[BioC] Problem installing Rsamtools and ShortRead under Fedora 10.
Martin Morgan
mtmorgan at fhcrc.org
Fri Oct 15 20:01:23 CEST 2010
On 10/15/2010 10:01 AM, Vincent Carey wrote:
> this looks like out-of-date Biostrings?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
There are suggestions for updating packages, relevant to a new release
of R, at
http://bioconductor.org/install/index.html#update-bioconductor-packages
Bioconductor is scheduled to release the version compatible with R 2-12
on Monday. Avoid needing to update packages twice by delaying your
update of R until then.
Martin
>
>> 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
>>
>> _______________________________________________
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>>
>
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