[Debian-med-packaging] Trying to update htsjdk but some tests are failing

[Vincent Danjean]

Le 20/05/2016 11:51, Andreas Tille a écrit :
> Hi,
> 
> I tried to upgrade htsjdk to the latest upstream version but some tests are failing.
> Vincent (or anybody else) could you please have a look at the current state in Git?

The error in the tests seems to come from a (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[...]"

So, I tried a very small patch to remove this test in the testsuite:
--- 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) {

And it seems to build correctly (all other tests passed on my machine)

I'm not sure if the right fix is in the test suite (as I propose)
or in the DeflaterFactory class. So, I did not commit anything for
now.

  Regards,
    Vincent

PS: thank to put me in CC: even if I'm subscribed, I do not read
d-med-packaging regularly.

> Kind regards
> 
>       Andreas.
>