[med-svn] [Git][med-team/htsjdk][master] remove a test failing no debian servers, needing ip/host resolution

Olivier Sallou gitlab at salsa.debian.org
Fri Nov 16 11:54:08 GMT 2018 

Olivier Sallou pushed to branch master at Debian Med / htsjdk


Commits:
8d38b196 by Olivier Sallou at 2018-11-16T11:07:34Z
remove a test failing no debian servers, needing ip/host resolution

- - - - -


2 changed files:

- debian/changelog
- debian/patches/13-skip_network_tests


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+htsjdk (2.16.1+dfsg-3) unstable; urgency=medium
+
+  * Fix FTBS on debian test servers due to ip/name resolution
+    Remove related test. Closes: #913839 
+
+ -- Olivier Sallou <osallou at debian.org>  Fri, 16 Nov 2018 11:06:41 +0000
+
 htsjdk (2.16.1+dfsg-2) unstable; urgency=medium
 
   * Fix FTBS with OpenJDK 11 (Closes: #913566) 


=====================================
debian/patches/13-skip_network_tests
=====================================
@@ -5,7 +5,7 @@ Description: remove network related tests
 Last-Updated: 2015-01-06
 --- a/src/test/java/htsjdk/samtools/seekablestream/SeekableBufferedStreamTest.java
 +++ b/src/test/java/htsjdk/samtools/seekablestream/SeekableBufferedStreamTest.java
-@@ -42,58 +42,7 @@ public class SeekableBufferedStreamTest
+@@ -42,58 +42,7 @@
      private final String BAM_URL_STRING = "http://broadinstitute.github.io/picard/testdata/index_test.bam";
      private static File TestFile = new File("src/test/resources/htsjdk/samtools/seekablestream/megabyteZeros.dat");
  
@@ -66,7 +66,7 @@ Last-Updated: 2015-01-06
      public void testSkip() throws IOException {
 --- a/src/test/java/htsjdk/samtools/sra/SRAIndexTest.java
 +++ b/src/test/java/htsjdk/samtools/sra/SRAIndexTest.java
-@@ -50,85 +50,4 @@ public class SRAIndexTest extends Abstra
+@@ -50,85 +50,4 @@
      private static final int LAST_BIN_LEVEL = GenomicIndexUtil.LEVEL_STARTS.length - 1;
      private static final int SRA_BIN_OFFSET = GenomicIndexUtil.LEVEL_STARTS[LAST_BIN_LEVEL];
  
@@ -154,7 +154,7 @@ Last-Updated: 2015-01-06
  }
 --- a/src/test/java/htsjdk/samtools/sra/SRATest.java
 +++ b/src/test/java/htsjdk/samtools/sra/SRATest.java
-@@ -56,378 +56,5 @@ import java.util.TreeSet;
+@@ -56,378 +56,5 @@
   */
  public class SRATest extends AbstractSRATest {
  
@@ -535,7 +535,7 @@ Last-Updated: 2015-01-06
  }
 --- a/src/test/java/htsjdk/tribble/util/ftp/FTPClientTest.java
 +++ b/src/test/java/htsjdk/tribble/util/ftp/FTPClientTest.java
-@@ -25,225 +25,4 @@ public class FTPClientTest extends Htsjd
+@@ -25,225 +25,4 @@
      static byte[] expectedBytes = "abcdefghijklmnopqrstuvwxyz\n".getBytes();
      FTPClient client;
  
@@ -763,7 +763,7 @@ Last-Updated: 2015-01-06
  }
 --- a/src/test/java/htsjdk/tribble/readers/TabixReaderTest.java
 +++ b/src/test/java/htsjdk/tribble/readers/TabixReaderTest.java
-@@ -135,30 +135,6 @@ public class TabixReaderTest extends Hts
+@@ -135,30 +135,6 @@
      }
  
      /**
@@ -796,7 +796,7 @@ Last-Updated: 2015-01-06
       * @throws java.io.IOException
 --- a/src/test/java/htsjdk/samtools/cram/ref/EnaRefServiceTest.java
 +++ b/src/test/java/htsjdk/samtools/cram/ref/EnaRefServiceTest.java
-@@ -15,8 +15,4 @@ public class EnaRefServiceTest extends H
+@@ -15,8 +15,4 @@
                  {"0000088cbcebe818eb431d58c908c698"}};
      }
  
@@ -807,7 +807,7 @@ Last-Updated: 2015-01-06
  }
 --- a/src/test/java/htsjdk/samtools/BAMRemoteFileTest.java
 +++ b/src/test/java/htsjdk/samtools/BAMRemoteFileTest.java
-@@ -44,276 +44,7 @@ import static org.testng.Assert.*;
+@@ -44,276 +44,7 @@
  public class BAMRemoteFileTest extends HtsjdkTest {
      private final File BAM_INDEX_FILE = new File("src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai");
      private final File BAM_FILE = new File("src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam");
@@ -1086,7 +1086,7 @@ Last-Updated: 2015-01-06
  }
 --- a/src/test/java/htsjdk/tribble/util/ftp/FTPUtilsTest.java
 +++ b/src/test/java/htsjdk/tribble/util/ftp/FTPUtilsTest.java
-@@ -15,18 +15,4 @@ import static org.testng.Assert.assertTr
+@@ -15,18 +15,4 @@
  */
  public class FTPUtilsTest extends HtsjdkTest {
  
@@ -1107,7 +1107,7 @@ Last-Updated: 2015-01-06
  }
 --- a/src/test/java/htsjdk/samtools/seekablestream/SeekableFTPStreamTest.java
 +++ b/src/test/java/htsjdk/samtools/seekablestream/SeekableFTPStreamTest.java
-@@ -40,67 +40,6 @@ import java.net.URL;
+@@ -40,67 +40,6 @@
  public class SeekableFTPStreamTest extends HtsjdkTest {
  
  
@@ -1177,7 +1177,7 @@ Last-Updated: 2015-01-06
  }
 --- a/src/test/java/htsjdk/tribble/util/ParsingUtilsTest.java
 +++ b/src/test/java/htsjdk/tribble/util/ParsingUtilsTest.java
-@@ -153,67 +153,12 @@ public class ParsingUtilsTest extends Ht
+@@ -153,67 +153,12 @@
          tstExists(file.toUri().toString(), false);
      }
  
@@ -1247,7 +1247,7 @@ Last-Updated: 2015-01-06
  }
 --- a/src/test/java/htsjdk/tribble/AbstractFeatureReaderTest.java
 +++ b/src/test/java/htsjdk/tribble/AbstractFeatureReaderTest.java
-@@ -52,54 +52,6 @@ public class AbstractFeatureReaderTest e
+@@ -52,54 +52,6 @@
      //wrapper which skips the first byte of a file and leaves the rest unchanged
      private static final Function<SeekableByteChannel, SeekableByteChannel> WRAPPER = SkippingByteChannel::new;
  
@@ -1302,3 +1302,18 @@ Last-Updated: 2015-01-06
  
      @DataProvider(name = "vcfFileAndWrapperCombinations")
      private static Object[][] vcfFileAndWrapperCombinations(){
+--- a/src/test/java/htsjdk/variant/PrintVariantsExampleTest.java
++++ b/src/test/java/htsjdk/variant/PrintVariantsExampleTest.java
+@@ -49,10 +49,12 @@
+                 tempFile.getAbsolutePath()
+         };
+         Assert.assertEquals(tempFile.length(), 0);
++        /*
+         PrintVariantsExample.main(args);
+         Assert.assertNotEquals(tempFile.length(), 0);
+ 
+         assertFilesEqualSkipHeaders(tempFile, f1);
++        */
+     }
+ 
+     private void assertFilesEqualSkipHeaders(File tempFile, File f1) throws FileNotFoundException {



View it on GitLab: https://salsa.debian.org/med-team/htsjdk/commit/8d38b196cdb812758f2e4666727f7e4aaabcff0f

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View it on GitLab: https://salsa.debian.org/med-team/htsjdk/commit/8d38b196cdb812758f2e4666727f7e4aaabcff0f
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