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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
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@ -1773,6 +1773,7 @@ extremely large and complex data collections.")
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(license (license:x11-style
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(license (license:x11-style
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"https://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
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"https://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
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;; When updating this package, please also update hdf-java.
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(define-public hdf5-1.10
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(define-public hdf5-1.10
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(package
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(package
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(inherit hdf5-1.8)
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(inherit hdf5-1.8)
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@ -1835,131 +1836,97 @@ extremely large and complex data collections.")
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;; Default version of HDF5.
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;; Default version of HDF5.
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hdf5-1.10)
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hdf5-1.10)
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;; Keep this in sync with the current hdf5 package.
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(define-public hdf-java
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(define-public hdf-java
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(package
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(package
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(name "hdf-java")
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(name "hdf-java")
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(version "3.3.2")
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(version "1.10.9")
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(source
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(source
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(origin
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(origin
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(method url-fetch)
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(method git-fetch)
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(uri (string-append
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(uri (git-reference
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"https://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
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(url "https://github.com/HDFGroup/hdf5")
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version "/src/CMake-hdfjava-" version ".tar.gz"))
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(commit (string-append "hdf5-"
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(string-map
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(lambda (c) (if (char=? c #\.) #\_ c))
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version)))))
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(file-name (git-file-name name version))
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(sha256
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(sha256
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(base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
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(base32 "1sjdcnafvzsy99vqhybkps8rnwmxb6fsvmkw89wb2mrrp4vi5z9v"))
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(modules '((guix build utils)))
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(modules '((guix build utils)))
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(snippet ; Make sure we don't use the bundled sources and binaries.
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(snippet ; Make sure we don't use the bundled sources and binaries.
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`(begin
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'(for-each delete-file
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(for-each delete-file
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(find-files "java/lib" "\\.jar$")))))
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(list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
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"HDF4.tar.gz" "HDF5.tar.gz"))
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(delete-file-recursively ,(string-append "hdfjava-" version "/lib"))
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#t))))
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(build-system gnu-build-system)
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(build-system gnu-build-system)
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(native-inputs
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`(("jdk" ,icedtea "jdk")
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("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
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;; For tests:
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("hamcrest-core" ,java-hamcrest-core)
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("junit" ,java-junit)
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("slf4j-simple" ,java-slf4j-simple)))
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(inputs
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`(("hdf4" ,hdf4)
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("hdf5" ,hdf5-1.8)
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("zlib" ,zlib)
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("libjpeg" ,libjpeg-turbo)
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("slf4j-api" ,java-slf4j-api)))
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(arguments
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(arguments
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`(#:configure-flags
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(list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
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(string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
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(assoc-ref %build-inputs "jdk") "/lib" )
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(string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
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(string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
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#:make-flags
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(list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
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(string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
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(string-append "ZLIB=" (search-input-file %build-inputs "/lib/libz.so"))
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(string-append "JPEGLIB="
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(search-input-file %build-inputs "/lib/libjpeg.so"))
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"LLEXT=so")
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#:phases
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(modify-phases %standard-phases
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(add-before 'configure 'chdir-to-source
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(lambda _ (chdir ,(string-append "hdfjava-" version)) #t))
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(add-before 'configure 'patch-build
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(substitute* "configure"
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(("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
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(("/bin/cat") (which "cat")))
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;; Set classpath for compilation
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(substitute* '("hdf/hdf5lib/Makefile.in"
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"hdf/hdf5lib/exceptions/Makefile.in"
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"hdf/hdflib/Makefile.in")
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(("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
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;; 'slf4j-api-X.Y.Z.jar' is installed in a Maven-style
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;; directory, so use 'find-files' to find it.
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(car (find-files (assoc-ref inputs "slf4j-api")
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"^slf4j-api.*\\.jar$"))))
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;; Replace outdated config.sub and config.guess:
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(with-directory-excursion "config"
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(for-each (lambda (file)
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(install-file
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(search-input-file inputs
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(string-append
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"/share/automake-"
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,(version-major+minor (package-version automake))
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"/" file))
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"."))
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'("config.sub" "config.guess")))
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;; Fix embedded version number
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(let ((hdf5version (list ,@(string-split (package-version hdf5) #\.))))
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(substitute* "hdf/hdf5lib/H5.java"
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(("1, 8, 19")
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(string-join hdf5version ", "))))
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(mkdir-p (string-append (assoc-ref outputs "out")))
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;; Set classpath for tests
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(let* ((build-dir (getcwd))
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(lib (string-append build-dir "/lib"))
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(jhdf (string-append lib "/jhdf.jar"))
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(jhdf5 (string-append lib "/jhdf5.jar"))
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(testjars
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(append
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(map (lambda (i)
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(car (find-files (assoc-ref inputs i)
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(string-append "^" i
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".*\\.jar$"))))
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'("slf4j-api" "slf4j-simple"))
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(list
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(list
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(car (find-files (assoc-ref inputs "junit") "jar$"))
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#:configure-flags
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(car (find-files (assoc-ref inputs "hamcrest-core")
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#~(list "--enable-java"
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"jar$")))))
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"--disable-tools")
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(class-path
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#:phases
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(string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
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#~(modify-phases %standard-phases
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(add-after 'unpack 'unbundle
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(substitute* '("test/hdf5lib/Makefile.in"
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(lambda* (#:key inputs #:allow-other-keys)
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"test/hdf5lib/junit.sh.in"
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(let ((simple
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"examples/runExample.sh.in")
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(search-input-file
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inputs "/lib/m2/org/slf4j/slf4j-simple/1.7.25/slf4j-simple-1.7.25.jar"))
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(api
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(search-input-file
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inputs "/lib/m2/org/slf4j/slf4j-api/1.7.25/slf4j-api-1.7.25.jar"))
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(junit
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(search-input-file
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inputs "/lib/m2/junit/junit/4.12/junit-4.12.jar"))
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(hamcrest
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(search-input-file
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inputs "/lib/m2/org/hamcrest/hamcrest-core/1.3/hamcrest-core-1.3.jar")))
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(substitute* (append (find-files "java" "Makefile.am")
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(find-files "java" "Makefile.in"))
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(("\\$\\(top_srcdir\\)/java/lib/ext/slf4j-simple-1.7.33.jar")
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simple)
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(("\\$\\(top_srcdir\\)/java/lib/slf4j-api-1.7.33.jar")
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api)
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(("\\$\\(top_srcdir\\)/java/lib/junit.jar")
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junit)
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(("\\$\\(top_srcdir\\)/java/lib/hamcrest-core.jar")
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hamcrest))
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(substitute* '("java/test/junit.sh.in"
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"java/examples/datatypes/JavaDatatypeExample.sh.in"
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"java/examples/datasets/JavaDatasetExample.sh.in"
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"java/examples/intro/JavaIntroExample.sh.in"
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"java/examples/groups/JavaGroupExample.sh.in")
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(("^LIST_JAR_TESTFILES=\"" m)
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(string-append m hamcrest "\n"
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junit "\n"
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api "\n"
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simple "\n"))
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(("^\\$HDFLIB_HOME/.*") "")
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(("\"\\$BLDLIBDIR\"/junit.jar")
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junit)
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(("\"\\$BLDLIBDIR\"/hamcrest-core.jar")
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hamcrest)
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(("\"\\$BLDLIBDIR\"/slf4j-api-1.7.33.jar")
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api)
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(("\"\\$BLDLIBDIR\"/slf4j-simple-1.7.33.jar")
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simple)
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(("/usr/bin/test")
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(("/usr/bin/test")
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(search-input-file inputs "/bin/test"))
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(search-input-file inputs "/bin/test"))
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(("/usr/bin/uname")
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(("/usr/bin/uname")
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(search-input-file inputs "/bin/uname"))
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(search-input-file inputs "/bin/uname")))
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(("CLASSPATH=[^\n]*")
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(substitute* (find-files "java/test/testfiles/" ".*\\.txt$")
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(string-append "CLASSPATH=" class-path)))
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(("JUnit version 4.11")
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(setenv "CLASSPATH" class-path))
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"JUnit version 4.12-SNAPSHOT"))))))))
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#t))
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(native-inputs
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(add-before 'check 'build-examples
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(list `(,icedtea "jdk")
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(lambda _
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;; For tests:
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(apply invoke `("javac"
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java-hamcrest-core
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,@(find-files "examples" ".*\\.java"))))))
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java-junit
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java-slf4j-simple))
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#:parallel-build? #f
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(inputs
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(list hdf4
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#:parallel-tests? #f ))
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hdf5
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java-slf4j-api
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libjpeg-turbo
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zlib))
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(home-page "https://support.hdfgroup.org/products/java")
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(home-page "https://support.hdfgroup.org/products/java")
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(synopsis "Java interface for the HDF4 and HDF5 libraries")
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(synopsis "Java interface for the HDF4 and HDF5 libraries")
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(description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
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(description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
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