mirror of
https://codeberg.org/guix/guix.git
synced 2025-10-02 02:15:12 +00:00
gnu: hdf-java: Update to 1.10.9.
The version string does not seem like an upgrade, but it is. hdf-java used to be released separately up to version 3.3.2. It is now part of the hdf5 sources. * gnu/packages/maths.scm (hdf-java): Update to 1.10.9. [source]: Fetch hdf5 sources from git. [arguments]: Adjust configure flags; add phase 'unbundle; remove phase 'build-examples. [native-inputs]: Drop labels. [inputs]: Replace hdf5-1.8 with hdf5; drop labels. Change-Id: I30ef41aa9255d6d4eb49f5382a6fe5a62080e6fa
This commit is contained in:
Ricardo Wurmus
parent
8ac97e627e
commit
b08a08448e
1 changed files with 82 additions and 115 deletions
|
|
@ -1773,6 +1773,7 @@ extremely large and complex data collections.")
|
|||
(license (license:x11-style
|
||||
"https://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
|
||||
|
||||
;; When updating this package, please also update hdf-java.
|
||||
(define-public hdf5-1.10
|
||||
(package
|
||||
(inherit hdf5-1.8)
|
||||
|
|
@ -1835,131 +1836,97 @@ extremely large and complex data collections.")
|
|||
;; Default version of HDF5.
|
||||
hdf5-1.10)
|
||||
|
||||
;; Keep this in sync with the current hdf5 package.
|
||||
(define-public hdf-java
|
||||
(package
|
||||
(name "hdf-java")
|
||||
(version "3.3.2")
|
||||
(version "1.10.9")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
"https://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
|
||||
version "/src/CMake-hdfjava-" version ".tar.gz"))
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/HDFGroup/hdf5")
|
||||
(commit (string-append "hdf5-"
|
||||
(string-map
|
||||
(lambda (c) (if (char=? c #\.) #\_ c))
|
||||
version)))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
|
||||
(base32 "1sjdcnafvzsy99vqhybkps8rnwmxb6fsvmkw89wb2mrrp4vi5z9v"))
|
||||
(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))))
|
||||
'(for-each delete-file
|
||||
(find-files "java/lib" "\\.jar$")))))
|
||||
(build-system gnu-build-system)
|
||||
(native-inputs
|
||||
`(("jdk" ,icedtea "jdk")
|
||||
("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
|
||||
;; For tests:
|
||||
("hamcrest-core" ,java-hamcrest-core)
|
||||
("junit" ,java-junit)
|
||||
("slf4j-simple" ,java-slf4j-simple)))
|
||||
(inputs
|
||||
`(("hdf4" ,hdf4)
|
||||
("hdf5" ,hdf5-1.8)
|
||||
("zlib" ,zlib)
|
||||
("libjpeg" ,libjpeg-turbo)
|
||||
("slf4j-api" ,java-slf4j-api)))
|
||||
(arguments
|
||||
`(#:configure-flags
|
||||
(list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
|
||||
(string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
|
||||
(assoc-ref %build-inputs "jdk") "/lib" )
|
||||
(string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
|
||||
(string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
|
||||
|
||||
#:make-flags
|
||||
(list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
|
||||
(string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
|
||||
(string-append "ZLIB=" (search-input-file %build-inputs "/lib/libz.so"))
|
||||
(string-append "JPEGLIB="
|
||||
(search-input-file %build-inputs "/lib/libjpeg.so"))
|
||||
"LLEXT=so")
|
||||
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-before 'configure 'chdir-to-source
|
||||
(lambda _ (chdir ,(string-append "hdfjava-" version)) #t))
|
||||
(add-before 'configure 'patch-build
|
||||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||||
(substitute* "configure"
|
||||
(("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
|
||||
(("/bin/cat") (which "cat")))
|
||||
;; Set classpath for compilation
|
||||
(substitute* '("hdf/hdf5lib/Makefile.in"
|
||||
"hdf/hdf5lib/exceptions/Makefile.in"
|
||||
"hdf/hdflib/Makefile.in")
|
||||
(("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
|
||||
;; 'slf4j-api-X.Y.Z.jar' is installed in a Maven-style
|
||||
;; directory, so use 'find-files' to find it.
|
||||
(car (find-files (assoc-ref inputs "slf4j-api")
|
||||
"^slf4j-api.*\\.jar$"))))
|
||||
;; Replace outdated config.sub and config.guess:
|
||||
(with-directory-excursion "config"
|
||||
(for-each (lambda (file)
|
||||
(install-file
|
||||
(search-input-file inputs
|
||||
(string-append
|
||||
"/share/automake-"
|
||||
,(version-major+minor (package-version automake))
|
||||
"/" file))
|
||||
"."))
|
||||
'("config.sub" "config.guess")))
|
||||
|
||||
;; Fix embedded version number
|
||||
(let ((hdf5version (list ,@(string-split (package-version hdf5) #\.))))
|
||||
(substitute* "hdf/hdf5lib/H5.java"
|
||||
(("1, 8, 19")
|
||||
(string-join hdf5version ", "))))
|
||||
|
||||
(mkdir-p (string-append (assoc-ref outputs "out")))
|
||||
;; Set classpath for tests
|
||||
(let* ((build-dir (getcwd))
|
||||
(lib (string-append build-dir "/lib"))
|
||||
(jhdf (string-append lib "/jhdf.jar"))
|
||||
(jhdf5 (string-append lib "/jhdf5.jar"))
|
||||
(testjars
|
||||
(append
|
||||
(map (lambda (i)
|
||||
(car (find-files (assoc-ref inputs i)
|
||||
(string-append "^" i
|
||||
".*\\.jar$"))))
|
||||
'("slf4j-api" "slf4j-simple"))
|
||||
(list
|
||||
(car (find-files (assoc-ref inputs "junit") "jar$"))
|
||||
(car (find-files (assoc-ref inputs "hamcrest-core")
|
||||
"jar$")))))
|
||||
(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")
|
||||
(search-input-file inputs "/bin/test"))
|
||||
(("/usr/bin/uname")
|
||||
(search-input-file inputs "/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-tests? #f ))
|
||||
(list
|
||||
#:configure-flags
|
||||
#~(list "--enable-java"
|
||||
"--disable-tools")
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
(add-after 'unpack 'unbundle
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(let ((simple
|
||||
(search-input-file
|
||||
inputs "/lib/m2/org/slf4j/slf4j-simple/1.7.25/slf4j-simple-1.7.25.jar"))
|
||||
(api
|
||||
(search-input-file
|
||||
inputs "/lib/m2/org/slf4j/slf4j-api/1.7.25/slf4j-api-1.7.25.jar"))
|
||||
(junit
|
||||
(search-input-file
|
||||
inputs "/lib/m2/junit/junit/4.12/junit-4.12.jar"))
|
||||
(hamcrest
|
||||
(search-input-file
|
||||
inputs "/lib/m2/org/hamcrest/hamcrest-core/1.3/hamcrest-core-1.3.jar")))
|
||||
(substitute* (append (find-files "java" "Makefile.am")
|
||||
(find-files "java" "Makefile.in"))
|
||||
(("\\$\\(top_srcdir\\)/java/lib/ext/slf4j-simple-1.7.33.jar")
|
||||
simple)
|
||||
(("\\$\\(top_srcdir\\)/java/lib/slf4j-api-1.7.33.jar")
|
||||
api)
|
||||
(("\\$\\(top_srcdir\\)/java/lib/junit.jar")
|
||||
junit)
|
||||
(("\\$\\(top_srcdir\\)/java/lib/hamcrest-core.jar")
|
||||
hamcrest))
|
||||
(substitute* '("java/test/junit.sh.in"
|
||||
"java/examples/datatypes/JavaDatatypeExample.sh.in"
|
||||
"java/examples/datasets/JavaDatasetExample.sh.in"
|
||||
"java/examples/intro/JavaIntroExample.sh.in"
|
||||
"java/examples/groups/JavaGroupExample.sh.in")
|
||||
(("^LIST_JAR_TESTFILES=\"" m)
|
||||
(string-append m hamcrest "\n"
|
||||
junit "\n"
|
||||
api "\n"
|
||||
simple "\n"))
|
||||
(("^\\$HDFLIB_HOME/.*") "")
|
||||
(("\"\\$BLDLIBDIR\"/junit.jar")
|
||||
junit)
|
||||
(("\"\\$BLDLIBDIR\"/hamcrest-core.jar")
|
||||
hamcrest)
|
||||
(("\"\\$BLDLIBDIR\"/slf4j-api-1.7.33.jar")
|
||||
api)
|
||||
(("\"\\$BLDLIBDIR\"/slf4j-simple-1.7.33.jar")
|
||||
simple)
|
||||
(("/usr/bin/test")
|
||||
(search-input-file inputs "/bin/test"))
|
||||
(("/usr/bin/uname")
|
||||
(search-input-file inputs "/bin/uname")))
|
||||
(substitute* (find-files "java/test/testfiles/" ".*\\.txt$")
|
||||
(("JUnit version 4.11")
|
||||
"JUnit version 4.12-SNAPSHOT"))))))))
|
||||
(native-inputs
|
||||
(list `(,icedtea "jdk")
|
||||
;; For tests:
|
||||
java-hamcrest-core
|
||||
java-junit
|
||||
java-slf4j-simple))
|
||||
(inputs
|
||||
(list hdf4
|
||||
hdf5
|
||||
java-slf4j-api
|
||||
libjpeg-turbo
|
||||
zlib))
|
||||
(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
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue