[Debian-med-packaging] Bug#730984: r-bioc-rsamtools: FTBFS: fatal error: XVector_defines.h: No such file or directory

[Roland Stigge]

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