[Debian-med-packaging] Bug#730574: r-bioc-genomicranges: FTBFS: error: unknown type name 'cachedCharSeq'

[Roland Stigge]

Package: r-bioc-genomicranges
Version: 1.12.4-1
Severity: serious

Hi,

r-bioc-genomicranges FTBFS like this:

...
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/usr/lib/R/site-library/IRanges/include"   -fpic  -O3 -pipe  -g  -c transcript_utils.c -o transcript_utils.o
transcript_utils.c:146:1: error: unknown type name 'cachedCharSeq'
transcript_utils.c: In function 'copy_exon':
transcript_utils.c:154:3: warning: implicit declaration of function 'Orevcopy_bytes_from_i1i2_with_lkup' [-Wimplicit-function-declaration]
transcript_utils.c:156:6: error: request for member 'seq' in something not a structure or union
transcript_utils.c:156:15: error: request for member 'length' in something not a structure or union
transcript_utils.c:159:3: warning: implicit declaration of function 'Ocopy_bytes_from_i1i2_with_lkup' [-Wimplicit-function-declaration]
transcript_utils.c:161:6: error: request for member 'seq' in something not a structure or union
transcript_utils.c:161:15: error: request for member 'length' in something not a structure or union
transcript_utils.c: At top level:
transcript_utils.c:167:1: error: unknown type name 'cachedCharSeq'
transcript_utils.c: In function 'extract_transcripts':
transcript_utils.c:260:2: error: unknown type name 'cachedCharSeq'
transcript_utils.c:262:2: error: unknown type name 'cachedXVectorList'
transcript_utils.c:266:2: warning: implicit declaration of function 'cache_XRaw' [-Wimplicit-function-declaration]
transcript_utils.c:269:2: error: request for member 'length' in something not a structure or union
transcript_utils.c:271:2: warning: implicit declaration of function 'alloc_XRawList' [-Wimplicit-function-declaration]
transcript_utils.c:271:2: warning: assignment makes pointer from integer without a cast [enabled by default]
transcript_utils.c:273:2: warning: implicit declaration of function 'cache_XVectorList' [-Wimplicit-function-declaration]
transcript_utils.c:274:2: warning: implicit declaration of function 'get_cachedXVectorList_length' [-Wimplicit-function-declaration]
transcript_utils.c:285:3: warning: implicit declaration of function 'get_cachedXRawList_elt' [-Wimplicit-function-declaration]
transcript_utils.c:288:29: error: request for member 'seq' in something not a structure or union
make[1]: *** [transcript_utils.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 'GenomicRanges'
* removing '/«PKGBUILDDIR»/debian/r-bioc-genomicranges/usr/lib/R/site-library/GenomicRanges'
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