gnu: Use 'search-input-file' when looking for .jar files.
* gnu/packages/bioinformatics.scm (java-picard-1.113): Use 'search-input-file' when looking for *.jar. (fastqc): Likewise. * gnu/packages/groovy.scm (groovy): Likewise. * gnu/packages/java.scm (ant-bootstrap): Likewise. (ecj-bootstrap): Likewise. (java-cisd-base): Likewise. (java-cisd-args4j): Likewise. (java-cisd-jhdf5): Likewise. (java-native-access): Likewise. (java-native-access-platform): Likewise. * gnu/packages/maths.scm (hdf-java): Likewise.master
Ludovic Courtès
parent
1ab95c2341
commit
828cfdc47e
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@ -4379,9 +4379,7 @@ VCF.")
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(lambda* (#:key inputs #:allow-other-keys)
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(substitute* "build.xml"
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(("\\$\\{lib\\}/apache-ant-1.8.2-bzip2.jar")
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(string-append (assoc-ref inputs "ant")
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"/lib/ant.jar")))
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#t))
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(search-input-file inputs "/lib/ant.jar")))))
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(add-after 'unpack 'make-test-target-independent
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(lambda* (#:key inputs #:allow-other-keys)
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(substitute* "build.xml"
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@ -4478,15 +4476,13 @@ VCF.")
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(lambda* (#:key inputs #:allow-other-keys)
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(substitute* "build.xml"
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(("jbzip2-0.9.jar")
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(string-append (assoc-ref inputs "java-jbzip2")
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"/share/java/jbzip2.jar"))
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(search-input-file inputs "/share/java/jbzip2.jar"))
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(("sam-1.103.jar")
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(string-append (assoc-ref inputs "java-picard-1.113")
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"/share/java/sam-1.112.jar"))
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(search-input-file inputs
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"/share/java/sam-1.112.jar"))
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(("cisd-jhdf5.jar")
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(string-append (assoc-ref inputs "java-cisd-jhdf5")
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"/share/java/sis-jhdf5.jar")))
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#t))
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(search-input-file inputs
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"/share/java/sis-jhdf5.jar")))))
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;; There is no installation target
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(replace 'install
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(lambda* (#:key inputs outputs #:allow-other-keys)
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@ -9137,8 +9133,8 @@ browser.")
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(substitute* "bin/linux/fseq"
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(("java") (which "java"))
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(("\\$REALDIR/../lib/commons-cli-1.1.jar")
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(string-append (assoc-ref inputs "java-commons-cli")
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"/share/java/commons-cli.jar"))
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(search-input-file inputs
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"/share/java/commons-cli.jar"))
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(("REALDIR=.*")
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(string-append "REALDIR=" bin "\n")))
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(install-file "README.txt" doc)
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@ -827,7 +827,7 @@ and modify groovy's @dfn{Abstract Syntax Tree} (AST)."))))
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"java-jansi" "java-jline-2"))
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;; antlr.jar is present twice in antlr2. Symlink doesn't like
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;; it, so we symlink it here.
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(symlink (string-append (assoc-ref inputs "antlr2") "/lib/antlr.jar")
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(symlink (search-input-file inputs "/lib/antlr.jar")
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(string-append out-lib "/antlr.jar"))
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(for-each
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(lambda (tool)
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@ -382,8 +382,7 @@ JNI.")
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(setenv "JAVAC"
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(search-input-file inputs "/bin/jikes"))
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(setenv "CLASSPATH"
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(string-append (assoc-ref inputs "jamvm")
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"/lib/rt.jar"))
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(search-input-file inputs "/lib/rt.jar"))
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;; Ant complains if this file doesn't exist.
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(setenv "HOME" "/tmp")
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@ -486,8 +485,7 @@ build process and its dependencies, whereas Make uses Makefile format.")
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(lambda* (#:key inputs #:allow-other-keys)
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(setenv "CLASSPATH"
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(string-join
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(cons (string-append (assoc-ref inputs "jamvm")
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"/lib/rt.jar")
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(cons (search-input-file inputs "/lib/rt.jar")
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(find-files (string-append
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(assoc-ref inputs "ant-bootstrap")
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"/lib")
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@ -3221,19 +3219,22 @@ Main-Class: org.eclipse.jdt.internal.compiler.batch.Main\n"
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(lambda* (#:key inputs #:allow-other-keys)
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(substitute* "build/build.xml"
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(("\\$\\{lib\\}/testng/testng-jdk15.jar")
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(string-append (assoc-ref inputs "java-testng")
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"/share/java/java-testng.jar"))
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(search-input-file inputs
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"/share/java/java-testng.jar"))
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(("\\$\\{lib\\}/commons-lang/commons-lang.jar")
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(string-append (assoc-ref inputs "java-commons-lang")
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"/share/java/commons-lang-"
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,(package-version java-commons-lang) ".jar"))
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(search-input-file inputs
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(string-append
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"/share/java/commons-lang-"
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,(package-version java-commons-lang)
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".jar")))
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(("\\$\\{lib\\}/commons-io/commons-io.jar")
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(string-append (assoc-ref inputs "java-commons-io")
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"/lib/m2/commons-io/commons-io/"
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,(package-version java-commons-io)
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"/commons-io-"
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,(package-version java-commons-io)
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".jar"))
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(search-input-file inputs
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(string-append
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"/lib/m2/commons-io/commons-io/"
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,(package-version java-commons-io)
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"/commons-io-"
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,(package-version java-commons-io)
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".jar")))
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;; Remove dependency on svn
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(("<build-info.*") "")
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(("\\$\\{revision.number\\}")
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@ -3406,8 +3407,7 @@ libraries from the SIS division at ETH Zurich like jHDF5.")
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(rename-file "build-common.xml.new" "build-common.xml"))
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(substitute* "build/build.xml"
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(("\\$\\{lib\\}/cisd-base/cisd-base.jar")
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(string-append (assoc-ref inputs "java-cisd-base")
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"/share/java/sis-base.jar"))
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(search-input-file inputs "/share/java/sis-base.jar"))
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;; Remove dependency on svn
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(("<build-info.*") "")
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(("\\$\\{revision.number\\}")
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@ -3509,29 +3509,32 @@ libraries from the SIS division at ETH Zurich like jHDF5.")
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(lambda* (#:key inputs #:allow-other-keys)
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(substitute* "../build_resources/ant/build-common.xml"
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(("../libraries/testng/testng-jdk15.jar")
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(string-append (assoc-ref inputs "java-testng")
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"/share/java/java-testng.jar")))
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(search-input-file inputs
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"/share/java/java-testng.jar")))
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(substitute* "build/build.xml"
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(("\\$\\{lib\\}/sis-base/sis-base.jar")
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(string-append (assoc-ref inputs "java-cisd-base")
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"/share/java/sis-base.jar"))
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(search-input-file inputs
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"/share/java/sis-base.jar"))
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(("\\$\\{lib\\}/cisd-args4j/cisd-args4j.jar")
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(string-append (assoc-ref inputs "java-cisd-args4j")
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"/share/java/cisd-args4j.jar"))
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(search-input-file inputs
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"/share/java/cisd-args4j.jar"))
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(("\\$\\{lib\\}/commons-lang/commons-lang.jar")
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(string-append (assoc-ref inputs "java-commons-lang")
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"/share/java/commons-lang-"
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,(package-version java-commons-lang) ".jar"))
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(search-input-file inputs
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(string-append
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"/share/java/commons-lang-"
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,(package-version java-commons-lang)
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".jar")))
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(("\\$\\{lib\\}/commons-io/commons-io.jar")
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(string-append (assoc-ref inputs "java-commons-io")
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"/lib/m2/commons-io/commons-io/"
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,(package-version java-commons-io)
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"/commons-io-"
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,(package-version java-commons-io)
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".jar"))
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(search-input-file inputs
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(string-append
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"/lib/m2/commons-io/commons-io/"
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,(package-version java-commons-io)
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"/commons-io-"
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,(package-version java-commons-io)
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".jar")))
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(("\\$\\{lib\\}/testng/testng-jdk15.jar")
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(string-append (assoc-ref inputs "java-testng")
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"/share/java/java-testng.jar"))
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(search-input-file inputs
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"/share/java/java-testng.jar"))
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(("\\$\\{lib\\}/junit4/junit.jar")
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(car (find-files (assoc-ref inputs "java-junit") "jar$")))
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(("\\$\\{lib\\}/jmock/hamcrest/hamcrest-core.jar")
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@ -12916,7 +12919,7 @@ from ORO, Inc.")
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(lambda* (#:key inputs #:allow-other-keys)
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(substitute* "build.xml"
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;; Since we removed the bundled ant.jar, give the correct path
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(("lib/ant.jar") (string-append (assoc-ref inputs "ant") "/lib/ant.jar"))
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(("lib/ant.jar") (search-input-file inputs "/lib/ant.jar"))
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;; We removed generated native libraries. We can only rebuild one
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;; so don't fail if we can't find a native library for another architecture.
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(("zipfileset") "zipfileset erroronmissingarchive=\"false\""))
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@ -12970,8 +12973,7 @@ Java method invocation.")
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(lambda* (#:key inputs #:allow-other-keys)
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(substitute* "nbproject/project.properties"
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(("../../build/jna.jar")
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(string-append (assoc-ref inputs "java-native-access")
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"/share/java/jna.jar"))
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(search-input-file inputs "/share/java/jna.jar"))
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(("../../lib/hamcrest-core-.*.jar")
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(car (find-files (assoc-ref inputs "java-hamcrest-core")
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"jar$")))
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@ -1347,8 +1347,7 @@ extremely large and complex data collections.")
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"hdf/hdf5lib/exceptions/Makefile.in"
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"hdf/hdflib/Makefile.in")
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(("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
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(string-append (assoc-ref inputs "slf4j-api")
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"/share/java/slf4j-api.jar")))
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(search-input-file inputs "/share/java/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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Reference in New Issue