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gnu: Use 'search-input-file' when looking for .jar files.

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* 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.
This commit is contained in:
Ludovic Courtès 2021-07-16 17:10:44 +02:00
parent 1ab95c2341
commit 828cfdc47e
No known key found for this signature in database
GPG key ID: 090B11993D9AEBB5
4 changed files with 49 additions and 52 deletions
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20
gnu/packages/bioinformatics.scm
View file

@ -4379,9 +4379,7 @@ VCF.")
(lambda* (#:key inputs #:allow-other-keys) (lambda* (#:key inputs #:allow-other-keys)
(substitute* "build.xml" (substitute* "build.xml"
(("\\$\\{lib\\}/apache-ant-1.8.2-bzip2.jar") (("\\$\\{lib\\}/apache-ant-1.8.2-bzip2.jar")
(string-append (assoc-ref inputs "ant") (search-input-file inputs "/lib/ant.jar")))))
"/lib/ant.jar")))
#t))
(add-after 'unpack 'make-test-target-independent (add-after 'unpack 'make-test-target-independent
(lambda* (#:key inputs #:allow-other-keys) (lambda* (#:key inputs #:allow-other-keys)
(substitute* "build.xml" (substitute* "build.xml"
@ -4478,15 +4476,13 @@ VCF.")
(lambda* (#:key inputs #:allow-other-keys) (lambda* (#:key inputs #:allow-other-keys)
(substitute* "build.xml" (substitute* "build.xml"
(("jbzip2-0.9.jar") (("jbzip2-0.9.jar")
(string-append (assoc-ref inputs "java-jbzip2") (search-input-file inputs "/share/java/jbzip2.jar"))
"/share/java/jbzip2.jar"))
(("sam-1.103.jar") (("sam-1.103.jar")
(string-append (assoc-ref inputs "java-picard-1.113") (search-input-file inputs
"/share/java/sam-1.112.jar")) "/share/java/sam-1.112.jar"))
(("cisd-jhdf5.jar") (("cisd-jhdf5.jar")
(string-append (assoc-ref inputs "java-cisd-jhdf5") (search-input-file inputs
"/share/java/sis-jhdf5.jar"))) "/share/java/sis-jhdf5.jar")))))
#t))
;; There is no installation target ;; There is no installation target
(replace 'install (replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys) (lambda* (#:key inputs outputs #:allow-other-keys)
@ -9137,8 +9133,8 @@ browser.")
(substitute* "bin/linux/fseq" (substitute* "bin/linux/fseq"
(("java") (which "java")) (("java") (which "java"))
(("\\$REALDIR/../lib/commons-cli-1.1.jar") (("\\$REALDIR/../lib/commons-cli-1.1.jar")
(string-append (assoc-ref inputs "java-commons-cli") (search-input-file inputs
"/share/java/commons-cli.jar")) "/share/java/commons-cli.jar"))
(("REALDIR=.*") (("REALDIR=.*")
(string-append "REALDIR=" bin "\n"))) (string-append "REALDIR=" bin "\n")))
(install-file "README.txt" doc) (install-file "README.txt" doc)

2
gnu/packages/groovy.scm
View file

@ -827,7 +827,7 @@ and modify groovy's @dfn{Abstract Syntax Tree} (AST)."))))
"java-jansi" "java-jline-2")) "java-jansi" "java-jline-2"))
;; antlr.jar is present twice in antlr2. Symlink doesn't like ;; antlr.jar is present twice in antlr2. Symlink doesn't like
;; it, so we symlink it here. ;; it, so we symlink it here.
(symlink (string-append (assoc-ref inputs "antlr2") "/lib/antlr.jar") (symlink (search-input-file inputs "/lib/antlr.jar")
(string-append out-lib "/antlr.jar")) (string-append out-lib "/antlr.jar"))
(for-each (for-each
(lambda (tool) (lambda (tool)

76
gnu/packages/java.scm
View file

@ -382,8 +382,7 @@ JNI.")
(setenv "JAVAC" (setenv "JAVAC"
(search-input-file inputs "/bin/jikes")) (search-input-file inputs "/bin/jikes"))
(setenv "CLASSPATH" (setenv "CLASSPATH"
(string-append (assoc-ref inputs "jamvm") (search-input-file inputs "/lib/rt.jar"))
"/lib/rt.jar"))
;; Ant complains if this file doesn't exist. ;; Ant complains if this file doesn't exist.
(setenv "HOME" "/tmp") (setenv "HOME" "/tmp")
@ -486,8 +485,7 @@ build process and its dependencies, whereas Make uses Makefile format.")
(lambda* (#:key inputs #:allow-other-keys) (lambda* (#:key inputs #:allow-other-keys)
(setenv "CLASSPATH" (setenv "CLASSPATH"
(string-join (string-join
(cons (string-append (assoc-ref inputs "jamvm") (cons (search-input-file inputs "/lib/rt.jar")
"/lib/rt.jar")
(find-files (string-append (find-files (string-append
(assoc-ref inputs "ant-bootstrap") (assoc-ref inputs "ant-bootstrap")
"/lib") "/lib")
@ -3221,19 +3219,22 @@ Main-Class: org.eclipse.jdt.internal.compiler.batch.Main\n"
(lambda* (#:key inputs #:allow-other-keys) (lambda* (#:key inputs #:allow-other-keys)
(substitute* "build/build.xml" (substitute* "build/build.xml"
(("\\$\\{lib\\}/testng/testng-jdk15.jar") (("\\$\\{lib\\}/testng/testng-jdk15.jar")
(string-append (assoc-ref inputs "java-testng") (search-input-file inputs
"/share/java/java-testng.jar")) "/share/java/java-testng.jar"))
(("\\$\\{lib\\}/commons-lang/commons-lang.jar") (("\\$\\{lib\\}/commons-lang/commons-lang.jar")
(string-append (assoc-ref inputs "java-commons-lang") (search-input-file inputs
"/share/java/commons-lang-" (string-append
,(package-version java-commons-lang) ".jar")) "/share/java/commons-lang-"
,(package-version java-commons-lang)
".jar")))
(("\\$\\{lib\\}/commons-io/commons-io.jar") (("\\$\\{lib\\}/commons-io/commons-io.jar")
(string-append (assoc-ref inputs "java-commons-io") (search-input-file inputs
"/lib/m2/commons-io/commons-io/" (string-append
,(package-version java-commons-io) "/lib/m2/commons-io/commons-io/"
"/commons-io-" ,(package-version java-commons-io)
,(package-version java-commons-io) "/commons-io-"
".jar")) ,(package-version java-commons-io)
".jar")))
;; Remove dependency on svn ;; Remove dependency on svn
(("<build-info.*") "") (("<build-info.*") "")
(("\\$\\{revision.number\\}") (("\\$\\{revision.number\\}")
@ -3406,8 +3407,7 @@ libraries from the SIS division at ETH Zurich like jHDF5.")
(rename-file "build-common.xml.new" "build-common.xml")) (rename-file "build-common.xml.new" "build-common.xml"))
(substitute* "build/build.xml" (substitute* "build/build.xml"
(("\\$\\{lib\\}/cisd-base/cisd-base.jar") (("\\$\\{lib\\}/cisd-base/cisd-base.jar")
(string-append (assoc-ref inputs "java-cisd-base") (search-input-file inputs "/share/java/sis-base.jar"))
"/share/java/sis-base.jar"))
;; Remove dependency on svn ;; Remove dependency on svn
(("<build-info.*") "") (("<build-info.*") "")
(("\\$\\{revision.number\\}") (("\\$\\{revision.number\\}")
@ -3509,29 +3509,32 @@ libraries from the SIS division at ETH Zurich like jHDF5.")
(lambda* (#:key inputs #:allow-other-keys) (lambda* (#:key inputs #:allow-other-keys)
(substitute* "../build_resources/ant/build-common.xml" (substitute* "../build_resources/ant/build-common.xml"
(("../libraries/testng/testng-jdk15.jar") (("../libraries/testng/testng-jdk15.jar")
(string-append (assoc-ref inputs "java-testng") (search-input-file inputs
"/share/java/java-testng.jar"))) "/share/java/java-testng.jar")))
(substitute* "build/build.xml" (substitute* "build/build.xml"
(("\\$\\{lib\\}/sis-base/sis-base.jar") (("\\$\\{lib\\}/sis-base/sis-base.jar")
(string-append (assoc-ref inputs "java-cisd-base") (search-input-file inputs
"/share/java/sis-base.jar")) "/share/java/sis-base.jar"))
(("\\$\\{lib\\}/cisd-args4j/cisd-args4j.jar") (("\\$\\{lib\\}/cisd-args4j/cisd-args4j.jar")
(string-append (assoc-ref inputs "java-cisd-args4j") (search-input-file inputs
"/share/java/cisd-args4j.jar")) "/share/java/cisd-args4j.jar"))
(("\\$\\{lib\\}/commons-lang/commons-lang.jar") (("\\$\\{lib\\}/commons-lang/commons-lang.jar")
(string-append (assoc-ref inputs "java-commons-lang") (search-input-file inputs
"/share/java/commons-lang-" (string-append
,(package-version java-commons-lang) ".jar")) "/share/java/commons-lang-"
,(package-version java-commons-lang)
".jar")))
(("\\$\\{lib\\}/commons-io/commons-io.jar") (("\\$\\{lib\\}/commons-io/commons-io.jar")
(string-append (assoc-ref inputs "java-commons-io") (search-input-file inputs
"/lib/m2/commons-io/commons-io/" (string-append
,(package-version java-commons-io) "/lib/m2/commons-io/commons-io/"
"/commons-io-" ,(package-version java-commons-io)
,(package-version java-commons-io) "/commons-io-"
".jar")) ,(package-version java-commons-io)
".jar")))
(("\\$\\{lib\\}/testng/testng-jdk15.jar") (("\\$\\{lib\\}/testng/testng-jdk15.jar")
(string-append (assoc-ref inputs "java-testng") (search-input-file inputs
"/share/java/java-testng.jar")) "/share/java/java-testng.jar"))
(("\\$\\{lib\\}/junit4/junit.jar") (("\\$\\{lib\\}/junit4/junit.jar")
(car (find-files (assoc-ref inputs "java-junit") "jar$"))) (car (find-files (assoc-ref inputs "java-junit") "jar$")))
(("\\$\\{lib\\}/jmock/hamcrest/hamcrest-core.jar") (("\\$\\{lib\\}/jmock/hamcrest/hamcrest-core.jar")
@ -12916,7 +12919,7 @@ from ORO, Inc.")
(lambda* (#:key inputs #:allow-other-keys) (lambda* (#:key inputs #:allow-other-keys)
(substitute* "build.xml" (substitute* "build.xml"
;; Since we removed the bundled ant.jar, give the correct path ;; Since we removed the bundled ant.jar, give the correct path
(("lib/ant.jar") (string-append (assoc-ref inputs "ant") "/lib/ant.jar")) (("lib/ant.jar") (search-input-file inputs "/lib/ant.jar"))
;; We removed generated native libraries. We can only rebuild one ;; We removed generated native libraries. We can only rebuild one
;; so don't fail if we can't find a native library for another architecture. ;; so don't fail if we can't find a native library for another architecture.
(("zipfileset") "zipfileset erroronmissingarchive=\"false\"")) (("zipfileset") "zipfileset erroronmissingarchive=\"false\""))
@ -12970,8 +12973,7 @@ Java method invocation.")
(lambda* (#:key inputs #:allow-other-keys) (lambda* (#:key inputs #:allow-other-keys)
(substitute* "nbproject/project.properties" (substitute* "nbproject/project.properties"
(("../../build/jna.jar") (("../../build/jna.jar")
(string-append (assoc-ref inputs "java-native-access") (search-input-file inputs "/share/java/jna.jar"))
"/share/java/jna.jar"))
(("../../lib/hamcrest-core-.*.jar") (("../../lib/hamcrest-core-.*.jar")
(car (find-files (assoc-ref inputs "java-hamcrest-core") (car (find-files (assoc-ref inputs "java-hamcrest-core")
"jar$"))) "jar$")))

3
gnu/packages/maths.scm
View file

@ -1347,8 +1347,7 @@ extremely large and complex data collections.")
"hdf/hdf5lib/exceptions/Makefile.in" "hdf/hdf5lib/exceptions/Makefile.in"
"hdf/hdflib/Makefile.in") "hdf/hdflib/Makefile.in")
(("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar") (("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
(string-append (assoc-ref inputs "slf4j-api") (search-input-file inputs "/share/java/slf4j-api.jar")))
"/share/java/slf4j-api.jar")))
;; Replace outdated config.sub and config.guess: ;; Replace outdated config.sub and config.guess:
(with-directory-excursion "config" (with-directory-excursion "config"
(for-each (lambda (file) (for-each (lambda (file)