[PATCH] gnu: r: Apply patch to fix linking against R.

[Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>]

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Hi Guix,

the attached upstream patch is required to fix linking problems when
linking external applications or libraries (such as Shogun) against R.
The problem was introduced with the upgrade to version 3.2.0 of R and
should be released with 3.2.1.


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From 0bb28820d47d9e02f4580253f11666e254841019 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 19 May 2015 11:53:47 +0200
Subject: [PATCH] gnu: r: Apply patch to fix linking against R.

* gnu/packages/patches/r-fix-15899.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/statistics.scm (r)[source]: Use it.
---
 gnu-system.am                          |  1 +
 gnu/packages/patches/r-fix-15899.patch | 17 +++++++++++++++++
 gnu/packages/statistics.scm            |  3 ++-
 3 files changed, 20 insertions(+), 1 deletion(-)
 create mode 100644 gnu/packages/patches/r-fix-15899.patch

diff --git a/gnu-system.am b/gnu-system.am
index 5ba48d1..6480a02 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -541,6 +541,7 @@ dist_patch_DATA =						\
   gnu/packages/patches/qt4-tests.patch				\
   gnu/packages/patches/qt5-conflicting-typedefs.patch		\
   gnu/packages/patches/qt5-runpath.patch			\
+  gnu/packages/patches/r-fix-15899.patch			\
   gnu/packages/patches/ratpoison-shell.patch			\
   gnu/packages/patches/readline-link-ncurses.patch		\
   gnu/packages/patches/ripperx-libm.patch			\
diff --git a/gnu/packages/patches/r-fix-15899.patch b/gnu/packages/patches/r-fix-15899.patch
new file mode 100644
index 0000000..40593d3
--- /dev/null
+++ b/gnu/packages/patches/r-fix-15899.patch
@@ -0,0 +1,17 @@
+Without the "extern" keyword external applications linking against R (such as
+Shogun, for example) might not be linkable.
+
+See https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15899 for details
+about this bug.
+
+--- a/src/include/Rinterface.h	(revision 66251)
++++ b/src/include/Rinterface.h	(working copy)
+@@ -84,7 +84,7 @@
+ void fpu_setup(Rboolean);
+ 
+ /* in unix/system.c */
+-int R_running_as_main_program; 
++extern int R_running_as_main_program; 
+ 
+ #ifdef CSTACK_DEFNS
+ /* duplicating Defn.h */
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 722e0df..9408705 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -50,7 +50,8 @@
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0dagyqgvi8i3nw158qi2zpwm04s4ffzvnmk5niaksvxs30zrbbpm"))))
+                "0dagyqgvi8i3nw158qi2zpwm04s4ffzvnmk5niaksvxs30zrbbpm"))
+              (patches (list (search-patch "r-fix-15899.patch")))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags
-- 
2.1.0