[med-svn] [htsjdk] 01/01: Skip tests checking the use of the local zip implementation

[Vincent Danjean]

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vdanjean pushed a commit to branch master
in repository htsjdk.

commit a456695c95d295b249e1934be6af0b95cd49450a
Author: Vincent Danjean <Vincent.Danjean at ens-lyon.org>
Date:   Fri May 20 21:06:40 2016 +0200

    Skip tests checking the use of the local zip implementation
---
 debian/changelog                        |  4 ++++
 debian/patches/14-skip_local_zlib_tests | 28 ++++++++++++++++++++++++++++
 debian/patches/series                   |  1 +
 3 files changed, 33 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 9cc0878..ac2a399 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,9 +1,13 @@
 htsjdk (2.3.0+dfsg.1-1) UNRELEASED; urgency=medium
 
+  [ Andreas Tille ]
   * New upstream version
   * Take over change from debian/jessie-backports branch to successfully obtain JAVA_HOME
   * Bump Standards-Version to 3.9.8
 
+  [ Vincent Danjean ]
+  * Skip tests checking the use of the local zip implementation
+
  -- Andreas Tille <tille at debian.org>  Fri, 20 May 2016 11:37:24 +0200
 
 htsjdk (2.1.1+dfsg.1-1) unstable; urgency=medium
diff --git a/debian/patches/14-skip_local_zlib_tests b/debian/patches/14-skip_local_zlib_tests
new file mode 100644
index 0000000..e314bd6
--- /dev/null
+++ b/debian/patches/14-skip_local_zlib_tests
@@ -0,0 +1,28 @@
+Skip test for the use of the local zlib implementation
+
+The error in the tests seems to come from the (local) zip lib that is not used.
+The comments in src/java/htsjdk/samtools/util/zip/DeflaterFactory.java
+seems to show that
+- this is not a big issue (at most, it will be a little slower)
+- this is uneeded with JDK8 (and it seems we are using it now):
+  "Note that this class will no longer be necessary once Java 8 is
+  required, because[...]"
+--- a/src/tests/java/htsjdk/samtools/util/IntelDeflaterTest.java
++++ b/src/tests/java/htsjdk/samtools/util/IntelDeflaterTest.java
+@@ -86,9 +86,13 @@
+         outputFile.deleteOnExit();
+ 
+ 
+-        Assert.assertTrue(DeflaterFactory.usingIntelDeflater(), "IntelDeflater is not loaded.");
+-        log.info("IntelDeflater is loaded");
+-
++        //Assert.assertTrue(DeflaterFactory.usingIntelDeflater(), "IntelDeflater is not loaded.");
++        //log.info("IntelDeflater is loaded");
++        if (DeflaterFactory.usingIntelDeflater()) {
++            log.info("IntelDeflater is loaded");
++        } else {
++            log.info("IntelDeflater is not loaded.");
++        }
+ 
+         SamReaderFactory readerFactory = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
+         if (eagerlyDecode) {
diff --git a/debian/patches/series b/debian/patches/series
index 41d8b1c..ac4be96 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,3 +2,4 @@
 11-snappy-java-compatibility.patch
 12-use_libjbzip2-java
 13-skip_network_tests
+14-skip_local_zlib_tests

-- 
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