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

Sat Oct 16 13:20:28 CEST 2010

Thank you for responding.

Biostrings was compiled with R-2.12.0 moments before my attempt at compiling Rsamtools and ShortRead. The version of Biostrings is 2.17.48. Installation was done by biocLite().

My failed attempt of compiling and installing Rsamtools and ShortRead was part of an attempt at installing Bioconductor into a fresh installation of R-2.12.0.

A moment ago, when I did an update.packages() Bioconductor 2.7 installed. It installed without errors, I suppose mostly rendering the point of my previous message moot.

Best regards,

Bernt Guldbrandtsen

________________________________________
Fra: Martin Morgan [mtmorgan at fhcrc.org]
Sendt: 15. oktober 2010 20:01
Til: Vincent Carey
Cc: Bernt Guldbrandtsen; bioconductor at stat.math.ethz.ch
Emne: Re: [BioC] Problem installing Rsamtools and ShortRead under Fedora 10.

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 this looks like out-of-date Biostrings?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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>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>>
>
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