From ce7e361fa30d3dbe5c1da35f52dade2eb829aed7 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 4 Jul 2017 15:21:33 +0300
Subject: [PATCH] gnu: gemma: Fix building on non-Intel architectures.

* gnu/packages/patches/gemma-intel-compat.patch: New file.
* gnu/packages/bioinformatics.scm (gemma)[source]: Add patch.
[arguments]: Add NO_INTEL_COMPAT flag on non-Intel architectures.
* gnu/local.mk (dist_patch_DATA): Register patch.
---
 gnu/local.mk                                  |  1 +
 gnu/packages/bioinformatics.scm               | 19 ++++----
 gnu/packages/patches/gemma-intel-compat.patch | 44 +++++++++++++++++++
 3 files changed, 56 insertions(+), 8 deletions(-)
 create mode 100644 gnu/packages/patches/gemma-intel-compat.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index ecd80acda5..8dbce7c052 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -622,6 +622,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/gd-freetype-test-failure.patch		\
   %D%/packages/patches/gd-php-73968-Fix-109-XBM-reading.patch		\
   %D%/packages/patches/gegl-CVE-2012-4433.patch			\
+  %D%/packages/patches/gemma-intel-compat.patch			\
   %D%/packages/patches/geoclue-config.patch			\
   %D%/packages/patches/ghc-dont-pass-linker-flags-via-response-files.patch	\
   %D%/packages/patches/ghostscript-CVE-2013-5653.patch		\
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0ff0bbb9e3..55c2975a1e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4,7 +4,7 @@
 ;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2016 Raoul Bonnal <ilpuccio.febo@gmail.com>
 ;;;
@@ -99,7 +99,7 @@
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg)
   #:use-module (srfi srfi-1)
-  #:use-module (srfi srfi-26))
+  #:use-module (ice-9 match))
 
 (define-public r-ape
   (package
@@ -2719,7 +2719,8 @@ comment or quality sections.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "055ynn16gd12pf78n4vr2a9jlwsbwzajpdnf2y2yilg1krfff222"))))
+                "055ynn16gd12pf78n4vr2a9jlwsbwzajpdnf2y2yilg1krfff222"))
+              (patches (search-patches "gemma-intel-compat.patch"))))
     (inputs
      `(("gsl" ,gsl)
        ("lapack" ,lapack)
@@ -2727,11 +2728,13 @@ comment or quality sections.")
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags
-       '(,@(if (any (cute string-prefix? <> (or (%current-system)
-                                                (%current-target-system)))
-                    '("x86_64" "mips64el" "aarch64"))
-             '("FORCE_DYNAMIC=1") ; use shared libs
-             '("FORCE_DYNAMIC=1" "FORCE_32BIT=1")))
+       '(,@(match (%current-system)
+         ("x86_64-linux"
+          '("FORCE_DYNAMIC=1"))
+         ("i686-linux"
+          '("FORCE_DYNAMIC=1" "FORCE_32BIT=1"))
+         (_
+          '("FORCE_DYNAMIC=1" "NO_INTEL_COMPAT=1"))))
        #:phases
        (modify-phases %standard-phases
          (delete 'configure)
diff --git a/gnu/packages/patches/gemma-intel-compat.patch b/gnu/packages/patches/gemma-intel-compat.patch
new file mode 100644
index 0000000000..f12ec56d9b
--- /dev/null
+++ b/gnu/packages/patches/gemma-intel-compat.patch
@@ -0,0 +1,44 @@
+From da1ed24209121f7b0f03f360b1029d7125a38e70 Mon Sep 17 00:00:00 2001
+From: Efraim Flashner <efraim@flashner.co.il>
+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
+