[med-svn] [Git][med-team/biojava4-live][master] 11 commits: Switch to libnetx-java from icedtea-netx
Michael R. Crusoe
gitlab at salsa.debian.org
Fri Jan 18 17:14:13 GMT 2019
Michael R. Crusoe pushed to branch master at Debian Med / biojava4-live
Commits:
34300bcf by Michael R. Crusoe at 2019-01-18T15:20:22Z
Switch to libnetx-java from icedtea-netx
- - - - -
a6c7b947 by Michael R. Crusoe at 2019-01-18T15:23:37Z
reorganize copyright as suggested by Lintian
- - - - -
5d6396c2 by Michael R. Crusoe at 2019-01-18T15:24:05Z
Don't run tests when DEB_BUILD_OPTIONS contains nocheck
- - - - -
7e5ee0d6 by Michael R. Crusoe at 2019-01-18T15:28:45Z
silence a new lintian warning about the libbiojava4-java wrapper package
- - - - -
00bf1468 by Michael R. Crusoe at 2019-01-18T16:55:37Z
Replace embedded copy of JavaScript libraries with symlinks to default-jdk-doc
- - - - -
b81eea52 by Michael R. Crusoe at 2019-01-18T16:55:37Z
enable log output of tests
- - - - -
51fb554e by Michael R. Crusoe at 2019-01-18T16:55:37Z
fix: libbiojava4-java-doc could be marked Multi-Arch: foreign
- - - - -
53565662 by Michael R. Crusoe at 2019-01-18T16:55:37Z
add explanation for repacked upstream tarball
- - - - -
172f8c1d by Michael R. Crusoe at 2019-01-18T16:55:38Z
correct two more paths in the copyright
- - - - -
d2c10a91 by Michael R. Crusoe at 2019-01-18T17:01:03Z
cme fix dpkg
- - - - -
3595d049 by Michael R. Crusoe at 2019-01-18T17:06:55Z
Upload to unstable
- - - - -
7 changed files:
- debian/README.Debian
- debian/build.xml
- debian/changelog
- debian/control
- debian/copyright
- debian/libbiojava4-java.lintian-overrides
- debian/rules
Changes:
=====================================
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
=====================================
@@ -1,3 +1,15 @@
+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 at 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
=====================================
@@ -1,37 +1,15 @@
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 at debian.org>
=====================================
debian/libbiojava4-java.lintian-overrides
=====================================
@@ -1,2 +1,3 @@
# 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
View it on GitLab: https://salsa.debian.org/med-team/biojava4-live/compare/ad7f5eff729f0950c3da55af89025172051c2226...3595d04921e80f64de0161a11dab2e14662e6689
--
View it on GitLab: https://salsa.debian.org/med-team/biojava4-live/compare/ad7f5eff729f0950c3da55af89025172051c2226...3595d04921e80f64de0161a11dab2e14662e6689
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