zimoun <zimon.touto...@gmail.com> writes:
> Thank you the explanations. > > >> New Bioconductor packages should go to bioconductor.scm. Eventually we >> may move all remaining R packages from bioinformatics to >> bioconductor.scm. > > I am a bit confused. > The file bioconductor.scm contains (or will contain) all R packages > from Bioconductor, right? Correct. > But R packages from CRAN used in Bioinformatics ? bioconductor.scm or > bioinformatics.scm? Neither :) We put them in cran.scm. At least that’s the new way of doing this. Previously it was all ad-hoc, meaning that packages would end up in bioinformatics.scm… Ideally, bioinformatics.scm would only contain non-R tools like samtools, bamtools, bioinfo pipelines, etc. > And I am asking myself if a massive import from Bioconductor should be > possible ? Certainly! I’ve done this before actually, but I hit two minor problems: 1. the bioconductor recursive importer does not *automatically* switch to “CRAN mode” when a dependent package isn’t found on Bioconductor. Not a big problem, but it means that teh import isn’t fully automatic. 2. compiling big Guile modules (such as a future (gnu packages cran)) require lots of memory since Guile 2.2(?), so I didn’t add all these packages. This is a bug and we’d have to split the module, probably, to work around it. -- Ricardo
