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