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-rw-r--r--gnu/packages/maths.scm514
1 files changed, 301 insertions, 213 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 5671b83c00..d59028599f 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -7,7 +7,7 @@
;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
-;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
+;;; Copyright © 2015, 2018 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2015, 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
@@ -606,8 +606,8 @@ problems in numerical linear algebra.")
routines on parallel distributed memory machines. ScaLAPACK solves dense and
banded linear systems, least squares problems, eigenvalue problems, and
singular value problems.")
- (license (license:bsd-style "file://LICENSE"
- "See LICENSE in the distribution."))))
+ (license (license:non-copyleft "file://LICENSE"
+ "See LICENSE in the distribution."))))
(define-public gnuplot
(package
@@ -650,13 +650,13 @@ plotting engine by third-party applications like Octave.")
(version "2.0.0")
(source
(origin
- (method url-fetch)
- (uri (string-append "https://github.com/OkoSanto/GCTP/archive/v"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/OkoSanto/GCTP.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
- (base32
- "0l9aqnqynh9laicn5dxf3rsb1n14xiks79wbyqccirzmjqd1c1x4"))))
+ (base32 "11wqmd443b4nksdbzp1msdws3av948nmwq1xz80w6hka3ss2aigd"))))
(native-inputs
`(("fortran" ,gfortran)))
(build-system gnu-build-system)
@@ -887,121 +887,130 @@ extremely large and complex data collections.")
(define-public hdf-java
(package
- (name "hdf-java")
- (version "3.3.2")
- (source
- (origin
- (method url-fetch)
- (uri (string-append
- "http://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
- version "/src/CMake-hdfjava-" version ".tar.gz"))
- (sha256
- (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
- (modules '((guix build utils)))
- (snippet ; Make sure we don't use the bundled sources and binaries.
- `(begin
- (for-each delete-file
- (list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
- "HDF4.tar.gz" "HDF5.tar.gz"))
- (delete-file-recursively ,(string-append "hdfjava-" version "/lib"))
- #t))))
- (build-system gnu-build-system)
- (native-inputs
- `(("jdk" ,icedtea "jdk")
- ("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
- ;; For tests:
- ("hamcrest-core" ,java-hamcrest-core)
- ("junit" ,java-junit)
- ("slf4j-simple" ,java-slf4j-simple)))
- (inputs
- `(("hdf4" ,hdf4)
- ("hdf5" ,hdf5)
- ("zlib" ,zlib)
- ("libjpeg" ,libjpeg)
- ("slf4j-api" ,java-slf4j-api)))
- (arguments
- `(#:configure-flags
- (list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
- (string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
- (assoc-ref %build-inputs "jdk") "/lib" )
- (string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
- (string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
-
- #:make-flags
- (list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
- (string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
- (string-append "ZLIB=" (assoc-ref %build-inputs "zlib") "/lib/libz.so")
- (string-append "JPEGLIB="
- (assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so")
- "LLEXT=so")
-
- #:phases
- (modify-phases %standard-phases
- (add-before 'configure 'chdir-to-source
- (lambda _ (chdir ,(string-append "hdfjava-" version))))
- (add-before 'configure 'patch-build
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (substitute* "configure"
- (("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
- (("/bin/cat") (which "cat")))
- ;; Set classpath for compilation
- (substitute* '("hdf/hdf5lib/Makefile.in"
- "hdf/hdf5lib/exceptions/Makefile.in"
- "hdf/hdflib/Makefile.in")
- (("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
- (string-append (assoc-ref inputs "slf4j-api")
- "/share/java/slf4j-api.jar")))
- ;; Replace outdated config.sub and config.guess:
- (with-directory-excursion "config"
- (for-each (lambda (file)
- (copy-file
- (string-append (assoc-ref inputs "automake")
- "/share/automake-1.15/" file) file))
- '("config.sub" "config.guess")))
- (mkdir-p (string-append (assoc-ref outputs "out")))
- ;; Set classpath for tests
- (let* ((build-dir (getcwd))
- (lib (string-append build-dir "/lib"))
- (jhdf (string-append lib "/jhdf.jar"))
- (jhdf5 (string-append lib "/jhdf5.jar"))
- (testjars
- (map (lambda (i)
- (string-append (assoc-ref inputs i)
- "/share/java/" i ".jar"))
- '("junit" "hamcrest-core" "slf4j-api" "slf4j-simple")))
- (class-path
- (string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
-
- (substitute* '("test/hdf5lib/Makefile.in"
- "test/hdf5lib/junit.sh.in"
- "examples/runExample.sh.in")
- (("/usr/bin/test")
- (string-append (assoc-ref inputs "coreutils")
- "/bin/test"))
- (("/usr/bin/uname")
- (string-append (assoc-ref inputs "coreutils")
- "/bin/uname"))
- (("CLASSPATH=[^\n]*")
- (string-append "CLASSPATH=" class-path)))
- (setenv "CLASSPATH" class-path))
- #t))
- (add-before 'check 'build-examples
- (lambda _
- (zero? (apply system* `("javac"
- ,@(find-files "examples" ".*\\.java")))))))
+ (name "hdf-java")
+ (version "3.3.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
+ version "/src/CMake-hdfjava-" version ".tar.gz"))
+ (sha256
+ (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
+ (modules '((guix build utils)))
+ (snippet ; Make sure we don't use the bundled sources and binaries.
+ `(begin
+ (for-each delete-file
+ (list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
+ "HDF4.tar.gz" "HDF5.tar.gz"))
+ (delete-file-recursively ,(string-append "hdfjava-" version "/lib"))
+ #t))))
+ (build-system gnu-build-system)
+ (native-inputs
+ `(("jdk" ,icedtea "jdk")
+ ("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
+ ;; For tests:
+ ("hamcrest-core" ,java-hamcrest-core)
+ ("junit" ,java-junit)
+ ("slf4j-simple" ,java-slf4j-simple)))
+ (inputs
+ `(("hdf4" ,hdf4)
+ ("hdf5" ,hdf5)
+ ("zlib" ,zlib)
+ ("libjpeg" ,libjpeg)
+ ("slf4j-api" ,java-slf4j-api)))
+ (arguments
+ `(#:configure-flags
+ (list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
+ (string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
+ (assoc-ref %build-inputs "jdk") "/lib" )
+ (string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
+ (string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
- #:parallel-build? #f
+ #:make-flags
+ (list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
+ (string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
+ (string-append "ZLIB=" (assoc-ref %build-inputs "zlib") "/lib/libz.so")
+ (string-append "JPEGLIB="
+ (assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so")
+ "LLEXT=so")
- #:parallel-tests? #f ))
- (home-page "https://support.hdfgroup.org/products/java")
- (synopsis "Java interface for the HDF4 and HDF5 libraries")
- (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
+ #:phases
+ (modify-phases %standard-phases
+ (add-before 'configure 'chdir-to-source
+ (lambda _ (chdir ,(string-append "hdfjava-" version)) #t))
+ (add-before 'configure 'patch-build
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (substitute* "configure"
+ (("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
+ (("/bin/cat") (which "cat")))
+ ;; Set classpath for compilation
+ (substitute* '("hdf/hdf5lib/Makefile.in"
+ "hdf/hdf5lib/exceptions/Makefile.in"
+ "hdf/hdflib/Makefile.in")
+ (("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
+ (string-append (assoc-ref inputs "slf4j-api")
+ "/share/java/slf4j-api.jar")))
+ ;; Replace outdated config.sub and config.guess:
+ (with-directory-excursion "config"
+ (for-each (lambda (file)
+ (install-file
+ (string-append (assoc-ref inputs "automake")
+ "/share/automake-"
+ ,(version-major+minor (package-version automake))
+ "/" file) "."))
+ '("config.sub" "config.guess")))
+
+ ;; Fix embedded version number
+ (let ((hdf5version (list ,@(string-split (package-version hdf5) #\.))))
+ (substitute* "hdf/hdf5lib/H5.java"
+ (("1, 8, 19")
+ (string-join hdf5version ", "))))
+
+ (mkdir-p (string-append (assoc-ref outputs "out")))
+ ;; Set classpath for tests
+ (let* ((build-dir (getcwd))
+ (lib (string-append build-dir "/lib"))
+ (jhdf (string-append lib "/jhdf.jar"))
+ (jhdf5 (string-append lib "/jhdf5.jar"))
+ (testjars
+ (map (lambda (i)
+ (string-append (assoc-ref inputs i)
+ "/share/java/" i ".jar"))
+ '("junit" "hamcrest-core" "slf4j-api" "slf4j-simple")))
+ (class-path
+ (string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
+
+ (substitute* '("test/hdf5lib/Makefile.in"
+ "test/hdf5lib/junit.sh.in"
+ "examples/runExample.sh.in")
+ (("/usr/bin/test")
+ (string-append (assoc-ref inputs "coreutils")
+ "/bin/test"))
+ (("/usr/bin/uname")
+ (string-append (assoc-ref inputs "coreutils")
+ "/bin/uname"))
+ (("CLASSPATH=[^\n]*")
+ (string-append "CLASSPATH=" class-path)))
+ (setenv "CLASSPATH" class-path))
+ #t))
+ (add-before 'check 'build-examples
+ (lambda _
+ (apply invoke `("javac"
+ ,@(find-files "examples" ".*\\.java"))))))
+
+ #:parallel-build? #f
+
+ #:parallel-tests? #f ))
+ (home-page "https://support.hdfgroup.org/products/java")
+ (synopsis "Java interface for the HDF4 and HDF5 libraries")
+ (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are
implemented in C.")
- ;; BSD-style license:
- (license (license:x11-style
- "https://support.hdfgroup.org/ftp/HDF5/hdf-java\
+ ;; BSD-style license:
+ (license (license:x11-style
+ "https://support.hdfgroup.org/ftp/HDF5/hdf-java\
/current/src/unpacked/COPYING"))))
(define-public hdf-eos2
@@ -1344,6 +1353,38 @@ large-scale nonlinear optimization. It provides C++, C, and Fortran
interfaces.")
(license license:epl1.0)))
+(define-public clp
+ (package
+ (name "clp")
+ (version "1.17.1")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://www.coin-or.org/download/source/"
+ "Clp/Clp-" version ".tgz"))
+ (sha256
+ (base32
+ "1wdg820g3iikf9344ijwsc8sy6c0m6im42bzzizm6rlmkvnmxhk9"))
+ (modules '((guix build utils)))
+ (snippet
+ ;; Make sure we don't use the bundled software.
+ '(begin
+ (delete-file-recursively "ThirdParty")
+ #t))))
+ (build-system gnu-build-system)
+ (native-inputs
+ `(("gfortran" ,gfortran)
+ ("pkg-config" ,pkg-config)))
+ (inputs
+ `(("openblas" ,openblas)))
+ (home-page "https://www.coin-or.org")
+ (synopsis "Linear programming solver")
+ (description
+ "CLP is a high quality linear programming solver. Its main strengths are
+its dual and primal Simplex algorithms. It also has a barrier algorithm for
+linear and quadratic objectives. There are limited facilities for nonlinear
+and quadratic objectives using the Simplex algorithm.")
+ (license license:epl1.0)))
+
(define-public ceres
(package
(name "ceres-solver")
@@ -1514,15 +1555,14 @@ script files.")
(version "0.17.2")
(source
(origin
- (method url-fetch)
- (uri (string-append
- "https://github.com/tpaviot/oce/archive/OCE-"
- version
- ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/tpaviot/oce.git")
+ (commit (string-append "OCE-" version))))
+ (file-name (git-file-name name version))
(patches (search-patches "opencascade-oce-glibc-2.26.patch"))
(sha256
- (base32
- "0vpmnb0k5y2f7lpmwx9pg9yfq24zjvnsak5alzacncfm1hv9b6cd"))))
+ (base32 "0rg5wzkvfmzfl6v2amyryb8dnjad0nn9kyr607wy2gch6rciah69"))))
(build-system cmake-build-system)
(arguments
'(#:configure-flags
@@ -2166,14 +2206,14 @@ sparse system of linear equations A x = b using Guassian elimination.")
(define-public r-quadprog
(package
(name "r-quadprog")
- (version "1.5-5")
+ (version "1.5-6")
(source
(origin
(method url-fetch)
(uri (cran-uri "quadprog" version))
(sha256
(base32
- "0jg3r6abmhp8r9vkbhpx9ldjfw6vyl1m4c5vwlyjhk1mi03656fr"))))
+ "1fnwaz70dhiq4av8apc4wr3yrrpwc2i6lksf8pfi6jw8vzzyahql"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
@@ -2187,12 +2227,12 @@ programming problems.")
(define-public r-pracma
(package
(name "r-pracma")
- (version "2.2.2")
+ (version "2.2.5")
(source (origin
(method url-fetch)
(uri (cran-uri "pracma" version))
(sha256
- (base32 "18zhni05gwnxbphl6bmjjxmsgg5wwnnkwlb4g971cqyw3dsd83ki"))))
+ (base32 "0isd3s0i4mzmva8lkh0j76hwjy1w50q7d1n9lhxsnnkgalx3xs1g"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/pracma/")
(synopsis "Practical numerical math functions")
@@ -2756,12 +2796,12 @@ to BMP, JPEG or PNG image formats.")
;; of Debian's Maxima package.
;; If Maxima can successfully run this, the binary to be installed
;; should be fine.
- (zero?
- (system
- (string-append "./maxima-local "
- "--lisp=gcl "
- "--batch-string=\"run_testsuite();\" "
- "| grep -q \"No unexpected errors found\"")))))
+ (invoke "sh" "-c"
+ (string-append
+ "./maxima-local "
+ "--lisp=gcl "
+ "--batch-string=\"run_testsuite();\" "
+ "| grep -q \"No unexpected errors found\""))))
;; Make sure the doc and emacs files are found in the
;; standard location. Also configure maxima to find gnuplot
;; without having it on the PATH.
@@ -2809,7 +2849,7 @@ point numbers.")
(define-public wxmaxima
(package
(name "wxmaxima")
- (version "19.01.3")
+ (version "19.03.1")
(source
(origin
(method git-fetch)
@@ -2819,7 +2859,7 @@ point numbers.")
(file-name (git-file-name name version))
(sha256
(base32
- "1vwahx3zxkn3qlv4z0fm7v8wh0wspvs026alrh7ff7s0c2dcy95x"))))
+ "1qkf4jg86xnn3wk3782ffmfz12axb92dkjagcz3ffzw2wi1rclml"))))
(build-system cmake-build-system)
(native-inputs
`(("gettext" ,gettext-minimal)))
@@ -2911,13 +2951,13 @@ associated functions (eg. contiguous and non-contiguous submatrix views).")
(version (string-append upstream-version "-" revision))
(source
(origin
- (method url-fetch)
- (uri (string-append "https://github.com/beltoforion/muparser/archive/v"
- upstream-version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/beltoforion/muparser.git")
+ (commit (string-append "v" upstream-version))))
+ (file-name (git-file-name name version))
(sha256
- (base32
- "0277qsi5l23jsck1vhn383bmvc2n9l4a1dl5r9bf7hvjv9ayyrh6"))))
+ (base32 "0f0g4995xngf1pp3zr4p6ai2f8v6f8bxwa0k8ayjjiv1l8h44m24"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags '("--enable-samples=no")
@@ -3047,13 +3087,13 @@ underway to allow BLIS to select the right optimized kernels at run time:
(lambda* (#:key outputs #:allow-other-keys)
;; This is a home-made 'configure' script.
(let ((out (assoc-ref outputs "out")))
- (zero? (system* "./configure" "-p" out
- "-d" "opt"
- "--disable-static"
- "--enable-shared"
- "--enable-threading=openmp"
+ (invoke "./configure" "-p" out
+ "-d" "opt"
+ "--disable-static"
+ "--enable-shared"
+ "--enable-threading=openmp"
- ,implementation)))))
+ ,implementation))))
(add-before 'check 'show-test-output
(lambda _
;; By default "make check" is silent. Make it verbose.
@@ -3105,13 +3145,13 @@ access to BLIS implementations via traditional BLAS routine calls.")
(version "0.6.0")
(source
(origin
- (method url-fetch)
- (uri (string-append "https://github.com/JuliaLang/openlibm/archive/v"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/JuliaLang/openlibm.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
- (base32
- "0a5fpm8nra5ldhjk0cqd2rx1qh32wiarkxmcqcm5xl8z7l4kjm6l"))))
+ (base32 "08wfchmmr5200fvmn1kwq9byc1fhsq46hn0y5k8scdl74771c7gh"))))
(build-system gnu-build-system)
(arguments
`(#:make-flags
@@ -3144,13 +3184,13 @@ environments.")
(version "0.5.3")
(source
(origin
- (method url-fetch)
- (uri (string-append "https://github.com/JuliaLang/openspecfun/archive/v"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/JuliaLang/openspecfun.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
- (base32
- "1rs1bv8jq751fv9vq79890wqf9xlbjc7lvz3ighzyfczbyjcf18m"))))
+ (base32 "0pfw6l3ch7isz403llx7inxlvavqh01jh1hb9dpidi86sjjx9kfh"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ; no "check" target
@@ -3260,7 +3300,6 @@ packages.")
#:substitutable? #f
#:modules ((srfi srfi-26)
- (srfi srfi-1)
(guix build gnu-build-system)
(guix build utils))
#:configure-flags
@@ -3293,11 +3332,11 @@ packages.")
(let ((doc (string-append (assoc-ref outputs "doc")
"/share/doc/atlas")))
(mkdir-p doc)
- (fold (lambda (file previous)
- (and previous (zero? (system* "cp" file doc))))
- #t (find-files "../ATLAS/doc" ".*")))))
+ (for-each (cut install-file <> doc)
+ (find-files "../ATLAS/doc" ".*"))
+ #t)))
(add-after 'check 'check-pt
- (lambda _ (zero? (system* "make" "ptcheck"))))
+ (lambda _ (invoke "make" "ptcheck")))
;; Fix files required to run configure.
(add-before 'configure 'fix-/bin/sh
(lambda _
@@ -3332,9 +3371,9 @@ packages.")
(chdir "../build")
(format #t "build directory: ~s~%" (getcwd))
(format #t "configure flags: ~s~%" flags)
- (zero? (apply system* bash
- (string-append srcdir "/configure")
- flags))))))))
+ (apply invoke bash
+ (string-append srcdir "/configure")
+ flags)))))))
(synopsis "Automatically Tuned Linear Algebra Software")
(description
"ATLAS is an automatically tuned linear algebra software library
@@ -3357,7 +3396,7 @@ Failure to do so will result in a library with poor performance.")
(define-public glm
(package
(name "glm")
- (version "0.9.9.4")
+ (version "0.9.9.5")
(source
(origin
(method url-fetch)
@@ -3365,7 +3404,7 @@ Failure to do so will result in a library with poor performance.")
version "/glm-" version ".zip"))
(sha256
(base32
- "17vxbqzy4pxciq5i39bgpxz54f7ifqqmcqwwq7m6xfgikwqqqawp"))))
+ "1vmg7hb4xvsa77zpbwiw6lqc7pyaj56dihx6xriny5b9rrh4iqsg"))))
(build-system cmake-build-system)
(native-inputs
`(("unzip" ,unzip)))
@@ -3641,31 +3680,32 @@ set.")
(define-public hypre
(package
(name "hypre")
- (version "2.14.0")
- (source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/LLNL/hypre/archive/"
- "v" version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
- (sha256
- (base32
- "0v515i73bvaz378h5465b1dy9v2gf924zy2q94cpq4qqarawvkqh"))
- (modules '((guix build utils)))
- (snippet
- '(begin
- ;; Remove use of __DATE__ and __TIME__ for reproducibility;
- ;; substitute the tarball creation time.
- (substitute* "src/utilities/HYPRE_utilities.h"
- (("Date Compiled: .*$")
- "Date Compiled: Apr 11 2018 16:24:59 +0000\"\n"))
- #t))))
+ (version "2.15.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/LLNL/hypre.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1lvh4ybqkriyqfg2zmic6mrg1981qv1i9vry1fdgsabn81hb71g4"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Remove use of __DATE__ and __TIME__ for reproducibility;
+ ;; substitute the release date.
+ (substitute* "src/utilities/HYPRE_utilities.h"
+ (("Date Compiled: .*$")
+ "Date Compiled: Oct 19 2018 15:23:00 +0000\"\n"))
+ #t))))
(build-system gnu-build-system)
- (outputs '("out" ;6.1 MiB of headers and libraries
- "doc")) ;4.8 MiB of documentation
+ (outputs '("out" ; 6.1 MiB of headers and libraries
+ "doc")) ; 4.8 MiB of documentation
(native-inputs
`(("doc++" ,doc++)
("netpbm" ,netpbm)
- ("perl" ,perl) ;needed to run 'ppmquant' during tests
+ ("perl" ,perl) ; needed to run 'ppmquant' during tests
("texlive" ,(texlive-union (list texlive-generic-xypic
texlive-fonts-xypic
texlive-latex-hyperref
@@ -3711,16 +3751,14 @@ set.")
(lambda _
(setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
(setenv "PATH" (string-append "." ":" (getenv "PATH")))
- (and (system* "make" "check" "CHECKRUN=")
- (fold (lambda (filename result)
- (and result
- (let ((size (stat:size (stat filename))))
- (when (not (zero? size))
- (format #t "~a size ~d; error indication~%"
- filename size))
- (zero? size))))
- #t
- (find-files "test" ".*\\.err$")))))
+ (invoke "make" "check" "CHECKRUN=")
+ (for-each (lambda (filename)
+ (let ((size (stat:size (stat filename))))
+ (when (positive? size)
+ (error (format #f "~a size ~d; error indication~%"
+ filename size)))))
+ (find-files "test" ".*\\.err$"))
+ #t))
(add-after 'install 'install-docs
(lambda* (#:key outputs #:allow-other-keys)
;; Custom install because docs/Makefile doesn't honor ${docdir}.
@@ -3729,7 +3767,7 @@ set.")
(with-directory-excursion "docs"
(for-each (lambda (base)
(install-file (string-append base ".pdf") docdir)
- (copy-recursively base docdir)) ;html docs
+ (copy-recursively base docdir)) ; html docs
'("HYPRE_usr_manual"
"HYPRE_ref_manual")))
#t))))))
@@ -3904,10 +3942,10 @@ Longest Commons Subsequence of a set of strings.")
(assoc-ref outputs "out"))
(chmod wrapper #o555))))
(replace 'configure
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (zero? (system* "./configure"
- (string-append "--prefix="
- (assoc-ref outputs "out")))))))))
+ (lambda* (#:key outputs #:allow-other-keys)
+ (invoke "./configure"
+ (string-append "--prefix="
+ (assoc-ref outputs "out"))))))))
(inputs `(("scm" ,scm)))
(native-inputs `(("unzip" ,unzip)
("texinfo" ,texinfo)))
@@ -3943,8 +3981,7 @@ as equations, scalars, vectors, and matrices.")
#t))
(add-before 'configure 'bootstrap
(lambda _
- (zero?
- (system* "python" "scripts/mk_make.py"))))
+ (invoke "python" "scripts/mk_make.py")))
;; work around gnu-build-system's setting --enable-fast-install
;; (z3's `configure' is a wrapper around the above python file,
;; which fails when passed --enable-fast-install)
@@ -3959,12 +3996,12 @@ as equations, scalars, vectors, and matrices.")
(add-before 'check 'make-test-z3
(lambda _
;; Build the test suite executable.
- (zero? (system* "make" "test-z3" "-j"
- (number->string (parallel-job-count))))))
+ (invoke "make" "test-z3" "-j"
+ (number->string (parallel-job-count)))))
(replace 'check
(lambda _
;; Run all the tests that don't require arguments.
- (zero? (system* "./test-z3" "/a")))))))
+ (invoke "./test-z3" "/a"))))))
(native-inputs
`(("which" ,which)
("python" ,python-wrapper)))
@@ -4820,3 +4857,54 @@ implemented as callable objects, and bases of finite element spaces.")
built on top of DUNE, the Distributed and Unified Numerics Environment.")
;; Either GPL version 2 with "runtime exception" or LGPLv3+.
(license (list license:lgpl3+ license:gpl2))))
+
+(define-public mlucas
+ (package
+ (name "mlucas")
+ (version "18")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://mersenneforum.org/mayer/src/C/mlucas_v" version ".txz"))
+ (sha256
+ (base32
+ "1ax12qj9lyvnx4vs3gx7l8r3wx5gjbsdswp5f00ik9z0wz7xf297"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("python2" ,python-2)))
+ (arguments
+ `(#:tests? #f ; no tests
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'configure
+ (lambda _
+ (chdir "src")
+ (call-with-output-file "Makefile"
+ (lambda (port)
+ (format port "CC = gcc
+CFLAGS = -O3 ~a -DUSE_THREADS
+LDLIBS = -lm -lpthread -lrt
+Mlucas: $(addsuffix .o,$(basename $(wildcard *.c)))
+"
+ ,(let ((system (or (%current-target-system)
+ (%current-system))))
+ (cond
+ ((string-prefix? "x86_64" system) "-DUSE_SSE2")
+ (else ""))))))
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (install-file "Mlucas" bin)
+ (install-file "primenet.py" bin))
+ #t)))))
+ (home-page "https://www.mersenne.org")
+ (synopsis "Great Internet Mersenne Prime Search (GIMPS) distributed computing client")
+ (description "Mlucas performs Lucas-Lehmer primality testing of Mersenne
+numbers in search of a world-record prime. You may use it to test any
+suitable number as you wish, but it is preferable that you do so in a
+coordinated fashion, as part of the Great Internet Mersenne Prime
+Search (GIMPS). Mlucas also includes a simple Python script for assignment
+management via the GIMPS project's Primenet server.")
+ (license license:gpl2+)))
generated by cgit v1.2.3 (git 2.45.0) at 2024-11-23 22:52:38 +0000