Hi Ricardo, On Tue, Dec 27, 2016 at 5:02 PM Ricardo Wurmus <rek...@elephly.net> wrote:
Hi Raoul, > in attachment a patch for the inclusion of an R/Bioconductor library named > "scran" https://bioconductor.org/packages/release/bioc/html/scran.html , > scran has a lot of dependencies and I placed those related to > bioinformatics/bioconductor into bioinformatics.scm and those related just > to R insto statistics.scm. Nice! Thank you for your efforts! Thanks, the result worth the effort. > Let me know if this big-patch is acceptable or how do I need to submit it. We have a policy of one commit per package. Each commit has a commit summary in a standard format (you’ll see when running git log). Ok, when I was adding r-scran I was just trying the make it the work. I'll go back and create a patch for each dependency. Going through the big patch I noticed a couple of things: * the indentation is rather uneven. If you’re using Emacs it’s very simple to correct this by using TAB and/or hitting C-M-q on the expression. (Also make sure parentheses are not all by themselves on an otherwise empty line.) I was using Vim, I will try with Emacs and also I was practicing a bit. * line length (especially in descriptions) exceeds the limits. * Please edit the descriptions. Package descriptions for Guix have to use full sentences. Judging from the indentation this doesn’t look like it was created by the *recursive* importer. Were there any problems using the recursive CRAN/Bioconductor importer? with guix 0.12.0 I was able to use guix import, I had some problem in the past due to certificates and x509. I used: guix import cran --archive=bioconductor scater I had to add the missing dependencies by hand, is there a recursive way to do so? The package for “r-shiny” needs a closer look. AFAIR it contains minified Javascript, which does not count as actual source code. If that’s in fact the case we would need to fiddle with the package a little to replace minified Javascript blobs with Javascript source files (which may be minified as part of the build process). I’d prefer if “r-shiny” were added to “web.scm”. Ok for web.scm. In the “r-statmod” package expression the comment above the gfortran input (which should be a native input) doesn’t seem to apply. Ok, bad comment placed there during tests. Please also double-check that the licenses are correct. The importer may not necessary get things right. Actually I noticed that and I fixed them, I will check again. Finally, please use lower-case words in the synopsis. In R packages this is often capitalised. Ok. Could you please send an updated patch set? Sure, in a couple of days, I think. -- Raoul
