Debian Patches
Status for picard-tools/3.3.0+dfsg-2
| Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
|---|---|---|---|---|---|---|
| 10-build.patch | Modifies the upstream build system. | Vincent Danjean <Vincent.Danjean@ens-lyon.org> | not-needed | |||
| 20-shadowjar.patch | do not use shadowjar | Sascha Steinbiss <satta@debian.org> | not-needed | |||
| 30-tests-fix-dataprovider.patch | fix data provider requirements | Sascha Steinbiss <satta@debian.org> | no | |||
| 40-tests-fix-testng.patch | Fix testng version and disable some tests. testng below or equal to 6.9.13.4 does not correctly map long and Integers. This leads to test issues when provider [0,9] values and methods expects a long (testng sends an Integer). This patch disable some tests around this |
Olivier Sallou | not-needed | 2018-09-18 | ||
| com_sun_javadoc_removal_in_openjdk17.patch | omitting the build of classes that use deprecated com.sun.javadoc package, which disappears in OpenJDK 17. | Pierre Gruet <pgt@debian.org> | no | debian | 2022-05-26 | |
| correct_dataprovider_TestDontMergeAbuttingData.patch | providing test with the right data types as arguments Test testActionsWithDontMergeAbutting needs to be provided with three arguments, the second of which has type long. But the current data provider sends an int. |
Pierre Gruet <pgt@debian.org> | yes | 2021-01-28 | ||
| fix_unreadabletests.patch | some tests try to check that a non readable file or directory is correctly managed. However during Debian build, sometimes user is root and unreadable is not effective. This patch removes related tests |
Olivier Sallou <osallou@debian.org> | not-needed | |||
| gradle_openjdk17_incompatibility.patch | according to https://docs.gradle.org/current/userguide/compatibility.html the version of Gradle we have in Debian currently does not support the default JDK, which is OpenJDK17. Until it does, some tests have to be deactivated as they cannot be provided with the --add-opens JVM args they need. |
Pierre Gruet <pgt@debian.org> | not-needed | 2022-11-02 | ||
| non-intel-skip-intel-tests | Skip Intel tests on non-Intel | Michael R. Crusoe <crusoe@debian.org> | no | |||
| omit_BamToBfq.patch | when switching from OpenJDK11 to OpenJDK17 in Debian, one byte became different between the reference and the generated file in BamToBfqTest: 00FF instead of OOOO. To be investigated... until it is, we remove the BamToBfq class from the build and thus don't ship this tool. |
Pierre Gruet <pgt@debian.org> | yes | 2022-11-03 | ||
| remove_google_nio.patch | Remove Google cloud storage | Olivier Sallou | not-needed | 2018-04-23 | ||
| test_accuracy.patch | allowing for some delta in test, to avoid java.lang.AssertionError: expected [100000] but found [100000.0] at org.testng.Assert.fail(Assert.java:94) at org.testng.Assert.failNotEquals(Assert.java:513) at org.testng.Assert.assertEqualsImpl(Assert.java:135) at org.testng.Assert.assertEquals(Assert.java:116) at org.testng.Assert.assertEquals(Assert.java:179) at picard.analysis.directed.CollectHsMetricsTest.testHsMetricsF80DoesNotUseCovCap(CollectHsMetricsTest.java:202) |
Pierre Gruet <pgt@debian.org> | yes | 2024-12-26 | ||
| tests_requiring_network.patch | disabling tests requiring the network | Pierre Gruet <pgt@debian.org> | not-needed | 2024-12-28 |
Showing 1 to 13 of 13 entries
All known versions for source package 'picard-tools'
- 3.3.0+dfsg-2 (sid, trixie)
- 2.27.5+dfsg-2 (bookworm)
- 2.24.1+dfsg-1 (bullseye)