[BioC] Where can i find/install package -"BSgenome.Mmusculus.UCSC.mm9" in BSgenome

[Hervé Pagès]

Hi Xiaojiang,

On 02/24/2011 06:32 AM, XIAOJIANG XU wrote:
> Hi Herve,
>     I try to install package "BSgenome.Mmusculus.UCSC.mm9", but BSgenome
> show me that it is not available. It's in the previous version. Do you
> know why? How can I install it? Thanks.

This is better asked on the mailing list (cc'ed). I get this on a fresh
R session:

 > library(BSgenome)
 > grep("Mmusculus", available.genomes(type="source"), value=TRUE)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
[1] "BSgenome.Mmusculus.UCSC.mm8" "BSgenome.Mmusculus.UCSC.mm9"

with both BioC-2.7/R-2.12 (current release) and BioC-2.8/R-2.13 (current
devel), so at least the source packages are available.

However, if you are on Mac, the situation seems to be a little bit more
complicated and confusing. If I remember correctly, it was decided
that, starting with BioC-2.7/R-2.12, the project would drop support for
Tiger (i.e. stop building binaries on a Tiger machine). This was just
following CRAN's authority on that matter, which dropped support for
Tiger starting with R-2.12. The consequence of this is that, if you
try to get the list of packages that are available on CRAN for Tiger,
it works with R < 2.12:

   > nrow(available.packages(type="mac.binary"))
   [1] 2240

but not with R >= 2.12:

   > nrow(available.packages(type="mac.binary"))
   Warning: unable to access index for repository 
http://cran.fhcrc.org/bin/macosx/universal/contrib/2.12
   [1] 0

Now available.genomes() should give something consistent with this but
it doesn't. With R 2.11:

   > library(BSgenome)
   > available.genomes(type="mac.binary")
   BioC_mirror = http://www.bioconductor.org
   Change using chooseBioCmirror().
   Warning: unable to access index for repository 
http://www.bioconductor.org/packages/2.6/data/annotation/bin/macosx/universal/contrib/2.11
   character(0)

And it seems that I get this problem whatever version of BioC/R I use
(I tried with 2.11, 2.12 and 2.13) when in fact, it should work
properly with R < 2.12 :-/
So I'll need to check on our end what is going on.

Now if you are on Leopard (or Snow Leopard), things look good with
BioC devel:

   > grep("Mmusculus", available.genomes(type="mac.binary.leopard"), 
value=TRUE)
   BioC_mirror = http://www.bioconductor.org
   Change using chooseBioCmirror().
   [1] "BSgenome.Mmusculus.UCSC.mm8" "BSgenome.Mmusculus.UCSC.mm9"

and they don't look too bad with BioC release:

   > grep("Mmusculus", available.genomes(type="mac.binary.leopard"), 
value=TRUE)
   BioC_mirror = http://www.bioconductor.org
   Change using chooseBioCmirror().
   [1] "BSgenome.Mmusculus.UCSC.mm8"

except that, as you can see, mm9 is missing. I will also need to check
this on our end.

In the mean time, if your machine is set up to install packages from
source, you can still use 'type="source"' in available.packages(),
available.genomes() and biocLite(). Sorry for the inconvenience.

We'll post again here when we have an update on the 2 issues spotted
above.

H.


-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024

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