[BioC] ERROR: compilation failed for package XVector

[Hervé Pagès]

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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-- 
Hervé Pagès

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