From ff2b1c17b824a2399cfdc11a9839ef3d5bb1a6ed Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 22 Apr 2015 11:58:44 +0200
Subject: gnu: r: Set library rpath.

* gnu/packages/statistics.scm (r)[arguments]: Add the rpath for lib directory
  of output to LDFLAGS.
---
 gnu/packages/statistics.scm | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

(limited to 'gnu/packages/statistics.scm')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 5fae6d7a3c..42c16cdb30 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -53,7 +53,11 @@
                 "0ypsm11c7n49pgh2ricyhhpfhas3famscdazzdp2zq70rapm1ldw"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:phases
+     `(#:make-flags
+       (list (string-append "LDFLAGS=-Wl,-rpath="
+                            (assoc-ref %outputs "out")
+                            "/lib/R/lib"))
+       #:phases
        (alist-cons-before
         'check 'set-timezone
         ;; Some tests require the timezone to be set.
-- 
cgit 1.4.1


From 3c43bcc68d4ad9caddbb64506b5c8f10fdb9c8f3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 22 Apr 2015 12:26:45 +0200
Subject: gnu: r: Update to 3.2.0.

* gnu/packages/statistics.scm (r): Update to 3.2.0.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/statistics.scm')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 42c16cdb30..722e0dfa49 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -42,7 +42,7 @@
 (define-public r
   (package
     (name "r")
-    (version "3.1.2")
+    (version "3.2.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cran/src/base/R-"
@@ -50,7 +50,7 @@
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0ypsm11c7n49pgh2ricyhhpfhas3famscdazzdp2zq70rapm1ldw"))))
+                "0dagyqgvi8i3nw158qi2zpwm04s4ffzvnmk5niaksvxs30zrbbpm"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags
-- 
cgit 1.4.1


From 9099e881828fd242cc26054c0f33670c46154d96 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: 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

(limited to 'gnu/packages/statistics.scm')

diff --git a/gnu-system.am b/gnu-system.am
index a26686b81b..297c8bcf6a 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -542,6 +542,7 @@ 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 0000000000..40593d34e6
--- /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 722e0dfa49..9408705d5e 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
-- 
cgit 1.4.1