[med-svn] r17679 - in trunk/packages/biojava3/trunk/debian: . patches
Olivier Sallou
osallou at moszumanska.debian.org
Sun Aug 10 22:16:03 UTC 2014
Author: osallou
Date: 2014-08-10 22:16:03 +0000 (Sun, 10 Aug 2014)
New Revision: 17679
Added:
trunk/packages/biojava3/trunk/debian/patches/java8_compatibility.patch
Modified:
trunk/packages/biojava3/trunk/debian/changelog
trunk/packages/biojava3/trunk/debian/get-orig-source
trunk/packages/biojava3/trunk/debian/patches/series
trunk/packages/biojava3/trunk/debian/patches/skip_network_related_tests
trunk/packages/biojava3/trunk/debian/patches/use_simple_json
Log:
new upstream release 3.0.8 plus patch for bug 745085
Modified: trunk/packages/biojava3/trunk/debian/changelog
===================================================================
--- trunk/packages/biojava3/trunk/debian/changelog 2014-08-10 18:09:22 UTC (rev 17678)
+++ trunk/packages/biojava3/trunk/debian/changelog 2014-08-10 22:16:03 UTC (rev 17679)
@@ -1,3 +1,11 @@
+biojava3-live (3.0.8-1) UNRELEASED; urgency=medium
+
+ * New upstream release
+ * Patch to fix Java 8 compatiblity (Closes: #745085).
+ Thanks to Emmanuel Bourg <ebourg at apache.org>.
+
+ -- Olivier Sallou <osallou at debian.org> Sun, 10 Aug 2014 23:51:14 +0200
+
biojava3-live (3.0.7+dfsg-3) unstable; urgency=medium
* d/control, d/build.xml: replace dependency to libcommons-collections3-java
Modified: trunk/packages/biojava3/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/biojava3/trunk/debian/get-orig-source 2014-08-10 18:09:22 UTC (rev 17678)
+++ trunk/packages/biojava3/trunk/debian/get-orig-source 2014-08-10 22:16:03 UTC (rev 17679)
@@ -25,11 +25,14 @@
mkdir -p biojava3-forester/src/main/java
cd biojava3-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
- jar xf forester-1.005-sources-1.005.jar
+ #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
+ jar xf forester-lgpl-1.005-sources.jar
find . -name *.class | xargs rm -f
rm -f resources/*.jar
- rm forester-1.005-sources-1.005.jar
+ rm forester-lgpl-1.005-sources.jar
+ #rm forester-1.005-sources-1.005.jar
cd ../../../..
cd ..
Added: trunk/packages/biojava3/trunk/debian/patches/java8_compatibility.patch
===================================================================
--- trunk/packages/biojava3/trunk/debian/patches/java8_compatibility.patch (rev 0)
+++ trunk/packages/biojava3/trunk/debian/patches/java8_compatibility.patch 2014-08-10 22:16:03 UTC (rev 17679)
@@ -0,0 +1,13 @@
+Description: Fix a test failure with Java 8
+Author: Emmanuel Bourg <ebourg at apache.org>
+Forwarded: no
+--- a/biojava3-core/src/main/java/org/biojava3/core/sequence/location/template/AbstractLocation.java
++++ b/biojava3-core/src/main/java/org/biojava3/core/sequence/location/template/AbstractLocation.java
+@@ -108,7 +108,7 @@
+ this.circular = circular;
+ this.betweenCompounds = betweenCompounds;
+ this.accession = accession;
+- this.subLocations = Collections.unmodifiableList(subLocations);
++ this.subLocations = subLocations != null ? Collections.unmodifiableList(subLocations) : Collections.<Location>emptyList();
+ assertLocation();
+ }
Modified: trunk/packages/biojava3/trunk/debian/patches/series
===================================================================
--- trunk/packages/biojava3/trunk/debian/patches/series 2014-08-10 18:09:22 UTC (rev 17678)
+++ trunk/packages/biojava3/trunk/debian/patches/series 2014-08-10 22:16:03 UTC (rev 17679)
@@ -2,4 +2,4 @@
fix_ascii_characters_mapping
skip_network_related_tests
fix_itext_class_updates
-fix_uselog4j1
+java8_compatibility.patch
Modified: trunk/packages/biojava3/trunk/debian/patches/skip_network_related_tests
===================================================================
--- trunk/packages/biojava3/trunk/debian/patches/skip_network_related_tests 2014-08-10 18:09:22 UTC (rev 17678)
+++ trunk/packages/biojava3/trunk/debian/patches/skip_network_related_tests 2014-08-10 22:16:03 UTC (rev 17679)
@@ -5,9 +5,30 @@
network access
Forwarded: yes
Bug: https://redmine.open-bio.org/issues/3402
+--- a/biojava3-core/src/test/java/org/biojava3/core/sequence/io/GenbankCookbookTest.java
++++ b/biojava3-core/src/test/java/org/biojava3/core/sequence/io/GenbankCookbookTest.java
+@@ -56,17 +56,7 @@
+ * Method 1: With the GenbankProxySequenceReader
+ */
+ //Try with the GenbankProxySequenceReader
+- GenbankProxySequenceReader<AminoAcidCompound> genbankProteinReader
+- = new GenbankProxySequenceReader<AminoAcidCompound>("/tmp", "NP_000257", AminoAcidCompoundSet.getAminoAcidCompoundSet());
+- ProteinSequence proteinSequence = new ProteinSequence(genbankProteinReader);
+- genbankProteinReader.getHeaderParser().parseHeader(genbankProteinReader.getHeader(), proteinSequence);
+- System.out.println("Sequence" + "(" + proteinSequence.getAccession() + "," + proteinSequence.getLength() + ")=" + proteinSequence.getSequenceAsString().substring(0, 10) + "...");
+-
+- GenbankProxySequenceReader<NucleotideCompound> genbankDNAReader
+- = new GenbankProxySequenceReader<NucleotideCompound>("/tmp", "NM_001126", DNACompoundSet.getDNACompoundSet());
+- DNASequence dnaSequence = new DNASequence(genbankDNAReader);
+- genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
+- System.out.println("Sequence" + "(" + dnaSequence.getAccession() + "," + dnaSequence.getLength() + ")=" + dnaSequence.getSequenceAsString().substring(0, 10) + "...");
++ // Skipping it due to network requirements
+ /*
+ * Method 2: With the GenbankReaderHelper
+ */
--- a/biojava3-protein-disorder/src/test/java/org/biojava3/ronn/NonstandardProteinCompoundTest.java
+++ b/biojava3-protein-disorder/src/test/java/org/biojava3/ronn/NonstandardProteinCompoundTest.java
-@@ -40,20 +40,7 @@
+@@ -43,21 +43,6 @@
public void testUniprot(String uniprotID) throws Exception{
@@ -23,30 +44,9 @@
-
-
-
+- @SuppressWarnings("unused")
- float[] values = Jronn.getDisorderScores(seq);
-
-+ // Skip network related tests
}
---- a/biojava3-core/src/test/java/org/biojava3/core/sequence/io/GenbankCookbookTest.java
-+++ b/biojava3-core/src/test/java/org/biojava3/core/sequence/io/GenbankCookbookTest.java
-@@ -56,17 +56,7 @@
- * Method 1: With the GenbankProxySequenceReader
- */
- //Try with the GenbankProxySequenceReader
-- GenbankProxySequenceReader<AminoAcidCompound> genbankProteinReader
-- = new GenbankProxySequenceReader<AminoAcidCompound>("/tmp", "NP_000257", AminoAcidCompoundSet.getAminoAcidCompoundSet());
-- ProteinSequence proteinSequence = new ProteinSequence(genbankProteinReader);
-- genbankProteinReader.getHeaderParser().parseHeader(genbankProteinReader.getHeader(), proteinSequence);
-- System.out.println("Sequence" + "(" + proteinSequence.getAccession() + "," + proteinSequence.getLength() + ")=" + proteinSequence.getSequenceAsString().substring(0, 10) + "...");
--
-- GenbankProxySequenceReader<NucleotideCompound> genbankDNAReader
-- = new GenbankProxySequenceReader<NucleotideCompound>("/tmp", "NM_001126", DNACompoundSet.getDNACompoundSet());
-- DNASequence dnaSequence = new DNASequence(genbankDNAReader);
-- genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
-- System.out.println("Sequence" + "(" + dnaSequence.getAccession() + "," + dnaSequence.getLength() + ")=" + dnaSequence.getSequenceAsString().substring(0, 10) + "...");
-+ // Skipping it due to network requirements
- /*
- * Method 2: With the GenbankReaderHelper
- */
Modified: trunk/packages/biojava3/trunk/debian/patches/use_simple_json
===================================================================
--- trunk/packages/biojava3/trunk/debian/patches/use_simple_json 2014-08-10 18:09:22 UTC (rev 17678)
+++ trunk/packages/biojava3/trunk/debian/patches/use_simple_json 2014-08-10 22:16:03 UTC (rev 17679)
@@ -18,7 +18,7 @@
/** Makes remote calls to the Hmmer3 web site and returns Pfam domain annotations for an input protein sequence.
-@@ -102,15 +103,13 @@
+@@ -103,15 +104,13 @@
SortedSet<HmmerResult> results = new TreeSet<HmmerResult>();
try {
@@ -38,7 +38,7 @@
//System.out.println("hit: "+ hit);
HmmerResult hmmResult = new HmmerResult();
-@@ -134,11 +133,11 @@
+@@ -135,11 +134,11 @@
hmmResult.setPvalue((Double)hit.get("pvalue"));
hmmResult.setScore(Float.parseFloat((String)hit.get("score")));
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