[BioC] ERROR: compilation failed for package XVector
Pengcheng Yang
pengchy at gmail.com
Thu Jul 25 02:48:15 CEST 2013
Hi Herve,
Originally, I wanted to install spliceR, which depends on GenomicRanges,
then which depends on XVector. I have installed other depended packages
successfully by local methods. But not XVector. Thanks Herve, I have
installed XVector now, but haven't tested it.
Best,
Pengcheng
On 2013/7/24 13:48, Hervé Pagès wrote:
> 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 ‘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/
>
> 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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