;;; Copyright © 2013, 2014, 2015, 2016 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
;;; Copyright © 2014, 2016, 2017 John Darrington <jmd@gnu.org>
-;;; Copyright © 2014, 2015, 2016 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2014, 2015, 2016, 2017 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
;;; 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>
;;;
;;; This file is part of GNU Guix.
;;;
(define-public glpk
(package
(name "glpk")
- (version "4.62")
+ (version "4.63")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "0w7s3869ybwyq9a4490dikpib1qp3jnn5nqz1vvwqy1qz3ilnvh9"))))
+ "1xp7nclmp8inp20968bvvfcwmz3mz03sbm0v3yjz8aqwlpqjfkci"))))
(build-system gnu-build-system)
(inputs
`(("gmp" ,gmp)))
(define-public hdf4
(package
(name "hdf4")
- (version "4.2.12")
+ (version "4.2.13")
(source
(origin
(method url-fetch)
(uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
version "/src/hdf-" version ".tar.bz2"))
(sha256
- (base32 "020jh563sjyxsgml8l809d2i1d4ms9shivwj3gbm7n0ilxbll8id"))
+ (base32 "1wz0586zh91pqb95wvr0pbh71a8rz358fdj6n2ksp85x2cis9lsm"))
(patches (search-patches "hdf4-architectures.patch"
"hdf4-reproducibility.patch"
"hdf4-shared-fortran.patch"))))
-
(build-system gnu-build-system)
(native-inputs
`(("gfortran" ,gfortran)
#:configure-flags '("--enable-shared")
#:phases
(modify-phases %standard-phases
+ ;; This is inspired by two of Debian's patches.
+ (add-before 'configure 'add-more-aarch64-support
+ (lambda _
+ (substitute* '("mfhdf/ncgen/ncgen.l"
+ "mfhdf/ncgen/ncgenyy.c"
+ "mfhdf/libsrc/netcdf.h.in")
+ (("AIX5L64") "__aarch64__"))
+ #t))
(add-before 'configure 'patchbuild
(lambda _
(substitute*
-R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
(("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
-R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
--R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") "")))))))
+-R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
+ #t)))))
(home-page "https://www.hdfgroup.org/products/hdf4/")
(synopsis
"Library and multi-object file format for storing and managing data")
(define-public petsc
(package
(name "petsc")
- (version "3.7.2")
+ (version "3.7.6")
(source
(origin
(method url-fetch)
(uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
"petsc-lite-" version ".tar.gz"))
(sha256
- (base32 "0jfrq6rd4zagw1iimz05m2w91k0jvz3qbik1lk8pqcxw3rvdqk5d"))))
+ (base32 "1y3f5jjq0v5b62i3sabp4kp5mgfyp3vnk0dxhwkrhpypax77nzxh"))))
(build-system gnu-build-system)
(native-inputs
`(("python" ,python-2)
(assoc-ref %build-inputs "superlu") "/include")
,(string-append "--with-superlu-lib="
(assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a"))
+ #:make-flags
+ ;; Honor (parallel-job-count) for build. Do not use --with-make-np,
+ ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
+ (list (format #f "MAKE_NP=~a" (parallel-job-count)))
#:phases
(modify-phases %standard-phases
(replace 'configure
(format #t "configure flags: ~s~%" flags)
(zero? (apply system* "./configure" flags)))))
(add-after 'configure 'clean-local-references
- (lambda* (#:key inputs outputs #:allow-other-keys)
+ (lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(substitute* (find-files "." "^petsc(conf|machineinfo).h$")
;; Prevent build directory from leaking into compiled code
(((getcwd)) out)
;; Scrub timestamp for reproducibility
((".*Libraries compiled on.*") ""))
+ (substitute* (find-files "." "petscvariables")
+ ;; Do not expose build machine characteristics, set to defaults.
+ (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
+ (("NPMAX = [:digit:]+") "NPMAX = 2"))
#t)))
(add-after 'install 'clean-install
;; Try to keep installed files from leaking build directory names.
(define-public slepc
(package
(name "slepc")
- (version "3.7.1")
+ (version "3.7.4")
(source
(origin
(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"))
+ (uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
+ version ".tar.gz"))
(sha256
(base32
- "1hijlmrvxvfqslnx8yydzw5xqbsn1yy02g32w0hln1z3cgr1c0k7"))))
+ "12pbl8yd6r8k9xjlr1qw25rs0k1acgic7hw1s6l6bhiv9s285drg"))))
(build-system gnu-build-system)
(native-inputs
`(("python" ,python-2)))
#:configure-flags
`(,(string-append "--with-arpack-dir="
(assoc-ref %build-inputs "arpack") "/lib"))
+ #:make-flags ;honor (parallel-job-count)
+ `(,(format #f "MAKE_NP=~a" (parallel-job-count)))
#:phases
(modify-phases %standard-phases
(replace 'configure
(define-public r-pracma
(package
(name "r-pracma")
- (version "2.0.4")
+ (version "2.0.7")
(source (origin
(method url-fetch)
(uri (cran-uri "pracma" version))
(sha256
- (base32 "1z3i90mkzwvp9di17caf4934z2xlb2imm3hwxllcrbwvmnmhrwyc"))))
+ (base32 "0hxa0rbbp54j0c05qj7vfwhqfdmiz5ax8vhqxd09g33x7c0hqbc5"))))
(build-system r-build-system)
(propagated-inputs
`(("r-quadprog" ,r-quadprog)))
(patches (search-patches "maxima-defsystem-mkdir.patch"))))
(build-system gnu-build-system)
(inputs
- `(("gcc" ,gcc)
- ("gcl" ,gcl)
+ `(("gcl" ,gcl)
("gnuplot" ,gnuplot) ;for plots
("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
(native-inputs
#:make-flags (list "TMPDIR=/tmp")
#:phases
(modify-phases %standard-phases
- (add-before 'configure 'set-gcc-path
- (lambda* (#:key inputs #:allow-other-keys)
- (substitute* "lisp-utils/defsystem.lisp"
- (("\\(defparameter \\*c-compiler\\* \"gcc\"\\)")
- (string-append "(defparameter *c-compiler* \""
- (assoc-ref inputs "gcc") "/bin/gcc\")")))
- #t))
(add-before 'check 'pre-check
(lambda _
(chmod "src/maxima" #o555)
(lambda* (#:key outputs inputs #:allow-other-keys)
(let* ((gnuplot (assoc-ref inputs "gnuplot"))
(out (assoc-ref outputs "out"))
- (datadir (string-append out "/share/maxima/" ,version)))
+ (datadir (string-append out "/share/maxima/" ,version))
+ (binutils (string-append (assoc-ref inputs "binutils")
+ "/bin")))
(with-directory-excursion out
(mkdir-p "share/emacs")
(mkdir-p "share/doc")
(format out "~a ~s~a~%"
"(setf $gnuplot_command "
(string-append gnuplot "/bin/gnuplot") ")")
- (dump-port in out)))))
+ (dump-port in out))))
+ ;; Ensure that Maxima will have access to the GNU binutils
+ ;; components at runtime.
+ (wrap-program (string-append out "/bin/maxima")
+ `("PATH" prefix (,binutils))))
#t)))))
(home-page "http://maxima.sourceforge.net")
(synopsis "Numeric and symbolic expression manipulation")
(define-public wxmaxima
(package
(name "wxmaxima")
- (version "17.05.0")
+ (version "17.05.1")
(source
(origin
(method url-fetch)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1bsyd7r12xm2crpizb9iyyki3j0mbazzzwbsh871m06dv2wk97gq"))))
+ "0dv0cy0cf46v0cbw32izscpkdmpxg1qhwq1f4cz46kkqd8k4yfbj"))))
(build-system gnu-build-system)
(native-inputs
`(("autoconf" ,autoconf)
("gtk+" ,gtk+)
("shared-mime-info" ,shared-mime-info)))
(arguments
- `(#:phases (modify-phases %standard-phases
- (add-before
- 'configure 'autoconf
- (lambda _
- (zero? (system* "./bootstrap"))))
- (add-after
- 'install 'wrap-program
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (wrap-program (string-append (assoc-ref outputs "out")
- "/bin/wxmaxima")
- `("PATH" ":" prefix
- (,(string-append (assoc-ref inputs "maxima")
- "/bin")))
- ;; For GtkFileChooserDialog.
- `("GSETTINGS_SCHEMA_DIR" =
- (,(string-append (assoc-ref inputs "gtk+")
- "/share/glib-2.0/schemas")))
- `("XDG_DATA_DIRS" ":" prefix
- (;; Needed by gdk-pixbuf to know supported icon formats.
- ,(string-append
- (assoc-ref inputs "shared-mime-info") "/share")
- ;; The default icon theme of GTK+.
- ,(string-append
- (assoc-ref inputs "adwaita-icon-theme") "/share"))))
- #t)))))
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'autoconf
+ (lambda _
+ (zero? (system* "sh" "bootstrap"))))
+ (add-after 'install 'wrap-program
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (wrap-program (string-append (assoc-ref outputs "out")
+ "/bin/wxmaxima")
+ `("PATH" ":" prefix
+ (,(string-append (assoc-ref inputs "maxima")
+ "/bin")))
+ ;; For GtkFileChooserDialog.
+ `("GSETTINGS_SCHEMA_DIR" =
+ (,(string-append (assoc-ref inputs "gtk+")
+ "/share/glib-2.0/schemas")))
+ `("XDG_DATA_DIRS" ":" prefix
+ (;; Needed by gdk-pixbuf to know supported icon formats.
+ ,(string-append
+ (assoc-ref inputs "shared-mime-info") "/share")
+ ;; The default icon theme of GTK+.
+ ,(string-append
+ (assoc-ref inputs "adwaita-icon-theme") "/share"))))
+ #t)))))
(home-page "https://andrejv.github.io/wxmaxima/")
(synopsis "Graphical user interface for the Maxima computer algebra system")
(description
(define-public suitesparse
(package
(name "suitesparse")
- (version "4.4.3")
+ (version "4.5.5")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "100hdzr0mf4mzlwnqpmwpfw4pymgsf9n3g0ywb1yps2nk1zbkdy5"))))
+ "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr"))
+ (modules '((guix build utils)))
+ (snippet
+ ;; Remove bundled metis source
+ '(delete-file-recursively "metis-5.1.0"))))
(build-system gnu-build-system)
(arguments
- '(#:parallel-build? #f ;cholmod build fails otherwise
- #:tests? #f ;no "check" target
+ '(#:tests? #f ;no "check" target
#:make-flags
(list "CC=gcc"
"BLAS=-lblas"
"TBB=-ltbb"
- "CHOLMOD_CONFIG=-DNPARTITION" ;required when METIS is not used
+ "MY_METIS_LIB=-lmetis"
(string-append "INSTALL_LIB="
(assoc-ref %outputs "out") "/lib")
(string-append "INSTALL_INCLUDE="
- (assoc-ref %outputs "out") "/include"))
+ (assoc-ref %outputs "out") "/include")
+ "library")
#:phases
- (alist-cons-before
- 'install 'prepare-out
- ;; README.txt states that the target directories must exist prior to
- ;; running "make install".
- (lambda _
- (mkdir-p (string-append (assoc-ref %outputs "out") "/lib"))
- (mkdir-p (string-append (assoc-ref %outputs "out") "/include")))
- ;; no configure script
- (alist-delete 'configure %standard-phases))))
+ (modify-phases %standard-phases
+ (delete 'configure)))) ;no configure script
(inputs
`(("tbb" ,tbb)
- ("lapack" ,lapack)))
+ ("lapack" ,lapack)
+ ("metis" ,metis)))
(home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
(synopsis "Suite of sparse matrix software")
(description
(define-public dealii
(package
(name "dealii")
- (version "8.4.1")
+ (version "8.5.0")
(source
(origin
(method url-fetch)
"download/v" version "/dealii-" version ".tar.gz"))
(sha256
(base32
- "1bdksvvyp1rj37df1ndh8j3x9nzpc3sazw8nd0hzvnlw0qnyk800"))
+ "0yfpy4zh8j7hmqakw17zdlmvfdcmhwgs66wcb716plc4y7v3z4g6"))
(modules '((guix build utils)))
(snippet
;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
("suitesparse" ,suitesparse))) ;for UMFPACK
(arguments
`(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
- #:configure-flags '("-DCOMPAT_FILES=OFF") ;Follow new directory structure
- #:phases (modify-phases %standard-phases
- (add-after
- 'install 'hint-example-prefix
- ;; Set Cmake hints in examples so that they can find this
- ;; deal.II when configuring.
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((out (assoc-ref %outputs "out"))
- (exmpl (string-append out "/share/doc"
- "/dealii/examples")))
- (substitute* (find-files exmpl "CMakeLists.txt")
- (("([[:space:]]*HINTS.*)\n" _ line)
- (string-append line " $ENV{HOME}/.guix-profile "
- out "\n")))
- #t))))))
+ #:configure-flags
+ ;; Work around a bug in libsuitesparseconfig linking
+ ;; see https://github.com/dealii/dealii/issues/4745
+ '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON")))
(home-page "https://www.dealii.org")
(synopsis "Finite element library")
(description
@item NVIDIA GPUs / CUDA (in development)
@end enumerate\n")
(home-page "https://github.com/VcDevel/Vc")
+ ;; "No support_???.cpp file exists for this architecture."
+ (supported-systems '("x86_64-linux" "i686-linux"))
(license license:bsd-3)))
(define-public reducelcs
(home-page "https://www.gnu.org/software/jacal/")
(license license:gpl3+)))
+(define-public z3
+ (package
+ (name "z3")
+ (version "4.5.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/Z3Prover/z3/archive/z3-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "032a5lvji2liwmc25jv52bdrhimqflvqbpg77ccaq1jykhiivbmf"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:configure-flags
+ (list "-DBUILD_PYTHON_BINDINGS=true"
+ "-DINSTALL_PYTHON_BINDINGS=true"
+ (string-append "-DCMAKE_INSTALL_PYTHON_PKG_DIR="
+ %output
+ "/lib/python2.7/site-packages")
+ (string-append "-DCMAKE_INSTALL_LIBDIR="
+ %output
+ "/lib"))
+
+ #:phases
+ (modify-phases %standard-phases
+ (add-before 'configure 'bootstrap
+ (lambda _
+ (zero?
+ (system* "python" "contrib/cmake/bootstrap.py" "create"))))
+ (add-before 'check 'make-test-z3
+ (lambda _
+ ;; Build the test suite executable.
+ (zero? (system* "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")))))))
+ (native-inputs
+ `(("python" ,python-2)))
+ (synopsis "Theorem prover")
+ (description "Z3 is a theorem prover and @dfn{satisfiability modulo
+theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.")
+ (home-page "https://github.com/Z3Prover/z3")
+ (license license:expat)))
+
+(define-public cubicle
+ (package
+ (name "cubicle")
+ (version "1.1.1")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "http://cubicle.lri.fr/cubicle-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1sny9c4fm14k014pk62ibpwbrjjirkx8xmhs9jg7q1hk7y7x3q2h"))))
+ (build-system gnu-build-system)
+ (native-inputs
+ `(("ocaml" ,ocaml)
+ ("which" ,(@@ (gnu packages base) which))))
+ (propagated-inputs
+ `(("z3" ,z3)))
+ (arguments
+ `(#:configure-flags (list "--with-z3")
+ #:tests? #f
+ #:phases
+ (modify-phases %standard-phases
+ (add-before 'configure 'configure-for-release
+ (lambda _
+ (substitute* "Makefile.in"
+ (("SVNREV=") "#SVNREV="))))
+ (add-before 'configure 'fix-/bin/sh
+ (lambda _
+ (substitute* "configure"
+ (("/bin/sh") (which "sh")))))
+ (add-before 'configure 'fix-smt-z3wrapper.ml
+ (lambda _
+ (substitute* "Makefile.in"
+ (("\\\\n") "")))))))
+ (home-page "http://cubicle.lri.fr/")
+ (synopsis "Model checker for array-based systems")
+ (description "Cubicle is an open source model checker for verifying safety
+properties of array-based systems. This is a syntactically restricted class of
+parametrized transition systems with states represented as arrays indexed by an
+arbitrary number of processes. Cache coherence protocols and mutual exclusion
+algorithms are typical examples of such systems.")
+ (license license:asl2.0)))
HCoop / jackhill / guix / guix.git / blobdiff