[BioC] Problem installing Rsamtools and ShortRead under Fedora 10.

[Bernt Guldbrandtsen]

Dear bioconductor,
 
After installing R-2.12.0 I tried to install a number of packages. Two Bioconductor appear to have problems.
 
The installation of Rsamtools dies with the error:

biocLite("Rsamtools")
...
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/opt/ghpc/R-2.12.0/lib64/R/library/Rsamtools/libs/Rsamtools.so':
  /opt/ghpc/R-2.12.0/lib64/R/library/Rsamtools/libs/Rsamtools.so: undefined symbol: new_XStringSet
ERROR: loading failed

The installation of ShortRead dies with the error:

biocLite("ShortRead")
...
g++ -I/opt/ghpc/R-2.12.0/lib64/R/include  "-I/opt/ghpc/include" -I"/opt/ghpc/R-2.12.0/lib64/R/library/IRanges/include" -I"/opt/ghpc/R-2.12.0/lib64/R/library/Biostrings/include"  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -DHAVE_LIBZ=1 -fpic  -g -O2 -c readBfaToc.cc -o readBfaToc.o
readBfaToc.cc: In function 'SEXPREC* readBfaToc(SEXPREC*)':
readBfaToc.cc:28: error: 'errno' was not declared in this scope
make: *** [readBfaToc.o] Error 1
ERROR: compilation failed for package 'ShortRead'

If I include errno.h in readBfaToc.cc then I subsequently get errors:

g++ -I/opt/ghpc/R-2.12.0/lib64/R/include  "-I/opt/ghpc/include" -I"/opt/ghpc/R-2.12.0/lib64/R/library/IRanges/include" -I"/opt/ghpc/R-2.12.0/lib64/R/library/Biostrings/include"  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -DHAVE_LIBZ=1 -fpic  -g -O2 -c read_maq_map.cc -o read_maq_map.o
read_maq_map.cc: In function 'SEXPREC* read_maq_map_B(SEXPREC*, SEXPREC*)':
read_maq_map.cc:52: error: 'errno' was not declared in this scope
read_maq_map.cc:149: error: there are no arguments to 'new_RoSeqs_from_CharAEAE' that depend on a template parameter, so a declaration of 'new_RoSeqs_from_CharAEAE' must be available
read_maq_map.cc:149: error: (if you use '-fpermissive', G++ will accept your code, but allowing the use of an undeclared name is deprecated)
read_maq_map.cc:150: error: there are no arguments to 'new_XStringSet_from_RoSeqs' that depend on a template parameter, so a declaration of 'new_XStringSet_from_RoSeqs' must be available
read_maq_map.cc:151: error: there are no arguments to 'new_RoSeqs_from_CharAEAE' that depend on a template parameter, so a declaration of 'new_RoSeqs_from_CharAEAE' must be available
read_maq_map.cc:152: error: there are no arguments to 'new_XStringSet_from_RoSeqs' that depend on a template parameter, so a declaration of 'new_XStringSet_from_RoSeqs' must be available
read_maq_map.cc:153: error: there are no arguments to 'new_RoSeqs_from_CharAEAE' that depend on a template parameter, so a declaration of 'new_RoSeqs_from_CharAEAE' must be available
read_maq_map.cc:154: error: there are no arguments to 'new_XStringSet_from_RoSeqs' that depend on a template parameter, so a declaration of 'new_XStringSet_from_RoSeqs' must be available
read_maq_map.cc: In function 'SEXPREC* read_maq_map_B(SEXPREC*, SEXPREC*) [with int max_readlen = 128]':
read_maq_map.cc:178:   instantiated from here
read_maq_map.cc:149: error: 'new_RoSeqs_from_CharAEAE' was not declared in this scope
read_maq_map.cc:150: error: 'new_XStringSet_from_RoSeqs' was not declared in this scope
read_maq_map.cc: In function 'SEXPREC* read_maq_map_B(SEXPREC*, SEXPREC*) [with int max_readlen = 64]':
read_maq_map.cc:180:   instantiated from here
read_maq_map.cc:149: error: 'new_RoSeqs_from_CharAEAE' was not declared in this scope
read_maq_map.cc:150: error: 'new_XStringSet_from_RoSeqs' was not declared in this scope
make: *** [read_maq_map.o] Error 1
ERROR: compilation failed for package 'ShortRead'

The packages compiled without problems under R-2.11.0. The packages when copied over to R-2.12.0 from our R-2.11.0 installation appear to load without problems. 

FYI:

> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US       LC_NUMERIC=C         LC_TIME=en_US
 [4] LC_COLLATE=en_US     LC_MONETARY=C        LC_MESSAGES=en_US
 [7] LC_PAPER=en_US       LC_NAME=C            LC_ADDRESS=C
[10] LC_TELEPHONE=C       LC_MEASUREMENT=en_US LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base 

I hope someone out there knows a solution.

Best regards,

Bernt Guldbrandtsen