Re: [PATCH] Add r-scran 1.2.0 and all its dependencies

[Ra <ilpuccio.febo@gmail.com>]

[-- Attachment #1: Type: text/plain, Size: 2856 bytes --]

Hi Ricardo,

On Tue, Dec 27, 2016 at 5:02 PM Ricardo Wurmus <rekado@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

[-- Attachment #2: Type: text/html, Size: 6619 bytes --]