debian/README.Debian

@@ -17,7 +17,7 @@ To make use of thos libraries, the following libraries are needed in the classpa
 				<include name="biojava4-forester.jar"/>
 ...
                         </fileset>
-                        <fileset dir="/usr/share/icedtea-web">
+                        <fileset dir="/usr/share/java">
                                 <include name="netx.jar"/>
                         </fileset>
 

debian/build.xml

@@ -28,7 +28,7 @@
 	<property environment="env"/>
 	<property name="project.jarfile.name" value="BJLIB.jar"/>	
 	
-	<property name="class.path" value="${lib.dir}/commons-logging.jar ${lib.dir}/commons-cli.jar ${lib.dir}/commons-collections3.jar ${lib.dir}/commons-dbcp.jar ${lib.dir}/junit4.jar ${lib.dir}/commons-pool.jar ${lib.dir}/guava.jar ${lib.dir}/jgrapht0.8.jar ${lib.dir}/Jmol.jar /usr/share/icedtea-web/netx.jar ${lib.dir}/hamcrest.jar ${lib.dir}/json_simple.jar ${lib.dir}/commons-codec.jar ${lib.dir}/itext5.jar ${lib.dir}/Jmol.jar ${lib.dir}/log4j2.jar ${lib.dir}/json-simple.jar ${lib.dir}/slf4j-api.jar ${lib.dir}/log4j-over-slf4j.jar ${lib.dir}/commons-math.jar ${lib.dir}/xmlunit.jar ${lib.dir}/vecmath.jar ${lib.dir}/jaxb-api.jar ${lib.dir}/jaxb-impl.jar"/>
+	<property name="class.path" value="${lib.dir}/commons-logging.jar ${lib.dir}/commons-cli.jar ${lib.dir}/commons-collections3.jar ${lib.dir}/commons-dbcp.jar ${lib.dir}/junit4.jar ${lib.dir}/commons-pool.jar ${lib.dir}/guava.jar ${lib.dir}/jgrapht0.8.jar ${lib.dir}/Jmol.jar /usr/share/java/netx.jar ${lib.dir}/hamcrest.jar ${lib.dir}/json_simple.jar ${lib.dir}/commons-codec.jar ${lib.dir}/itext5.jar ${lib.dir}/Jmol.jar ${lib.dir}/log4j2.jar ${lib.dir}/json-simple.jar ${lib.dir}/slf4j-api.jar ${lib.dir}/log4j-over-slf4j.jar ${lib.dir}/commons-math.jar ${lib.dir}/xmlunit.jar ${lib.dir}/vecmath.jar ${lib.dir}/jaxb-api.jar ${lib.dir}/jaxb-impl.jar /usr/share/java/slf4j-simple.jar"/>
 								
 	<path id="compile.classpath">
                         <fileset dir="${lib.dir}">
@@ -58,7 +58,7 @@
 			<fileset dir="${dist.dir}">
 				<include name="*.jar"/>
 			</fileset>
-                        <fileset dir="/usr/share/icedtea-web">
+                        <fileset dir="/usr/share/java">
                                 <include name="netx.jar"/>
                         </fileset>
 	</path>

debian/changelog

+biojava4-live (4.2.12+dfsg-2) unstable; urgency=medium
+
+  * Team upload.
+  * Switch to libnetx-java from icedtea-netx and downgrade to a Suggests.
+    It is only needed by biojava-structure-gui for one operation, which is
+    done by reflection.
+  * Replace embedded copy of JavaScript libraries with symlinks to the
+    dependency of default-jdk-doc.
+  * debian/copyright: added explanation for repacked upstream tarball
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Fri, 18 Jan 2019 09:01:52 -0800
+
 biojava4-live (4.2.12+dfsg-1) unstable; urgency=medium
 
   * Team upload.

debian/control

@@ -17,12 +17,11 @@ Build-Depends-Indep: libcommons-dbcp-java,
                      libitext5-java (>= 5.4.1),
                      libjmol-java (>= 14.6.4),
                      libvecmath-java,
-                     default-jdk (>= 1:1.6),
+                     default-jdk-headless,
                      junit4,
                      javahelper,
                      ant-optional,
                      ant-contrib,
-                     icedtea-netx,
                      libhamcrest-java,
                      libjson-simple-java (>= 1.1.1),
                      liblog4j2-java,
@@ -30,7 +29,10 @@ Build-Depends-Indep: libcommons-dbcp-java,
                      libxmlunit-java,
                      libjgrapht-java,
                      libjaxb-api-java,
-                     libjaxb-java
+                     libjaxb-java,
+                     libnetx-java,
+                     default-jdk-doc,
+                     rdfind
 Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/biojava4-live
 Vcs-Git: https://salsa.debian.org/med-team/biojava4-live.git
@@ -46,7 +48,6 @@ Depends: ${java:Depends},
          libcommons-logging-java,
          libhsqldb-java,
          libbytecode-java,
-         icedtea-netx,
          libjson-simple-java,
          libcommons-codec-java,
          libitext5-java (>= 5.4.1),
@@ -59,7 +60,8 @@ Depends: ${java:Depends},
          libvecmath-java
 Suggests: java-virtual-machine,
           libbiojava4-java,
-          libbiojava4-java-doc
+          libbiojava4-java-doc,
+          libnetx-java
 Description: Java API to biological data and applications (version 4)
  This package presents the Open Source Java API to biological databases
  and a series of mostly sequence-based algorithms.
@@ -94,8 +96,10 @@ Description: Java API to biological data and applications (default version)
 
 Package: libbiojava4-java-doc
 Architecture: all
+Multi-Arch: foreign
 Section: doc
-Depends: ${misc:Depends}
+Depends: ${misc:Depends},
+         default-jdk-doc
 Suggests: libbiojava4-java-demos,
           libbiojava4-java
 Description: [Biology] Documentation for BioJava

debian/copyright

 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: biojava4
 Source: http://www.biojava.org/
-
-Files: biojava-jcolorbrewer
-Copyright: 2011 University of California San Diego
-           2011 J.L. Moreland
-           2011 A.Gramada
-           2011 O.V. Buzko
-           2011 Qing Zhang
-           2011 P.E. Bourne
-License: LGPL-2.1+
-
-Files: biojava-forester
-Copyright: 2008-2009 Christian M. Zmasek
-           2008-2009 Burnham Institute for Medical Research
-License: LGPL-2.1+
-
-License: LGPL-2.1+
- This package is free software; you can redistribute it and/or modify
- it under the terms of the GNU Lesser General Public License as published by
- the Free Software Foundation; either version 2 .1 of the License, or
- (at your option) any later version.
- .
- This package is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- GNU General Public License for more details.
+Comment:
+ Biojava uses the forester library version 0.955.
+ The source version is hosted in maven/biojava repo only and does not
+ match any release available in forester web site. To manage,
+ a specific biojava4-forester library is created.
  .
- You should have received a copy of the GNU Lesser General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>
+ Same for jcolorbrewer
  .
- On Debian systems, the complete text of the GNU Lesser General
- Public License version 2 can be found in "/usr/share/common-licenses/LGPL-2.1".
+ The get-orig-source embeds this library version in the code.
 
 Files: *
 Copyright: 2008-2012 the Individual authors who contributed the code,
@@ -65,6 +43,36 @@ License: LGPL-2.1
  On Debian systems, the complete text of the GNU Lesser General
  Public License version 2 can be found in "/usr/share/common-licenses/LGPL-2.1".
 
+Files: biojava-jcolorbrewer/*
+Copyright: 2011 University of California San Diego
+           2011 J.L. Moreland
+           2011 A.Gramada
+           2011 O.V. Buzko
+           2011 Qing Zhang
+           2011 P.E. Bourne
+License: LGPL-2.1+
+
+Files: biojava-forester/*
+Copyright: 2008-2009 Christian M. Zmasek
+           2008-2009 Burnham Institute for Medical Research
+License: LGPL-2.1+
+
+License: LGPL-2.1+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation; either version 2 .1 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU Lesser General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU Lesser General
+ Public License version 2 can be found in "/usr/share/common-licenses/LGPL-2.1".
 
 Files: debian/*
 Copyright: 2015 Olivier Sallou <osallou@debian.org>

debian/libbiojava4-java.lintian-overrides

 # Wrapper package to ease upgrades 
 libbiojava4-java: empty-binary-package
+libbiojava4-java: javalib-but-no-public-jars

debian/rules

@@ -55,7 +55,17 @@ override_dh_auto_build:
 	cd biojavadoc && ant javadocs
 	# rm -rf biojavadoc
 
+override_jh_installjavadoc:
+	jh_installjavadoc
+	rdfind -makesymlinks true -followsymlinks true \
+		/usr/share/doc/openjdk-11-jre-headless \
+		debian/libbiojava4-java-doc/usr/share/doc/libbiojava4-java/
+ifeq ($(DH_VERBOSE),1)
+	cat results.txt || /bin/true; rm -f results.txt
+endif
+
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	echo '*********************************************************************************'
 	echo '* The following test is ignored since under certain circumstances it might fail *'
 	echo '* Please check the result!                                                      *'
@@ -79,6 +89,7 @@ override_dh_auto_test:
 	#cd biojava-structure && ant test
 	cd biojava-structure-gui && ant test
 	cd biojava-ontology && ant test
+endif
 
 override_dh_clean:
 	dh_clean