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

[Vincent Carey]

this looks like out-of-date Biostrings?  since you note an attempt to
copy packages between R 2.11 and R 2.12, i note
this is not advisable.  update.packages should be used.  i just did a
build/install from source via biocLite without difficulty.  but i just
noted that some of my packages (such as Biostrings) are themselves out
of date...  here is my sessionInfo subsequent to installing and
loading Rsamtools via biocLite

> sessionInfo()
R version 2.12.0 Patched (2010-10-15 r53329)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

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

other attached packages:
[1] Rsamtools_1.1.17     Biostrings_2.17.47   GenomicRanges_1.1.29
[4] IRanges_1.7.37

loaded via a namespace (and not attached):
[1] Biobase_2.9.2 tools_2.12.0


On Fri, Oct 15, 2010 at 12:02 PM, Bernt Guldbrandtsen
<Bernt.Guldbrandtsen at agrsci.dk> wrote:
> 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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>