[med-svn] [Git][med-team/biojava4-live][master] 3 commits: Depending again on libjgrapht0.8-java instead of libjgrapht-java so that the package builds

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch master at Debian Med / biojava4-live


Commits:
b5af80df by Pierre Gruet at 2021-12-12T21:09:36+01:00
Depending again on libjgrapht0.8-java instead of libjgrapht-java so that the package builds

- - - - -
b531add7 by Pierre Gruet at 2021-12-12T22:14:46+01:00
Excluding more tests needing the network

- - - - -
5e4f9a2c by Pierre Gruet at 2021-12-12T22:52:30+01:00
Upload to unstable

- - - - -


3 changed files:

- debian/changelog
- debian/control
- debian/patches/skip_network_related_tests


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+biojava4-live (4.2.12+dfsg-6) unstable; urgency=medium
+
+  * Team upload.
+  * Depending again on libjgrapht0.8-java instead of libjgrapht-java
+  * Excluding more tests needing the network
+
+ -- Pierre Gruet <pgt at debian.org>  Sun, 12 Dec 2021 22:15:47 +0100
+
 biojava4-live (4.2.12+dfsg-5) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -27,7 +27,7 @@ Build-Depends-Indep: libcommons-dbcp-java,
                      liblog4j2-java,
                      libslf4j-java,
                      libxmlunit-java,
-                     libjgrapht-java,
+                     libjgrapht0.8-java,
                      libjaxb-api-java,
                      libjaxb-java,
                      libnetx-java,
@@ -56,7 +56,7 @@ Depends: ${java:Depends},
          libguava-java,
          libslf4j-java,
          libcommons-math-java,
-         libjgrapht-java,
+         libjgrapht0.8-java,
          libvecmath-java
 Suggests: java-virtual-machine,
           libbiojava4-java,


=====================================
debian/patches/skip_network_related_tests
=====================================
@@ -5,7 +5,7 @@ Last-Updated: 2016-12-09
 Forwarded: no
 --- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
 +++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
-@@ -67,21 +67,6 @@ public class GenbankCookbookTest {
+@@ -67,21 +67,6 @@
  	@Test
  	public void testProcess() throws Throwable {
  		/*
@@ -29,7 +29,7 @@ Forwarded: no
  		//Try with the GenbankReaderHelper
 --- a/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java
 +++ b/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java
-@@ -67,20 +67,6 @@ public class NonstandardProteinCompoundT
+@@ -67,20 +67,6 @@
  
  	private void testUniprot(String uniprotID) throws CompoundNotFoundException, IOException {
  
@@ -52,7 +52,7 @@ Forwarded: no
  
 --- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
 +++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
-@@ -75,90 +75,11 @@ public class GenbankProxySequenceReaderT
+@@ -75,90 +75,11 @@
  
  	@Test
  	public void testFeatures() throws IOException, InterruptedException, CompoundNotFoundException {
@@ -143,3 +143,47 @@ Forwarded: no
  
  	}
  }
+--- a/biojava-core/src/test/java/org/biojava/nbio/core/search/io/SearchIOTest.java
++++ b/biojava-core/src/test/java/org/biojava/nbio/core/search/io/SearchIOTest.java
+@@ -27,6 +27,7 @@
+ import org.junit.AfterClass;
+ import org.junit.Before;
+ import org.junit.BeforeClass;
++import org.junit.Ignore;
+ import org.junit.Test;
+ import static org.junit.Assert.*;
+ 
+@@ -78,6 +79,7 @@
+ 	/**
+ 	 * Constructor test specifying Factory
+ 	 */
++        @Ignore("Attemps to use the network")
+ 	@Test
+ 	public void testConstructorWithoutFactoryGuess() {
+ 		String resource = "/org/biojava/nbio/core/search/io/blast/testBlastReport.blastxml";
+@@ -95,6 +97,7 @@
+ 	/**
+ 	 * Constructor test specifying Factory and using a evalue threshold filter
+ 	 */
++        @Ignore("Attemps to use the network")
+ 	@Test
+ 	public void testConstructorWithEvalueHspFilter() {
+ 		//
+--- a/biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastXMLParserTest.java
++++ b/biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastXMLParserTest.java
+@@ -31,6 +31,7 @@
+ import org.junit.AfterClass;
+ import org.junit.Before;
+ import org.junit.BeforeClass;
++import org.junit.Ignore;
+ import org.junit.Test;
+ import static org.junit.Assert.*;
+ import org.junit.Ignore;
+@@ -84,6 +85,7 @@
+ 	/**
+ 	 * Test of createObjects method, of class BlastXMLParser.
+ 	 */
++        @Ignore("Attempts to use the network")
+ 	@Test
+ 	public void testCreateObjects() throws Exception {
+ 		System.out.println("createObjects");



View it on GitLab: https://salsa.debian.org/med-team/biojava4-live/-/compare/6ea5ecb247ea1e7f69d9848466f33049770178f3...5e4f9a2ce270623849dd7648843f2365e06ca6c6

-- 
View it on GitLab: https://salsa.debian.org/med-team/biojava4-live/-/compare/6ea5ecb247ea1e7f69d9848466f33049770178f3...5e4f9a2ce270623849dd7648843f2365e06ca6c6
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