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-rw-r--r--gnu/packages/maths.scm240
1 files changed, 185 insertions, 55 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 962bcd8278..f183cce8b3 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -14,11 +14,12 @@
;;; Copyright © 2016 Kei Kebreau <kkebreau@posteo.net>
;;; Copyright © 2016, 2017 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
-;;; Copyright © 2016 Thomas Danckaert <post@thomasdanckaert.be>
+;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
;;; Copyright © 2017 Paul Garlick <pgarlick@tourbillion-technology.com>
;;; Copyright © 2017 ng0 <contact.ng0@cryptolab.net>
;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
-;;; Copyright © 2017 Theodoros Foradis <theodoros.for@openmailbox.org>
+;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
+;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -69,6 +70,7 @@
#:use-module (gnu packages graphviz)
#:use-module (gnu packages gtk)
#:use-module (gnu packages image)
+ #:use-module (gnu packages java)
#:use-module (gnu packages less)
#:use-module (gnu packages lisp)
#:use-module (gnu packages logging)
@@ -456,13 +458,14 @@ large scale eigenvalue problems.")
;; Build the 'LAPACKE_clatms' functions.
"-DLAPACKE_WITH_TMG=ON")
- #:phases (alist-cons-before
- 'check 'patch-python
- (lambda* (#:key inputs #:allow-other-keys)
- (let ((python (assoc-ref inputs "python")))
- (substitute* "lapack_testing.py"
- (("/usr/bin/env python") python))))
- %standard-phases)))
+ #:phases
+ (modify-phases %standard-phases
+ (add-before 'check 'patch-python
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((python (assoc-ref inputs "python")))
+ (substitute* "lapack_testing.py"
+ (("/usr/bin/env python") python)))
+ #t)))))
(synopsis "Library for numerical linear algebra")
(description
"LAPACK is a Fortran 90 library for solving the most commonly occurring
@@ -742,6 +745,124 @@ extremely large and complex data collections.")
(license (license:x11-style
"http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
+(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"))))))
+ (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")))))))
+
+ #: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\
+/current/src/unpacked/COPYING"))))
+
(define-public hdf-eos2
(package
(name "hdf-eos2")
@@ -1126,7 +1247,7 @@ can solve two kinds of problems:
(license license:bsd-3)))
;; For a fully featured Octave, users are strongly recommended also to install
-;; the following packages: texinfo, less, ghostscript, gnuplot.
+;; the following packages: less, ghostscript, gnuplot.
(define-public octave
(package
(name "octave")
@@ -1158,6 +1279,7 @@ can solve two kinds of problems:
("glu" ,glu)
("zlib" ,zlib)
("curl" ,curl)
+ ("texinfo" ,texinfo)
("graphicsmagick" ,graphicsmagick)))
(native-inputs
`(("lzip" ,lzip)
@@ -1172,14 +1294,23 @@ can solve two kinds of problems:
;; will still run without them, albeit without the features they
;; provide.
("less" ,less)
- ("texinfo" ,texinfo)
("ghostscript" ,ghostscript)
("gnuplot" ,gnuplot)))
(arguments
`(#:configure-flags
(list (string-append "--with-shell="
(assoc-ref %build-inputs "bash")
- "/bin/sh"))))
+ "/bin/sh"))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'configure 'configure-makeinfo
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "libinterp/corefcn/help.cc"
+ (("Vmakeinfo_program = \"makeinfo\"")
+ (string-append "Vmakeinfo_program = \""
+ (assoc-ref inputs "texinfo")
+ "/bin/makeinfo\"")))
+ #t)))))
(home-page "https://www.gnu.org/software/octave/")
(synopsis "High-level language for numerical computation")
(description "GNU Octave is a high-level interpreted language that is
@@ -1866,12 +1997,12 @@ void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
(arguments
`(#:parallel-build? #f ;race conditions using ar
#:phases
- (alist-replace
- 'configure
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (call-with-output-file "make.inc"
- (lambda (port)
- (format port "
+ (modify-phases %standard-phases
+ (replace 'configure
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (call-with-output-file "make.inc"
+ (lambda (port)
+ (format port "
PLAT =
DSuperLUroot = ~a
DSUPERLULIB = ~a/lib/libsuperlu_dist.a
@@ -1894,47 +2025,46 @@ FORTRAN = mpifort
FFLAGS = -O2 -g $(PIC)
LOADER = $(CC)
CDEFS = -DAdd_"
- (getcwd)
- (assoc-ref outputs "out")
- (assoc-ref inputs "lapack")
- (assoc-ref inputs "pt-scotch")))))
- (alist-cons-after
- 'unpack 'remove-broken-symlinks
- (lambda _
- (for-each delete-file
- (find-files "MAKE_INC" "\\.#make\\..*")))
- (alist-cons-before
- 'build 'create-install-directories
- (lambda* (#:key outputs #:allow-other-keys)
- (for-each
- (lambda (dir)
- (mkdir-p (string-append (assoc-ref outputs "out")
- "/" dir)))
- '("lib" "include")))
- (alist-replace
- 'check
+ (getcwd)
+ (assoc-ref outputs "out")
+ (assoc-ref inputs "lapack")
+ (assoc-ref inputs "pt-scotch"))))
+ #t))
+ (add-after 'unpack 'remove-broken-symlinks
+ (lambda _
+ (for-each delete-file
+ (find-files "MAKE_INC" "\\.#make\\..*"))
+ #t))
+ (add-before 'build 'create-install-directories
+ (lambda* (#:key outputs #:allow-other-keys)
+ (for-each
+ (lambda (dir)
+ (mkdir-p (string-append (assoc-ref outputs "out")
+ "/" dir)))
+ '("lib" "include"))
+ #t))
+ (replace 'check
(lambda _
(with-directory-excursion "EXAMPLE"
(and
(zero? (system* "mpirun" "-n" "2"
"./pddrive" "-r" "1" "-c" "2" "g20.rua"))
(zero? (system* "mpirun" "-n" "2"
- "./pzdrive" "-r" "1" "-c" "2" "cg20.cua")))))
- (alist-replace
- 'install
- (lambda* (#:key outputs #:allow-other-keys)
- ;; Library is placed in lib during the build phase. Copy over
- ;; headers to include.
- (let* ((out (assoc-ref outputs "out"))
- (incdir (string-append out "/include")))
- (for-each (lambda (file)
- (let ((base (basename file)))
- (format #t "installing `~a' to `~a'~%"
- base incdir)
- (copy-file file
- (string-append incdir "/" base))))
- (find-files "SRC" ".*\\.h$"))))
- %standard-phases)))))))
+ "./pzdrive" "-r" "1" "-c" "2" "cg20.cua"))))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; Library is placed in lib during the build phase. Copy over
+ ;; headers to include.
+ (let* ((out (assoc-ref outputs "out"))
+ (incdir (string-append out "/include")))
+ (for-each (lambda (file)
+ (let ((base (basename file)))
+ (format #t "installing `~a' to `~a'~%"
+ base incdir)
+ (copy-file file
+ (string-append incdir "/" base))))
+ (find-files "SRC" ".*\\.h$")))
+ #t)))))
(home-page (package-home-page superlu))
(synopsis "Parallel supernodal direct solver")
(description
@@ -2621,7 +2751,7 @@ access to BLIS implementations via traditional BLAS routine calls.")
(list (string-append "prefix=" (assoc-ref %outputs "out")))
#:phases
;; no configure script
- (alist-delete 'configure %standard-phases)
+ (modify-phases %standard-phases (delete 'configure))
#:tests? #f)) ;the tests are part of the default target
(home-page "http://openlibm.org/")
(synopsis "Portable C mathematical library (libm)")
@@ -2660,7 +2790,7 @@ environments.")
#:make-flags
(list (string-append "prefix=" (assoc-ref %outputs "out")))
;; no configure script
- #:phases (alist-delete 'configure %standard-phases)))
+ #:phases (modify-phases %standard-phases (delete 'configure))))
(inputs
`(("fortran" ,gfortran)))
(home-page "https://github.com/JuliaLang/openspecfun")
generated by cgit v1.2.3 (git 2.45.2) at 2024-07-22 20:34:01 +0000