From: Ricardo Wurmus <rekado@elephly.net>
To: "Ludovic Courtès" <ludo@gnu.org>
Cc: guix-devel <guix-devel@gnu.org>
Subject: Re: [PATCH] Add cufflinks.
Date: Sat, 23 Jan 2016 09:14:41 +0100 [thread overview]
Message-ID: <874me4vhji.fsf@elephly.net> (raw)
In-Reply-To: <871tdycmtr.fsf@gnu.org>
Ludovic Courtès <ludo@gnu.org> writes:
> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
>
>> From e8186326701df11ee4bdb22d4717cf4b8c27dd50 Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>> Date: Wed, 16 Sep 2015 17:42:41 +0200
>> Subject: [PATCH] gnu: Add cufflinks.
>>
>> * gnu/packages/bioinformatics.scm (boost-1.55, cufflinks): New
>> variables.
>
> [...]
>
>> +(define boost-1.55
>> + (package (inherit boost)
>
> I would keep it next to ‘boost’.
Since the update to boost 1.60 this is no longer needed.
>> + (lambda* (#:key inputs #:allow-other-keys)
>> + ;; The includes for "eigen" are located in a subdirectory.
>> + (setenv "CPATH" (string-append (assoc-ref inputs "eigen")
>> + "/include/eigen3/" ":"
>> + (or (getenv "CPATH") "")))
>
> It should be using ‘pkg-config eigen3 --cflags’, but pkg-config is
> missing.
>
> Could you check if adding pkg-config makes this hack unnecessary?
>
> Otherwise LGTM.
Cufflinks does not use pkg-config. I have modified this to use
EIGEN_CPPFLAGS instead of the much broader CPATH:
+ (arguments
+ `(#:make-flags
+ (list
+ ;; The includes for "eigen" are located in a subdirectory.
+ (string-append "EIGEN_CPPFLAGS="
+ "-I" (assoc-ref %build-inputs "eigen")
+ "/include/eigen3/")
I have also cleaned up the package to use “modify-phases”, clarified the
description (“transcript” -> “RNA transcript”), and replaced the license
with “license:boost1.0”.
~~ Ricardo
next prev parent reply other threads:[~2016-01-23 8:14 UTC|newest]
Thread overview: 17+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-09-16 15:45 [PATCH] Add cufflinks Ricardo Wurmus
2015-09-16 17:10 ` Ludovic Courtès
2015-09-16 19:56 ` Andreas Enge
2015-09-16 20:06 ` Ludovic Courtès
2015-09-16 20:07 ` Ricardo Wurmus
2016-01-23 8:14 ` Ricardo Wurmus [this message]
-- strict thread matches above, loose matches on Subject: below --
2016-01-20 10:02 [PATCH 0/1] Provide icons for transmission-gtk Leo Famulari
2016-01-20 10:02 ` [PATCH 1/1] gnu: transmission-gtk: Add icon dependencies Leo Famulari
2016-01-22 17:15 ` Ludovic Courtès
2016-01-22 19:27 ` Leo Famulari
2016-01-23 16:36 ` Ludovic Courtès
2016-01-23 18:11 ` Add "guix update" command Fabian Harfert
2016-01-23 18:28 ` Friedrich Herbst
2016-01-23 19:37 ` Thompson, David
2016-01-23 21:35 ` Ludovic Courtès
2016-01-28 4:44 ` [PATCH 1/1] gnu: transmission-gtk: Add icon dependencies Leo Famulari
2016-01-31 9:38 ` Ludovic Courtès
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