;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2013, 2014, 2015
, 2016 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
-;;; Copyright © 2014 John Darrington <jmd@gnu.org>
-;;; Copyright © 2014, 2015 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2014, 2016 John Darrington <jmd@gnu.org>
+;;; Copyright © 2014, 2015, 2016 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
-;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
+;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module (guix build utils)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
+ #:use-module (guix build-system r)
#:use-module (gnu packages algebra)
#:use-module (gnu packages bison)
#:use-module (gnu packages boost)
#:use-module (gnu packages cmake)
#:use-module (gnu packages compression)
#:use-module (gnu packages curl)
+ #:use-module (gnu packages documentation)
#:use-module (gnu packages elf)
#:use-module (gnu packages flex)
#:use-module (gnu packages fltk)
#:use-module (gnu packages gcc)
#:use-module (gnu packages gd)
#:use-module (gnu packages ghostscript)
- #:use-module (gnu packages glib)
#:use-module (gnu packages gtk)
#:use-module (gnu packages image)
#:use-module (gnu packages less)
#:use-module (gnu packages lisp)
#:use-module (gnu packages gnome)
+ #:use-module (gnu packages guile)
#:use-module (gnu packages xorg)
#:use-module (gnu packages gl)
#:use-module (gnu packages m4)
#:use-module (gnu packages mpi)
#:use-module (gnu packages multiprecision)
+ #:use-module (gnu packages netpbm)
#:use-module (gnu packages pcre)
#:use-module (gnu packages popt)
#:use-module (gnu packages perl)
#:use-module (gnu packages zip)
#:use-module (srfi srfi-1))
+(define-public c-graph
+ (package
+ (name "c-graph")
+ (version "2.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://gnu/c-graph/c-graph-" version
+ ".tar.gz"))
+ (sha256 (base32
+ "1hlvpzrh7hzzf533diyfiabzskddi8zx92av9hwkjw3l46z7qv01"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("fortran" ,gfortran)))
+ (synopsis "Visualize and analyze convolution operations")
+ (description
+ "GNU C-Graph demonstrates the theory of convolution underlying
+engineering systems and signal analysis.")
+ (license license:gpl3+)
+ (home-page "http://www.gnu.org/software/c-graph/")))
+
(define-public units
(package
(name "units")
(define-public glpk
(package
(name "glpk")
- (version "4.58")
+ (version "4.60")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "1jmrya04hgwnrxrqqs40i6m9cqka3q601cx3nh9ijyvlg90zlq24"))))
+ "15z2ymzqhxwss6wgdj5f7vkyqlqdsjgrvm0x871kmlx0n0664mhk"))))
(build-system gnu-build-system)
(inputs
`(("gmp" ,gmp)))
LP/MIP solver is included in the package.")
(license license:gpl3+)))
-(define-public pspp
+(define-public 4ti2
(package
- (name "pspp")
- (version "0.8.5")
+ (name "4ti2")
+ (version "1.6.7")
(source
(origin
(method url-fetch)
- (uri (string-append "mirror://gnu/pspp/pspp-"
- version ".tar.gz"))
+ (uri (string-append "http://www.4ti2.de/version_" version
+ "/4ti2-" version ".tar.gz"))
(sha256
(base32
- "0c8326yykidi94xi7jn27j8iqxc38vc07d4wf5zyk0l8lpzx5vz7"))))
+ "1frix3rnm9ffr93alqzw4cavxbfpf524l8rfbmcpyhwd3n1km0yl"))))
(build-system gnu-build-system)
- (inputs
- `(("cairo" ,cairo)
- ("fontconfig" ,fontconfig)
- ("gettext" ,gnu-gettext)
- ("gsl" ,gsl)
- ("libxml2" ,libxml2)
- ("pango" ,pango)
- ("readline" ,readline)
- ("gtk" ,gtk+-2)
- ("gtksourceview" ,gtksourceview-2)
- ("zlib" ,zlib)))
(native-inputs
- `(("glib" ,glib "bin") ;for glib-genmarshal
- ("perl" ,perl)
- ("texinfo" ,texinfo)
- ("pkg-config" ,pkg-config)))
- (home-page "http://www.gnu.org/software/pspp/")
- (synopsis "Statistical analysis")
+ `(("which" ,(@ (gnu packages base) which)))) ; for the tests
+ (inputs
+ `(("glpk" ,glpk)
+ ("gmp" ,gmp)))
+ (home-page "http://www.4ti2.de/")
+ (synopsis "Mathematical tool suite for problems on linear spaces")
(description
- "GNU PSPP is a statistical analysis program. It can perform
-descriptive statistics, T-tests, linear regression and non-parametric tests.
-It features both a graphical interface as well as command-line input. PSPP
-is designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data
-can be imported from spreadsheets, text files and database sources and it can
-be output in text, PostScript, PDF or HTML.")
- (license license:gpl3+)))
+ "4ti2 implements algorithms for solving algebraic, geometric and
+combinatorial problems on linear spaces. Among others, it solves systems
+of linear equations, computes extreme rays of polyhedral cones, solves
+integer programming problems and computes Markov bases for statistics.")
+ (license license:gpl2+)))
+
+(define-public cddlib
+ (package
+ (name "cddlib")
+ (version "0.94h")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "ftp://ftp.ifor.math.ethz.ch/pub/fukuda/cdd/cddlib-"
+ (string-delete #\. version) ".tar.gz"))
+ (sha256
+ (base32
+ "1dasasscwfg793q8fwzgwf64xwj7w62yfvszpr8x8g38jka08vgy"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("gmp" ,gmp)))
+ (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
+ (synopsis "Library for convex hulls and extreme rays of polyhedra")
+ (description
+ "The C-library cddlib implements the Double Description Method of
+Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
+rays of a general convex polyhedron given by a system of linear inequalities
+in arbitrary dimension. It can also be used for the converse operation of
+computing convex hulls.")
+ (license license:gpl2+)))
(define-public arpack-ng
(package
(define-public hdf5
(package
(name "hdf5")
- (version "1.8.12")
+ (version "1.8.17")
(source
(origin
(method url-fetch)
version "/src/hdf5-"
version ".tar.bz2"))
(sha256
- (base32 "0f9n0v3p3lwc7564791a39c6cn1d3dbrn7d1j3ikqsi27a8hy23d"))))
+ (base32 "0sj8x0gfs5fb28gipnynb9wpkz113h8wq9sva9mxx66kv27xsdgw"))
+ (patches (list (search-patch "hdf5-config-date.patch")))))
(build-system gnu-build-system)
(inputs
`(("zlib" ,zlib)))
(arguments
`(#:phases
- (alist-cons-before
- 'configure 'patch-configure
- (lambda _
- (substitute* "configure"
- (("/bin/mv") "mv")))
- %standard-phases)))
+ (modify-phases %standard-phases
+ (add-before 'configure 'patch-configure
+ (lambda _
+ (substitute* "configure"
+ (("/bin/mv") "mv"))
+ #t))
+ (add-after 'install 'patch-references
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
+ (zlib (assoc-ref inputs "zlib")))
+ (substitute* (find-files bin "h5p?cc")
+ (("-lz" lib)
+ (string-append "-L" zlib "/lib " lib)))
+ #t))))))
(home-page "http://www.hdfgroup.org")
(synopsis "Management suite for extremely large and complex data")
(description "HDF5 is a suite that makes possible the management of
(license (license:x11-style
"http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
+(define-public hdf5-parallel-openmpi
+ (package (inherit hdf5)
+ (name "hdf5-parallel-openmpi")
+ (inputs
+ `(("mpi" ,openmpi)
+ ,@(package-inputs hdf5)))
+ (arguments
+ (substitute-keyword-arguments `(#:configure-flags '("--enable-parallel")
+ ,@(package-arguments hdf5))
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (add-before 'check 'patch-tests
+ (lambda _
+ ;; OpenMPI's mpirun will exit with non-zero status if it
+ ;; detects an "abnormal termination", i.e. any process not
+ ;; calling MPI_Finalize(). Since the test is explicitely
+ ;; avoiding MPI_Finalize so as not to have at_exit and thus
+ ;; H5C_flush_cache from being called, mpirun will always
+ ;; complain, so turn this test off.
+ (substitute* "testpar/Makefile"
+ (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
+ (string-append front back "\n")))
+ (substitute* "tools/h5diff/testph5diff.sh"
+ (("/bin/sh") (which "sh")))
+ #t))))))
+ (synopsis "Management suite for data with parallel IO support")))
+
+(define-public h5check
+ (package
+ (name "h5check")
+ (version "2.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/"
+ "h5check/src/h5check-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
+ (build-system gnu-build-system)
+ (inputs `(("hdf5" ,hdf5))) ;h5cc for tests
+ (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
+ (synopsis "HDF5 format checker")
+ (description "@code{h5check} is a validation tool for verifying that an
+HDF5 file is encoded according to the HDF File Format Specification.")
+ (license (license:x11-style "file://COPYING"))))
+
+(define-public nlopt
+ (package
+ (name "nlopt")
+ (version "2.4.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
+ version ".tar.gz"))
+ (sha256
+ (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(;; Shared libraries are not built by default. They are required to
+ ;; build the Guile, Octave, and Python bindings.
+ #:configure-flags '("--enable-shared")
+
+ #:phases
+ (modify-phases %standard-phases
+ (add-before 'configure 'set-libnlopt-file-name
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; Make sure the Scheme module refers to the library by its
+ ;; absolute file name (we cannot do that from a snippet
+ ;; because the expansion of @libdir@ contains
+ ;; ${exec_prefix}.)
+ (let ((out (assoc-ref outputs "out")))
+ (substitute* "swig/nlopt.scm.in"
+ (("libnlopt")
+ (string-append out "/lib/libnlopt")))
+ #t))))))
+ (inputs `(("guile" ,guile-2.0)))
+ (native-inputs `(("pkg-config" ,pkg-config)))
+ (home-page "http://ab-initio.mit.edu/wiki/")
+ (synopsis "Library for nonlinear optimization")
+ (description "NLopt is a library for nonlinear optimization, providing a
+common interface for a number of different free optimization routines available
+online as well as original implementations of various other algorithms.")
+ (license license:lgpl2.1+)))
;; For a fully featured Octave, users are strongly recommended also to install
;; the following packages: texinfo, less, ghostscript, gnuplot.
'install 'clean-install
;; Try to keep installed files from leaking build directory names.
(lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out"))
- (fortran (assoc-ref inputs "gfortran")))
+ (let ((out (assoc-ref outputs "out")))
(substitute* (map (lambda (file)
(string-append out "/lib/petsc/conf/" file))
'("petscvariables" "PETScConfig.cmake"))
(((getcwd)) out))
;; Make compiler references point to the store
(substitute* (string-append out "/lib/petsc/conf/petscvariables")
- (("= g(cc|\\+\\+|fortran)" _ suffix)
- (string-append "= " fortran "/bin/g" suffix)))
+ (("= (gcc|g\\+\\+|gfortran)" _ compiler)
+ (string-append "= " (which compiler))))
;; PETSc installs some build logs, which aren't necessary.
(for-each (lambda (file)
(let ((f (string-append out "/lib/petsc/conf/" file)))
(method url-fetch)
(uri (string-append "http://slepc.upv.es/download/download.php?"
"filename=slepc-" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1pv5iqz2kc8sj49zsabyz4arnfpana8mjrhq31vzgk16xldk3d1a"))))
(sha256
(base32
"1820jfp3mbl7n85765v5mp6p0gzqpgr4d2lrnhwj4gl7cwp5ndah"))
- (patches (list (search-patch "mumps-build-parallelism.patch")))))
+ (patches (search-patches "mumps-build-parallelism.patch"))))
(build-system gnu-build-system)
(inputs
`(("fortran" ,gfortran)
(inputs
(alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
+(define-public r-pracma
+ (package
+ (name "r-pracma")
+ (version "1.8.8")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "pracma" version))
+ (sha256
+ (base32 "0ans9l5rrb7a38gyi4qx4258sd5r5668vyrk02yzjpg9k3h8l165"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/pracma")
+ (synopsis "Practical numerical math functions")
+ (description "This package provides functions for numerical analysis and
+linear algebra, numerical optimization, differential equations, plus some
+special functions. It uses Matlab function names where appropriate to simplify
+porting.")
+ (license license:gpl3+)))
+
(define-public superlu
(package
(name "superlu")
"superlu_dist_" version ".tar.gz"))
(sha256
(base32 "1hnak09yxxp026blq8zhrl7685yip16svwngh1wysqxf8z48vzfj"))
- (patches (list (search-patch "superlu-dist-scotchmetis.patch")))))
+ (patches (search-patches "superlu-dist-scotchmetis.patch"))))
(build-system gnu-build-system)
(native-inputs
`(("tcsh" ,tcsh)))
"scotch_" version ".tar.gz"))
(sha256
(base32 "1ir088mvrqggyqdkx9qfynmiaffqbyih5qfl5mga2nrlm1qlsgzm"))
- (patches (list (search-patch "scotch-test-threading.patch")
- (search-patch "pt-scotch-build-parallelism.patch")))))
+ (patches (search-patches "scotch-test-threading.patch"
+ "pt-scotch-build-parallelism.patch"))))
(build-system gnu-build-system)
(inputs
`(("zlib" ,zlib)
(sha256
(base32
"0x1rk659sn3cq0n5c90848ilzr1gb1wf0072fl6jhkdq00qgh2s0"))
- (patches (list (search-patch "maxima-defsystem-mkdir.patch")))))
+ (patches (search-patches "maxima-defsystem-mkdir.patch"))))
(build-system gnu-build-system)
(inputs
`(("gcl" ,gcl)
(define-public armadillo
(package
(name "armadillo")
- (version "6.400.3")
+ (version "6.700.4")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/arma/armadillo-"
version ".tar.gz"))
(sha256
(base32
- "0bsgrmldlx77w5x26n3axj1hg6iw6csyw0dwl1flrbdwl51f9701"))))
+ "0dsdjcps5l2nhg0455rrc708inffarzj7n435vj4sm9lxwf21wg9"))))
(build-system cmake-build-system)
(arguments `(#:tests? #f)) ;no test target
(inputs
(define-public armadillo-for-rcpparmadillo
(package (inherit armadillo)
- (version "6.200.2")
+ (version "6.700.3")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/arma/armadillo-"
version ".tar.gz"))
(sha256
(base32
- "1f69rlqhnf2wv8khyn2a8vi6gx1i72qgfy8b9b760ssk85dcl763"))))))
+ "1vnhifa7d0aij3kv5bxf6m91d99h3y2fyj48jrx7jcvwyb1q5wwq"))))))
(define-public muparser
(package
(sha256
(base32
"185jych0gdnpkjwxni7pd0dda149492zwq2457xdjg76bzj78mnp"))
- (patches (list (search-patch "dealii-p4est-interface.patch")))
+ (patches (search-patches "dealii-p4est-interface.patch"))
(modules '((guix build utils)))
(snippet
;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
set.")
(home-page "http://www.gnu.org/software/xaos/")
(license license:gpl2+)))
+
+(define-public hypre
+ (package
+ (name "hypre")
+ (version "2.11.0")
+ (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
+ "0q69ia0jivzcr8p049dn3mg8yjpn6nwq4sw9iqac8vr63vi54l6m"))
+ (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: Mar 28 2016 20:19:59 +0000\"\n"))
+ #t))))
+ (build-system gnu-build-system)
+ (outputs '("out" ;6.1 MiB of headers and libraries
+ "doc")) ;4.8 MiB of documentation
+ (native-inputs
+ `(("doc++" ,doc++)
+ ("netpbm" ,netpbm)
+ ("texlive" ,texlive) ;full package required for fonts
+ ("ghostscript" ,ghostscript)))
+ (inputs
+ `(("blas" ,openblas)
+ ("lapack" ,lapack)))
+ (arguments
+ `(#:modules ((srfi srfi-1)
+ ,@%gnu-build-system-modules)
+ #:configure-flags '("--enable-shared"
+ "--disable-fortran"
+ "--without-MPI"
+ "--with-openmp"
+ "--with-fei"
+ "--with-lapack"
+ "--with-blas")
+ #:phases
+ (modify-phases %standard-phases
+ (add-before 'configure 'chdir-src
+ (lambda _ (chdir "src")))
+ (replace 'configure
+ (lambda* (#:key build target configure-flags
+ #:allow-other-keys #:rest args)
+ (let* ((configure (assoc-ref %standard-phases 'configure)))
+ (apply configure
+ (append args
+ (list #:configure-flags
+ (cons (string-append
+ "--host=" (or target build))
+ configure-flags)))))))
+ (add-after 'build 'build-docs
+ (lambda _
+ (zero? (system* "make" "-Cdocs" "pdf" "html"))))
+ (replace 'check
+ (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$")))))
+ (add-after 'install 'install-docs
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; Custom install because docs/Makefile doesn't honor ${docdir}.
+ (let* ((doc (assoc-ref outputs "doc"))
+ (docdir (string-append doc "/share/doc/hypre-" ,version)))
+ (mkdir-p docdir)
+ (with-directory-excursion "docs"
+ (for-each (lambda (base)
+ (install-file (string-append base ".pdf") docdir)
+ (copy-recursively base docdir)) ;html docs
+ '("HYPRE_usr_manual"
+ "HYPRE_ref_manual")))
+ #t))))))
+ (home-page "http://www.llnl.gov/casc/hypre/")
+ (synopsis "Library of solvers and preconditioners for linear equations")
+ (description
+ "HYPRE is a software library of high performance preconditioners and
+solvers for the solution of large, sparse linear systems of equations. It
+features multigrid solvers for both structured and unstructured grid
+problems.")
+ (license license:lgpl2.1)))
+
+(define-public hypre-openmpi
+ (package (inherit hypre)
+ (name "hypre-openmpi")
+ (inputs
+ `(("mpi" ,openmpi)
+ ,@(package-inputs hypre)))
+ (arguments
+ (substitute-keyword-arguments (package-arguments hypre)
+ ((#:configure-flags flags)
+ ``("--with-MPI"
+ ,@(delete "--without-MPI" ,flags)))))
+ (synopsis "Parallel solvers and preconditioners for linear equations")
+ (description
+ "HYPRE is a software library of high performance preconditioners and
+solvers for the solution of large, sparse linear systems of equations on
+parallel computers. It features parallel multigrid solvers for both
+structured and unstructured grid problems.")))
HCoop / jackhill / guix / guix.git / blobdiff