Merge branch 'master' into core-updates

1 files changed, 1170 insertions, 179 deletions

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index d3fa88adbd..b4f64e2c2e 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -59,6 +59,7 @@
   #:use-module (gnu packages image)
   #:use-module (gnu packages libffi)
   #:use-module (gnu packages linux) ;alsa
+  #:use-module (gnu packages maths)
   #:use-module (gnu packages web)
   #:use-module (gnu packages wget)
   #:use-module (gnu packages pkg-config)
@@ -1587,7 +1588,8 @@ IcedTea build harness.")
                 (modules '((guix build utils)))
                 (snippet
                  '(begin
-                    (substitute* "acinclude.m4"
+                    (substitute* '("configure"
+                                   "acinclude.m4")
                       ;; Do not embed build time
                       (("(DIST_ID=\"Custom build).*$" _ prefix)
                        (string-append prefix "\"\n"))
@@ -1596,65 +1598,90 @@ IcedTea build harness.")
                        "DIST_NAME=\"guix\""))
                     #t))))
       (arguments
-       (substitute-keyword-arguments (package-arguments icedtea-7)
-         ((#:configure-flags flags)
-          `(let ((jdk (assoc-ref %build-inputs "jdk")))
-             `(;;"--disable-bootstrap"
-               "--enable-bootstrap"
-               "--enable-nss"
-               "--disable-downloading"
-               "--disable-system-pcsc"
-               "--disable-system-sctp"
-               "--disable-tests"      ;they are run in the check phase instead
-               "--with-openjdk-src-dir=./openjdk.src"
-               ,(string-append "--with-jdk-home=" jdk))))
-         ((#:phases phases)
-          `(modify-phases ,phases
-             (delete 'fix-x11-extension-include-path)
-             (delete 'patch-paths)
-             (delete 'set-additional-paths)
-             (delete 'patch-patches)
-             (add-after 'unpack 'patch-jni-libs
-               ;; Hardcode dynamically loaded libraries.
-               (lambda _
-                 (let* ((library-path (search-path-as-string->list
-                                       (getenv "LIBRARY_PATH")))
-                        (find-library (lambda (name)
-                                        (search-path
-                                         library-path
-                                         (string-append "lib" name ".so")))))
-                   (for-each
-                    (lambda (file)
-                      (catch 'decoding-error
-                        (lambda ()
-                          (substitute* file
-                            (("VERSIONED_JNI_LIB_NAME\\(\"(.*)\", \"(.*)\"\\)"
-                              _ name version)
-                             (format #f "\"~a\""  (find-library name)))
-                            (("JNI_LIB_NAME\\(\"(.*)\"\\)" _ name)
-                             (format #f "\"~a\"" (find-library name)))))
-                        (lambda _
-                          ;; Those are safe to skip.
-                          (format (current-error-port)
-                                  "warning: failed to substitute: ~a~%"
-                                  file))))
-                    (find-files "openjdk.src/jdk/src/solaris/native"
-                                "\\.c|\\.h"))
-                   #t)))
-             (replace 'install
-               (lambda* (#:key outputs #:allow-other-keys)
-                 (let ((doc (string-append (assoc-ref outputs "doc")
-                                           "/share/doc/icedtea"))
-                       (jre (assoc-ref outputs "out"))
-                       (jdk (assoc-ref outputs "jdk")))
-                   (copy-recursively "openjdk.build/docs" doc)
-                   (copy-recursively "openjdk.build/images/j2re-image" jre)
-                   (copy-recursively "openjdk.build/images/j2sdk-image" jdk)
-                   ;; Install the nss.cfg file to JRE to enable SSL/TLS
-                   ;; support via NSS.
-                   (copy-file (string-append jdk "/jre/lib/security/nss.cfg")
-                              (string-append jre "/lib/security/nss.cfg"))
-                   #t)))))))
+       `(#:imported-modules
+         ((guix build ant-build-system)
+          (guix build syscalls)
+          ,@%gnu-build-system-modules)
+         ,@(substitute-keyword-arguments (package-arguments icedtea-7)
+             ((#:modules modules)
+              `((guix build utils)
+                (guix build gnu-build-system)
+                ((guix build ant-build-system) #:prefix ant:)
+                (ice-9 match)
+                (ice-9 popen)
+                (srfi srfi-19)
+                (srfi srfi-26)))
+             ((#:configure-flags flags)
+              `(let ((jdk (assoc-ref %build-inputs "jdk")))
+                 `( ;;"--disable-bootstrap"
+                   "--enable-bootstrap"
+                   "--enable-nss"
+                   "--disable-downloading"
+                   "--disable-system-pcsc"
+                   "--disable-system-sctp"
+                   "--disable-tests"  ;they are run in the check phase instead
+                   "--with-openjdk-src-dir=./openjdk.src"
+                   ,(string-append "--with-jdk-home=" jdk))))
+             ((#:phases phases)
+              `(modify-phases ,phases
+                 (delete 'fix-x11-extension-include-path)
+                 (delete 'patch-paths)
+                 (delete 'set-additional-paths)
+                 (delete 'patch-patches)
+                 ;; Prevent the keytool from recording the current time when
+                 ;; adding certificates at build time.
+                 (add-after 'unpack 'patch-keystore
+                   (lambda _
+                     (substitute* "openjdk.src/jdk/src/share/classes/sun/security/provider/JavaKeyStore.java"
+                       (("date = new Date\\(\\);")
+                        "\
+date = (System.getenv(\"SOURCE_DATE_EPOCH\") != null) ?\
+new Date(Long.parseLong(System.getenv(\"SOURCE_DATE_EPOCH\"))) :\
+new Date();"))
+                     #t))
+                 (add-after 'unpack 'patch-jni-libs
+                   ;; Hardcode dynamically loaded libraries.
+                   (lambda _
+                     (let* ((library-path (search-path-as-string->list
+                                           (getenv "LIBRARY_PATH")))
+                            (find-library (lambda (name)
+                                            (search-path
+                                             library-path
+                                             (string-append "lib" name ".so")))))
+                       (for-each
+                        (lambda (file)
+                          (catch 'decoding-error
+                            (lambda ()
+                              (substitute* file
+                                (("VERSIONED_JNI_LIB_NAME\\(\"(.*)\", \"(.*)\"\\)"
+                                  _ name version)
+                                 (format #f "\"~a\""  (find-library name)))
+                                (("JNI_LIB_NAME\\(\"(.*)\"\\)" _ name)
+                                 (format #f "\"~a\"" (find-library name)))))
+                            (lambda _
+                              ;; Those are safe to skip.
+                              (format (current-error-port)
+                                      "warning: failed to substitute: ~a~%"
+                                      file))))
+                        (find-files "openjdk.src/jdk/src/solaris/native"
+                                    "\\.c|\\.h"))
+                       #t)))
+                 (replace 'install
+                   (lambda* (#:key outputs #:allow-other-keys)
+                     (let ((doc (string-append (assoc-ref outputs "doc")
+                                               "/share/doc/icedtea"))
+                           (jre (assoc-ref outputs "out"))
+                           (jdk (assoc-ref outputs "jdk")))
+                       (copy-recursively "openjdk.build/docs" doc)
+                       (copy-recursively "openjdk.build/images/j2re-image" jre)
+                       (copy-recursively "openjdk.build/images/j2sdk-image" jdk)
+                       ;; Install the nss.cfg file to JRE to enable SSL/TLS
+                       ;; support via NSS.
+                       (copy-file (string-append jdk "/jre/lib/security/nss.cfg")
+                                  (string-append jre "/lib/security/nss.cfg"))
+                       #t)))
+                 (add-after 'install 'strip-jar-timestamps
+                   (assoc-ref ant:%standard-phases 'strip-jar-timestamps)))))))
       (native-inputs
        `(("jdk" ,icedtea-7 "jdk")
          ("openjdk-src"
@@ -2015,6 +2042,510 @@ debugging, etc.")
              (delete-file-recursively "lib") #t))
          (replace 'install (install-jars "bin/lib")))))))
 
+;; This is the last 3.x release of ECJ
+(define-public java-ecj-3
+  (package
+    (name "java-ecj")
+    (version "3.8.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://archive.eclipse.org/eclipse/"
+                                  "downloads/drops/R-" version
+                                  "-201301310800/ecjsrc-" version ".jar"))
+              (sha256
+               (base32
+                "01mdj14jw11g1jfnki4fi8229p0c6zzckd38zqy2w4m3cjcvsx04"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:tests? #f ; none included
+       #:jdk ,icedtea-7 ; doesn't build with JDK8+
+       #:make-flags (list "-f" "src/build.xml")
+       #:build-target "build"
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-manifest
+           (lambda _
+             ;; Record the main class to make ecj executable.
+             (with-atomic-file-replacement "src/META-INF/MANIFEST.MF"
+               (lambda (in out)
+                 (display "Manifest-Version: 1.0
+Main-Class: org.eclipse.jdt.internal.compiler.batch.Main\n"
+                          out)))))
+         (replace 'install (install-jars ".")))))
+    (home-page "https://eclipse.org")
+    (synopsis "Eclipse Java development tools core batch compiler")
+    (description "This package provides the Eclipse Java core batch compiler.")
+    (license license:epl1.0)))
+
+;; This is needed for java-cisd-args4j
+(define-public java-ecj-3.5
+  (package (inherit java-ecj-3)
+    (version "3.5.1")
+    (source (origin
+              (method url-fetch/zipbomb)
+              (uri (string-append "http://archive.eclipse.org/eclipse/"
+                                  "downloads/drops/R-" version
+                                  "-200909170800/ecjsrc-" version ".zip"))
+              (sha256
+               (base32
+                "1vnl2mavisc567bip736xzsvvbjif5279wc4a7pbdik5wlir8qr7"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:tests? #f ; none included
+       #:jdk ,icedtea-7 ; doesn't build with JDK8+
+       #:build-target "build"
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-manifest
+           (lambda _
+             ;; Record the main class to make ecj executable.
+             (with-atomic-file-replacement "META-INF/MANIFEST.MF"
+               (lambda (in out)
+                 (dump-port in out)
+                 (display "Main-Class: org.eclipse.jdt.internal.compiler.batch.Main\n"
+                          out)))))
+         (replace 'install (install-jars ".")))))
+    (native-inputs
+     `(("unzip" ,unzip)))))
+
+(define-public java-cisd-base
+  (let ((revision 38938)
+        (base-version "14.12.0"))
+    (package
+      (name "java-cisd-base")
+      (version (string-append base-version "-" (number->string revision)))
+      (source (origin
+                (method svn-fetch)
+                (uri (svn-reference
+                      (url (string-append "http://svnsis.ethz.ch/repos/cisd/"
+                                          "base/tags/release/"
+                                          (version-major+minor base-version)
+                                          ".x/" base-version "/base/"))
+                      (revision revision)))
+                (file-name (string-append "java-cisd-base-" version "-checkout"))
+                (sha256
+                 (base32
+                  "1i5adyf7nzclb0wydgwa1az04qliid8035vpahaandmkmigbnxiy"))
+                (modules '((guix build utils)))
+                (snippet
+                 '(begin
+                    ;; Delete included gradle jar
+                    (delete-file-recursively "gradle/wrapper")
+                    ;; Delete pre-built native libraries
+                    (delete-file-recursively "libs")
+                    #t))))
+      (build-system ant-build-system)
+      (arguments
+       `(#:make-flags '("-file" "build/build.xml")
+         #:test-target "jar-test"
+         #:jdk ,icedtea-8
+         #:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'unpack-build-resources
+             (lambda* (#:key inputs #:allow-other-keys)
+               (copy-recursively (assoc-ref inputs "build-resources")
+                                 "../build_resources")
+               #t))
+           (add-after 'unpack-build-resources 'fix-dependencies
+             (lambda* (#:key inputs #:allow-other-keys)
+               (substitute* "build/build.xml"
+                 (("\\$\\{lib\\}/testng/testng-jdk15.jar")
+                  (string-append (assoc-ref inputs "java-testng")
+                                 "/share/java/java-testng.jar"))
+                 (("\\$\\{lib\\}/commons-lang/commons-lang.jar")
+                  (string-append (assoc-ref inputs "java-commons-lang")
+                                 "/share/java/commons-lang-"
+                                 ,(package-version java-commons-lang) ".jar"))
+                 (("\\$\\{lib\\}/commons-io/commons-io.jar")
+                  (string-append (assoc-ref inputs "java-commons-io")
+                                 "/share/java/commons-io-"
+                                 ,(package-version java-commons-io)
+                                 "-SNAPSHOT.jar"))
+                 ;; Remove dependency on svn
+                 (("<build-info.*") "")
+                 (("\\$\\{revision.number\\}")
+                  ,(number->string revision))
+                 (("\\$\\{version.number\\}") ,base-version))
+               ;; Remove dependency on classycle
+               (substitute* "../build_resources/ant/build-common.xml"
+                 (("<taskdef name=\"dependency-checker.*") "")
+                 (("classname=\"classycle.*") "")
+                 (("classpath=\"\\$\\{lib\\}/classycle.*") ""))
+               #t))
+           ;; A few tests fail because of the lack of a proper /etc/groups and
+           ;; /etc/passwd file in the build container.
+           (add-after 'unpack 'disable-broken-tests
+             (lambda _
+               (substitute* "sourceTest/java/ch/systemsx/cisd/base/AllTests.java"
+                 (("Unix.isOperational\\(\\)") "false"))
+               #t))
+           ;; These decorators are almost useless and pull in an unpackaged
+           ;; dependency.
+           (add-after 'unpack 'remove-useless-decorators
+             (lambda _
+               (substitute* "source/java/ch/systemsx/cisd/base/unix/Unix.java"
+                 (("@Private") "")
+                 (("import ch.rinn.restrictions.Private;") ""))
+               (substitute* "sourceTest/java/ch/systemsx/cisd/base/unix/UnixTests.java"
+                 (("@Friend.*") "")
+                 (("import ch.rinn.restrictions.Friend;") ""))
+               #t))
+           (add-before 'configure 'build-native-code
+             (lambda* (#:key inputs #:allow-other-keys)
+               (let ((jdk (assoc-ref inputs "jdk"))
+                     (dir ,(match (%current-system)
+                             ("i686-linux"
+                              "i386-Linux")
+                             ((or "armhf-linux" "aarch64-linux")
+                              "arm-Linux")
+                             ((or "x86_64-linux")
+                              "amd64-Linux")
+                             (_ "unknown-Linux"))))
+                 (with-directory-excursion "source/c"
+                   (invoke "gcc" "-shared" "-O3" "-fPIC" "unix.c"
+                           (string-append "-I" jdk "/include")
+                           (string-append "-I" jdk "/include/linux")
+                           "-o" "libunix.so")
+                   (invoke "gcc" "-shared" "-O3" "-fPIC"
+                           "-DMACHINE_BYTE_ORDER=1"
+                           "copyCommon.c"
+                           "copyByteChar.c"
+                           "copyByteDouble.c"
+                           "copyByteFloat.c"
+                           "copyByteInt.c"
+                           "copyByteLong.c"
+                           "copyByteShort.c"
+                           (string-append "-I" jdk "/include")
+                           (string-append "-I" jdk "/include/linux")
+                           "-o" "libnativedata.so"))
+                 (install-file "source/c/libunix.so"
+                               (string-append "libs/native/unix/" dir))
+                 (install-file "source/c/libnativedata.so"
+                               (string-append "libs/native/nativedata/" dir))
+                 #t)))
+           ;; In the "check" phase we only build the test executable.
+           (add-after 'check 'run-tests
+             (lambda _
+               (invoke "java" "-jar" "targets/dist/sis-base-test.jar")
+               (delete-file "targets/dist/sis-base-test.jar")
+               #t))
+           (replace 'install (install-jars "targets/dist")))))
+      (native-inputs
+       `(("jdk" ,icedtea-8)
+         ("java-commons-lang" ,java-commons-lang)
+         ("java-commons-io" ,java-commons-io)
+         ("java-testng" ,java-testng)
+         ("build-resources"
+          ,(origin
+             (method svn-fetch)
+             (uri (svn-reference
+                   (url (string-append "http://svnsis.ethz.ch/repos/cisd/"
+                                       "base/tags/release/"
+                                       (version-major+minor base-version)
+                                       ".x/" base-version
+                                       "/build_resources/"))
+                   (revision revision)))
+             (sha256
+              (base32
+               "0b6335gkm4x895rac6kfg9d3rpq0sy19ph4zpg2gyw6asfsisjhk"))))))
+      (home-page "http://svnsis.ethz.ch")
+      (synopsis "Utility classes for libraries from ETH Zurich")
+      (description "This library supplies some utility classes needed for
+libraries from the SIS division at ETH Zurich like jHDF5.")
+      ;; The C sources are under a non-copyleft license, which looks like a
+      ;; variant of the BSD licenses.  The whole package is under the ASL2.0.
+      (license (list license:asl2.0
+                     (license:non-copyleft "file://source/c/COPYING"))))))
+
+(define-public java-cisd-args4j
+  (let ((revision 39162)
+        (base-version "9.11.2"))
+    (package
+      (name "java-cisd-args4j")
+      (version (string-append base-version "-" (number->string revision)))
+      (source (origin
+                (method svn-fetch)
+                (uri (svn-reference
+                      (url (string-append "http://svnsis.ethz.ch/repos/cisd/"
+                                          "args4j/tags/release/"
+                                          (version-major+minor base-version)
+                                          ".x/" base-version "/args4j/"))
+                      (revision revision)))
+                (file-name (string-append "java-cisd-args4j-" version "-checkout"))
+                (sha256
+                 (base32
+                  "0hhqznjaivq7ips7mkwas78z42s6djsm20rrs7g1zd59rcsakxn2"))))
+      (build-system ant-build-system)
+      (arguments
+       `(#:make-flags '("-file" "build/build.xml")
+         #:tests? #f ; there are no tests
+         ;; There are weird build failures with JDK8, such as: "The type
+         ;; java.io.ObjectInputStream cannot be resolved. It is indirectly
+         ;; referenced from required .class files"
+         #:jdk ,icedtea-7
+         #:modules ((guix build ant-build-system)
+                    (guix build utils)
+                    (guix build java-utils)
+                    (sxml simple)
+                    (sxml transform)
+                    (sxml xpath))
+         #:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'unpack-build-resources
+             (lambda* (#:key inputs #:allow-other-keys)
+               (mkdir-p "../build_resources")
+               (invoke "tar" "xf" (assoc-ref inputs "build-resources")
+                       "-C" "../build_resources"
+                       "--strip-components=1")
+               (mkdir-p "../build_resources/lib")
+               #t))
+           (add-after 'unpack-build-resources 'fix-dependencies
+             (lambda* (#:key inputs #:allow-other-keys)
+               ;; FIXME: There should be a more convenient abstraction for
+               ;; editing XML files.
+               (with-directory-excursion "../build_resources/ant/"
+                 (chmod "build-common.xml" #o664)
+                 (call-with-output-file "build-common.xml.new"
+                   (lambda (port)
+                     (sxml->xml
+                      (pre-post-order
+                       (with-input-from-file "build-common.xml"
+                         (lambda _ (xml->sxml #:trim-whitespace? #t)))
+                       `(;; Remove dependency on classycle and custom ant tasks
+                         (taskdef   . ,(lambda (tag . kids)
+                                         (let ((name ((sxpath '(name *text*)) kids)))
+                                           (if (or (member "build-info" name)
+                                                   (member "dependency-checker" name)
+                                                   (member "build-java-subprojects" name)
+                                                   (member "project-classpath" name))
+                                               '() ; skip
+                                               `(,tag ,@kids)))))
+                         (typedef   . ,(lambda (tag . kids)
+                                         (let ((name ((sxpath '(name *text*)) kids)))
+                                           (if (member "recursive-jar" name)
+                                               '() ; skip
+                                               `(,tag ,@kids)))))
+                         (build-java-subprojects . ,(lambda _ '()))
+                         ;; Ignore everything else
+                         (*default* . ,(lambda (tag . kids) `(,tag ,@kids)))
+                         (*text*    . ,(lambda (_ txt) txt))))
+                      port)))
+                 (rename-file "build-common.xml.new" "build-common.xml"))
+               (substitute* "build/build.xml"
+                 (("\\$\\{lib\\}/cisd-base/cisd-base.jar")
+                  (string-append (assoc-ref inputs "java-cisd-base")
+                                 "/share/java/sis-base.jar"))
+                 ;; Remove dependency on svn
+                 (("<build-info.*") "")
+                 (("\\$\\{revision.number\\}")
+                  ,(number->string revision))
+                 (("\\$\\{version.number\\}") ,base-version)
+                 ;; Don't use custom ant tasks.
+                 (("recursive-jar") "jar")
+                 (("<project-classpath.*") ""))
+               #t))
+           (replace 'install (install-jars "targets/dist")))))
+      (inputs
+       `(("java-cisd-base" ,java-cisd-base)))
+      (native-inputs
+       `(("ecj" ,java-ecj-3.5)
+         ("build-resources"
+          ,(origin
+             (method svn-fetch)
+             (uri (svn-reference
+                   (url (string-append "http://svnsis.ethz.ch/repos/cisd/"
+                                       "args4j/tags/release/"
+                                       (version-major+minor base-version)
+                                       ".x/" base-version
+                                       "/build_resources/"))
+                   (revision revision)))
+             (sha256
+              (base32
+               "056cam4k8pll7ass31sy6gwn8g8719njc41yf4l02b0342nilkyf"))
+             (modules '((guix build utils)))
+             ;; Delete bundled pre-built jars.
+             (snippet
+              '(begin (delete-file-recursively "lib/") #t))))))
+      (home-page "http://svnsis.ethz.ch")
+      (synopsis "Command line parser library")
+      (description "This package provides a parser for command line arguments.")
+      (license license:asl2.0))))
+
+(define-public java-cisd-jhdf5
+  (let ((revision 39162)
+        (base-version "14.12.6"))
+    (package
+      (name "java-cisd-jhdf5")
+      (version (string-append base-version "-" (number->string revision)))
+      (source (origin
+                (method svn-fetch)
+                (uri (svn-reference
+                      (url (string-append "http://svnsis.ethz.ch/repos/cisd/"
+                                          "jhdf5/tags/release/"
+                                          (version-major+minor base-version)
+                                          ".x/" base-version "/jhdf5/"))
+                      (revision revision)))
+                (file-name (string-append "java-cisd-jhdf5-" version "-checkout"))
+                (sha256
+                 (base32
+                  "13i17s2hn0q9drdqvp8csy7770p3hdbh9rp30ihln2ldkfawdmz0"))
+                (modules '((guix build utils)))
+                (snippet
+                 '(begin
+                    ;; Delete included gradle jar
+                    (delete-file-recursively "gradle/wrapper")
+                    ;; Delete pre-built native libraries
+                    (delete-file-recursively "libs")
+                    #t))))
+      (build-system ant-build-system)
+      (arguments
+       `(#:make-flags '("-file" "build/build.xml")
+         #:build-target "jar-all"
+         #:test-target "jar-test"
+         #:jdk ,icedtea-8
+         #:phases
+         (modify-phases %standard-phases
+           ;; Don't erase results from the build phase when building tests.
+           (add-after 'unpack 'separate-test-target-from-clean
+             (lambda _
+               (substitute* "build/build.xml"
+                 (("\"jar-test\" depends=\"clean, ")
+                  "\"jar-test\" depends=\""))
+               #t))
+           (add-after 'unpack 'unpack-build-resources
+             (lambda* (#:key inputs #:allow-other-keys)
+               (copy-recursively (assoc-ref inputs "build-resources")
+                                 "../build_resources")
+               (delete-file-recursively "../build_resources/lib/")
+               (mkdir-p "../build_resources/lib")
+               ;; Remove dependency on classycle
+               (substitute* "../build_resources/ant/build-common.xml"
+                 (("<taskdef name=\"dependency-checker.*") "")
+                 (("classname=\"classycle.*") "")
+                 (("classpath=\"\\$\\{lib\\}/classycle.*") ""))
+               ;; Remove dependency on svn
+               (substitute* "build/build.xml"
+                 (("<build-info.*") "")
+                 (("\\$\\{revision.number\\}")
+                  ,(number->string revision))
+                 (("\\$\\{version.number\\}") ,base-version))
+               #t))
+           (add-after 'unpack-build-resources 'fix-dependencies
+             (lambda* (#:key inputs #:allow-other-keys)
+               (substitute* "../build_resources/ant/build-common.xml"
+                 (("../libraries/testng/testng-jdk15.jar")
+                  (string-append (assoc-ref inputs "java-testng")
+                                 "/share/java/java-testng.jar")))
+               (substitute* "build/build.xml"
+                 (("\\$\\{lib\\}/sis-base/sis-base.jar")
+                  (string-append (assoc-ref inputs "java-cisd-base")
+                                 "/share/java/sis-base.jar"))
+                 (("\\$\\{lib\\}/cisd-args4j/cisd-args4j.jar")
+                  (string-append (assoc-ref inputs "java-cisd-args4j")
+                                 "/share/java/cisd-args4j.jar"))
+                 (("\\$\\{lib\\}/commons-lang/commons-lang.jar")
+                  (string-append (assoc-ref inputs "java-commons-lang")
+                                 "/share/java/commons-lang-"
+                                 ,(package-version java-commons-lang) ".jar"))
+                 (("\\$\\{lib\\}/commons-io/commons-io.jar")
+                  (string-append (assoc-ref inputs "java-commons-io")
+                                 "/share/java/commons-io-"
+                                 ,(package-version java-commons-io)
+                                 "-SNAPSHOT.jar"))
+                 (("\\$\\{lib\\}/testng/testng-jdk15.jar")
+                  (string-append (assoc-ref inputs "java-testng")
+                                 "/share/java/java-testng.jar"))
+                 (("\\$\\{lib\\}/junit4/junit.jar")
+                  (string-append (assoc-ref inputs "java-junit")
+                                 "/share/java/junit.jar"))
+                 (("\\$\\{lib\\}/jmock/hamcrest/hamcrest-core.jar")
+                  (string-append (assoc-ref inputs "java-hamcrest-core")
+                                 "/share/java/hamcrest-core.jar")))
+               ;; Remove dependency on ch.rinn.restrictions
+               (with-directory-excursion "source/java/ch/systemsx/cisd/hdf5/"
+                 (substitute* '("BitSetConversionUtils.java"
+                                "HDF5Utils.java")
+                   (("import ch.rinn.restrictions.Private;") "")
+                   (("@Private") "")))
+               (with-directory-excursion "sourceTest/java/ch/systemsx/cisd/hdf5/"
+                 (substitute* '("BitSetConversionTest.java"
+                                "h5ar/HDF5ArchiverTest.java")
+                   (("import ch.rinn.restrictions.Friend;") "")
+                   (("@Friend.*") ""))
+                 ;; Remove leftovers from removing @Friend
+                 (substitute* "h5ar/HDF5ArchiverTest.java"
+                   (("\\{ HDF5Archiver.class, IdCache.class, LinkRecord.class \\}\\)")
+                    "")))
+               #t))
+           (add-before 'configure 'build-native-library
+             (lambda* (#:key inputs #:allow-other-keys)
+               (let ((jdk  (assoc-ref inputs "jdk"))
+                     (hdf5 (assoc-ref inputs "hdf5"))
+                     (dir  ,(match (%current-system)
+                              ("i686-linux"
+                               "i386-Linux")
+                              ((or "armhf-linux" "aarch64-linux")
+                               "arm-Linux")
+                              ((or "x86_64-linux")
+                               "amd64-Linux")
+                              (_ "unknown-Linux"))))
+                 (with-directory-excursion "source/c"
+                   (apply invoke `("gcc" "-shared" "-O3"
+                                   "-fPIC"
+                                   "-Wl,--exclude-libs,ALL"
+                                   ,@(find-files "jhdf5" "\\.c$")
+                                   ,@(find-files "hdf-java" "\\.c$")
+                                   ,(string-append "-I" hdf5 "/include")
+                                   ,(string-append "-I" jdk "/include")
+                                   ,(string-append "-I" jdk "/include/linux")
+                                   ,(string-append hdf5 "/lib/libhdf5.a")
+                                   "-o" "libjhdf5.so" "-lz")))
+                 (install-file "source/c/libjhdf5.so"
+                               (string-append "libs/native/jhdf5/" dir))
+                 #t)))
+           ;; In the "check" phase we only build the test executable.
+           (add-after 'check 'run-tests
+             (lambda _
+               (invoke "java" "-jar" "targets/dist/sis-jhdf5-test.jar")
+               (delete-file "targets/dist/sis-jhdf5-test.jar")
+               #t))
+           (replace 'install
+             (install-jars "targets/dist")))))
+      (inputs
+       `(("java-cisd-base" ,java-cisd-base)
+         ("java-cisd-args4j" ,java-cisd-args4j)
+         ("java-commons-lang" ,java-commons-lang)
+         ("java-commons-io" ,java-commons-io)
+         ("hdf5" ,hdf5)
+         ("zlib" ,zlib)))
+      (native-inputs
+       `(("jdk" ,icedtea-8)
+         ("java-testng" ,java-testng)
+         ("java-junit" ,java-junit)
+         ("java-jmock" ,java-jmock)
+         ("java-hamcrest-core" ,java-hamcrest-core)
+         ("build-resources"
+          ,(origin
+             (method svn-fetch)
+             (uri (svn-reference
+                   (url (string-append "http://svnsis.ethz.ch/repos/cisd/"
+                                       "jhdf5/tags/release/"
+                                       (version-major+minor base-version)
+                                       ".x/" base-version
+                                       "/build_resources/"))
+                   (revision revision)))
+             (sha256
+              (base32
+               "0b6335gkm4x895rac6kfg9d3rpq0sy19ph4zpg2gyw6asfsisjhk"))))))
+      (home-page "https://wiki-bsse.ethz.ch/display/JHDF5/")
+      (synopsis "Java binding for HDF5")
+      (description "JHDF5 is a high-level API in Java for reading and writing
+HDF5 files, building on the libraries provided by the HDF Group.")
+      ;; The C sources are under a non-copyleft license, which looks like a
+      ;; variant of the BSD licenses.  The whole package is under the ASL2.0.
+      (license (list license:asl2.0
+                     (license:non-copyleft "file://source/c/COPYING"))))))
+
 (define-public java-classpathx-servletapi
   (package
     (name "java-classpathx-servletapi")
@@ -2480,7 +3011,7 @@ mechanism of Java.  It is especially useful for dynamic loading of application
 components.")
     (license license:asl2.0)))
 
-(define-public java-plexus-container-default-bootstrap
+(define java-plexus-container-default-bootstrap
   (package
     (name "java-plexus-container-default-bootstrap")
     (version "1.7.1")
@@ -2657,6 +3188,418 @@ archives (jar).")
      `(("archiver" ,java-plexus-archiver)
        ("hamcrest" ,java-hamcrest-core)))))
 
+(define-public java-plexus-component-annotations
+  (package
+    (inherit java-plexus-container-default)
+    (name "java-plexus-component-annotations")
+    (arguments
+     `(#:jar-name "plexus-component-annotations.jar"
+       #:source-dir "plexus-component-annotations/src/main/java"
+       #:tests? #f)); no tests
+    (inputs '())
+    (native-inputs '())
+    (synopsis "Plexus descriptors generator")
+    (description "This package is a Maven plugin to generate Plexus descriptors
+from source tags and class annotations.")))
+
+(define-public java-plexus-cipher
+  (package
+    (name "java-plexus-cipher")
+    (version "1.7")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/codehaus-plexus/plexus-cipher"
+                                  "/archive/plexus-cipher-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1j3r8xzlxlk340snkjp6lk2ilkxlkn8qavsfiq01f43xmvv8ymk3"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "plexus-cipher.jar"
+       #:source-dir "src/main/java"
+       #:jdk ,icedtea-8
+       #:tests? #f; FIXME: requires sisu-inject-bean
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'copy-resources
+           (lambda _
+             (copy-recursively "src/main/resources" "build/classes")
+             (mkdir-p "build/classes/META-INF/sisu")
+             (with-output-to-file "build/classes/META-INF/sisu/javax.inject.Named"
+               (lambda _
+                 (display "org.sonatype.plexus.components.cipher.DefaultPlexusCipher\n")))
+             #t)))))
+    (inputs
+     `(("java-cdi-api" ,java-cdi-api)
+       ("java-javax-inject" ,java-javax-inject)))
+    (home-page "https://github.com/sonatype/plexus-cipher")
+    (synopsis "Encryption/decryption Component")
+    (description "Plexus-cipher contains a component to deal with encryption
+and decryption.")
+    (license license:asl2.0)))
+
+(define-public java-plexus-compiler-api
+  (package
+    (name "java-plexus-compiler-api")
+    (version "2.8.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/codehaus-plexus/plexus-compiler"
+                                  "/archive/plexus-compiler-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0g3x26pymcdnfnwv2a1i57pd5s26f5zqfi1rdy98z1bn01klx25k"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "plexus-compiler-api.jar"
+       #:source-dir "plexus-compiler-api/src/main/java"
+       #:jdk ,icedtea-8
+       #:test-dir "plexus-compiler-api/src/test"))
+    (inputs
+     `(("java-plexus-container-default" ,java-plexus-container-default)
+       ("java-plexus-util" ,java-plexus-utils)))
+    (native-inputs
+     `(("java-junit" ,java-junit)))
+    (home-page "https://github.com/codehaus-plexus/plexus-compiler")
+    (synopsis "Plexus Compilers component's API to manipulate compilers")
+    (description "This package contains the API used by components to manipulate
+compilers.")
+    (license (list license:asl2.0
+                   license:expat))))
+
+(define-public java-plexus-compiler-javac
+  (package
+    (inherit java-plexus-compiler-api)
+    (name "java-plexus-compiler-javac")
+    (arguments
+     `(#:jar-name "plexus-compiler-javac.jar"
+       #:source-dir "plexus-compilers/plexus-compiler-javac/src/main/java"
+       #:jdk ,icedtea-8
+       #:tests? #f; depends on compiler-test -> maven-core -> ... -> this package.
+       #:test-dir "plexus-compilers/plexus-compiler-javac/src/test"))
+    (inputs
+     `(("java-plexus-compiler-api" ,java-plexus-compiler-api)
+       ("java-plexus-utils" ,java-plexus-utils)
+       ("java-plexus-container-default" ,java-plexus-container-default)))
+    (native-inputs
+     `(("java-junit" ,java-junit)))
+    (synopsis "Javac Compiler support for Plexus Compiler component")
+    (description "This package contains the Javac Compiler support for Plexus
+Compiler component.")))
+
+(define-public java-plexus-sec-dispatcher
+  (package
+    (name "java-plexus-sec-dispatcher")
+    (version "1.4") ;; Newest release listed at the Maven Central Repository.
+    (source (origin
+              ;; This project doesn't tag releases or publish tarballs, so we take
+              ;; the "prepare release plexus-sec-dispatcher-1.4" git commit.
+              (method url-fetch)
+              (uri (string-append "https://github.com/sonatype/plexus-sec-dispatcher/"
+                                  "archive/7db8f88048.tar.gz"))
+              (sha256
+               (base32
+                "1smfrk4n7xbrsxpxcp2j4i0j8q86j73w0w6xg7qz83dp6dagdjgp"))
+              (file-name (string-append name "-" version ".tar.gz"))))
+    (arguments
+     `(#:jar-name "plexus-sec-dispatcher.jar"
+       #:source-dir "src/main/java"
+       #:jdk ,icedtea-8
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'generate-models
+           (lambda* (#:key inputs #:allow-other-keys)
+             (define (modello-single-mode file version mode)
+               (zero? (system* "java"
+                               "org.codehaus.modello.ModelloCli"
+                               file mode "src/main/java" version
+                               "false" "true")))
+             (let ((file "src/main/mdo/settings-security.mdo"))
+               (and
+               (modello-single-mode file "1.0.0" "java")
+               (modello-single-mode file "1.0.0" "xpp3-reader")
+               (modello-single-mode file "1.0.0" "xpp3-writer")))))
+         (add-before 'build 'generate-components.xml
+           (lambda _
+             (mkdir-p "build/classes/META-INF/plexus")
+             (with-output-to-file "build/classes/META-INF/plexus/components.xml"
+               (lambda _
+                 (display
+                   "<component-set>\n
+  <components>\n
+    <component>\n
+      <role>org.sonatype.plexus.components.sec.dispatcher.SecDispatcher</role>\n
+      <role-hint>default</role-hint>\n
+      <implementation>org.sonatype.plexus.components.sec.dispatcher.DefaultSecDispatcher</implementation>\n
+      <description></description>\n
+      <requirements>\n
+        <requirement>\n
+          <role>org.sonatype.plexus.components.cipher.PlexusCipher</role>\n
+          <field-name>_cipher</field-name>\n
+        </requirement>\n
+        <requirement>\n
+          <role>org.sonatype.plexus.components.sec.dispatcher.PasswordDecryptor</role>\n
+          <field-name>_decryptors</field-name>\n
+        </requirement>\n
+      </requirements>\n
+      <configuration>\n
+        <_configuration-file>~/.settings-security.xml</_configuration-file>\n
+      </configuration>\n
+    </component>\n
+  </components>\n
+</component-set>\n")))))
+         (add-before 'check 'fix-paths
+           (lambda _
+             (copy-recursively "src/test/resources" "target"))))))
+    (inputs
+     `(("java-plexus-cipher" ,java-plexus-cipher)))
+    (native-inputs
+     `(("java-modello-core" ,java-modello-core)
+       ;; for modello:
+       ("java-plexus-container-default" ,java-plexus-container-default)
+       ("java-plexus-classworlds" ,java-plexus-classworlds)
+       ("java-plexus-utils" ,java-plexus-utils)
+       ("java-guava" ,java-guava)
+       ("java-geronimo-xbean-reflect" ,java-geronimo-xbean-reflect)
+       ("java-sisu-build-api" ,java-sisu-build-api)
+       ;; modello plugins:
+       ("java-modellop-plugins-java" ,java-modello-plugins-java)
+       ("java-modellop-plugins-xml" ,java-modello-plugins-xml)
+       ("java-modellop-plugins-xpp3" ,java-modello-plugins-xpp3)
+       ;; for tests
+       ("java-junit" ,java-junit)))
+    (build-system ant-build-system)
+    (home-page "https://github.com/sonatype/plexus-sec-dispatcher")
+    (synopsis "Plexus Security Dispatcher Component")
+    (description "This package is the Plexus Security Dispatcher Component.
+This component decrypts a string passed to it.")
+    (license license:asl2.0)))
+
+(define-public java-sisu-build-api
+  (package
+    (name "java-sisu-build-api")
+    (version "0.0.7")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/sonatype/sisu-build-api/"
+                                  "archive/plexus-build-api-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1c3rrpma3x634xp2rm2p5iskfhzdyc7qfbhjzr70agrl1jwghgy2"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "sisu-build-api.jar"
+       #:source-dir "src/main/java"
+       #:jdk ,icedtea-8
+       #:tests? #f; FIXME: how to run the tests?
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'copy-resources
+           (lambda _
+             (copy-recursively "src/main/resources" "build/classes")
+             (substitute* (find-files "build/classes")
+               (("\\$\\{project.version\\}") ,version))
+             #t))
+         (add-before 'build 'generate-plexus-compontent
+           (lambda _
+             (mkdir-p "build/classes/META-INF/plexus")
+             ;; This file is required for plexus to inject this package.
+             ;; FIXME: how is it generated?
+             (with-output-to-file "build/classes/META-INF/plexus/components.xml"
+               (lambda _
+                 (display
+                   "<component-set>\n
+  <components>\n
+    <component>\n
+      <role>org.sonatype.plexus.build.incremental.BuildContext</role>\n
+      <role-hint>default</role-hint>\n
+      <implementation>org.sonatype.plexus.build.incremental.DefaultBuildContext</implementation>\n
+      <description>Filesystem based non-incremental build context implementation\n
+which behaves as if all files were just created.</description>\n
+    </component>\n
+  </components>\n
+</component-set>\n")))
+             #t)))))
+    (inputs
+     `(("java-plexus-utils" ,java-plexus-utils)
+       ("java-plexus-container-default" ,java-plexus-container-default)))
+    (home-page "https://github.com/sonatype/sisu-build-api/")
+    (synopsis "Base build API for maven")
+    (description "This package contains the base build API for maven and
+a default implementation of it.  This API is about scanning files in a
+project and determining what files need to be rebuilt.")
+    (license license:asl2.0)))
+
+(define-public java-modello-core
+  (package
+    (name "java-modello-core")
+    (version "1.9.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/codehaus-plexus/modello"
+                                  "/archive/modello-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0l2pvns8pmlrmjm3iknp7gpg3654y1m8qhy55b19sdwdchdcyxfh"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "modello-core.jar"
+       #:source-dir "modello-core/src/main/java"
+       #:test-dir "modello-core/src/test"
+       #:main-class "org.codehaus.modello.ModelloCli"
+       #:jdk ,icedtea-8
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'copy-resources
+           (lambda _
+             (mkdir-p "build/classes/META-INF/plexus")
+             (copy-file "modello-core/src/main/resources/META-INF/plexus/components.xml"
+                        "build/classes/META-INF/plexus/components.xml")
+             #t))
+         (add-before 'check 'fix-tests
+           (lambda _
+             (with-directory-excursion "modello-core/src/test/java/org/codehaus"
+               (substitute* '("modello/core/DefaultModelloCoreTest.java"
+                              "modello/core/io/ModelReaderTest.java")
+                 (("src/test") "modello-core/src/test")))
+             #t)))))
+    (inputs
+     `(("java-plexus-utils" ,java-plexus-utils)
+       ("java-plexus-container-default" ,java-plexus-container-default)
+       ("java-sisu-build-api" ,java-sisu-build-api)))
+    (native-inputs
+     `(("java-junit" ,java-junit)
+       ("java-plexus-classworlds" ,java-plexus-classworlds)
+       ("java-geronimo-xbean-reflect" ,java-geronimo-xbean-reflect)
+       ("java-guava" ,java-guava)))
+    (home-page "http://codehaus-plexus.github.io/modello/")
+    (synopsis "Framework for code generation from a simple model")
+    (description "Modello is a framework for code generation from a simple model.
+
+Modello generates code from a simple model format: based on a plugin
+architecture, various types of code and descriptors can be generated from the
+single model, including Java POJOs, XML/JSON/YAML marshallers/unmarshallers,
+XSD and documentation.")
+    (license (list
+               license:expat
+               ;; Although this package uses only files licensed under expat,
+               ;; other parts of the source are licensed under different
+               ;; licenses.  We include them to be inherited by other packages.
+               license:asl2.0
+               ;; Some files in modello-plugin-java are licensed under a
+               ;; 5-clause BSD license.
+               (license:non-copyleft
+                 (string-append "file:///modello-plugins/modello-plugin-java/"
+                                "src/main/java/org/codehaus/modello/plugin/"
+                                "java/javasource/JNaming.java"))))))
+
+(define-public java-modello-plugins-java
+  (package
+    (inherit java-modello-core)
+    (name "java-modello-plugins-java")
+    (arguments
+     `(#:jar-name "modello-plugins-java.jar"
+       #:source-dir "modello-plugins/modello-plugin-java/src/main/java"
+       #:test-dir "modello-plugins/modello-plugin-java/src/test"
+       #:jdk ,icedtea-8
+       #:tests? #f; requires maven-model, which depends on this package
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'copy-resources
+           (lambda _
+             (mkdir-p "build/classes")
+             (copy-recursively "modello-plugins/modello-plugin-java/src/main/resources"
+                               "build/classes")
+             #t)))))
+    (inputs
+     `(("java-modello-core" ,java-modello-core)
+       ,@(package-inputs java-modello-core)))
+    (synopsis "Modello Java Plugin")
+    (description "Modello Java Plugin generates Java objects for the model.")))
+
+(define-public java-modello-plugins-xml
+  (package
+    (inherit java-modello-core)
+    (name "java-modello-plugins-xml")
+    (arguments
+     `(#:jar-name "modello-plugins-xml.jar"
+       #:source-dir "modello-plugins/modello-plugin-xml/src/main/java"
+       #:test-dir "modello-plugins/modello-plugin-xml/src/test"
+       #:jdk ,icedtea-8
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'copy-resources
+           (lambda _
+             (mkdir-p "build/classes")
+             (copy-recursively
+               "modello-plugins/modello-plugin-xml/src/main/resources"
+               "build/classes")
+             #t))
+         (add-before 'check 'fix-paths
+           (lambda _
+             (with-directory-excursion "modello-plugins/modello-plugin-xml/src/test"
+               (substitute*
+                 "java/org/codehaus/modello/plugins/xml/XmlModelloPluginTest.java"
+                 (("src/test") "modello-plugins/modello-plugin-xml/src/test"))))))))
+    (inputs
+     `(("java-modello-core" ,java-modello-core)
+       ("java-modello-plugins-java" ,java-modello-plugins-java)
+       ,@(package-inputs java-modello-core)))
+    (synopsis "Modello XML Plugin")
+    (description "Modello XML Plugin contains shared code for every plugins
+working on XML representation of the model.")))
+
+(define-public java-modello-test
+  (package
+    (inherit java-modello-core)
+    (name "java-modello-test")
+    (arguments
+     `(#:jar-name "modello-test.jar"
+       #:source-dir "modello-test/src/main/java"
+       #:tests? #f; no tests
+       #:jdk ,icedtea-8))
+    (inputs
+     `(("java-plexus-utils" ,java-plexus-utils)
+       ("java-plexus-compiler-api" ,java-plexus-compiler-api)
+       ("java-plexus-compiler-javac" ,java-plexus-compiler-javac)
+       ("java-plexus-container-default" ,java-plexus-container-default)))
+    (synopsis "Modello test package")
+    (description "The modello test package contains the basis to create
+Modello generator unit-tests, including sample models and xml files to test
+every feature for every plugin.")))
+
+(define-public java-modello-plugins-xpp3
+  (package
+    (inherit java-modello-core)
+    (name "java-modello-plugins-xpp3")
+    (arguments
+     `(#:jar-name "modello-plugins-xpp3.jar"
+       #:source-dir "modello-plugins/modello-plugin-xpp3/src/main/java"
+       #:test-dir "modello-plugins/modello-plugin-xpp3/src/test"
+       ;; One of the test dependencies is maven-model which depends on this package.
+       #:tests? #f
+       #:jdk ,icedtea-8
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'copy-resources
+           (lambda _
+             (mkdir-p "build/classes")
+             (copy-recursively "modello-plugins/modello-plugin-xpp3/src/main/resources"
+                               "build/classes")
+             #t)))))
+    (inputs
+     `(("java-modello-core" ,java-modello-core)
+       ("java-modello-plugins-java" ,java-modello-plugins-java)
+       ("java-modello-plugins-xml" ,java-modello-plugins-xml)
+       ,@(package-inputs java-modello-core)))
+    (native-inputs
+     `(("java-xmlunit" ,java-xmlunit)
+       ("java-modello-test" ,java-modello-test)
+       ,@(package-native-inputs java-modello-core)))
+    (synopsis "Modello XPP3 Plugin")
+    (description "The modello XPP3 plugin generates XML readers and writers based
+on the XPP3 API (XML Pull Parser).")))
+
 (define-public java-asm
   (package
     (name "java-asm")
@@ -2940,39 +3883,30 @@ The jMock library
   (package (inherit java-hamcrest-core)
     (name "java-hamcrest-all")
     (arguments
-     (substitute-keyword-arguments (package-arguments java-hamcrest-core)
-       ;; FIXME: a unit test fails because org.hamcrest.SelfDescribing is not
-       ;; found, although it is part of the hamcrest-core library that has
-       ;; just been built.
-       ;;
-       ;; Fixing this one test is insufficient, though, and upstream confirmed
-       ;; that the latest hamcrest release fails its unit tests when built
-       ;; with Java 7.  See https://github.com/hamcrest/JavaHamcrest/issues/30
-       ((#:tests? _) #f)
-       ((#:build-target _) "bigjar")
-       ((#:phases phases)
-        `(modify-phases ,phases
-           ;; Some build targets override the classpath, so we need to patch
-           ;; the build.xml to ensure that required dependencies are on the
-           ;; classpath.
-           (add-after 'unpack 'patch-classpath-for-integration
-             (lambda* (#:key inputs #:allow-other-keys)
-               (substitute* "build.xml"
-                 ((" build/hamcrest-library-\\$\\{version\\}.jar" line)
-                  (string-join
-                   (cons line
-                         (append
-                          (find-files (assoc-ref inputs "java-hamcrest-core") "\\.jar$")
-                          (find-files (assoc-ref inputs "java-junit") "\\.jar$")
-                          (find-files (assoc-ref inputs "java-jmock") "\\.jar$")
-                          (find-files (assoc-ref inputs "java-easymock") "\\.jar$")))
-                   ";")))
-               #t))))))
+     `(#:jdk ,icedtea-8
+       ,@(substitute-keyword-arguments (package-arguments java-hamcrest-core)
+           ((#:build-target _) "bigjar")
+           ((#:phases phases)
+            `(modify-phases ,phases
+               ;; Some build targets override the classpath, so we need to patch
+               ;; the build.xml to ensure that required dependencies are on the
+               ;; classpath.
+               (add-after 'unpack 'patch-classpath-for-integration
+                 (lambda* (#:key inputs #:allow-other-keys)
+                   (substitute* "build.xml"
+                     ((" build/hamcrest-library-\\$\\{version\\}.jar" line)
+                      (string-join
+                       (cons line
+                             (append
+                              (find-files (assoc-ref inputs "java-junit") "\\.jar$")
+                              (find-files (assoc-ref inputs "java-jmock") "\\.jar$")
+                              (find-files (assoc-ref inputs "java-easymock") "\\.jar$")))
+                       ";")))
+                   #t)))))))
     (inputs
      `(("java-junit" ,java-junit)
        ("java-jmock" ,java-jmock-1)
        ("java-easymock" ,java-easymock)
-       ("java-hamcrest-core" ,java-hamcrest-core)
        ,@(package-inputs java-hamcrest-core)))))
 
 (define-public java-jopt-simple
@@ -5103,7 +6037,9 @@ tree walking, and translation.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0qgg5vgsm4l1d6dj9pfbaa25dpv2ry2gny8ajy4vvgvfklw97b3m"))))
+                "0qgg5vgsm4l1d6dj9pfbaa25dpv2ry2gny8ajy4vvgvfklw97b3m"))
+              (patches
+               (search-patches "antlr3-3_3-fix-java8-compilation.patch"))))
     (arguments
      `(#:jar-name (string-append ,name "-" ,version ".jar")
        #:source-dir (string-join '("tool/src/main/java"
@@ -5185,7 +6121,6 @@ import org.antlr.grammar.v2.ANTLRTreePrinter;"))
 (define antlr3-3.1
   (package
     (inherit antlr3)
-    (name "antlr3-3.1")
     (version "3.1")
     (source (origin
               (method url-fetch)
@@ -5194,9 +6129,11 @@ import org.antlr.grammar.v2.ANTLRTreePrinter;"))
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0sfimc9cpbgrihz4giyygc8afgpma2c93yqpwb951giriri6x66z"))))
+                "0sfimc9cpbgrihz4giyygc8afgpma2c93yqpwb951giriri6x66z"))
+              (patches
+               (search-patches "antlr3-3_1-fix-java8-compilation.patch"))))
     (arguments
-     `(#:jar-name (string-append ,name "-" ,version ".jar")
+     `(#:jar-name (string-append "antlr3-" ,version ".jar")
        #:source-dir "src:runtime/Java/src"
        #:tests? #f
        #:phases
@@ -5228,12 +6165,13 @@ import org.antlr.grammar.v2.ANTLRTreePrinter;"))
                (for-each (lambda (file)
                            (display file)
                            (newline)
-                           (system* "antlr" "-o" dir (string-append dir file)))
+                           (invoke "antlr" "-o" dir (string-append dir file)))
                          '("antlr.g" "antlr.print.g" "assign.types.g"
                            "buildnfa.g" "define.g")))
              (format #t "codegen.g\n")
-             (system* "antlr" "-o" "src/org/antlr/codegen"
-                      "src/org/antlr/codegen/codegen.g")))
+             (invoke "antlr" "-o" "src/org/antlr/codegen"
+                     "src/org/antlr/codegen/codegen.g")
+             #t))
          (add-before 'build 'fix-build-xml
            (lambda _
              (substitute* "build.xml"
@@ -6056,7 +6994,8 @@ it manages project dependencies, gives diffs jars, and much more.")
              ;; packaging.  It uses the version referenced in pom.xml.  We replace
              ;; it with our own version.
              (substitute* "src/test/java/org/ops4j/pax/tinybundles/bnd/BndTest.java"
-               (("2.4.0.201411031534") "3.4.0")))))))
+               (("[0-9][0-9]*\\.[0-9][0-9]*\\.[0-9][0-9]*\\.[0-9][0-9]*")
+                ,(package-version java-aqute-bndlib))))))))
     (inputs
      `(("lang" ,java-ops4j-base-lang)
        ("io" ,java-ops4j-base-io)
@@ -6365,6 +7304,7 @@ configuration.")
               (method url-fetch)
               (uri (string-append "https://bitbucket.org/asomov/snakeyaml/get/v"
                                   version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
                 "0rf5ha6w0waz50jz2479jsrbgmd0dnx0gs337m126j5z7zlmg7mg"))))
@@ -6956,7 +7896,7 @@ those in Perl and JavaScript.")
 (define-public java-testng
   (package
     (name "java-testng")
-    (version "6.14.2")
+    (version "6.14.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -6965,7 +7905,7 @@ those in Perl and JavaScript.")
               (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "0ngj88dpbqqdx9084cmiasmn9q3v5dgx45qbvxpip47nxc5x14xy"))))
+                "0y6vq30i5g276kw0v2bhbvci22ijg7ax49ap2611yqlhbs4d6dqv"))))
     (build-system ant-build-system)
     (arguments
      `(#:jdk ,icedtea-8; java.util.function
@@ -7030,54 +7970,56 @@ to use.")
     (license license:asl2.0)))
 
 (define-public java-jnacl
-  (package
-    (name "java-jnacl")
-    (version "0.1.0")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                     (url "https://github.com/neilalexander/jnacl")
-                     (commit "40c322e0a42637ab17cdf941138eeaf2494055f8")))
-              (sha256
-               (base32
-                "1pspnmp44q61a2q4bpslpxw86rfn8s5l0xgvyrikqgdvg7ypx597"))))
-    (build-system ant-build-system)
-    (arguments
-     `(#:jar-name "java-jnacl.jar"
-       #:source-dir "src/main/java"
-       #:jdk ,icedtea-8
-       #:phases
-       (modify-phases %standard-phases
-         (add-before 'build 'fix-tests
-           (lambda _
-             (substitute* "src/test/java/com/neilalexander/jnacl/NaClTest.java"
-               (("assertions.Assertions") "assertions.api.Assertions"))
-             (substitute* "src/test/java/com/neilalexander/jnacl/NaclSecretBoxTest.java"
-               (("assertions.Assertions") "assertions.api.Assertions"))
-             #t))
-         (replace 'check
-           (lambda _
-             (system* "ant" "compile-tests")
-             (and
-               (zero? (system* "java" "-cp" (string-append (getenv "CLASSPATH")
-                                                           ":build/classes"
-                                                           ":build/test-classes")
-                               "org.testng.TestNG" "-testclass"
-                               "build/test-classes/com/neilalexander/jnacl/NaclSecretBoxTest.class"))
-               (zero? (system* "java" "-cp" (string-append (getenv "CLASSPATH")
-                                                           ":build/classes"
-                                                           ":build/test-classes")
-                               "org.testng.TestNG" "-testclass"
-                               "build/test-classes/com/neilalexander/jnacl/NaClTest.class"))))))))
-    (native-inputs
-     `(("java-testng" ,java-testng)
-       ("java-fest-util" ,java-fest-util)
-       ("java-fest-assert" ,java-fest-assert)))
-    (home-page "https://github.com/neilalexander/jnacl")
-    (synopsis "Java implementation of NaCl")
-    (description "Pure Java implementation of the NaCl: Networking and
+  (let ((commit "094e819afdd63ea81a499b3bcb42a271006bebd9")
+        (revision "2"))
+    (package
+      (name "java-jnacl")
+      (version (string-append "0.1.0-" revision "." (string-take commit 7)))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/neilalexander/jnacl.git")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1d6g6xhn83byv5943n7935wwjsk0ibk0qdvqgr699qqgqqmwisbb"))))
+      (build-system ant-build-system)
+      (arguments
+       `(#:jar-name "jnacl.jar"
+         #:source-dir "src/main/java"
+         #:jdk ,icedtea-8
+         #:phases
+         (modify-phases %standard-phases
+           (add-before 'build 'fix-tests
+             (lambda _
+               (substitute* '("src/test/java/com/neilalexander/jnacl/NaClTest.java"
+                              "src/test/java/com/neilalexander/jnacl/NaclSecretBoxTest.java")
+                 (("assertions.Assertions") "assertions.api.Assertions"))
+               #t))
+           (replace 'check
+             (lambda _
+               (invoke "ant" "compile-tests")
+               (invoke "java" "-cp" (string-append (getenv "CLASSPATH")
+                                                   ":build/classes"
+                                                   ":build/test-classes")
+                       "org.testng.TestNG" "-testclass"
+                       "build/test-classes/com/neilalexander/jnacl/NaclSecretBoxTest.class")
+               (invoke "java" "-cp" (string-append (getenv "CLASSPATH")
+                                                   ":build/classes"
+                                                   ":build/test-classes")
+                       "org.testng.TestNG" "-testclass"
+                       "build/test-classes/com/neilalexander/jnacl/NaClTest.class")
+               #t)))))
+      (native-inputs
+       `(("java-testng" ,java-testng)
+         ("java-fest-util" ,java-fest-util)
+         ("java-fest-assert" ,java-fest-assert)))
+      (home-page "https://github.com/neilalexander/jnacl")
+      (synopsis "Java implementation of NaCl")
+      (description "Pure Java implementation of the NaCl: Networking and
 Cryptography library.")
-    (license license:mpl2.0)))
+      (license license:bsd-2))))
 
 (define-public java-mvel2
   (package
@@ -7172,8 +8114,9 @@ configuration and string construction.")
          (add-before 'build 'run-javacc
            (lambda _
              (with-directory-excursion "src/main/java/org/apache/commons/jexl2/parser/"
-               (and (zero? (system* "java" "jjtree" "Parser.jjt"))
-                    (zero? (system* "java" "javacc" "Parser.jj")))))))))
+               (invoke "java" "jjtree" "Parser.jjt")
+               (invoke "java" "javacc" "Parser.jj"))
+             #t)))))
     (inputs
      `(("java-commons-logging-minimal" ,java-commons-logging-minimal)))
     (native-inputs
@@ -7213,7 +8156,8 @@ by technical operatives or consultants working with enterprise platforms.")
          (add-before 'configure 'generate-source
            (lambda _
              (with-directory-excursion "src/build/source_templates"
-               (zero? (system* "mvel2" "../gen_sources.mvel" "../../java"))))))))
+               (invoke "mvel2" "../gen_sources.mvel" "../../java"))
+             #t)))))
     (native-inputs
      `(("mvel" ,java-mvel2)))
     (home-page "https://jpountz.github.io/lz4-java")
@@ -7243,7 +8187,8 @@ algorithms and xxHash hashing algorithm.")
            (lambda _
              (mkdir-p "src")
              (with-directory-excursion "src"
-               (zero? (system* "unzip" "../src.zip"))))))))
+               (invoke "unzip" "../src.zip"))
+             #t)))))
     (native-inputs
      `(("unzip" ,unzip)
        ("junit" ,java-junit)))
@@ -7274,7 +8219,8 @@ for the Java programming language.")
            (lambda _
              (mkdir-p "src")
              (with-directory-excursion "src"
-               (zero? (system* "unzip" "../src.zip"))))))))
+               (invoke "unzip" "../src.zip"))
+             #t)))))
     (native-inputs
      `(("unzip" ,unzip)
        ("junit" ,java-junit)))
@@ -7631,7 +8577,8 @@ protocol-independent framework to build mail and messaging applications.")
               (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "1gxkp7lv2ahymgrqdw94ncq54bmp4m4sw5m1x9gkp7l5bxn0xsyj"))))
+                "1gxkp7lv2ahymgrqdw94ncq54bmp4m4sw5m1x9gkp7l5bxn0xsyj"))
+              (patches (search-patches "java-jeromq-fix-tests.patch"))))
     (build-system ant-build-system)
     (arguments
      `(#:jar-name "java-jeromq.jar"
@@ -7645,7 +8592,13 @@ protocol-independent framework to build mail and messaging applications.")
          ;; Failures
          "**/DealerSpecTest.java"
          "**/CustomDecoderTest.java"
-         "**/CustomEncoderTest.java")))
+         "**/CustomEncoderTest.java"
+         "**/ConnectRidTest.java"
+         "**/ReqSpecTest.java"
+         "**/PushPullSpecTest.java"
+         "**/PubSubHwmTest.java"
+         "**/RouterSpecTest.java"
+         "**/ProxyTest.java")))
     (inputs
      `(("java-jnacl" ,java-jnacl)))
     (native-inputs
@@ -7901,26 +8854,23 @@ including pre-existing objects that you do not have source-code of.")
        (modify-phases %standard-phases
          (add-before 'build 'build-native
            (lambda* (#:key inputs #:allow-other-keys)
-             (with-directory-excursion "hawtjni-generator/src/main/resources/"
-               (and
-                 (system* "gcc" "-c" "hawtjni.c" "-o" "hawtjni.o"
-                          "-fPIC" "-O2"
-                          (string-append "-I" (assoc-ref inputs "jdk") "/include/linux"))
-                 (system* "gcc" "-c" "hawtjni-callback.c" "-o" "hawtjni-callback.o"
-                          "-fPIC" "-O2"
-                          (string-append "-I" (assoc-ref inputs "jdk") "/include/linux"))
-                 (system* "gcc" "-o" "libhawtjni.so" "-shared"
-                          "hawtjni.o" "hawtjni-callback.o")))))
+             (let ((include (string-append "-I" (assoc-ref inputs "jdk") "/include/linux")))
+               (with-directory-excursion "hawtjni-generator/src/main/resources/"
+                 (invoke "gcc" "-c" "hawtjni.c" "-o" "hawtjni.o"
+                         "-fPIC" "-O2" include)
+                 (invoke "gcc" "-c" "hawtjni-callback.c" "-o" "hawtjni-callback.o"
+                         "-fPIC" "-O2" include)
+                 (invoke "gcc" "-o" "libhawtjni.so" "-shared"
+                         "hawtjni.o" "hawtjni-callback.o")))
+             #t))
          (add-after 'install 'install-native
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
                     (lib (string-append out "/lib"))
                     (inc (string-append out "/include")))
-               (mkdir-p lib)
-               (mkdir-p inc)
                (with-directory-excursion "hawtjni-generator/src/main/resources/"
-                 (copy-file "libhawtjni.so" (string-append lib "/libhawtjni.so"))
-                 (copy-file "hawtjni.h" (string-append inc "/hawtjni.h"))))
+                 (install-file "libhawtjni.so" lib)
+                 (install-file "hawtjni.h" inc)))
              #t)))))
     (inputs
      `(("java-commons-cli" ,java-commons-cli)
@@ -7957,14 +8907,14 @@ that is part of the SWT Tools project.")
              (with-directory-excursion "src/main/native-package/src"
                (substitute* "jansi_ttyname.c"
                  (("#include \"jansi_.*") ""))
-               (and
-                 (system* "gcc" "-c" "jansi_ttyname.c" "-o" "jansi_ttyname.o"
-                          (string-append "-I" (assoc-ref inputs "java-hawtjni")
-                                         "/include")
-                          (string-append "-I" (assoc-ref inputs "jdk")
-                                         "/include/linux")
-                          "-fPIC" "-O2")
-                 (system* "gcc" "-o" "libjansi.so" "-shared" "jansi_ttyname.o")))))
+               (invoke "gcc" "-c" "jansi_ttyname.c" "-o" "jansi_ttyname.o"
+                       (string-append "-I" (assoc-ref inputs "java-hawtjni")
+                                      "/include")
+                       (string-append "-I" (assoc-ref inputs "jdk")
+                                      "/include/linux")
+                       "-fPIC" "-O2")
+               (invoke "gcc" "-o" "libjansi.so" "-shared" "jansi_ttyname.o")
+               #t)))
          (add-before 'build 'install-native
            (lambda _
              (let ((dir (string-append "build/classes/META-INF/native/"
@@ -7977,7 +8927,6 @@ that is part of the SWT Tools project.")
              #t))
          (add-after 'install 'install-native
            (lambda* (#:key outputs #:allow-other-keys)
-             (mkdir-p (string-append (assoc-ref outputs "out") "/include"))
              (install-file "src/main/native-package/src/jansi.h"
                            (string-append (assoc-ref outputs "out") "/include"))
              #t)))))
@@ -7985,8 +8934,9 @@ that is part of the SWT Tools project.")
      `(("java-hawtjni" ,java-hawtjni)))
     (home-page "https://fusesource.github.io/jansi/")
     (synopsis "Native library for jansi")
-    (description "Java-jansi-native contains the native library for the jansi
-frobnication library/framework.")
+    (description "This package provides the native library for jansi, a small
+Java library that allows you to use ANSI escape sequences to format your
+console output.")
     (license license:asl2.0)))
 
 (define-public java-jansi
@@ -8370,3 +9320,44 @@ against expected outcomes.")
        ("java-junit" ,java-junit)))
     (native-inputs
      `(("java-mockito-1" ,java-mockito-1)))))
+
+(define-public java-openchart2
+  (package
+    (name "java-openchart2")
+    (version "1.4.3")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://download.approximatrix.com/openchart2/"
+                                  "openchart2-" version ".source.zip"))
+              (sha256
+               (base32
+                "1xq96zm5r02n1blja0072jmmsifmxc40lbyfbnmcnr6mw42frh4g"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:test-target "test"
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-junit-errors
+           (lambda _
+             (with-directory-excursion "unittest/src/com/approximatrix/charting/"
+               (substitute* '("coordsystem/ticklocator/NumericXTickLocatorTest.java"
+                              "coordsystem/ticklocator/NumericYTickLocatorTest.java"
+                              "coordsystem/ticklocator/ObjectXTickLocatorTest.java"
+                              "model/DefaultChartDataModelConstraintsTest.java"
+                              "model/MultiScatterDataModelConstraintsTest.java"
+                              "model/threedimensional/DotPlotDataModelConstraintsTest.java")
+                 (("(assertEquals[^;]+);" before _)
+                  (string-append (string-drop-right before 2) ", 1E-6);"))))
+             #t))
+         (replace 'install (install-jars ".")))))
+    (native-inputs
+     `(("unzip" ,unzip)
+       ("java-junit" ,java-junit)
+       ("java-hamcrest-core" ,java-hamcrest-core)))
+    (home-page "http://approximatrix.com/products/openchart2/")
+    (synopsis "Simple plotting for Java")
+    (description "Openchart2 provides a simple, yet powerful, interface for
+Java programmers to create two-dimensional charts and plots.  The library
+features an assortment of graph styles, including advanced scatter plots, bar
+graphs, and pie charts.")
+    (license license:lgpl2.1+)))