[BioC] can't load affycoretools because GOstats is broken. Can I load affycoretools without dependencies to use some functions?

[James W. MacDonald]

Hi Mark,

Mark W Kimpel wrote:
> GOstats is broken in BioC 2.0, and I think in 1.9. Seth and Robert are 
> working on a fix but are en-route to New Zealand for a conference. Can I 
> load affycoretools without one or more dependencies? I just want to use 
> the venn diagram functions.

Yeah, if you can build binaries. All you would need to do is download 
the source version of affycoretools and strip out the dependencies that 
you don't want from the DESCRIPTION file. Then build/install the package 
(or you can really just install straight away - you will just be missing 
the vignette). Unfortunately it doesn't seem that you can just delete 
GOstats from the dependency field in a binary affycoretools, because it 
will still (attempt to) be loaded.

Anyway, I saw the error you mention in the build for affycoretools 
yesterday, but it isn't there today so I imagine whatever was causing 
the problem has been resolved. Maybe when you re-installed you got a bum 
version. You might try re-installing GOstats and see if that helps.

If you are set up to build binaries, you can try biocLite("GOstats", 
type="source") to install from the source version. If you aren't set up 
to build binaries you should be.

Anybody who wants to play around with the devel versions of R/BioC 
_should_ be set up to build the binaries. Between releases when people 
are changing their packages it is not uncommon for a package to fail to 
build. With something like affycoretools that depends on a gazillion 
other packages it is not uncommon to go for a long time without building 
on the Seattle servers (esp. the windows server) because of missing 
dependencies. This is especially true with the biomaRt dependency, since 
it depends on RCurl and RMySQL which are not completely straightforward 
to build on windows.

And you certainly wouldn't want to ask about a bug on R-devel that was 
fixed in svn like three hours ago, so you might also want to be building 
R-devel from source as well.

Anyway, long story short, between the release cycle I am often required 
to use biocLite("somel337package", type="source") because the package is 
not available on windows.

Best,

Jim


> 
> Mark


-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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