Ludovic Courtès <[email protected]> writes: > Ricardo Wurmus <[email protected]> skribis: > >> From e8186326701df11ee4bdb22d4717cf4b8c27dd50 Mon Sep 17 00:00:00 2001 >> From: Ricardo Wurmus <[email protected]> >> 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
