[BioC] ERROR: compilation failed for package XVector

[Dan Tenenbaum]

On Tue, Jul 23, 2013 at 6:44 PM, Pengcheng Yang <pengchy at gmail.com> wrote:
> 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)
> ======================================
>


Note that it says you are running Bioconductor 2.12. As Hervé
mentioned, you need to be running Bioconductor 2.13.

You can upgrade either by giving the
useDevel()
command, or setting up a separate installation of R and then running
useDevel() in that version of R.

Or you can follow the detailed instructions here:

http://bioconductor.org/developers/how-to/useDevel/

Dan



> 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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>>
>
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