From e7d16ad1616878f28b9e0eb403be845d3892a4aa Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 24 Nov 2016 14:58:40 +0100
Subject: [PATCH] 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 0ba33165d68..dcf6dbe6262 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3342,6 +3342,58 @@ (define-public r-googlesheets
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:
+
+@enumerate
+@item Dictionary learning and matrix factorization (NMF, sparse @dfn{principle
+ component analysis} (PCA), ...)
+@item Solving sparse decomposition problems with LARS, coordinate descent,
+ OMP, SOMP, proximal methods
+@item Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse
+ group lasso, tree-structured regularization, structured sparsity with
+ overlapping groups,...).
+@end enumerate\n")
+ (license license:gpl3+)))
+
(define-public r-rpart
(package
(name "r-rpart")
--
GitLab