[med-svn] r18659 - in trunk/packages/biojava4-live/trunk/debian: . patches
Olivier Sallou
osallou at moszumanska.debian.org
Sat Jan 31 11:39:36 UTC 2015
Author: osallou
Date: 2015-01-31 11:39:35 +0000 (Sat, 31 Jan 2015)
New Revision: 18659
Added:
trunk/packages/biojava4-live/trunk/debian/patches/fix_import
Modified:
trunk/packages/biojava4-live/trunk/debian/README.Debian
trunk/packages/biojava4-live/trunk/debian/README.source
trunk/packages/biojava4-live/trunk/debian/changelog
trunk/packages/biojava4-live/trunk/debian/get-orig-source
trunk/packages/biojava4-live/trunk/debian/libbiojava4.0-java.jlibs
trunk/packages/biojava4-live/trunk/debian/patches/series
trunk/packages/biojava4-live/trunk/debian/rules
Log:
integrate jcolorbrewer in code source and build mngt to get all libs built
Modified: trunk/packages/biojava4-live/trunk/debian/README.Debian
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/README.Debian 2015-01-31 10:13:01 UTC (rev 18658)
+++ trunk/packages/biojava4-live/trunk/debian/README.Debian 2015-01-31 11:39:35 UTC (rev 18659)
@@ -13,8 +13,9 @@
<include name="jgrapht0.8.jar"/>
<include name="Jmol.jar"/>
<include name="json-lib.jar"/>
- <include name="biojava3-core.jar"/>
- <include name="biojava3-forester.jar"/>
+ <include name="biojava4-core.jar"/>
+ <include name="biojava4-forester.jar"/>
+...
</fileset>
<fileset dir="/usr/share/icedtea-web">
<include name="netx.jar"/>
Modified: trunk/packages/biojava4-live/trunk/debian/README.source
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/README.source 2015-01-31 10:13:01 UTC (rev 18658)
+++ trunk/packages/biojava4-live/trunk/debian/README.source 2015-01-31 11:39:35 UTC (rev 18659)
@@ -1,11 +1,13 @@
biojava for Debian
------------------
-Biojava3 uses the forester library version 0.955.
+Biojava uses the forester library version 0.955.
The source version is hosted in Biojava repo only and does not
match any release available in forester web site. To manage,
-a specific biojava3-forester library is created.
+a specific biojava4-forester library is created.
+Same for jcolorbrewer
+
The get-orig-source embeds this library version in the code.
json.org dependency is replaced by json-simple with a patch for biojava3-ws.
Modified: trunk/packages/biojava4-live/trunk/debian/changelog
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/changelog 2015-01-31 10:13:01 UTC (rev 18658)
+++ trunk/packages/biojava4-live/trunk/debian/changelog 2015-01-31 11:39:35 UTC (rev 18659)
@@ -1,7 +1,11 @@
biojava4-live (4.0.0+dfsg-1) UNRELEASED; urgency=medium
* BioJava4 packaging
- [ needs Jmol upgrade, build of biojava-structure-gui meanwhile ]
+ [ needs jcolorbrewer from org.biojava, integrate in source code, need to
+ add copyright info
+
+ ]
+ [ needs Jmol upgrade? to be confirmed, build of biojava-structure-gui meanwhile ]
[ failing test :
commented for the moment, to be investigated
]
Modified: trunk/packages/biojava4-live/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/get-orig-source 2015-01-31 10:13:01 UTC (rev 18658)
+++ trunk/packages/biojava4-live/trunk/debian/get-orig-source 2015-01-31 11:39:35 UTC (rev 18659)
@@ -22,8 +22,8 @@
rm -rf target
rm -rf biojava/dist/*.jar
-mkdir -p biojava4-forester/src/main/java
-cd biojava4-forester/src/main/java
+mkdir -p biojava-forester/src/main/java
+cd biojava-forester/src/main/java
#wget http://www.biojava.org/download/maven/org/forester/forester-1.005-sources/1.005/forester-1.005-sources-1.005.jar
wget http://www.biojava.org/download/maven/org/forester/forester-lgpl/1.005/forester-lgpl-1.005-sources.jar
#jar xf forester-1.005-sources-1.005.jar
@@ -33,6 +33,12 @@
rm forester-lgpl-1.005-sources.jar
#rm forester-1.005-sources-1.005.jar
cd ../../../..
+mkdir -p biojava-jcolorbrewer/src/main/java
+cd biojava-jcolorbrewer/src/main/java
+ wget -O jcolorbrewer-5.2-sources.jar "https://search.maven.org/remotecontent?filepath=org/biojava/jcolorbrewer/5.2/jcolorbrewer-5.2-sources.jar"
+ jar xf jcolorbrewer-5.2-sources.jar
+ rm jcolorbrewer-5.2-sources.jar
+cd ../../../..
cd ..
BZIP2="--best" tar -cjf ${PKG}_${VERSION}+dfsg.orig.tar.bz2 ${PKG}-${VERSION}.orig
Modified: trunk/packages/biojava4-live/trunk/debian/libbiojava4.0-java.jlibs
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/libbiojava4.0-java.jlibs 2015-01-31 10:13:01 UTC (rev 18658)
+++ trunk/packages/biojava4-live/trunk/debian/libbiojava4.0-java.jlibs 2015-01-31 11:39:35 UTC (rev 18659)
@@ -13,3 +13,4 @@
dist/biojava4-ws.jar
dist/biojava4-ontology.jar
dist/biojava4-survival.jar
+dist/biojava4-jcolorbrewer.jar
Added: trunk/packages/biojava4-live/trunk/debian/patches/fix_import
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/fix_import (rev 0)
+++ trunk/packages/biojava4-live/trunk/debian/patches/fix_import 2015-01-31 11:39:35 UTC (rev 18659)
@@ -0,0 +1,31 @@
+Subject: missing imports
+Description: some classes are not imported
+Author: Olivier Sallou
+Last-Updated: 2015-01-31
+Forwarded: no
+--- a/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java
++++ b/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java
+@@ -39,6 +39,13 @@
+ import java.io.InputStream;
+ import java.io.UnsupportedEncodingException;
+
++import org.biojava.nbio.structure.StructureException;
++import org.biojava.nbio.structure.Structure;
++import org.biojava.nbio.structure.StructureTools;
++import org.biojava.nbio.structure.Atom;
++import org.biojava.nbio.structure.ResidueNumber;
++
++
+ /**
+ * Demo of how to use the {@link FastaStructureParser} class to read protein
+ * structures from a FASTA file.
+--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MyJmolStatusListener.java
++++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MyJmolStatusListener.java
+@@ -130,7 +130,6 @@
+ }
+
+
+- @Override
+ public Map<String, Object> getProperty(String arg0) {
+ // TODO Auto-generated method stub
+ return null;
Modified: trunk/packages/biojava4-live/trunk/debian/patches/series
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/series 2015-01-31 10:13:01 UTC (rev 18658)
+++ trunk/packages/biojava4-live/trunk/debian/patches/series 2015-01-31 11:39:35 UTC (rev 18659)
@@ -1,2 +1,3 @@
fix_itext_class_updates
use_simple_json
+fix_import
Modified: trunk/packages/biojava4-live/trunk/debian/rules
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/rules 2015-01-31 10:13:01 UTC (rev 18658)
+++ trunk/packages/biojava4-live/trunk/debian/rules 2015-01-31 11:39:35 UTC (rev 18659)
@@ -26,8 +26,10 @@
sed -e 's/BJLIB/biojava4-ontology/g' debian/build.xml > biojava-ontology/build.xml
sed -e 's/BJLIB/biojava4-protein-comparison-tool/g' debian/build.xml > biojava-protein-comparison-tool/build.xml
sed -e 's/BJLIB/biojava4-survival/g' debian/build.xml > biojava-survival/build.xml
+ sed -e 's/BJLIB/biojava4-jcolorbrewer/g' debian/build.xml > biojava-jcolorbrewer/build.xml
override_dh_auto_build:
+ cd biojava-jcolorbrewer && ant jar
cd biojava-forester && ant jar
cd biojava-core && ant jar
cd biojava-phylo && ant jar
@@ -36,7 +38,7 @@
cd biojava-genome && ant jar
cd biojava-sequencing && ant jar
cd biojava-structure && ant jar
-# cd biojava-structure-gui && ant jar
+ cd biojava-structure-gui && ant jar
cd biojava-modfinder && ant jar
cd biojava-ontology && ant jar
cd biojava-protein-disorder && ant jar
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