[BioC] ERROR: compilation failed for package XVector

[Pengcheng Yang]

Hi Herve,

I did have tested using biocLite() method to install XVector. Here is 
the message:


======================================
 > biocLite("XVector")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.12 (BiocInstaller 1.10.2), R version 3.0.0.
Installing package(s) 'XVector'
Warning message:
package ‘XVector’ is not available (for R version 3.0.0)
======================================

Best,
Pengcheng

On 2013/7/23 10:48, Hervé Pagès wrote:
> Hi Yang,
>
> XVector only exists in Bioc-devel (BioC 2.13) and you're trying
> to install it with Bioc-release (Bioc 2.12). Mixing packages from
> release and devel is generally a bad thing and can easily be avoided
> by installing packages with biocLite(), as explained on our website.
>
> Cheers,
> H.
>
>
> On 07/22/2013 06:30 PM, Pengcheng Yang wrote:
>> Hi all,
>>
>> *Here is the sessionInfo.*
>> ========================================================
>> > sessionInfo()
>> R version 3.0.0 (2013-04-03)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=C LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] parallel stats graphics grDevices utils datasets methods
>> [8] base
>>
>> other attached packages:
>> [1] Biobase_2.20.0 IRanges_1.18.0 BiocGenerics_0.6.0
>>
>> loaded via a namespace (and not attached):
>> [1] stats4_3.0.0
>>
>> =========================================================
>>
>> *And here is the error messages when installing XVector_0.1.0*
>> =====================================================
>> >
>> install.packages(repos=NULL,pkgs="R_package_archive/XVector_0.1.0.tar.gz") 
>>
>> * installing *source* package âEUR~XVectorâEUR^(TM) ...
>> ** libs
>> gcc -std=gnu99 -I/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/include
>> -DNDEBUG -I/usr/local/include
>> -I"/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/include" 
>>
>> -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
>> gcc -std=gnu99 -I/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/include
>> -DNDEBUG -I/usr/local/include
>> -I"/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/include" 
>>
>> -fpic -g -O2 -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
>> In file included from XVector.h:1,
>> from Ocopy_byteblocks.c:1:
>> ../inst/include/XVector_defines.h:24: error: redefinition of âEUR~struct
>> cached_charseqâEUR^(TM)
>> ../inst/include/XVector_defines.h:27: error: redefinition of typedef
>> âEUR~cachedCharSeqâEUR^(TM)
>> /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/include/IRanges_defines.h:115: 
>>
>> error: previous declaration of âEUR~cachedCharSeqâEUR^(TM) was here
>> ../inst/include/XVector_defines.h:29: error: redefinition of âEUR~struct
>> cached_intseqâEUR^(TM)
>> ../inst/include/XVector_defines.h:32: error: redefinition of typedef
>> âEUR~cachedIntSeqâEUR^(TM)
>> /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/include/IRanges_defines.h:120: 
>>
>> error: previous declaration of âEUR~cachedIntSeqâEUR^(TM) was here
>> ../inst/include/XVector_defines.h:34: error: redefinition of âEUR~struct
>> cached_doubleseqâEUR^(TM)
>> ../inst/include/XVector_defines.h:37: error: redefinition of typedef
>> âEUR~cachedDoubleSeqâEUR^(TM)
>> /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/include/IRanges_defines.h:125: 
>>
>> error: previous declaration of âEUR~cachedDoubleSeqâEUR^(TM) was here
>> ../inst/include/XVector_defines.h:39: error: redefinition of âEUR~struct
>> cached_xvectorlistâEUR^(TM)
>> ../inst/include/XVector_defines.h:47: error: redefinition of typedef
>> âEUR~cachedXVectorListâEUR^(TM)
>> /panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/IRanges/include/IRanges_defines.h:135: 
>>
>> error: previous declaration of âEUR~cachedXVectorListâEUR^(TM) was here
>> make: *** [Ocopy_byteblocks.o] Error 1
>> ERROR: compilation failed for package âEUR~XVectorâEUR^(TM)
>> * removing
>> âEUR~/panfs/home/kang/yangpc/soft/R/R-3.0.0/lib64/R/library/XVectorâEUR^(TM) 
>>
>> Warning message:
>> In install.packages(repos = NULL, pkgs =
>> "R_package_archive/XVector_0.1.0.tar.gz") :
>> installation of package
>> âEUR~R_package_archive/XVector_0.1.0.tar.gzâEUR^(TM) had non-zero exit
>> status
>> =======================================================
>>
>> Thank you in advance.
>>
>> Best,
>> Pengcheng Yang
>>
>> [[alternative HTML version deleted]]
>>
>>
>>
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>