;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
;;; Copyright © 2017, 2018 Paul Garlick <pgarlick@tourbillion-technology.com>
-;;; Copyright © 2017 Nils Gillmann <ng0@n0.is>
+;;; Copyright © 2017 ng0 <ng0@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 © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Dave Love <me@fx@gnu.org>
;;; Copyright © 2018 Jan Nieuwenhuizen <janneke@gnu.org>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
(define-public gnuplot
(package
(name "gnuplot")
- (version "5.2.4")
+ (version "5.2.6")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
version "/gnuplot-"
version ".tar.gz"))
(sha256
- (base32
- "1jvh8xmd2cvrhlsg88kxwh55wkwx31sg50v1n59slfippl0g058m"))))
+ (base32 "1vllgap08nhvdmc03idmkdnk9cfl2bp81hps50q1pqrr640qzp9m"))))
(build-system gnu-build-system)
(inputs `(("readline" ,readline)
("cairo" ,cairo)
(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"))
- #t))))
- (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")))))))
+ (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"))
+ #t))))
+ (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)) #t))
+ (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)
+ (install-file
+ (string-append (assoc-ref inputs "automake")
+ "/share/automake-"
+ ,(version-major+minor (package-version automake))
+ "/" file) "."))
+ '("config.sub" "config.guess")))
+
+ ;; Fix embedded version number
+ (let ((hdf5version (list ,@(string-split (package-version hdf5) #\.))))
+ (substitute* "hdf/hdf5lib/H5.java"
+ (("1, 8, 19")
+ (string-join hdf5version ", "))))
+
+ (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 _
+ (apply invoke `("javac"
+ ,@(find-files "examples" ".*\\.java"))))))
- #:parallel-build? #f
+ #: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
+ #: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\
+ ;; BSD-style license:
+ (license (license:x11-style
+ "https://support.hdfgroup.org/ftp/HDF5/hdf-java\
/current/src/unpacked/COPYING"))))
(define-public hdf-eos2
(define-public ipopt
(package
(name "ipopt")
- (version "3.12.5")
+ (version "3.12.12")
(source (origin
(method url-fetch)
(uri (string-append
version".tgz"))
(sha256
(base32
- "09bk2hqy2vgi4yi76xng9zxakddwqy3wij9nx7wf2vfbxxpazrsk"))
+ "07yn9rzdswjk8n246qq6ci9ssf2bcplkifcpsfz9j6cdxw9vgbkv"))
(modules '((guix build utils)))
(snippet
;; Make sure we don't use the bundled software.
(define-public petsc
(package
(name "petsc")
- (version "3.10.3")
+ (version "3.10.4")
(source
(origin
(method url-fetch)
(uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
"petsc-lite-" version ".tar.gz"))
(sha256
- (base32 "10p9ap1rp6k8k2g8zdc505kdlsc3976fjymyp393sccjapm50dph"))))
- (outputs '("out" ;libraries and headers
- "examples")) ;~30MiB of examples
+ (base32 "0fk16944zh3473ra198kdkxdn08rq7b6ap838hxy1mh1i0hb488r"))))
+ (outputs '("out" ; libraries and headers
+ "examples")) ; ~30MiB of examples
(build-system gnu-build-system)
(native-inputs
`(("python" ,python-2)))
))
(arguments
`(#:test-target "test"
- #:parallel-build? #f ;build is parallel by default
+ #:parallel-build? #f ; build is parallel by default
#:configure-flags
`("--with-mpi=0"
"--with-openmp=1"
(define-public glm
(package
(name "glm")
- (version "0.9.9.3")
+ (version "0.9.9.4")
(source
(origin
(method url-fetch)
version "/glm-" version ".zip"))
(sha256
(base32
- "0yqk5r3qh60d4r2iab5q7wq0fryn8p3pz6s28y1i7amqj1aqavj9"))))
+ "17vxbqzy4pxciq5i39bgpxz54f7ifqqmcqwwq7m6xfgikwqqqawp"))))
(build-system cmake-build-system)
(native-inputs
`(("unzip" ,unzip)))
built on top of DUNE, the Distributed and Unified Numerics Environment.")
;; Either GPL version 2 with "runtime exception" or LGPLv3+.
(license (list license:lgpl3+ license:gpl2))))
+
+(define-public mlucas
+ (package
+ (name "mlucas")
+ (version "18")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://mersenneforum.org/mayer/src/C/mlucas_v" version ".txz"))
+ (sha256
+ (base32
+ "1ax12qj9lyvnx4vs3gx7l8r3wx5gjbsdswp5f00ik9z0wz7xf297"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("python2" ,python-2)))
+ (arguments
+ `(#:tests? #f ; no tests
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'configure
+ (lambda _
+ (chdir "src")
+ (call-with-output-file "Makefile"
+ (lambda (port)
+ (format port "CC = gcc
+CFLAGS = -O3 ~a -DUSE_THREADS
+LDLIBS = -lm -lpthread -lrt
+Mlucas: $(addsuffix .o,$(basename $(wildcard *.c)))
+"
+ ,(let ((system (or (%current-target-system)
+ (%current-system))))
+ (cond
+ ((string-prefix? "x86_64" system) "-DUSE_SSE2")
+ (else ""))))))
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (install-file "Mlucas" bin)
+ (install-file "primenet.py" bin))
+ #t)))))
+ (home-page "https://www.mersenne.org")
+ (synopsis "Great Internet Mersenne Prime Search (GIMPS) distributed computing client")
+ (description "Mlucas performs Lucas-Lehmer primality testing of Mersenne
+numbers in search of a world-record prime. You may use it to test any
+suitable number as you wish, but it is preferable that you do so in a
+coordinated fashion, as part of the Great Internet Mersenne Prime
+Search (GIMPS). Mlucas also includes a simple Python script for assignment
+management via the GIMPS project's Primenet server.")
+ (license license:gpl2+)))
HCoop / jackhill / guix / guix.git / blobdiff