02/02: gnu: gemma: Update to 0.98.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit 152bebd9e0c7fc0863d6b82af014e61a8cb6a488
Author: Ricardo Wurmus <address@hidden>
Date:   Wed Nov 7 20:24:18 2018 +0100

    gnu: gemma: Update to 0.98.
    
    * gnu/local.mk (dist_patch_DATA): Remove patch.
    * gnu/packages/patches/gemma-intel-compat.patch: Remove file.
    * gnu/packages/bioinformatics.scm (gemma): Update to 0.98.
    [source]: Remove patch.
    [inputs]: Add eigen, gfortran:lib, and openblas.
    [arguments]: Add phase "find-eigen".
---
 gnu/local.mk                                  |  1 -
 gnu/packages/bioinformatics.scm               | 19 +++++++++---
 gnu/packages/patches/gemma-intel-compat.patch | 44 ---------------------------
 3 files changed, 15 insertions(+), 49 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index bfe9315..9a8330a 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -722,7 +722,6 @@ dist_patch_DATA =                                           
\
   %D%/packages/patches/gd-fix-tests-on-i686.patch              \
   %D%/packages/patches/gd-freetype-test-failure.patch          \
   %D%/packages/patches/gdm-CVE-2018-14424.patch                        \
-  %D%/packages/patches/gemma-intel-compat.patch                        \
   %D%/packages/patches/geoclue-config.patch                    \
   %D%/packages/patches/ghc-8.0-fall-back-to-madv_dontneed.patch \
   %D%/packages/patches/ghc-dont-pass-linker-flags-via-response-files.patch     
\
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3cd0e03..5337b7b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2829,7 +2829,7 @@ comment or quality sections.")
 (define-public gemma
   (package
     (name "gemma")
-    (version "0.96")
+    (version "0.98")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -2838,11 +2838,13 @@ comment or quality sections.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0sa4mllp7890v5pss0mm02ik8yixl7az3vprcw3kp7qmr9gwrdai"))
-              (patches (search-patches "gemma-intel-compat.patch"))))
+                "1s3ncnbn45r2hh1cvrqky1kbqq6546biypr4f5mkw1kqlrgyh0yg"))))
     (inputs
-     `(("gsl" ,gsl)
+     `(("eigen" ,eigen)
+       ("gfortran" ,gfortran "lib")
+       ("gsl" ,gsl)
        ("lapack" ,lapack)
+       ("openblas" ,openblas)
        ("zlib" ,zlib)))
     (build-system gnu-build-system)
     (arguments
@@ -2857,6 +2859,15 @@ comment or quality sections.")
        #:phases
        (modify-phases %standard-phases
          (delete 'configure)
+         (add-after 'unpack 'find-eigen
+           (lambda* (#:key inputs #:allow-other-keys)
+             ;; Ensure that Eigen headers can be found
+             (setenv "CPLUS_INCLUDE_PATH"
+                     (string-append (getenv "CPLUS_INCLUDE_PATH")
+                                    ":"
+                                    (assoc-ref inputs "eigen")
+                                    "/include/eigen3"))
+             #t))
          (add-before 'build 'bin-mkdir
           (lambda _
             (mkdir-p "bin")
diff --git a/gnu/packages/patches/gemma-intel-compat.patch 
b/gnu/packages/patches/gemma-intel-compat.patch
deleted file mode 100644
index f12ec56..0000000
--- a/gnu/packages/patches/gemma-intel-compat.patch
+++ /dev/null
@@ -1,44 +0,0 @@
-From da1ed24209121f7b0f03f360b1029d7125a38e70 Mon Sep 17 00:00:00 2001
-From: Efraim Flashner <address@hidden>
-Date: Tue, 4 Jul 2017 12:44:53 +0300
-Subject: [PATCH] Add NO_INTEL_COMPAT flag to Makefile.
-
-see also: https://github.com/xiangzhou/GEMMA/pull/47
-
----
- Makefile | 12 ++++++++----
- 1 file changed, 8 insertions(+), 4 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 5bb8748..712b1ad 100644
---- a/Makefile
-+++ b/Makefile
-@@ -11,6 +11,7 @@
- SYS = LNX
- # Leave blank after "=" to disable; put "= 1" to enable
- WITH_LAPACK = 1
-+NO_INTEL_COMPAT = 
- FORCE_32BIT = 
- FORCE_DYNAMIC = 
- DIST_NAME = gemma-0.96
-@@ -64,10 +65,13 @@ endif
-   HDR += $(SRC_DIR)/lapack.h
- endif
- 
--ifdef FORCE_32BIT
--  CPPFLAGS += -m32
--else
--  CPPFLAGS += -m64
-+ifdef NO_INTEL_COMPAT
-+  else
-+  ifdef FORCE_32BIT
-+    CPPFLAGS += -m32
-+  else
-+    CPPFLAGS += -m64
-+  endif
- endif
- 
- ifdef FORCE_DYNAMIC
--- 
-2.13.2
-