diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 240 |
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") |