[BioC] gmapR for R 3.0.0 installation problem?

[Dan Tenenbaum]

On Wed, Apr 3, 2013 at 4:39 PM, ying chen <ying_chen at live.com> wrote:
>
> Hi guys, I tried to install gmapR in R3.0.0 in windows 7, but kept having troubles: > biocLite("gmapR")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.12 (BiocInstaller 1.9.11), R version 3.0.0.
> Installing package(s) 'gmapR'   package ‘gmapR’ is available as a source package but not as a binaryWarning message:
> package ‘gmapR’ is not available (for R version 3.0.0) >
>> biocLite("gmapR",type="source")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.12 (BiocInstaller 1.9.11), R version 3.0.0.
> Installing package(s) 'gmapR'
> trying URL 'http://bioconductor.org/packages/2.12/bioc/src/contrib/gmapR_1.1.16.tar.gz'
> Content type 'application/x-gzip' length 4473453 bytes (4.3 Mb)
> opened URL
> downloaded 4.3 Mb* installing *source* package 'gmapR' ...
> ** libs*** arch - i386
> ERROR: compilation failed for package 'gmapR'
> * removing 'C:/Program Files/R/R-3.0.0/library/gmapR'The downloaded source packages are in
>         ‘C:\Users\Administrator\AppData\Local\Temp\Rtmp2nMJFF\downloaded_packages’
> Warning messages:
> 1: running command '"C:/PROGRA~1/R/R-30~1.0/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.0.0\library" C:\Users\ADMINI~1\AppData\Local\Temp\Rtmp2nMJFF/downloaded_packages/gmapR_1.1.16.tar.gz' had status 1
> 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>   installation of package ‘gmapR’ had non-zero exit status
>>
>> install.packages("gmapR_1.1.16.tar.gz",repos=NULL,type="source")
> * installing *source* package 'gmapR' ...
> ** libs*** arch - i386
> ERROR: compilation failed for package 'gmapR'
> * removing 'C:/Program Files/R/R-3.0.0/library/gmapR'
> Warning messages:
> 1: running command '"C:/PROGRA~1/R/R-30~1.0/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.0.0\library" "gmapR_1.1.16.tar.gz"' had status 1
> 2: In install.packages("gmapR_1.1.16.tar.gz", repos = NULL, type = "source") :
>   installation of package ‘gmapR_1.1.16.tar.gz’ had non-zero exit status
> Does gmapR work in windows? Thanks, Ying

Unfortunately, no gmapR is not supported on Windows.

Dan


> sessionInfo()
> R version 3.0.0 (2013-04-03)
> Platform: x86_64-w64-mingw32/x64 (64-bit)locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252    attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     other attached packages:
> [1] BiocInstaller_1.9.11loaded via a namespace (and not attached):
> [1] tools_3.0.0
>>
>
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>
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