@@ 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$")))))
(build-system gnu-build-system)
+ (arguments
+ (list
+ #:configure-flags
+ #~(list "--enable-java"
+ "--disable-tools")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'unbundle
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((simple
+ (search-input-file
+ inputs "/lib/m2/org/slf4j/slf4j-simple/1.7.25/slf4j-simple-1.7.25.jar"))
+ (api
+ (search-input-file
+ inputs "/lib/m2/org/slf4j/slf4j-api/1.7.25/slf4j-api-1.7.25.jar"))
+ (junit
+ (search-input-file
+ inputs "/lib/m2/junit/junit/4.12/junit-4.12.jar"))
+ (hamcrest
+ (search-input-file
+ inputs "/lib/m2/org/hamcrest/hamcrest-core/1.3/hamcrest-core-1.3.jar")))
+ (substitute* (append (find-files "java" "Makefile.am")
+ (find-files "java" "Makefile.in"))
+ (("\\$\\(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$")
+ (("JUnit version 4.11")
+ "JUnit version 4.12-SNAPSHOT"))))))))
(native-inputs
- `(("jdk" ,icedtea "jdk")
- ("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
- ;; For tests:
- ("hamcrest-core" ,java-hamcrest-core)
- ("junit" ,java-junit)
- ("slf4j-simple" ,java-slf4j-simple)))
+ (list `(,icedtea "jdk")
+ ;; For tests:
+ java-hamcrest-core
+ java-junit
+ java-slf4j-simple))
(inputs
- `(("hdf4" ,hdf4)
- ("hdf5" ,hdf5-1.8)
- ("zlib" ,zlib)
- ("libjpeg" ,libjpeg-turbo)
- ("slf4j-api" ,java-slf4j-api)))
- (arguments
- `(#:configure-flags
- (list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
- (string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
- (assoc-ref %build-inputs "jdk") "/lib" )
- (string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
- (string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
-
- #:make-flags
- (list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
- (string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
- (string-append "ZLIB=" (search-input-file %build-inputs "/lib/libz.so"))
- (string-append "JPEGLIB="
- (search-input-file %build-inputs "/lib/libjpeg.so"))
- "LLEXT=so")
-
- #:phases
- (modify-phases %standard-phases
- (add-before 'configure 'chdir-to-source
- (lambda _ (chdir ,(string-append "hdfjava-" version)) #t))
- (add-before 'configure 'patch-build
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (substitute* "configure"
- (("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
- (("/bin/cat") (which "cat")))
- ;; Set classpath for compilation
- (substitute* '("hdf/hdf5lib/Makefile.in"
- "hdf/hdf5lib/exceptions/Makefile.in"
- "hdf/hdflib/Makefile.in")
- (("\\$\\(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 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