04/18: gnu: Add r-spams.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit e7d16ad1616878f28b9e0eb403be845d3892a4aa
Author: Ricardo Wurmus <address@hidden>
Date:   Thu Nov 24 14:58:40 2016 +0100

    gnu: Add r-spams.
    
    * gnu/packages/statistics.scm (r-spams): New variable.
---
 gnu/packages/statistics.scm |   52 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 52 insertions(+)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 0ba3316..dcf6dbe 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3342,6 +3342,58 @@ character vector.")
 from within R.")
     (license license:expat)))
 
+(define-public r-spams
+  (package
+    (name "r-spams")
+    (version "2.5-svn2014-07-04")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://gforge.inria.fr/frs/download.php/33815/";
+                           "spams-R-v" version ".tar.gz"))
+       (sha256
+        (base32
+         "1k459jg9a334slkw31w63l4d39xszjzsng7dv5j1mp78zifz7hvx"))))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'chdir
+           (lambda _ (chdir "spams") #t))
+         ;; Since R 3.3.0 including R headers inside of an extern "C" block
+         ;; causes C headers to be included, which results in a lot of
+         ;; duplicate definitions.  This can be avoided by defining
+         ;; NO_C_HEADERS before including the R headers.
+         (add-after 'chdir 'patch-use-of-R-headers
+           (lambda _
+             (substitute* "src/spams.cpp"
+               (("#include <R.h>" line)
+                (string-append "#define NO_C_HEADERS\n" line)))
+             #t))
+         ;; This looks like a syntax error.
+         (add-after 'chdir 'patch-isnan
+           (lambda _
+             (substitute* '"src/spams/linalg/linalg.h"
+               (("if isnan\\(lambda\\) \\{")
+                "if (isnan(lambda)) {"))
+             #t)))))
+    (home-page "http://spams-devel.gforge.inria.fr";)
+    (synopsis "Toolbox for solving sparse estimation problems")
+    (description "SPAMS (SPArse Modeling Software) is an optimization toolbox
+for solving various sparse estimation problems.  It includes tools for the
+following problems:
+
address@hidden
address@hidden Dictionary learning and matrix factorization (NMF, sparse 
@dfn{principle
+ component analysis} (PCA), ...)
address@hidden Solving sparse decomposition problems with LARS, coordinate 
descent,
+ OMP, SOMP, proximal methods
address@hidden Solving structured sparse decomposition problems (l1/l2, 
l1/linf, sparse
+ group lasso, tree-structured regularization, structured sparsity with
+ overlapping groups,...).
address@hidden enumerate\n")
+    (license license:gpl3+)))
+
 (define-public r-rpart
   (package
     (name "r-rpart")