Re: [Bioc-devel] zzz.R in GenoView

I'm not sure I like that idea, because then we are propagating packages that do not build and/or check (even though there's a big fat warning when you load them). Also I don't like the idea of modifying the build system so close to the release, and I don't have a lot of time to do that. We

Re: [Bioc-devel] zzz.R in GenoView

If it is total failure, we could consider having an empty package just saying does not work or something when loaded. Not sure that is great, but at least it tells people the problem. If you put on the release hat, the package shouldn't get released if we know it doesn't work. It is preferable

Re: [Bioc-devel] zzz.R in GenoView

Yes, this is part of a larger problem we need to think about. I marked several packages as deprecated. In each case, the package has not built successfully (and propagated) in some time. So the deprecation message will not propagate to the end user, and the special landing page text will not

Re: [Bioc-devel] zzz.R in GenoView

On 10/05/2015 05:45 PM, Dan Tenenbaum wrote: I'm not sure I like that idea, because then we are propagating packages that do not build and/or check (even though there's a big fat warning when you load them). Right but if the package was passing build and check, there wouldn't be much reason

Re: [Bioc-devel] IPI numbers in annotation packages

Hi Marc, That script has this in it: ## For now just get data for the ones that we have traditionally supported ## I don't even know if the other species are available... speciesList = c("chipsrc_human.sqlite", "chipsrc_rat.sqlite", "chipsrc_chicken.sqlite", "chipsrc_zebrafish.sqlite", #

Re: [Bioc-devel] IPI numbers in annotation packages

You need to scroll down that script a ways... Look for 'yeast'. On Mon, Oct 5, 2015 at 6:11 AM, James W. MacDonald wrote: > Hi Marc, > > That script has this in it: > > ## For now just get data for the ones that we have traditionally supported > ## I don't even know if the

Re: [Bioc-devel] IPI numbers in annotation packages

Ah. That's the problem. The script in getdb.sh has R --slave < /home/ubuntu/cpb_anno/AnnotationBuildPipeline/annosrc/uniprot/script/ uniprot.ws/inst/script/processDataForBuild.R which is a modification of what is in svn (to match the directory structure of the AMI), which calls on a script in a