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-rw-r--r--gnu/packages/maths.scm67
1 files changed, 50 insertions, 17 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 9930f491a2..e3d3216eab 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -26,7 +26,7 @@
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018 Nadya Voronova <voronovank@gmail.com>
;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com>
-;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2018, 2020 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2018 Eric Brown <brown@fastmail.com>
;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
;;; Copyright © 2018 Amin Bandali <bandali@gnu.org>
@@ -460,23 +460,45 @@ precision floating point numbers.")
(define-public gsl
(package
(name "gsl")
- (version "2.5")
+ (version "2.6")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/gsl/gsl-"
version ".tar.gz"))
(sha256
(base32
- "1395y9hlhqadn5g9j8q22224fds5sd92jxi9czfavjj24myasq04"))
- (patches (search-patches "gsl-test-i686.patch"))))
+ "1a460zj9xmbgvcymkdhqh313c4l29mn9cffbi5vf33x3qygk70mp"))))
(build-system gnu-build-system)
(arguments
- `(;; Currently there are numerous tests that fail on "exotic"
- ;; architectures such as aarch64 and ppc64le.
- ,@(if (string-prefix? "aarch64-linux"
- (or (%current-target-system) (%current-system)))
- '(#:tests? #f)
- '())))
+ (let ((system (%current-system)))
+ (cond
+ ((string-prefix? "aarch64" system)
+ ;; Some sparse matrix tests are failing on AArch64:
+ ;; https://lists.gnu.org/archive/html/bug-gsl/2020-04/msg00001.html
+ '(#:phases (modify-phases %standard-phases
+ (add-before 'check 'disable-failing-tests
+ (lambda _
+ (substitute* "spmatrix/test.c"
+ ((".*test_complex.*") "\n"))
+ #t)))))
+ ((string-prefix? "i686" system)
+ ;; There are rounding issues with these tests on i686:
+ ;; https://lists.gnu.org/archive/html/bug-gsl/2016-10/msg00000.html
+ ;; https://lists.gnu.org/archive/html/bug-gsl/2020-04/msg00000.html
+ '(#:phases (modify-phases %standard-phases
+ (add-before 'check 'disable-failing-tests
+ (lambda _
+ (substitute* "linalg/test.c"
+ ((".*gsl_test\\(test_LU_decomp.*") "\n")
+ ((".*gsl_test\\(test_LUc_decomp.*") "\n")
+ ((".*gsl_test\\(test_cholesky_decomp.*") "\n")
+ ((".*gsl_test\\(test_COD_lssolve2.*") "\n"))
+ (substitute* "spmatrix/test.c"
+ ((".*test_all.*") "\n")
+ ((".*test_float.*") "\n")
+ ((".*test_complex.*") "\n"))
+ #t)))))
+ (else '()))))
(home-page "https://www.gnu.org/software/gsl/")
(synopsis "Numerical library for C and C++")
(description
@@ -856,7 +878,7 @@ computations.")
("flex" ,flex)))
(inputs
`(("zlib" ,zlib)
- ("libjpeg" ,libjpeg)
+ ("libjpeg" ,libjpeg-turbo)
("libtirpc" ,libtirpc)))
(arguments
`(#:parallel-tests? #f
@@ -1096,7 +1118,7 @@ extremely large and complex data collections.")
`(("hdf4" ,hdf4)
("hdf5" ,hdf5)
("zlib" ,zlib)
- ("libjpeg" ,libjpeg)
+ ("libjpeg" ,libjpeg-turbo)
("slf4j-api" ,java-slf4j-api)))
(arguments
`(#:configure-flags
@@ -1213,7 +1235,7 @@ implemented in C.")
`(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
;; XXX: These inputs are really dependencies of hdf4.
("zlib" ,zlib)
- ("libjpeg" ,libjpeg)
+ ("libjpeg" ,libjpeg-turbo)
("libtirpc" ,libtirpc)
("gctp" ,gctp)))
@@ -1373,7 +1395,7 @@ similar to MATLAB, GNU Octave or SciPy.")
`(("hdf4" ,hdf4-alt)
("hdf5" ,hdf5)
("zlib" ,zlib)
- ("libjpeg" ,libjpeg)))
+ ("libjpeg" ,libjpeg-turbo)))
(arguments
`(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
@@ -1646,6 +1668,12 @@ can solve two kinds of problems:
("glpk" ,glpk)
("glu" ,glu)
("graphicsmagick" ,graphicsmagick)
+
+ ;; TODO: libjpeg-turbo is indirectly required through libtiff. In
+ ;; the next rebuild cycle, add an absolute reference for -ljpeg in
+ ;; libtiff.la instead of having to provide it here.
+ ("libjpeg" ,libjpeg-turbo)
+
("hdf5" ,hdf5)
("lapack" ,lapack)
("libsndfile" ,libsndfile)
@@ -1684,7 +1712,12 @@ can solve two kinds of problems:
`(#:configure-flags
(list (string-append "--with-shell="
(assoc-ref %build-inputs "bash")
- "/bin/sh"))
+ "/bin/sh")
+
+ ;; XXX: Without this flag, linking octave-cli fails with
+ ;; undefined references to 'logf@GLIBCXX_3.4' et.al. due to
+ ;; not pulling in liboctinterp.la for -lstdc++.
+ "--enable-link-all-dependencies")
#:phases
(modify-phases %standard-phases
(add-after 'configure 'configure-makeinfo
@@ -3243,7 +3276,7 @@ parts of it.")
(define-public openblas
(package
(name "openblas")
- (version "0.3.7")
+ (version "0.3.9")
(source
(origin
(method url-fetch)
@@ -3252,7 +3285,7 @@ parts of it.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0jbdjsi0qsxahdcm42agnn1y7xpmg0hrhwjsxg0zbhs9wwy3p568"))))
+ "14iz9xnrb9xiwgj84j94mc74gg0zn2vsy9fmsijxxma1n7dck4w3"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"