From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: bioinformatics.scm vs bioconductor.scm ? Date: Tue, 18 Dec 2018 23:45:48 +0100 Message-ID: <87mup2tpwj.fsf@elephly.net> References: <87a7lb5rza.fsf@elephly.net> <87y38u52xq.fsf@elephly.net> 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]:59830) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gZO80-0002qk-Se for guix-devel@gnu.org; Tue, 18 Dec 2018 17:46:17 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gZO7x-0006g8-2j for guix-devel@gnu.org; Tue, 18 Dec 2018 17:46:16 -0500 Received: from sender-of-o53.zoho.com ([135.84.80.218]:21705) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1gZO7r-0006cF-B6 for guix-devel@gnu.org; Tue, 18 Dec 2018 17:46:09 -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: zimoun Cc: Guix Devel Hi, > Is the bioconductor importer usable from `guix import` ? yes. You may encounter minor problems when using the recursive bioconductor importer, as it may try to look up CRAN packages on Bioconductor. > This package is on Bioconductor: > https://bioconductor.org/packages/release/bioc/html/flowCore.html I=E2=80=99d do ./pre-inst-env guix import cran -a bioconductor -r flowCore This fails because it wants corpcor from CRAN. So we do: ./pre-inst-env guix import cran -r corpcor We dump the result (with minor changes) in (gnu packages cran) and try again to import flowCore. This time it succeeds. > Hum, the package BiocGenerics needs the version >=3D 0.1.14, and it is > not defined in the package. We have r-biocgenerics 0.28.0 in gnu/packages/bioinformatics.scm. That=E2=80=99s one of the packages that should move eventually. > Then, the package grDevices, graphics, methods, stats, stats4 are > required (see bioconductor webpage) but not defined elsewhere. Is it > good ? These are all default packages that are part of R itself. The importer skips them. > What is the convention about license ? > (license name) or (license license:name) This depends on the target module. cran.scm, bioinformatics.scm, and bioconductor.scm all use the =E2=80=9Clicense:=E2=80=9D prefix. web.scm on= the other hand uses the =E2=80=9Cl:=E2=80=9D prefix. Take a look at the #:use-module= clause at the top of the module. -- Ricardo