From mboxrd@z Thu Jan 1 00:00:00 1970 From: Roel Janssen Subject: Re: [PATCH 2/7] gnu: Add r-rbgl. Date: Mon, 19 Sep 2016 13:31:02 +0200 Message-ID: <87y42o15zd.fsf@gnu.org> References: <87k2eds89x.fsf@gnu.org> <87k2e8mc9q.fsf@elephly.net> <87zin419gv.fsf@gnu.org> <87intsma6c.fsf@elephly.net> Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:42883) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1blwm4-0007BT-Tp for guix-devel@gnu.org; Mon, 19 Sep 2016 07:30:14 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1blwlz-0004XV-88 for guix-devel@gnu.org; Mon, 19 Sep 2016 07:30:11 -0400 In-reply-to: <87intsma6c.fsf@elephly.net> 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: Ricardo Wurmus Cc: guix-devel@gnu.org Ricardo Wurmus writes: > Roel Janssen writes: > >> Ricardo Wurmus writes: >> >>> Roel Janssen writes: >>> >>>> * gnu/packages/bioinformatics.scm (r-rbgl): New variable. >>>> --- >>>> gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++ >>>> 1 file changed, 24 insertions(+) >>>> >>>> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm >>>> index ffb9692..3d607cc 100644 >>>> --- a/gnu/packages/bioinformatics.scm >>>> +++ b/gnu/packages/bioinformatics.scm >>>> @@ -5309,6 +5309,30 @@ packages.") >>>> CRAN, and (some) github packages.") >>>> (license license:artistic2.0))) >>>> >>>> +(define-public r-rbgl >>>> + (package >>>> + (name "r-rbgl") >>>> + (version "1.49.3") >>>> + (source (origin >>>> + (method url-fetch) >>>> + (uri (string-append >>>> + "https://bioconductor.org/packages/3.4/bioc/src/contrib/" >>>> + "RBGL_" version ".tar.gz")) >>> >>> Shouldn’t this be “(bioconductor-uri "RBGL" version)”? >> >> You are right, it should be “(bioconductor-uri "RBGL" version)”. > > Okay. I’ll make the change before pushing. If you want I can do the modifications as well and push. Saves you some valuable time :) >>>> + (sha256 >>>> + (base32 >>>> + "0rpiqpalbxk82jkwv3l0fimq9y2hrdi0f7ca4v21318541vfsncs")))) >>>> + (properties >>>> + `((upstream-name . "RBGL"))) >>>> + (build-system r-build-system) >>>> + (propagated-inputs >>>> + `(("r-graph" ,r-graph))) >>>> + (home-page "http://bioconductor.org/packages/RBGL") >>>> + (synopsis "Interface to the graph algorithms from Boost") >>>> + (description >>>> + "This package provides a fairly extensive and comprehensive interface to >>>> +the graph algorithms contained in the Boost library.") >>>> + (license license:artistic2.0))) >>>> + >>> >>> This package looks very familiar. Chances are that I packaged this >>> already and forgot about it… :) >> >> Do you whether you stripped the Boost source code in this package and >> used the Boost library from Guix? I wanted to do so, but couldn't >> figure out how it gets build! Plus, they use Boost 1.61.0 on this RBGL >> release, and we are stuck at 1.60.0. > > I didn’t try to swap out the sources. In my opinion this should be > treated as a fork. It’s a subset of Boost with R-specific adaptations. > Other R packages may depend on this particular “flavour” and might not > work well otherwise. > > If someone made the effort to change this, it would need to be checked > each time we updated our Boost package. I don’t think we have the > infrastructure to keep track of these things, so I’d rather err on the > side of keeping things as upstream has them. Right. I didn't compare the original boost sources with the one provided with the RBGL package, so I didn't know there were differences in code. I agree to keep the "forked" Boost code instead of using the upstream Boost code for additional reasons: 1. It makes the package recipe much simpler. 2. It keeps the package as the maintainer of RBGL meant to distribute it. The compile-time overhead is manageable (building the package on my machine takes less than ten minutes). I will take care of upstreaming this package and the other six I proposed. Kind regards, Roel Janssen