From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: [PATCH] Add r-scran 1.2.0 and all its dependencies Date: Tue, 27 Dec 2016 17:02:44 +0100 Message-ID: <87k2aljr6j.fsf@elephly.net> References: Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:42307) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cLuDJ-00025B-AQ for guix-devel@gnu.org; Tue, 27 Dec 2016 11:02:58 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cLuDG-00084N-7t for guix-devel@gnu.org; Tue, 27 Dec 2016 11:02:57 -0500 Received: from sender163-mail.zoho.com ([74.201.84.163]:21374) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1cLuDG-00083g-01 for guix-devel@gnu.org; Tue, 27 Dec 2016 11:02:54 -0500 In-reply-to: List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: Ra Cc: guix-devel Hi Raoul, > in attachment a patch for the inclusion of an R/Bioconductor library nam= ed > "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! > 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=E2=80=99ll see when running git log). Going through the big patch I noticed a couple of things: * the indentation is rather uneven. If you=E2=80=99re using Emacs it=E2=80= =99s 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.) * 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=E2=80=99t look like it was created = by the *recursive* importer. Were there any problems using the recursive CRAN/Bioconductor importer? The package for =E2=80=9Cr-shiny=E2=80=9D needs a closer look. AFAIR it co= ntains minified Javascript, which does not count as actual source code. If that=E2=80=99s 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=E2=80=99d prefer if =E2=80=9Cr-shiny=E2=80=9D were added to =E2=80=9Cweb.scm=E2=80=9D. In the =E2=80=9Cr-statmod=E2=80=9D package expression the comment above the= gfortran input (which should be a native input) doesn=E2=80=99t seem to apply. Please also double-check that the licenses are correct. The importer may not necessary get things right. Finally, please use lower-case words in the synopsis. In R packages this is often capitalised. Could you please send an updated patch set? --=20 Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC http://elephly.net