r-cran-snow sbuild-build-depends-r-bioc-rsamtools-dummy ucf
unzip x11-common xauth xdg-utils zip zlib1g-dev
0 upgraded, 130 newly installed, 0 to remove and 5 not upgraded.
Need to get 113 MB of archives.
After this operation, 277 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-1woqyx/apt_archive ./ sbuild-build-depends-r-bioc-rsamtools-dummy 0.invalid.0 [838 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-8 [1087 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.12 [178 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.2.0-1 [61.7 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libpng16-16 armhf 1.6.25-2 [261 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf libfreetype6 armhf 2.6.3-3+b1 [385 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf ucf all 3.0036 [70.2 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf fonts-dejavu-core all 2.37-1 [1068 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf fontconfig-config all 2.11.0-6.7 [271 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libfontconfig1 armhf 2.11.0-6.7 [313 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf fontconfig armhf 2.11.0-6.7 [402 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libjbig0 armhf 2.1-3.1 [27.5 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libpaper1 armhf 1.1.24+nmu4 [21.4 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libpcrecpp0v5 armhf 2:8.39-2 [149 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libxdmcp6 armhf 1:1.1.2-1.1 [24.9 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libxcb1 armhf 1.12-1 [129 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libx11-data all 2:1.6.3-1 [128 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libx11-6 armhf 2:1.6.3-1 [678 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libxext6 armhf 2:1.3.3-1 [48.1 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libxrender1 armhf 1:0.9.9-2 [28.9 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libxft2 armhf 2.3.2-1 [48.3 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf x11-common all 1:7.7+16 [251 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libxss1 armhf 1:1.2.2-1 [16.8 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.29-1 [219 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.29-1 [104 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.29-1 [63.3 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libkrb5support0 armhf 1.14.3+dfsg-2 [57.5 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libk5crypto3 armhf 1.14.3+dfsg-2 [110 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libkrb5-3 armhf 1.14.3+dfsg-2 [262 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libgssapi-krb5-2 armhf 1.14.3+dfsg-2 [131 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-4 [7407 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2 [805 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20160430.1 [72.6 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf openssl armhf 1.0.2j-1 [671 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf ca-certificates all 20160104 [200 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf cdbs all 0.4.148 [82.3 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf dctrl-tools armhf 2.24-2 [94.4 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.028-1 [14.6 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.028-1 [9020 B]
Get:55 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.0-2+rpi1 [2523 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-2 [131 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10.2.2 [826 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf zip armhf 3.0-11 [212 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf unzip armhf 6.0-20 [142 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf libpaper-utils armhf 1.1.24+nmu4 [17.2 kB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf xdg-utils all 1.1.1-1 [71.1 kB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 6.2.0-6+rpi1 [165 kB]
Get:67 http://172.17.0.1/private stretch-staging/main armhf libblas-common armhf 3.6.1-2 [13.9 kB]
Get:68 http://172.17.0.1/private stretch-staging/main armhf libblas3 armhf 3.6.1-2 [112 kB]
Get:69 http://172.17.0.1/private stretch-staging/main armhf libpixman-1-0 armhf 0.34.0-1 [451 kB]
Get:70 http://172.17.0.1/private stretch-staging/main armhf libxcb-render0 armhf 1.12-1 [104 kB]
Get:71 http://172.17.0.1/private stretch-staging/main armhf libxcb-shm0 armhf 1.12-1 [95.9 kB]
Get:72 http://172.17.0.1/private stretch-staging/main armhf libcairo2 armhf 1.14.6-1+b1 [686 kB]
Get:73 http://172.17.0.1/private stretch-staging/main armhf libnghttp2-14 armhf 1.16.0-1 [72.5 kB]
Get:74 http://172.17.0.1/private stretch-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:75 http://172.17.0.1/private stretch-staging/main armhf libssh2-1 armhf 1.7.0-1 [125 kB]
Get:76 http://172.17.0.1/private stretch-staging/main armhf libcurl3 armhf 7.50.1-1 [251 kB]
Get:77 http://172.17.0.1/private stretch-staging/main armhf libice6 armhf 2:1.0.9-1+b1 [51.9 kB]
Get:78 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo armhf 1:1.5.1-2 [109 kB]
Get:79 http://172.17.0.1/private stretch-staging/main armhf liblapack3 armhf 3.6.1-2 [1392 kB]
Get:80 http://172.17.0.1/private stretch-staging/main armhf libthai-data all 0.1.25-2 [165 kB]
Get:81 http://172.17.0.1/private stretch-staging/main armhf libdatrie1 armhf 0.2.10-4 [32.8 kB]
Get:82 http://172.17.0.1/private stretch-staging/main armhf libthai0 armhf 0.1.25-2 [48.7 kB]
Get:83 http://172.17.0.1/private stretch-staging/main armhf libpango-1.0-0 armhf 1.40.3-2 [300 kB]
Get:84 http://172.17.0.1/private stretch-staging/main armhf libgraphite2-3 armhf 1.3.8-1 [62.5 kB]
Get:85 http://172.17.0.1/private stretch-staging/main armhf libharfbuzz0b armhf 1.2.7-1+b1 [589 kB]
Get:86 http://172.17.0.1/private stretch-staging/main armhf libpangoft2-1.0-0 armhf 1.40.3-2 [196 kB]
Get:87 http://172.17.0.1/private stretch-staging/main armhf libpangocairo-1.0-0 armhf 1.40.3-2 [186 kB]
Get:88 http://172.17.0.1/private stretch-staging/main armhf libsm6 armhf 2:1.2.2-1+b1 [31.2 kB]
Get:89 http://172.17.0.1/private stretch-staging/main armhf libtcl8.6 armhf 8.6.6+dfsg-1 [861 kB]
Get:90 http://172.17.0.1/private stretch-staging/main armhf libtiff5 armhf 4.0.6-2 [203 kB]
Get:91 http://172.17.0.1/private stretch-staging/main armhf libtk8.6 armhf 8.6.6-1 [659 kB]
Get:92 http://172.17.0.1/private stretch-staging/main armhf libxt6 armhf 1:1.1.5-1 [155 kB]
Get:93 http://172.17.0.1/private stretch-staging/main armhf r-base-core armhf 3.3.1.20161024-1 [20.8 MB]
Get:94 http://172.17.0.1/private stretch-staging/main armhf libgfortran-6-dev armhf 6.2.0-6+rpi1 [199 kB]
Get:95 http://172.17.0.1/private stretch-staging/main armhf gfortran-6 armhf 6.2.0-6+rpi1 [5405 kB]
Get:96 http://172.17.0.1/private stretch-staging/main armhf gfortran armhf 4:6.1.1-1 [1370 B]
Get:97 http://172.17.0.1/private stretch-staging/main armhf libblas-dev armhf 3.6.1-2 [18.9 kB]
Get:98 http://172.17.0.1/private stretch-staging/main armhf liblapack-dev armhf 3.6.1-2 [1379 kB]
Get:99 http://172.17.0.1/private stretch-staging/main armhf libtinfo-dev armhf 6.0+20160917-1 [65.4 kB]
Get:100 http://172.17.0.1/private stretch-staging/main armhf libncurses5-dev armhf 6.0+20160917-1 [245 kB]
Get:101 http://172.17.0.1/private stretch-staging/main armhf libreadline-dev armhf 7.0-1 [109 kB]
Get:102 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.1-2 [181 kB]
Get:103 http://172.17.0.1/private stretch-staging/main armhf libjpeg-dev all 1:1.5.1-2 [56.1 kB]
Get:104 http://172.17.0.1/private stretch-staging/main armhf libpcre16-3 armhf 2:8.39-2 [235 kB]
Get:105 http://172.17.0.1/private stretch-staging/main armhf libpcre32-3 armhf 2:8.39-2 [227 kB]
Get:106 http://172.17.0.1/private stretch-staging/main armhf libpcre3-dev armhf 2:8.39-2 [568 kB]
Get:107 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:108 http://172.17.0.1/private stretch-staging/main armhf libpng-dev armhf 1.6.25-2 [230 kB]
Get:109 http://172.17.0.1/private stretch-staging/main armhf libbz2-dev armhf 1.0.6-8 [27.8 kB]
Get:110 http://172.17.0.1/private stretch-staging/main armhf liblzma-dev armhf 5.2.2-1.2 [284 kB]
Get:111 http://172.17.0.1/private stretch-staging/main armhf icu-devtools armhf 57.1-4 [156 kB]
Get:112 http://172.17.0.1/private stretch-staging/main armhf libicu-dev armhf 57.1-4 [15.7 MB]
Get:113 http://172.17.0.1/private stretch-staging/main armhf libxmuu1 armhf 2:1.1.2-2 [23.0 kB]
Get:114 http://172.17.0.1/private stretch-staging/main armhf xauth armhf 1:1.0.9-1 [35.6 kB]
Get:115 http://172.17.0.1/private stretch-staging/main armhf r-base-dev all 3.3.1.20161024-1 [4298 B]
Get:116 http://172.17.0.1/private stretch-staging/main armhf dh-r all 20160916 [7378 B]
Get:117 http://172.17.0.1/private stretch-staging/main armhf libbam-dev armhf 0.1.19-2 [109 kB]
Get:118 http://172.17.0.1/private stretch-staging/main armhf r-bioc-biocgenerics all 0.20.0-1 [483 kB]
Get:119 http://172.17.0.1/private stretch-staging/main armhf r-cran-lambda.r all 1.1.7-3 [66.4 kB]
Get:120 http://172.17.0.1/private stretch-staging/main armhf r-cran-futile.options all 1.0.0-2 [15.4 kB]
Get:121 http://172.17.0.1/private stretch-staging/main armhf r-cran-futile.logger all 1.4.1-3 [84.3 kB]
Get:122 http://172.17.0.1/private stretch-staging/main armhf r-cran-snow all 1:0.4.2-1 [65.0 kB]
Get:123 http://172.17.0.1/private stretch-staging/main armhf r-bioc-biocparallel all 1.8.0-2 [633 kB]
Get:124 http://172.17.0.1/private stretch-staging/main armhf r-bioc-s4vectors armhf 0.10.2-1 [917 kB]
Get:125 http://172.17.0.1/private stretch-staging/main armhf r-bioc-iranges armhf 2.6.1-1 [1418 kB]
Get:126 http://172.17.0.1/private stretch-staging/main armhf r-bioc-xvector armhf 0.12.0-2 [328 kB]
Get:127 http://172.17.0.1/private stretch-staging/main armhf r-bioc-biostrings armhf 2.40.2-1 [13.5 MB]
Get:128 http://172.17.0.1/private stretch-staging/main armhf r-bioc-genomeinfodb all 1.10.0-1 [14.7 MB]
Get:129 http://172.17.0.1/private stretch-staging/main armhf r-bioc-genomicranges armhf 1.24.0-1 [1301 kB]
Get:130 http://172.17.0.1/private stretch-staging/main armhf r-cran-bitops armhf 1.0-6-1 [23.6 kB]
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Setting up cdbs (0.4.148) ...
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No schema files found: doing nothing.
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Setting up libdatrie1:armhf (0.2.10-4) ...
Setting up libtiff5:armhf (4.0.6-2) ...
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Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
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Setting up libpixman-1-0:armhf (0.34.0-1) ...
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update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
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Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
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Setting up libkeyutils1:armhf (1.5.9-9) ...
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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 x11-common (1:7.7+16) ...
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
Running in chroot, ignoring request.
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of start.
Setting up xdg-utils (1.1.1-1) ...
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Creating config file /etc/papersize with new version
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Setting up libharfbuzz0b:armhf (1.2.7-1+b1) ...
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Setting up libice6:armhf (2:1.0.9-1+b1) ...
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
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Setting up libtool (2.4.6-2) ...
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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 libfontconfig1:armhf (2.11.0-6.7) ...
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Setting up libk5crypto3:armhf (1.14.3+dfsg-2) ...
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Setting up po-debconf (1.0.20) ...
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update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode
Setting up libx11-6:armhf (2:1.6.3-1) ...
Setting up libxmuu1:armhf (2:1.1.2-2) ...
Setting up libxcb-shm0:armhf (1.12-1) ...
Setting up libxt6:armhf (1:1.1.5-1) ...
Setting up libxrender1:armhf (1:0.9.9-2) ...
Setting up libkrb5-3:armhf (1.14.3+dfsg-2) ...
Setting up libxft2:armhf (2.3.2-1) ...
Setting up fontconfig (2.11.0-6.7) ...
Regenerating fonts cache... done.
Setting up liblapack-dev (3.6.1-2) ...
update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode
Setting up libxext6:armhf (2:1.3.3-1) ...
Setting up libxss1:armhf (1:1.2.2-1) ...
Setting up libgssapi-krb5-2:armhf (1.14.3+dfsg-2) ...
Setting up xauth (1:1.0.9-1) ...
Setting up libpango-1.0-0:armhf (1.40.3-2) ...
Setting up libcairo2:armhf (1.14.6-1+b1) ...
Setting up libcurl3:armhf (7.50.1-1) ...
Setting up libtk8.6:armhf (8.6.6-1) ...
Setting up libpangoft2-1.0-0:armhf (1.40.3-2) ...
Setting up libpangocairo-1.0-0:armhf (1.40.3-2) ...
Setting up r-base-core (3.3.1.20161024-1) ...
Creating config file /etc/R/Renviron with new version
Setting up r-base-dev (3.3.1.20161024-1) ...
Setting up r-bioc-biocgenerics (0.20.0-1) ...
Setting up r-cran-bitops (1.0-6-1) ...
Setting up r-cran-futile.options (1.0.0-2) ...
Setting up r-cran-lambda.r (1.1.7-3) ...
Setting up r-cran-snow (1:0.4.2-1) ...
Setting up r-bioc-s4vectors (0.10.2-1) ...
Setting up r-cran-futile.logger (1.4.1-3) ...
Setting up r-bioc-iranges (2.6.1-1) ...
Setting up r-bioc-biocparallel (1.8.0-2) ...
Setting up r-bioc-genomeinfodb (1.10.0-1) ...
Setting up r-bioc-xvector (0.12.0-2) ...
Setting up r-bioc-biostrings (2.40.2-1) ...
Setting up r-bioc-genomicranges (1.24.0-1) ...
Setting up dh-autoreconf (12) ...
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Setting up debhelper (10.2.2) ...
Setting up dh-r (20160916) ...
Setting up sbuild-build-depends-r-bioc-rsamtools-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-5+rpi1) ...
Processing triggers for systemd (231-9) ...
Processing triggers for ca-certificates (20160104) ...
Updating certificates in /etc/ssl/certs...
173 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.6.0-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.27-9 dpkg-dev_1.18.10 g++-6_6.2.0-6+rpi1 gcc-6_6.2.0-6+rpi1 libc6-dev_2.24-5+rpi1 libstdc++-6-dev_6.2.0-6+rpi1 libstdc++6_6.2.0-6+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.3.1 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.8.1-1 autotools-dev_20160430.1 base-files_9.6+rpi1 base-passwd_3.5.40 bash_4.4-1 binutils_2.27-9 bsdmainutils_9.0.12 bsdutils_1:2.28.2-1 build-essential_12.2 bzip2_1.0.6-8 ca-certificates_20160104 cdbs_0.4.148 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:6.1.1-1 cpp-6_6.2.0-6+rpi1 dash_0.5.8-2.3 dctrl-tools_2.24-2 debconf_1.5.59 debfoster_2.7-2.1 debhelper_10.2.2 debianutils_4.8 dh-autoreconf_12 dh-r_20160916 dh-strip-nondeterminism_0.028-1 diffutils_1:3.5-1 dirmngr_2.1.15-4 dmsetup_2:1.02.133-1 dpkg_1.18.10 dpkg-dev_1.18.10 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 fakeroot_1.21-2 file_1:5.29-1 findutils_4.6.0+git+20160703-2 fontconfig_2.11.0-6.7 fontconfig-config_2.11.0-6.7 fonts-dejavu-core_2.37-1 fuse2fs_1.43.3-1 g++_4:6.1.1-1 g++-6_6.2.0-6+rpi1 gcc_4:6.1.1-1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-6_6.2.0-6+rpi1 gcc-6-base_6.2.0-6+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gfortran_4:6.1.1-1 gfortran-6_6.2.0-6+rpi1 gnupg_2.1.15-4 gnupg-agent_2.1.15-4 gnupg-l10n_2.1.15-4 gpgv_2.1.15-4 grep_2.26-1 groff-base_1.22.3-8 gzip_1.6-5 hostname_3.18 icu-devtools_57.1-4 init_1.45 init-system-helpers_1.45 initscripts_2.88dsf-59.8 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libapparmor1_2.10.95-5 libapt-pkg5.0_1.3.1 libarchive-zip-perl_1.59-1 libasan3_6.2.0-6+rpi1 libassuan0_2.4.3-1 libatomic1_6.2.0-6+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.7-1 libaudit1_1:2.6.7-1 libbam-dev_0.1.19-2 libblas-common_3.6.1-2 libblas-dev_3.6.1-2 libblas3_3.6.1-2 libblkid1_2.28.2-1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libbz2-dev_1.0.6-8 libc-bin_2.24-5+rpi1 libc-dev-bin_2.24-5+rpi1 libc6_2.24-5+rpi1 libc6-dev_2.24-5+rpi1 libcairo2_1.14.6-1+b1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.2.0-6+rpi1 libcomerr2_1.43.3-1 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.2-5 libcurl3_7.50.1-1 libdatrie1_0.2.10-4 libdb5.3_5.3.28-12 libdbus-1-3_1.10.12-1 libdebconfclient0_0.218 libdevmapper1.02.1_2:1.02.133-1 libdpkg-perl_1.18.10 libdrm2_2.4.71-1 libexpat1_2.2.0-1 libfakeroot_1.21-2 libfdisk1_2.28.2-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.028-1 libfontconfig1_2.11.0-6.7 libfreetype6_2.6.3-3+b1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.2.0-6+rpi1 libgcc1_1:6.2.0-6+rpi1 libgcrypt20_1.7.3-2 libgdbm3_1.8.3-14 libgfortran-6-dev_6.2.0-6+rpi1 libgfortran3_6.2.0-6+rpi1 libglib2.0-0_2.50.0-2+rpi1 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.5.5-2 libgomp1_6.2.0-6+rpi1 libgpg-error0_1.24-1 libgraphite2-3_1.3.8-1 libgssapi-krb5-2_1.14.3+dfsg-2 libharfbuzz0b_1.2.7-1+b1 libhogweed4_3.3-1 libice6_2:1.0.9-1+b1 libicu-dev_57.1-4 libicu57_57.1-4 libidn11_1.33-1 libip4tc0_1.6.0-4 libisl15_0.17.1-1 libjbig0_2.1-3.1 libjpeg-dev_1:1.5.1-2 libjpeg62-turbo_1:1.5.1-2 libjpeg62-turbo-dev_1:1.5.1-2 libk5crypto3_1.14.3+dfsg-2 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_22-1.1 libkrb5-3_1.14.3+dfsg-2 libkrb5support0_1.14.3+dfsg-2 libksba8_1.3.5-2 liblapack-dev_3.6.1-2 liblapack3_3.6.1-2 libldap-2.4-2_2.4.42+dfsg-2+rpi1+b3 liblz4-1_0.0~r131-2 liblzma-dev_5.2.2-1.2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.29-1 libmagic1_1:5.29-1 libmount1_2.28.2-1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20160917-1 libncurses5-dev_6.0+20160917-1 libncursesw5_6.0+20160917-1 libnettle6_3.3-1 libnghttp2-14_1.16.0-1 libnpth0_1.2-3 libp11-kit0_0.23.2-5 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpango-1.0-0_1.40.3-2 libpangocairo-1.0-0_1.40.3-2 libpangoft2-1.0-0_1.40.3-2 libpaper-utils_1.1.24+nmu4 libpaper1_1.1.24+nmu4 libpcre16-3_2:8.39-2 libpcre3_2:8.39-2 libpcre3-dev_2:8.39-2 libpcre32-3_2:8.39-2 libpcrecpp0v5_2:8.39-2 libperl5.24_5.24.1~rc3-3 libpipeline1_1.4.1-2 libpixman-1-0_0.34.0-1 libpng-dev_1.6.25-2 libpng12-0_1.2.54-6 libpng16-16_1.6.25-2 libprocps6_2:3.3.12-2 libreadline-dev_7.0-1 libreadline7_7.0-1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libseccomp2_2.3.1-2 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsm6_2:1.2.2-1+b1 libsmartcols1_2.28.2-1 libsqlite3-0_3.14.2-1 libss2_1.43.3-1 libssh2-1_1.7.0-1 libssl1.0.2_1.0.2j-1 libstdc++-6-dev_6.2.0-6+rpi1 libstdc++6_6.2.0-6+rpi1 libsystemd0_231-9 libtasn1-6_4.9-4 libtcl8.6_8.6.6+dfsg-1 libthai-data_0.1.25-2 libthai0_0.1.25-2 libtiff5_4.0.6-2 libtimedate-perl_2.3000-2 libtinfo-dev_6.0+20160917-1 libtinfo5_6.0+20160917-1 libtk8.6_8.6.6-1 libtool_2.4.6-2 libubsan0_6.2.0-6+rpi1 libudev1_231-9 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28.2-1 libx11-6_2:1.6.3-1 libx11-data_2:1.6.3-1 libxau6_1:1.0.8-1 libxcb-render0_1.12-1 libxcb-shm0_1.12-1 libxcb1_1.12-1 libxdmcp6_1:1.1.2-1.1 libxext6_2:1.3.3-1 libxft2_2.3.2-1 libxml2_2.9.4+dfsg1-2 libxmuu1_2:1.1.2-2 libxrender1_1:0.9.9-2 libxss1_1:1.2.2-1 libxt6_1:1.1.5-1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.2 lsb-base_9.20160629+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.08-1 mawk_1.3.3-17 mount_2.28.2-1 multiarch-support_2.24-5+rpi1 nano_2.7.0-1 ncurses-base_6.0+20160917-1 ncurses-bin_6.0+20160917-1 openssl_1.0.2j-1 passwd_1:4.2-3.2 patch_2.7.5-1 perl_5.24.1~rc3-3 perl-base_5.24.1~rc3-3 perl-modules-5.24_5.24.1~rc3-3 pinentry-curses_0.9.7-6 po-debconf_1.0.20 procps_2:3.3.12-2 r-base-core_3.3.1.20161024-1 r-base-dev_3.3.1.20161024-1 r-bioc-biocgenerics_0.20.0-1 r-bioc-biocparallel_1.8.0-2 r-bioc-biostrings_2.40.2-1 r-bioc-genomeinfodb_1.10.0-1 r-bioc-genomicranges_1.24.0-1 r-bioc-iranges_2.6.1-1 r-bioc-s4vectors_0.10.2-1 r-bioc-xvector_0.12.0-2 r-cran-bitops_1.0-6-1 r-cran-futile.logger_1.4.1-3 r-cran-futile.options_1.0.0-2 r-cran-lambda.r_1.1.7-3 r-cran-snow_1:0.4.2-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-rsamtools-dummy_0.invalid.0 sed_4.2.2-8 sensible-utils_0.0.9 startpar_0.59-3.1 systemd_231-9 systemd-sysv_231-9 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1 tzdata_2016h-1 ucf_3.0036 udev_231-9 unzip_6.0-20 util-linux_2.28.2-1 x11-common_1:7.7+16 xauth_1:1.0.9-1 xdg-utils_1.1.1-1 xz-utils_5.2.2-1.2 zip_3.0-11 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| 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 Oct 26 15:18:08 2016 UTC
gpgv: using RSA key 578A0494D1C646D1
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./r-bioc-rsamtools_1.26.1-1.dsc
dpkg-source: info: extracting r-bioc-rsamtools in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking r-bioc-rsamtools_1.26.1.orig.tar.gz
dpkg-source: info: unpacking r-bioc-rsamtools_1.26.1-1.debian.tar.xz
dpkg-source: info: applying use_debian_packaged_zlib.patch
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=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-a6082793-3aa4-4b51-83b0-f31592c1935f
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package r-bioc-rsamtools
dpkg-buildpackage: info: source version 1.26.1-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build r-bioc-rsamtools-1.26.1
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --buildsystem R
dh_testdir -O--buildsystem=R
dh_auto_clean -O--buildsystem=R
dh_clean -O--buildsystem=R
debian/rules build-arch
dh build-arch --buildsystem R
dh_testdir -a -O--buildsystem=R
dh_update_autotools_config -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
fakeroot debian/rules binary-arch
dh binary-arch --buildsystem R
dh_testroot -a -O--buildsystem=R
dh_prep -a -O--buildsystem=R
dh_installdirs -a -O--buildsystem=R
dh_auto_install -a -O--buildsystem=R
I: R Package: Rsamtools Version: 1.26.1
I: Building using R version 3.3.1.20161024-1
I: R API version: r-api-3
I: Using built-time from d/changelog: Wed, 26 Oct 2016 17:15:09 +0200
mkdir -p /<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library
R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library --clean . "--built-timestamp='Wed, 26 Oct 2016 17:15:09 +0200'"
* installing *source* package 'Rsamtools' ...
** 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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c IRanges_stubs.c -o IRanges_stubs.o
g++ -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" -I"/usr/lib/R/site-library/Biostrings/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c PileupBuffer.cpp -o PileupBuffer.o
g++ -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" -I"/usr/lib/R/site-library/Biostrings/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c PosCacheColl.cpp -o PosCacheColl.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_init_Rsamtools.c -o R_init_Rsamtools.o
g++ -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" -I"/usr/lib/R/site-library/Biostrings/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ResultManager.cpp -o ResultManager.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c as_bam.c -o as_bam.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bam_data.c -o bam_data.o
g++ -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" -I"/usr/lib/R/site-library/Biostrings/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bam_mate_iter.cpp -o bam_mate_iter.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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bambuffer.c -o bambuffer.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bamfile.c -o bamfile.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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bcffile.c -o bcffile.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c encode.c -o encode.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fafile.c -o fafile.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c idxstats.c -o idxstats.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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c io_sam.c -o io_sam.o
g++ -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" -I"/usr/lib/R/site-library/Biostrings/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
g++ -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" -I"/usr/lib/R/site-library/Biostrings/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pileup.cpp -o pileup.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pileupbam.c -o pileupbam.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools_patch.c -o samtools_patch.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c scan_bam_data.c -o scan_bam_data.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tabixfile.c -o tabixfile.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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tagfilter.c -o tagfilter.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utilities.c -o utilities.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c zip_compression.c -o zip_compression.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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bgzf.c -o samtools/bgzf.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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/kstring.c -o samtools/kstring.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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam_aux.c -o samtools/bam_aux.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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam.c -o samtools/bam.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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam_import.c -o samtools/bam_import.o
In file included from /usr/include/limits.h:25:0,
from /usr/lib/gcc/arm-linux-gnueabihf/6/include-fixed/limits.h:168,
from /usr/lib/gcc/arm-linux-gnueabihf/6/include-fixed/syslimits.h:7,
from /usr/lib/gcc/arm-linux-gnueabihf/6/include-fixed/limits.h:34,
from /usr/include/arm-linux-gnueabihf/zconf.h:395,
from /usr/include/zlib.h:34,
from samtools/bam_import.c:3:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/sam.c -o samtools/sam.o
In file included from /usr/include/string.h:25:0,
from samtools/sam.c:3:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam_index.c -o samtools/bam_index.o
samtools/bam_index.c: In function 'bam_index_load_core':
samtools/bam_index.c:335:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(magic, 1, 4, fp);
^~~~~~~~~~~~~~~~~~~~~~
samtools/bam_index.c:342:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&idx->n, 4, 1, fp);
^~~~~~~~~~~~~~~~~~~~~~~~
samtools/bam_index.c:355:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&size, 4, 1, fp);
^~~~~~~~~~~~~~~~~~~~~~
samtools/bam_index.c:358:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&key, 4, 1, fp);
^~~~~~~~~~~~~~~~~~~~~
samtools/bam_index.c:362:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&p->n, 4, 1, fp);
^~~~~~~~~~~~~~~~~~~~~~
samtools/bam_index.c:366:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(p->list, 16, p->n, fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
samtools/bam_index.c:376:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&index2->n, 4, 1, fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
samtools/bam_index.c:380:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(index2->offset, index2->n, 8, fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam_pileup.c -o samtools/bam_pileup.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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam_lpileup.c -o samtools/bam_lpileup.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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam_md.c -o samtools/bam_md.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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/razf.c -o samtools/razf.o
samtools/razf.c: In function 'razf_flush':
samtools/razf.c:221:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samtools/razf.c:234:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samtools/razf.c: In function '_razf_write':
samtools/razf.c:201:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samtools/razf.c: In function 'razf_close':
samtools/razf.c:810:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->x.fpw, &rz->in, sizeof(int64_t));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samtools/razf.c:811:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->x.fpw, &rz->out, sizeof(int64_t));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samtools/razf.c:814:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->x.fpw, &v64, sizeof(int64_t));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samtools/razf.c:816:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->x.fpw, &v64, sizeof(int64_t));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samtools/razf.c: In function 'razf_end_flush':
samtools/razf.c:258:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samtools/razf.c: In function 'save_zindex':
samtools/razf.c:96:12: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
if(is_be) write(fd, &rz->index->size, sizeof(int));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samtools/razf.c:99:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(fd, &v32, sizeof(uint32_t));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samtools/razf.c:106:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samtools/razf.c:107:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/faidx.c -o samtools/faidx.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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/knetfile.c -o samtools/knetfile.o
In file included from /usr/include/time.h:27:0,
from samtools/knetfile.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from samtools/knetfile.c:49:0:
samtools/knetfile.c: In function 'kftp_send_cmd':
samtools/knetfile.h:9:32: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
#define netwrite(fd, ptr, len) write(fd, ptr, len)
^~~~~~~~~~~~~~~~~~~
samtools/knetfile.c:239:2: note: in expansion of macro 'netwrite'
netwrite(ftp->ctrl_fd, cmd, strlen(cmd));
^~~~~~~~
samtools/knetfile.c: In function 'khttp_connect_file':
samtools/knetfile.h:9:32: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
#define netwrite(fd, ptr, len) write(fd, ptr, len)
^~~~~~~~~~~~~~~~~~~
samtools/knetfile.c:418:2: note: in expansion of macro 'netwrite'
netwrite(fp->fd, buf, l);
^~~~~~~~
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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam_sort.c -o samtools/bam_sort.o
In file included from /usr/include/stdlib.h:24:0,
from samtools/bam_sort.c:3:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/sam_header.c -o samtools/sam_header.o
In file included from /usr/include/stdio.h:27:0,
from samtools/sam_header.c:3:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bam_reheader.c -o samtools/bam_reheader.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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/kprobaln.c -o samtools/kprobaln.o
ar -crus libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/razf.o samtools/faidx.o samtools/knetfile.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools_patch.o
ar: `u' modifier ignored since `D' is the default (see `U')
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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
In file included from /usr/include/limits.h:25:0,
from /usr/lib/gcc/arm-linux-gnueabihf/6/include-fixed/limits.h:168,
from /usr/lib/gcc/arm-linux-gnueabihf/6/include-fixed/syslimits.h:7,
from /usr/lib/gcc/arm-linux-gnueabihf/6/include-fixed/limits.h:34,
from /usr/include/arm-linux-gnueabihf/zconf.h:395,
from /usr/include/zlib.h:34,
from samtools/bcftools/vcf.c:3:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
In file included from /usr/include/alloca.h:21:0,
from samtools/bcftools/bcfutils.c:3:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/index.c -o samtools/bcftools/index.o
In file included from /usr/include/assert.h:35:0,
from samtools/bcftools/index.c:2:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/fet.c -o samtools/bcftools/fet.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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o
ar -crus libbcf.a samtools/bcftools/bcf.o samtools/bcftools/vcf.o samtools/bcftools/bcfutils.o samtools/bcftools/prob1.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o
ar: `u' modifier ignored since `D' is the default (see `U')
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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tabix/index.c -o tabix/index.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" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tabix/bedidx.c -o tabix/bedidx.o
ar -crus libtabix.a samtools/bgzf.o samtools/kstring.o samtools/knetfile.o tabix/index.o tabix/bedidx.o samtools_patch.o
ar: `u' modifier ignored since `D' is the default (see `U')
mkdir -p "/<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/samtools/bcftools"
mkdir -p "/<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/tabix"
cp samtools/*.h "/<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "/<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "/<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/tabix/"
cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
"/<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/tabix/"
mkdir -p "/<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib"
cp libbam.a libbcf.a libtabix.a "/<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib"
g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -o Rsamtools.so Biostrings_stubs.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam_data.o bam_mate_iter.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o -pthread -fopenmp /<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib/libbam.a /<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib/libbcf.a /<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib/libtabix.a -lz -L/usr/lib/R/lib -lR
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
installing to /<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/libs
** R
** inst
** preparing package for lazy loading
Warning: multiple methods tables found for 'which.max'
Warning: multiple methods tables found for 'which.min'
Warning: multiple methods tables found for 'which'
Warning: replacing previous import 'BiocGenerics::which' by 'IRanges::which' when loading 'GenomeInfoDb'
Warning: replacing previous import 'BiocGenerics::which.min' by 'IRanges::which.min' when loading 'GenomeInfoDb'
Warning: replacing previous import 'BiocGenerics::which.max' by 'IRanges::which.max' when loading 'GenomeInfoDb'
Warning: replacing previous import 'BiocGenerics::which' by 'IRanges::which' when loading 'GenomicRanges'
Warning: replacing previous import 'BiocGenerics::which.min' by 'IRanges::which.min' when loading 'GenomicRanges'
Warning: replacing previous import 'BiocGenerics::which.max' by 'IRanges::which.max' when loading 'GenomicRanges'
Warning: replacing previous import 'BiocGenerics::which' by 'IRanges::which' when loading 'XVector'
Warning: replacing previous import 'BiocGenerics::which.min' by 'IRanges::which.min' when loading 'XVector'
Warning: replacing previous import 'BiocGenerics::which.max' by 'IRanges::which.max' when loading 'XVector'
Warning: replacing previous import 'BiocGenerics::which' by 'IRanges::which' when loading 'Biostrings'
Warning: replacing previous import 'BiocGenerics::which.min' by 'IRanges::which.min' when loading 'Biostrings'
Warning: replacing previous import 'BiocGenerics::which.max' by 'IRanges::which.max' when loading 'Biostrings'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: multiple methods tables found for 'which.max'
Warning: multiple methods tables found for 'which.min'
Warning: multiple methods tables found for 'which'
Warning: replacing previous import 'BiocGenerics::which' by 'IRanges::which' when loading 'GenomeInfoDb'
Warning: replacing previous import 'BiocGenerics::which.min' by 'IRanges::which.min' when loading 'GenomeInfoDb'
Warning: replacing previous import 'BiocGenerics::which.max' by 'IRanges::which.max' when loading 'GenomeInfoDb'
Warning: replacing previous import 'BiocGenerics::which' by 'IRanges::which' when loading 'GenomicRanges'
Warning: replacing previous import 'BiocGenerics::which.min' by 'IRanges::which.min' when loading 'GenomicRanges'
Warning: replacing previous import 'BiocGenerics::which.max' by 'IRanges::which.max' when loading 'GenomicRanges'
Warning: replacing previous import 'BiocGenerics::which' by 'IRanges::which' when loading 'XVector'
Warning: replacing previous import 'BiocGenerics::which.min' by 'IRanges::which.min' when loading 'XVector'
Warning: replacing previous import 'BiocGenerics::which.max' by 'IRanges::which.max' when loading 'XVector'
Warning: replacing previous import 'BiocGenerics::which' by 'IRanges::which' when loading 'Biostrings'
Warning: replacing previous import 'BiocGenerics::which.min' by 'IRanges::which.min' when loading 'Biostrings'
Warning: replacing previous import 'BiocGenerics::which.max' by 'IRanges::which.max' when loading 'Biostrings'
* DONE (Rsamtools)
rm -f /<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/LICENSE
I: Using r-bioc-genomeinfodb for Depends:GenomeInfoDb (>= 1.1.3)
I: Using r-bioc-genomicranges for Depends:GenomicRanges (>= 1.21.6)
I: Using r-bioc-biostrings for Depends:Biostrings (>= 2.37.1)
I: Using r-bioc-genomicalignments for Suggests:GenomicAlignments
I: Using r-bioc-shortread for Suggests:ShortRead (>= 1.19.10)
I: Using r-bioc-genomicfeatures for Suggests:GenomicFeatures
W: Cannot find a debian package for Suggests:TxDb.Dmelanogaster.UCSC.dm3.ensGene
W: Cannot find a debian package for Suggests:KEGG.db
W: Cannot find a debian package for Suggests:TxDb.Hsapiens.UCSC.hg18.knownGene
W: Cannot find a debian package for Suggests:RNAseqData.HNRNPC.bam.chr14
W: Cannot find a debian package for Suggests:BSgenome.Hsapiens.UCSC.hg19
W: Cannot find a debian package for Suggests:pasillaBamSubset
I: Using r-cran-runit for Suggests:RUnit
W: Cannot find a debian package for Suggests:BiocStyle
I: Using r-bioc-biocgenerics for Imports:BiocGenerics (>= 0.1.3)
I: Using r-bioc-s4vectors for Imports:S4Vectors (>= 0.7.11)
I: Using r-bioc-iranges for Imports:IRanges (>= 2.3.7)
I: Using r-bioc-xvector for Imports:XVector (>= 0.9.1)
I: Using r-cran-bitops for Imports:bitops
I: Using r-bioc-biocparallel for Imports:BiocParallel
dh_install -a -O--buildsystem=R
dh_installdocs -a -O--buildsystem=R
dh_installchangelogs -a -O--buildsystem=R
dh_installexamples -a -O--buildsystem=R
dh_installman -a -O--buildsystem=R
dh_installcatalogs -a -O--buildsystem=R
dh_installcron -a -O--buildsystem=R
dh_installdebconf -a -O--buildsystem=R
dh_installemacsen -a -O--buildsystem=R
dh_installifupdown -a -O--buildsystem=R
dh_installinfo -a -O--buildsystem=R
dh_installinit -a -O--buildsystem=R
dh_installmenu -a -O--buildsystem=R
dh_installmime -a -O--buildsystem=R
dh_installmodules -a -O--buildsystem=R
dh_installlogcheck -a -O--buildsystem=R
dh_installlogrotate -a -O--buildsystem=R
dh_installpam -a -O--buildsystem=R
dh_installppp -a -O--buildsystem=R
dh_installudev -a -O--buildsystem=R
dh_installgsettings -a -O--buildsystem=R
dh_bugfiles -a -O--buildsystem=R
dh_ucf -a -O--buildsystem=R
dh_lintian -a -O--buildsystem=R
dh_gconf -a -O--buildsystem=R
dh_icons -a -O--buildsystem=R
dh_perl -a -O--buildsystem=R
dh_usrlocal -a -O--buildsystem=R
dh_link -a -O--buildsystem=R
dh_installwm -a -O--buildsystem=R
dh_installxfonts -a -O--buildsystem=R
dh_strip_nondeterminism -a -O--buildsystem=R
dh_compress -a -O--buildsystem=R
dh_fixperms -a -O--buildsystem=R
dh_strip -a -O--buildsystem=R
dh_makeshlibs -a -O--buildsystem=R
dh_shlibdeps -a -O--buildsystem=R
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/libs/Rsamtools.so was not linked against libgomp.so.1 (it uses none of the library's symbols)
dh_installdeb -a -O--buildsystem=R
dh_gencontrol -a -O--buildsystem=R
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a -O--buildsystem=R
dh_builddeb -a -O--buildsystem=R
dpkg-deb: building package 'r-bioc-rsamtools-dbgsym' in '../r-bioc-rsamtools-dbgsym_1.26.1-1_armhf.deb'.
dpkg-deb: building package 'r-bioc-rsamtools' in '../r-bioc-rsamtools_1.26.1-1_armhf.deb'.
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../r-bioc-rsamtools_1.26.1-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build r-bioc-rsamtools-1.26.1
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2016-11-01T13:18:26Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
r-bioc-rsamtools_1.26.1-1_armhf.changes:
----------------------------------------
Format: 1.8
Date: Wed, 26 Oct 2016 17:15:09 +0200
Source: r-bioc-rsamtools
Binary: r-bioc-rsamtools
Architecture: armhf
Version: 1.26.1-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
r-bioc-rsamtools - GNU R binary alignment (BAM), variant call (BCF), or tabix file i
Changes:
r-bioc-rsamtools (1.26.1-1) unstable; urgency=medium
.
* New upstream version
* Convert to dh-r
* Generic BioConductor homepage
Checksums-Sha1:
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9fc9f5b4922051bf4685ee3f47c24a2d5efba8cd 3196010 r-bioc-rsamtools_1.26.1-1_armhf.deb
Checksums-Sha256:
91c0d3cc5b38fdf6f35a3ac473311a8719d89d2d88d7d6188ff51c45d9147e3e 816488 r-bioc-rsamtools-dbgsym_1.26.1-1_armhf.deb
8c374978863c8dd5a5561b097beae5b4531c5d7755b8a59b11ddd6bddaa45db7 3196010 r-bioc-rsamtools_1.26.1-1_armhf.deb
Files:
1a006f00da73aa32a567a6b50bf447ab 816488 debug extra r-bioc-rsamtools-dbgsym_1.26.1-1_armhf.deb
b2bdc62e5e140e5cc44bf453a95f463f 3196010 gnu-r optional r-bioc-rsamtools_1.26.1-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
r-bioc-rsamtools-dbgsym_1.26.1-1_armhf.deb
------------------------------------------
new debian package, version 2.0.
size 816488 bytes: control archive=495 bytes.
460 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: r-bioc-rsamtools-dbgsym
Source: r-bioc-rsamtools
Version: 1.26.1-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 862
Depends: r-bioc-rsamtools (= 1.26.1-1)
Section: debug
Priority: extra
Homepage: https://bioconductor.org/packages/Rsamtools/
Description: Debug symbols for r-bioc-rsamtools
Auto-Built-Package: debug-symbols
Build-Ids: 6e6a1c057a98ec6cc7f38e0754202b7e1f3d05ff
drwxr-xr-x root/root 0 2016-10-26 15:15 ./
drwxr-xr-x root/root 0 2016-10-26 15:15 ./usr/
drwxr-xr-x root/root 0 2016-10-26 15:15 ./usr/lib/
drwxr-xr-x root/root 0 2016-10-26 15:15 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-10-26 15:15 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-10-26 15:15 ./usr/lib/debug/.build-id/6e/
-rw-r--r-- root/root 872108 2016-10-26 15:15 ./usr/lib/debug/.build-id/6e/6a1c057a98ec6cc7f38e0754202b7e1f3d05ff.debug
drwxr-xr-x root/root 0 2016-10-26 15:15 ./usr/share/
drwxr-xr-x root/root 0 2016-10-26 15:15 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-10-26 15:15 ./usr/share/doc/r-bioc-rsamtools-dbgsym -> r-bioc-rsamtools
r-bioc-rsamtools_1.26.1-1_armhf.deb
-----------------------------------
new debian package, version 2.0.
size 3196010 bytes: control archive=4606 bytes.
1069 bytes, 15 lines control
12078 bytes, 132 lines md5sums
Package: r-bioc-rsamtools
Version: 1.26.1-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5044
Depends: r-base-core (>= 3.3.1.20161024-1), r-api-3, r-bioc-genomeinfodb (>= 1.1.3), r-bioc-genomicranges (>= 1.21.6), r-bioc-biostrings (>= 2.37.1), r-bioc-biocgenerics (>= 0.1.3), r-bioc-s4vectors (>= 0.7.11), r-bioc-iranges (>= 2.3.7), r-bioc-xvector (>= 0.9.1), r-cran-bitops, r-bioc-biocparallel, libc6 (>= 2.15), libgcc1 (>= 1:3.5), libgomp1 (>= 4.2.1), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.3.3)
Suggests: r-bioc-genomicalignments, r-bioc-shortread (>= 1.19.10), r-bioc-genomicfeatures, r-cran-runit
Section: gnu-r
Priority: optional
Homepage: https://bioconductor.org/packages/Rsamtools/
Description: GNU R binary alignment (BAM), variant call (BCF), or tabix file import
This package provides an interface to the 'samtools', 'bcftools', and
'tabix' utilities for manipulating SAM (Sequence Alignment / Map),
binary variant call (BCF) and compressed indexed tab-delimited (tabix)
files.
drwxr-xr-x root/root 0 2016-10-26 15:15 ./
drwxr-xr-x root/root 0 2016-10-26 15:15 ./usr/
drwxr-xr-x root/root 0 2016-10-26 15:15 ./usr/lib/
drwxr-xr-x root/root 0 2016-10-26 15:15 ./usr/lib/R/
drwxr-xr-x root/root 0 2016-10-26 15:15 ./usr/lib/R/site-library/
drwxr-xr-x root/root 0 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/
-rw-r--r-- root/root 1558 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/DESCRIPTION
-rw-r--r-- root/root 2136 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/INDEX
drwxr-xr-x root/root 0 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/Meta/
-rw-r--r-- root/root 3140 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/Meta/Rd.rds
-rw-r--r-- root/root 3271 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/Meta/hsearch.rds
-rw-r--r-- root/root 2388 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/Meta/links.rds
-rw-r--r-- root/root 765 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/Meta/nsInfo.rds
-rw-r--r-- root/root 1569 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/Meta/package.rds
-rw-r--r-- root/root 284 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/Meta/vignette.rds
-rw-r--r-- root/root 1407 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/NAMESPACE
-rw-r--r-- root/root 13411 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/NEWS
drwxr-xr-x root/root 0 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/R/
-rw-r--r-- root/root 1056 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/R/Rsamtools
-rw-r--r-- root/root 393177 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/R/Rsamtools.rdb
-rw-r--r-- root/root 6332 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/R/Rsamtools.rdx
drwxr-xr-x root/root 0 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/doc/
-rw-r--r-- root/root 9645 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-Overview.R
-rw-r--r-- root/root 19842 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-Overview.Rnw
-rw-r--r-- root/root 140755 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-Overview.pdf
-rw-r--r-- root/root 221 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-UsingCLibraries.R
-rw-r--r-- root/root 3843 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-UsingCLibraries.Rnw
-rw-r--r-- root/root 85416 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-UsingCLibraries.pdf
-rw-r--r-- root/root 1976 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/doc/index.html
drwxr-xr-x root/root 0 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/
-rw-r--r-- root/root 176 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/ce2dict1.fa
-rw-r--r-- root/root 112 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/ce2dict1.fa.fai
-rw-r--r-- root/root 126539 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bam
-rw-r--r-- root/root 176 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bam.bai
-rw-r--r-- root/root 74700 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bcf
-rw-r--r-- root/root 77 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bcf.bci
-rw-r--r-- root/root 559422 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.sam
-rw-r--r-- root/root 3778 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/example.gtf.gz
-rw-r--r-- root/root 259 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/example.gtf.gz.tbi
-rw-r--r-- root/root 348 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/example_from_SAM_Spec.bam
-rw-r--r-- root/root 96 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/example_from_SAM_Spec.bam.bai
-rw-r--r-- root/root 368 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/example_from_SAM_Spec.sam
-rw-r--r-- root/root 203 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_buffered_pileup.bam
-rw-r--r-- root/root 176 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_buffered_pileup.bam.bai
-rw-r--r-- root/root 240 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_buffered_pileup.sam
-rw-r--r-- root/root 198 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_whole_file.bam
-rw-r--r-- root/root 176 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_whole_file.bam.bai
-rw-r--r-- root/root 168 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_whole_file.sam
-rw-r--r-- root/root 1663363 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/olaps.Rda
-rw-r--r-- root/root 138598 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/pileup.txt
-rw-r--r-- root/root 181 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/querybins.bam
-rw-r--r-- root/root 96 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/querybins.bam.bai
-rw-r--r-- root/root 117 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/querybins.sam
-rw-r--r-- root/root 381 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/revbins.bam
-rw-r--r-- root/root 416 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/revbins.bam.bai
-rw-r--r-- root/root 770 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/revbins.sam
-rw-r--r-- root/root 31 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/samtools-github.txt
-rw-r--r-- root/root 2808 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/slxMaq09_urls.txt
-rw-r--r-- root/root 333 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/tagfilter.bam
-rw-r--r-- root/root 656 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/tagfilter.bam.bai
-rw-r--r-- root/root 804 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/tagfilter.sam
-rw-r--r-- root/root 1167 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/tiny.bam
-rw-r--r-- root/root 2336 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/tiny.bam.bai
-rw-r--r-- root/root 4102 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/tiny.sam
drwxr-xr-x root/root 0 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/
-rw-r--r-- root/root 36 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/README
-rw-r--r-- root/root 36039 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/accepted_hits.sam
-rw-r--r-- root/root 4381 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/coverage.wig
-rw-r--r-- root/root 196 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/junctions.bed
drwxr-xr-x root/root 0 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/help/
-rw-r--r-- root/root 11103 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/help/AnIndex
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-rw-r--r-- root/root 369 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/help/paths.rds
drwxr-xr-x root/root 0 2016-10-26 15:15 ./usr/lib/R/site-library/Rsamtools/html/
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Build Architecture: armhf
Build-Space: 17816
Build-Time: 362
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 801
Job: r-bioc-rsamtools_1.26.1-1
Machine Architecture: armhf
Package: r-bioc-rsamtools
Package-Time: 1215
Source-Version: 1.26.1-1
Space: 17816
Status: successful
Version: 1.26.1-1
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Finished at 2016-11-01T13:18:26Z
Build needed 00:20:15, 17816k disc space