Hi,

I noticed htsjdk FTBFS in sid:

Gradle Test Executor 1 finished executing tests.
Results: FAILURE (35741 tests, 35722 successes, 9 failures, 10 skipped)

35741 tests completed, 9 failed, 10 skipped
Finished generating test XML results (0.354 secs) into:
/home/merkys/htsjdk-3.0.5+dfsg/build/test-results/testWithDefaultReference
Generating HTML test report...
Finished generating test html results (0.42 secs) into:
/home/merkys/htsjdk-3.0.5+dfsg/build/reports/tests/testWithDefaultReference
:testWithDefaultReference FAILED
:testWithDefaultReference (Thread[Task worker for ':' Thread 2,5,main])
completed. Took 11 mins 7.989 secs.

FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':testWithDefaultReference'.
 > There were failing tests. See the report at:
file:///home/merkys/htsjdk-3.0.5+dfsg/build/reports/tests/testWithDefaultReference/index.html

Andrius

Hi Andrius,

Thanks for the bug report. It was not easy to reproduce this one!

On Mon, 6 Nov 2023 14:35:05 +0200 Andrius Merkys <merkys@debian.org> wrote:
 > Source: htsjdk
 > Version: 3.0.5+dfsg-1
 > Severity: serious
 > Justification: FTBFS
 > Tags: sid ftbfs
 >
 > Hi,
 >
 > I noticed htsjdk FTBFS in sid:
 >
 > Gradle Test Executor 1 finished executing tests.
 > Results: FAILURE (35741 tests, 35722 successes, 9 failures, 10 skipped)
 >
 > 35741 tests completed, 9 failed, 10 skipped
 > Finished generating test XML results (0.354 secs) into:
 >
/home/merkys/htsjdk-3.0.5+dfsg/build/test-results/testWithDefaultReference
 > Generating HTML test report...
 > Finished generating test html results (0.42 secs) into:
 >
/home/merkys/htsjdk-3.0.5+dfsg/build/reports/tests/testWithDefaultReference
 > :testWithDefaultReference FAILED
 > :testWithDefaultReference (Thread[Task worker for ':' Thread 2,5,main])
 > completed. Took 11 mins 7.989 secs.
 >
 > FAILURE: Build failed with an exception.
 >
 > * What went wrong:
 > Execution failed for task ':testWithDefaultReference'.
 > > There were failing tests. See the report at:
 >
file:///home/merkys/htsjdk-3.0.5+dfsg/build/reports/tests/testWithDefaultReference/index.html

I found out some the failing tests were trying to create temporary files
in directories that did not exist, possibly they rely on other tests to
create them and tests are not run in the same order in every build? I am
unsure how to address the test order so that it is always the same.

Anyway, I added a check of the existence of directories before
attempting to put anything inside them.

 >
 > Andrius
 >
 >

Best,

Hi Pierre,

Interesting, I ran rebuild two times and both times it failed :) I
spotted this issue during ratt-rebuild of a bunch of other packages, did
not really give a decent look.

Great, thanks!

Best wishes,
Andrius

We believe that the bug you reported is fixed in the latest version of
htsjdk, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1055447@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Pierre Gruet <pgt@debian.org> (supplier of updated htsjdk package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)
Format: 1.8
Date: Wed, 08 Nov 2023 10:13:12 +0100
Source: htsjdk
Architecture: source
Version: 3.0.5+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Pierre Gruet <pgt@debian.org>
Closes: 1055447
Changes:
 htsjdk (3.0.5+dfsg-2) unstable; urgency=medium
 .
   * Ensuring directories exist before the unit tests attempt to create files
     inside (Closes: #1055447)
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