[BioC] BSgenome.Dmelanogaster.UCSC.dm3 package for R 3.0.0 beta?

[James W. MacDonald]

Hi Ying,

On 3/27/2013 2:49 PM, ying chen wrote:
> Hi guys, Is there a BSgenome.Dmelanogaster.UCSC.dm3 package for R 3.0.0 beta? I tried one under BioC devel (http://www.bioconductor.org/packages/2.12/data/annotation/html/BSgenome.Dmelanogaster.UCSC.dm3.html), but had no success.>  install.packages("BSgenome.Dmelanogaster.UCSC.dm3_1.3.19.tar.gz",repos="null",type="source")
> Warning: unable to access index for repository null/src/contrib
> Warning message:
> package ‘BSgenome.Dmelanogaster.UCSC.dm3_1.3.19.tar.gz’ is not available (for R version 3.0.0 beta)

You have found the correct package on the devel page, so I don't think 
your question is whether or not one exists. Instead, it appears you are 
wondering why it didn't install.

This is why we tell people (for example here: 
http://www.bioconductor.org/install/) to do something like

|source("http://bioconductor.org/biocLite.R")
biocLite("BSgenome.Dmelanogaster.UCSC.dm3")

|||

Because a) you don't have to go searching around for the right package 
and b) it just works.

So try installing the package the recommended way, and let us know if 
you have problems.

Best,

Jim


||

>> sessionInfo()
> R version 3.0.0 beta (2013-03-24 r62395)
> 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     loaded via a namespace (and not attached):
> [1] tools_3.0.0
> Thanks, Ying 		 	   		
> 	[[alternative HTML version deleted]]
>
>
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099