[BioC] ERROR: compilation failed for package XVector

Wed Jul 24 07:48:52 CEST 2013

Hi Pengcheng,

On 07/23/2013 07:21 PM, Dan Tenenbaum wrote:
> 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 â€˜XVectorâ€™ 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/

That's if you really want to install the XVector package but why
you'd want to do that? I mean, this is an infrastructure package
that is new in Bioc-devel. You don't need it in Bioc-release (and
it's incompatible with Bioc-release anyway, as you've learned),
and you don't need to install it explicitly in Bioc-devel since
it will get automatically installed when you install other (more
useful) packages that depend on it.

H.

>
> 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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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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