Question: can't load affycoretools because GOstats is broken. Can I load affycoretools without dependencies to use some functions?
0
gravatar for Mark W Kimpel
12.9 years ago by
Mark W Kimpel830
Mark W Kimpel830 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. Mark -- Mark W. Kimpel MD Neuroinformatics Department of Psychiatry Indiana University School of Medicine
affycoretools • 432 views
ADD COMMENTlink modified 12.9 years ago by James W. MacDonald52k • written 12.9 years ago by Mark W Kimpel830
Answer: can't load affycoretools because GOstats is broken. Can I load affycoretools wit
0
gravatar for James W. MacDonald
12.9 years ago by
United States
James W. MacDonald52k wrote:
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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
ADD COMMENTlink written 12.9 years ago by James W. MacDonald52k
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