[Debian-med-packaging] Bug#730592: r-bioc-biostrings: FTBFS: error: unknown type name 'cachedCharSeq'

[Roland Stigge]

Package: r-bioc-biostrings
Version: 2.28.0-1
Severity: serious

Hi,

r-bioc-biostrings 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 BAB_class.c -o BAB_class.o
In file included from Biostrings.h:1:0,
                 from BAB_class.c:5:
../inst/include/Biostrings_defines.h:50:2: error: unknown type name 'cachedCharSeq'
../inst/include/Biostrings_defines.h:59:1: error: unknown type name 'cachedXVectorList'
In file included from BAB_class.c:5:0:
Biostrings.h:32:2: error: unknown type name 'cachedCharSeq'
Biostrings.h:51:2: error: unknown type name 'cachedCharSeq'
Biostrings.h:56:2: error: unknown type name 'cachedCharSeq'
Biostrings.h:104:2: error: unknown type name 'cachedCharSeq'
Biostrings.h:112:2: error: unknown type name 'cachedCharSeq'
Biostrings.h:144:1: error: unknown type name 'cachedCharSeq'
Biostrings.h:514:2: error: unknown type name 'cachedCharSeq'
Biostrings.h:515:2: error: unknown type name 'cachedCharSeq'
Biostrings.h:526:2: error: unknown type name 'cachedCharSeq'
Biostrings.h:527:2: error: unknown type name 'cachedCharSeq'
Biostrings.h:535:2: error: unknown type name 'cachedCharSeq'
Biostrings.h:536:2: error: unknown type name 'cachedCharSeq'
Biostrings.h:577:2: error: unknown type name 'cachedCharSeq'
Biostrings.h:578:2: error: unknown type name 'cachedCharSeq'
Biostrings.h:591:2: error: unknown type name 'cachedCharSeq'
Biostrings.h:592:2: error: unknown type name 'cachedCharSeq'
Biostrings.h:604:2: error: unknown type name 'cachedCharSeq'
Biostrings.h:605:2: error: unknown type name 'cachedCharSeq'
Biostrings.h:617:2: error: unknown type name 'cachedCharSeq'
Biostrings.h:618:2: error: unknown type name 'cachedCharSeq'
Biostrings.h:627:2: error: unknown type name 'cachedCharSeq'
Biostrings.h:628:2: error: unknown type name 'cachedCharSeq'
Biostrings.h:947:2: error: unknown type name 'cachedCharSeq'
Biostrings.h:958:2: error: unknown type name 'cachedCharSeq'
Biostrings.h:977:2: error: unknown type name 'cachedCharSeq'
Biostrings.h:1029:2: error: unknown type name 'cachedCharSeq'
Biostrings.h:1037:2: error: unknown type name 'cachedCharSeq'
make[1]: *** [BAB_class.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 'Biostrings'
* removing '/«PKGBUILDDIR»/debian/r-bioc-biostrings/usr/lib/R/site-library/Biostrings'
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)

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