;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020 Eric Bavier <bavier@posteo.net>
;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
-;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
;;; 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>
;;; Copyright © 2016, 2018, 2020 Kei Kebreau <kkebreau@posteo.net>
-;;; Copyright © 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
;;; Copyright © 2017, 2018, 2019, 2020 Paul Garlick <pgarlick@tourbillion-technology.com>
-;;; Copyright © 2017 ng0 <ng0@n0.is>
+;;; Copyright © 2017 Nikita <nikita@n0.is>
;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
;;; Copyright © 2017, 2019 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018 Nadya Voronova <voronovank@gmail.com>
;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com>
-;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2018, 2020 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2018 Eric Brown <brown@fastmail.com>
;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
;;; Copyright © 2018 Amin Bandali <bandali@gnu.org>
(define-public gsl
(package
(name "gsl")
- (version "2.5")
+ (version "2.6")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/gsl/gsl-"
version ".tar.gz"))
(sha256
(base32
- "1395y9hlhqadn5g9j8q22224fds5sd92jxi9czfavjj24myasq04"))
- (patches (search-patches "gsl-test-i686.patch"))))
+ "1a460zj9xmbgvcymkdhqh313c4l29mn9cffbi5vf33x3qygk70mp"))))
(build-system gnu-build-system)
(arguments
- `(;; Currently there are numerous tests that fail on "exotic"
- ;; architectures such as aarch64 and ppc64le.
- ,@(if (string-prefix? "aarch64-linux"
- (or (%current-target-system) (%current-system)))
- '(#:tests? #f)
- '())))
+ (let ((system (%current-system)))
+ (cond
+ ((string-prefix? "aarch64" system)
+ ;; Some sparse matrix tests are failing on AArch64:
+ ;; https://lists.gnu.org/archive/html/bug-gsl/2020-04/msg00001.html
+ '(#:phases (modify-phases %standard-phases
+ (add-before 'check 'disable-failing-tests
+ (lambda _
+ (substitute* "spmatrix/test.c"
+ ((".*test_complex.*") "\n"))
+ #t)))))
+ ((string-prefix? "i686" system)
+ ;; There are rounding issues with these tests on i686:
+ ;; https://lists.gnu.org/archive/html/bug-gsl/2016-10/msg00000.html
+ ;; https://lists.gnu.org/archive/html/bug-gsl/2020-04/msg00000.html
+ '(#:phases (modify-phases %standard-phases
+ (add-before 'check 'disable-failing-tests
+ (lambda _
+ (substitute* "linalg/test.c"
+ ((".*gsl_test\\(test_LU_decomp.*") "\n")
+ ((".*gsl_test\\(test_LUc_decomp.*") "\n")
+ ((".*gsl_test\\(test_cholesky_decomp.*") "\n")
+ ((".*gsl_test\\(test_COD_lssolve2.*") "\n"))
+ (substitute* "spmatrix/test.c"
+ ((".*test_all.*") "\n")
+ ((".*test_float.*") "\n")
+ ((".*test_complex.*") "\n"))
+ #t)))))
+ (else '()))))
(home-page "https://www.gnu.org/software/gsl/")
(synopsis "Numerical library for C and C++")
(description
("flex" ,flex)))
(inputs
`(("zlib" ,zlib)
- ("libjpeg" ,libjpeg)
+ ("libjpeg" ,libjpeg-turbo)
("libtirpc" ,libtirpc)))
(arguments
`(#:parallel-tests? #f
`(("hdf4" ,hdf4)
("hdf5" ,hdf5)
("zlib" ,zlib)
- ("libjpeg" ,libjpeg)
+ ("libjpeg" ,libjpeg-turbo)
("slf4j-api" ,java-slf4j-api)))
(arguments
`(#:configure-flags
`(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
;; XXX: These inputs are really dependencies of hdf4.
("zlib" ,zlib)
- ("libjpeg" ,libjpeg)
+ ("libjpeg" ,libjpeg-turbo)
("libtirpc" ,libtirpc)
("gctp" ,gctp)))
#t))))))
(synopsis "Management suite for data with parallel IO support")))
+(define-public hdf5-blosc
+ (package
+ (name "hdf5-blosc")
+ (version "1.0.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/Blosc/hdf5-blosc.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1nj2bm1v6ymm3fmyvhbn6ih5fgdiapavlfghh1pvbmhw71cysyqs"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:configure-flags
+ (list (string-append "-DBLOSC_INSTALL_DIR="
+ (assoc-ref %build-inputs "c-blosc"))
+ (string-append "-DPLUGIN_INSTALL_PATH="
+ (assoc-ref %outputs "out")
+ "/hdf5/lib/plugin"))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'do-not-build-blosc
+ (lambda _
+ (substitute* "CMakeLists.txt"
+ (("set\\(BLOSC_INSTALL_DIR.*") "")
+ (("ExternalProject_Add\\(project_blosc") "message("))
+ #t)))))
+ (inputs
+ `(("c-blosc" ,c-blosc)
+ ("hdf5" ,hdf5-1.10)))
+ (home-page "https://github.com/Blosc/hdf5-blosc")
+ (synopsis "Filter for HDF5 using the Blosc compressor")
+ (description "This is a filter for HDF5 that uses the Blosc compressor; by
+installing this filter, you can read and write HDF5 files with
+Blosc-compressed datasets.")
+ (license license:expat)))
+
(define-public h5check
(package
(name "h5check")
`(("hdf4" ,hdf4-alt)
("hdf5" ,hdf5)
("zlib" ,zlib)
- ("libjpeg" ,libjpeg)))
+ ("libjpeg" ,libjpeg-turbo)))
(arguments
`(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
("glpk" ,glpk)
("glu" ,glu)
("graphicsmagick" ,graphicsmagick)
+
+ ;; TODO: libjpeg-turbo is indirectly required through libtiff. In
+ ;; the next rebuild cycle, add an absolute reference for -ljpeg in
+ ;; libtiff.la instead of having to provide it here.
+ ("libjpeg" ,libjpeg-turbo)
+
("hdf5" ,hdf5)
("lapack" ,lapack)
("libsndfile" ,libsndfile)
`(#:configure-flags
(list (string-append "--with-shell="
(assoc-ref %build-inputs "bash")
- "/bin/sh"))
+ "/bin/sh")
+
+ ;; XXX: Without this flag, linking octave-cli fails with
+ ;; undefined references to 'logf@GLIBCXX_3.4' et.al. due to
+ ;; not pulling in liboctinterp.la for -lstdc++.
+ "--enable-link-all-dependencies")
#:phases
(modify-phases %standard-phases
(add-after 'configure 'configure-makeinfo
(define-public openblas
(package
(name "openblas")
- (version "0.3.7")
+ (version "0.3.9")
(source
(origin
(method url-fetch)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0jbdjsi0qsxahdcm42agnn1y7xpmg0hrhwjsxg0zbhs9wwy3p568"))))
+ "14iz9xnrb9xiwgj84j94mc74gg0zn2vsy9fmsijxxma1n7dck4w3"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
(define-public glm
(package
(name "glm")
- (version "0.9.9.6")
+ (version "0.9.9.8")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/g-truc/glm/releases/download/"
version "/glm-" version ".zip"))
(sha256
- (base32 "1l0pi1qi37mk6s0yrkrw07lspv4gcqnr9ryg3521hrl77ff37dwx"))
- (patches (search-patches "glm-restore-install-target.patch"))))
+ (base32 "0k6yk9v46h690rshdx49x98y5qspkzibld1wb51jwcm35vba7qip"))))
(build-system cmake-build-system)
+ (arguments
+ `(#:phases (modify-phases %standard-phases
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; Since version 0.9.9.6, 'make install' is not supported
+ ;; and we have to do it "manually". Upstream discussion:
+ ;; <https://github.com/g-truc/glm/pull/968>.
+ (let* ((source (string-append "../glm"))
+ (out (assoc-ref outputs "out"))
+ (inc (string-append out "/include"))
+ (lib (string-append out "/lib"))
+ (pkgconfig (string-append lib "/pkgconfig")))
+ (with-directory-excursion source
+ (mkdir-p inc)
+ (mkdir-p pkgconfig)
+ (copy-recursively "glm" (string-append inc "/glm"))
+ (copy-recursively "cmake" (string-append lib "/cmake"))
+ (call-with-output-file (string-append pkgconfig "/glm.pc")
+ (lambda (port)
+ (format port
+ "prefix=~a
+includedir=${prefix}/include
+
+Name: GLM
+Description: OpenGL Mathematics
+Version: ~a
+Cflags: -I${includedir}~%" out ,(version-prefix version 3)))))
+ #t))))))
(native-inputs
`(("unzip" ,unzip)))
(home-page "https://glm.g-truc.net/")
(define-public flann
(package
(name "flann")
- (version "1.8.4")
+ (version "1.9.1")
+ (home-page "https://github.com/mariusmuja/flann/")
(source
(origin
- (method url-fetch)
- (uri
- (string-append
- "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
- version "-src.zip"))
+ (method git-fetch)
+ (uri (git-reference (url home-page) (commit version)))
+ (file-name (git-file-name name version))
(sha256
(base32
- "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))
+ "0p56fl2yx1r86ds1mgjq40926jdcgq3hka7p3l1hv2acv9jxp15x"))
(patches (search-patches "flann-cmake-3.11.patch"))))
(build-system cmake-build-system)
- (outputs '("out"
- "octave")) ;46 MiB .mex file that pulls Octave
+ (outputs '("out"))
(native-inputs
`(("unzip" ,unzip)))
(inputs
`(("hdf5" ,hdf5)
- ("octave" ,octave-cli)
+ ;; FIXME: 'mkoctfile' fails with a linker error:
+ ;; ld: cannot find -loctinterp
+ ;; ld: cannot find -loctave
+ ;; Disable it for now.
+ ;;("octave" ,octave-cli)
("python" ,python-2) ; print syntax
;; ("python2-numpy" ,python2-numpy) ; only required for the tests
("zlib" ,zlib)))
;; Save 12 MiB by not installing .a files. Passing
;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
#:phases (modify-phases %standard-phases
- (add-before 'configure 'set-octave-directory
- (lambda* (#:key outputs #:allow-other-keys)
- ;; Install the .mex file in the "octave" output.
- (let ((out (assoc-ref outputs "octave")))
- (substitute* "src/matlab/CMakeLists.txt"
- (("share/flann/octave")
- (string-append out "/share/flann/octave")))
- #t)))
(add-after 'install 'remove-static-libraries
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
#t))))
#:tests? #f)) ; The test data are downloaded from the Internet.
- (home-page "http://www.cs.ubc.ca/research/flann/")
(synopsis "Library for approximate nearest neighbors computation")
(description "FLANN is a library for performing fast approximate
nearest neighbor searches in high dimensional spaces. It implements a
(define-public dune-common
(package
(name "dune-common")
- (version "2.6.0")
+ (version "2.7.0")
(source
(origin
(method url-fetch)
version "/dune-common-" version ".tar.gz"))
(sha256
(base32
- "019wcr1qf7jwyxx1y5y290wdlglylskvbb2m01ljkzcza2xnlmhw"))))
+ "140q1zh44cr5yrjwg4b5ga803rkqv55vk30l2cqm29aklj1wb0rw"))))
(build-system cmake-build-system)
(arguments
`(#:phases
(define-public dune-geometry
(package
(name "dune-geometry")
- (version "2.6.0")
+ (version "2.7.0")
(source
(origin
(method url-fetch)
version "/dune-geometry-" version ".tar.gz"))
(sha256
(base32
- "0hlaaxjyv9j05blasvb67sy02hd0w4g9znf68gdh3l731dd1aqbn"))))
+ "1cicvlwbyyw76npicnblxckyvhbfn3ip8isydiv3hlrlz8zcg5nr"))))
(build-system cmake-build-system)
(arguments
`(#:phases
(define-public dune-uggrid
(package
(name "dune-uggrid")
- (version "2.6.0")
+ (version "2.7.0")
(source
(origin
- (method url-fetch)
- (uri (string-append "https://dune-project.org/download/"
- version "/dune-uggrid-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://gitlab.dune-project.org/staging/dune-uggrid.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "05l7a1gb78mny49anyxk6rjvn66rhgm30y72v5cjg0m5kfgr1a1f"))))
+ "192miqgmfj6jwk969gydzpbv9ki7jg5nky3ydnrwa2nq29b5xkh0"))))
(build-system cmake-build-system)
(arguments
`(#:phases
(define-public dune-grid
(package
(name "dune-grid")
- (version "2.6.0")
+ (version "2.7.0")
(source
(origin
(method url-fetch)
version "/dune-grid-" version ".tar.gz"))
(sha256
(base32
- "1jp4vscm9yb9xg0lh7apzccfkhvgbnk652yahigmh3cvzpl4acd0"))))
+ "17fjz30qazjgl11sryyxnw9klai4yz1ji4bs68013xcxc5hdv27s"))))
(build-system cmake-build-system)
(arguments
`(#:phases
(define-public dune-istl
(package
(name "dune-istl")
- (version "2.6.0")
+ (version "2.7.0")
(source
(origin
(method url-fetch)
version "/dune-istl-" version ".tar.gz"))
(sha256
(base32
- "0l2gyrvys5w6wsmk0ckbb7295s80b7yk7qrl7x66akv2jv1nzq2w"))))
+ "0gl3wgz5rs6sb4m83440ny45sbx7z7lnbi3gx6r9nm3rvy5j33f9"))
+ (patches (search-patches "dune-istl-2.7-fix-non-mpi-tests.patch"))))
(build-system cmake-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
+ ;; XXX: istl/test/matrixtest.cc includes <fenv.h> and fails to find
+ ;; the stdlib types when the gfortran header is used. Remove gfortran
+ ;; from CPLUS_INCLUDE_PATH as a workaround.
+ (add-after 'set-paths 'hide-gfortran
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((gfortran (assoc-ref inputs "gfortran")))
+ (setenv "CPLUS_INCLUDE_PATH"
+ (string-join
+ (delete (string-append gfortran "/include/c++")
+ (string-split (getenv "CPLUS_INCLUDE_PATH") #\:))
+ ":"))
+ #t)))
(add-after 'build 'build-tests
(lambda* (#:key make-flags #:allow-other-keys)
(apply invoke "make" "build_tests" make-flags))))))
(define-public dune-localfunctions
(package
(name "dune-localfunctions")
- (version "2.6.0")
+ (version "2.7.0")
(source
(origin
(method url-fetch)
version "/dune-localfunctions-" version ".tar.gz"))
(sha256
(base32
- "19c6zjinwwpy8jh4v4prhphyd438rapd4x80fj93apmwgw04nrhl"))))
+ "1yih59h6vngii696bx1c2vil02lriij4kz0nc583mjn9kiaqxfqd"))))
(build-system cmake-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
+ ;; XXX: localfunctions/test/lagrangeshapefunctiontest.cc includes <fenv.h>
+ ;; and fails to find the stdlib types when the gfortran header is used.
+ ;; Hide gfortran from CPLUS_INCLUDE_PATH to ensure we get the GCC header.
+ (add-after 'set-paths 'hide-gfortran
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((gfortran (assoc-ref inputs "gfortran")))
+ (setenv "CPLUS_INCLUDE_PATH"
+ (string-join
+ (delete (string-append gfortran "/include/c++")
+ (string-split (getenv "CPLUS_INCLUDE_PATH") #\:))
+ ":"))
+ #t)))
(add-after 'build 'build-tests
(lambda* (#:key make-flags #:allow-other-keys)
(apply invoke "make" "build_tests" make-flags))))))
(define-public dune-alugrid
(package
(name "dune-alugrid")
- (version "2.6.0")
+ (version "2.7.0-git-81d35682")
(source
(origin
- (method url-fetch)
- (uri (string-append "https://dune-project.org/download/"
- version "/dune-alugrid-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://gitlab.dune-project.org/extensions/dune-alugrid.git")
+ (commit "81d356827c84454b971937db02c02b90bbcd7fe5")))
+ (file-name (git-file-name name version))
(sha256
(base32
- "1l9adgyjpra8mvwm445s0lpjshnb63jag85fb2hisbjn6bm320yj"))))
+ "0z54lwfp53prcrs94k8gwh047l9z642jll3l56xlyfr69z0b2zz1"))))
(build-system cmake-build-system)
(arguments
`(#:phases
(define-public dune-subgrid
(package
(name "dune-subgrid")
- (version "2.6.0")
+ (version "2.7.0-git-2103a363")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://git.imp.fu-berlin.de/agnumpde/dune-subgrid")
- (commit "releases/2.6-1")))
+ (commit "2103a363f32e8d7b60e66eee7ddecf969f6cf762")))
(file-name (git-file-name name version))
(sha256
(base32
- "1gcv35rx3knqd54r4pp9rzd639db4j8w2r2ibq43w1mgwdcqhs64"))))
+ "1wsjlypd3835c3arqjkw836cxx5q67zy447wa65q634lf6f6v9ia"))))
(build-system cmake-build-system)
(arguments
`(#:phases
(define-public dune-typetree
(package
(name "dune-typetree")
- (version "2.6.0")
+ (version "2.7.0")
(source
(origin
(method git-fetch)
(file-name (git-file-name name version))
(sha256
(base32
- "0mnv6w2f22lz3j4bdpdjq55vjm8xxfx9v4vvhg9bd36xpsbjpjp9"))))
+ "1rhv25yg0q1hw50c8wlfqhgwrjl4mh62zq9v14ilwgzbfgxmpiy7"))))
(build-system cmake-build-system)
(arguments
`(#:phases
(define-public dune-functions
(package
(name "dune-functions")
- (version "2.6.0")
+ (version "2.7.0")
(source
(origin
(method git-fetch)
(file-name (git-file-name name version))
(sha256
(base32
- "1an8gb477n8j0kzpbrv7nr1snh8pxip0gsxq6w63jc83gg3dj200"))))
+ "1na4gcih0kin37ksj2xj07ds04v7zx53pjdhm1hzy55jjfqdjk8h"))))
(build-system cmake-build-system)
(arguments
`(#:phases
(define-public dune-pdelab
(package
(name "dune-pdelab")
- (version "2.6.0-rc1")
+ (version "2.7.0-git-476fe437")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://gitlab.dune-project.org/pdelab/dune-pdelab")
- (commit (string-append "v" version))))
+ (commit "476fe43763fa6f459c5e4658e2a2b4b5582db834")))
(file-name (git-file-name name version))
(sha256
(base32
- "07g0s9448z65vjrq88g5rv3340iifil85k170n8kbqchsvi4ny5v"))))
+ "0cs36piqzn6rq0j2ih3ab3q3q9yg199wk72k5qi86pkzh7i7fdn1"))))
(build-system cmake-build-system)
(arguments '(#:tests? #f)) ; XXX: the tests cannot be compiled
(inputs
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "1vbaza9c7159xf2ym90l0xkyj2mp6c3hbghhsqn29yvz08fda9df"))))
+ (base32 "1vbaza9c7159xf2ym90l0xkyj2mp6c3hbghhsqn29yvz08fda9df"))
+ (patches
+ (search-patches "libqalculate-3.8.0-libcurl-ssl-fix.patch"))))
(build-system gnu-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)
HCoop / jackhill / guix / guix.git / blobdiff