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12/13: gnu: r-spams: Update to 2.6.1.
From: |
guix-commits |
Subject: |
12/13: gnu: r-spams: Update to 2.6.1. |
Date: |
Mon, 3 Oct 2022 11:19:18 -0400 (EDT) |
apteryx pushed a commit to branch master
in repository guix.
commit 67e9513e40715083ad23089ff093cf47565f1eb7
Author: Maxim Cournoyer <maxim.cournoyer@gmail.com>
AuthorDate: Mon Oct 3 09:33:56 2022 -0400
gnu: r-spams: Update to 2.6.1.
* gnu/packages/statistics.scm (r-spams): Update to 2.6.1.
[source]: Migrate from gforge.inria.fr to gitlab.inria.fr, fetching from
git.
[phases]: Use gexps.
{patch-paths, mkdist}: New phases.
{no-mtune}: Delete trailing #t.
[native-inputs]: New field.
[home-page]: Update URL.
---
gnu/packages/statistics.scm | 72 ++++++++++++++++++++++++++++++---------------
1 file changed, 49 insertions(+), 23 deletions(-)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 6e57eb2f4f..7a9c4414b1 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -12,7 +12,7 @@
;;; Copyright © 2017 Alex Kost <alezost@gmail.com>
;;; Copyright © 2018 Alex Branham <alex.branham@gmail.com>
;;; Copyright © 2020 Tim Howes <timhowes@lavabit.com>
-;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2021, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2021 Bonface Munyoki Kilyungi <me@bonfacemunyoki.com>
;;; Copyright © 2021 Lars-Dominik Braun <lars@6xq.net>
;;; Copyright © 2021 Frank Pursel <frank.pursel@gmail.com>
@@ -73,6 +73,7 @@
#:use-module (gnu packages maths)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages ncurses)
+ #:use-module (gnu packages ocaml)
#:use-module (gnu packages pcre)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
@@ -83,6 +84,7 @@
#:use-module (gnu packages shells)
#:use-module (gnu packages sphinx)
#:use-module (gnu packages ssh)
+ #:use-module (gnu packages swig)
#:use-module (gnu packages tcl)
#:use-module (gnu packages tex)
#:use-module (gnu packages texinfo)
@@ -4407,31 +4409,55 @@ from within R.")
(define-public r-spams
(package
(name "r-spams")
- (version "2.6-2017-03-22")
- (source
- (origin
- (method url-fetch)
- ;; Use the ‘Latest version’ link for a stable URI across releases.
- (uri (string-append "https://gforge.inria.fr/frs/download.php/"
- "latestfile/4531/spams-R-v" version ".tar.gz"))
- (sha256
- (base32
- "13z2293jixf1r9g8dyy856xrhvpjr2ln2n9smn6644126r9hmhkx"))))
+ (version "2.6.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://gitlab.inria.fr/thoth/spams-devel")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0qvj87fw4sm54c7dvhxjgmgvnyyrrz9fk6dqp3ak0gwgb42gqh60"))))
(build-system r-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'chdir
- (lambda _ (chdir "spams") #t))
- ;; Don't tune for the building machine.
- (add-after 'chdir 'no-mtune
- (lambda _
- (substitute* "src/Makevars"
- (("-mtune=native") ""))
- #t)))))
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'patch-generated-file-shebangs 'patch-paths
+ (lambda _
+ (substitute* (cons* "swig/setRelease"
+ "swig/R/docmatlab2R"
+ "swig/R/mkdist"
+ (find-files "." "(^mk|\\.sh$)"))
+ (("/bin/pwd") "pwd")
+ (("/bin/rm") "rm"))))
+ (add-after 'patch-paths 'mkdist
+ (lambda _
+ (chdir "swig/R")
+ (setenv "TEXINPUTS" (string-append (getcwd) "/../../doc:"))
+ (substitute* "mkdist"
+ (("^SWIG=.*")
+ (string-append "SWIG=" (which "swig")))
+ (("^../mkdoc") "")) ;requires texlive-aeguill
+ (invoke "./mkdist")
+ (chdir "dist/spams-R/spams")))
+ ;; Don't tune for the building machine.
+ (add-after 'mkdist 'no-mtune
+ (lambda _
+ (substitute* "src/Makevars"
+ (("-mtune=native") "")))))))
+ (native-inputs
+ (list hevea
+ perl
+ swig
+ ;;texlive-aeguill ;;FIXME: package me!
+ texlive-base
+ texlive-jknappen))
(propagated-inputs
- (list r-lattice r-matrix))
- (home-page "https://spams-devel.gforge.inria.fr")
+ (list r-lattice
+ r-matrix))
+ (home-page "https://gitlab.inria.fr/thoth/spams-devel/")
(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
- 03/13: gnu: gf2x: Update to 1.3.0., (continued)
- 03/13: gnu: gf2x: Update to 1.3.0., guix-commits, 2022/10/03
- 05/13: gnu: gappa: Update to 1.4.1., guix-commits, 2022/10/03
- 01/13: gnu-maintenance: Remove retired 'gforge.inria.fr' site., guix-commits, 2022/10/03
- 07/13: gnu: isl: Remove outdated comment., guix-commits, 2022/10/03
- 08/13: gnu: mpfi: Use gexps and remove input labels., guix-commits, 2022/10/03
- 10/13: gnu: Remove unused scotch patches., guix-commits, 2022/10/03
- 02/13: gnu: gf2x: Migrate from gforge.inria.fr to gitlab.inria.fr., guix-commits, 2022/10/03
- 04/13: gnu: gmp-ecm: Update to 7.0.5., guix-commits, 2022/10/03
- 06/13: gnu: gappa: Honor TESTS?., guix-commits, 2022/10/03
- 11/13: gnu: ocaml-dose3: Migrate from gforce.inria.fr., guix-commits, 2022/10/03
- 12/13: gnu: r-spams: Update to 2.6.1.,
guix-commits <=
- 09/13: gnu: mpfi: Update to 1.5.4-1.b982534., guix-commits, 2022/10/03
- 13/13: gnu: Remove ocaml-craml., guix-commits, 2022/10/03