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

[Andreas Tille]

Hi Vincent,

On Fri, May 20, 2016 at 09:18:09PM +0200, Vincent Danjean wrote:
> > 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[...]"

Thanks for checking.  We should probably add a versioned Depends since
if we backport to Jessie this becomes important.
 
> 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.

Please be so kind to commit.  Thanks.
 
> PS: thank to put me in CC: even if I'm subscribed, I do not read
> d-med-packaging regularly.

I think I'm somehow aware of this - at least when I wrote the mail today
I was vaguely remembering.  Thanks for refreshing. ;-)
 
Kind regards

      Andreas. 

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