Your message dated Sun, 01 Dec 2013 09:20:03 +0000
with message-id <e1vn3c7-0005se...@franck.debian.org>
and subject line Bug#730984: fixed in r-bioc-rsamtools 1.14.2-1
has caused the Debian Bug report #730984,
regarding r-bioc-rsamtools: FTBFS: fatal error: XVector_defines.h: No such file
or directory
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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immediately.)
--
730984: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=730984
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: r-bioc-rsamtools
Version: 1.12.4-1
Severity: serious
Hi,
r-bioc-rsamtools FTBFS like this:
...
dh_installdirs usr/lib/R/site-library
echo "R:Depends=r-base-core (>= 3.0.2-1)" >> debian/r-bioc-rsamtools.substvars
if test -f /usr/bin/xvfb-run; then \
xvfb-run -a \
R CMD INSTALL -l
/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library --clean \
. ; \
else \
R CMD INSTALL -l
/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library \
--clean . ;\
fi
* 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/Biostrings/include"
-I"/usr/lib/R/site-library/IRanges/include" -fopenmp -D_USE_KNETFILE
-D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf
-Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
-I./samtools/bcftools -I./tabix -fpic -O3 -pipe -g -c Biostrings_stubs.c -o
Biostrings_stubs.o
In file included from
/usr/lib/R/site-library/Biostrings/include/Biostrings_interface.h:114:0,
from
/usr/lib/R/site-library/Biostrings/include/_Biostrings_stubs.c:1,
from Biostrings_stubs.c:1:
/usr/lib/R/site-library/Biostrings/include/Biostrings_defines.h:19:29: fatal
error: XVector_defines.h: No such file or directory
compilation terminated.
make[1]: *** [Biostrings_stubs.o] Error 1
make[1]: Leaving directory `/«PKGBUILDDIR»/src'
make[1]: Entering directory `/«PKGBUILDDIR»/src'
make[1]: Leaving directory `/«PKGBUILDDIR»/src'
ERROR: compilation failed for package 'Rsamtools'
* removing
'/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools'
make: *** [R_any_arch] Error 1
...
Roland
-- System Information:
Debian Release: 7.0
APT prefers unreleased
APT policy: (500, 'unreleased'), (500, 'unstable')
Architecture: powerpcspe (ppc)
Kernel: Linux 3.9.0-dirty (SMP w/2 CPU cores)
Locale: LANG=en_GB.UTF-8, LC_CTYPE=en_GB.UTF-8 (charmap=UTF-8) (ignored: LC_ALL
set to en_GB.UTF-8)
Shell: /bin/sh linked to /bin/dash
--- End Message ---
--- Begin Message ---
Source: r-bioc-rsamtools
Source-Version: 1.14.2-1
We believe that the bug you reported is fixed in the latest version of
r-bioc-rsamtools, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 730...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated r-bioc-rsamtools package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Format: 1.8
Date: Sun, 01 Dec 2013 09:45:58 +0100
Source: r-bioc-rsamtools
Binary: r-bioc-rsamtools
Architecture: source amd64
Version: 1.14.2-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
r-bioc-rsamtools - GNU R binary alignment (BAM), variant call (BCF), or tabix
file i
Closes: 730984
Changes:
r-bioc-rsamtools (1.14.2-1) unstable; urgency=low
.
* New upstream version (adapted patch)
Closes: #730984
* Build-Depends: r-bioc-xvector
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r-bioc-rsamtools_1.14.2.orig.tar.gz
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r-bioc-rsamtools_1.14.2-1.debian.tar.gz
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r-bioc-rsamtools_1.14.2-1_amd64.deb
Checksums-Sha256:
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r-bioc-rsamtools_1.14.2-1.dsc
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r-bioc-rsamtools_1.14.2.orig.tar.gz
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r-bioc-rsamtools_1.14.2-1.debian.tar.gz
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r-bioc-rsamtools_1.14.2-1_amd64.deb
Files:
593350f73a4d57386a0a3ec9faaad49d 1588 gnu-r optional
r-bioc-rsamtools_1.14.2-1.dsc
83aa5c41214583f83c86bcc90355d59e 2954830 gnu-r optional
r-bioc-rsamtools_1.14.2.orig.tar.gz
168279be05272a81bccbc9f1c49185a0 6548 gnu-r optional
r-bioc-rsamtools_1.14.2-1.debian.tar.gz
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r-bioc-rsamtools_1.14.2-1_amd64.deb
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--- End Message ---
