Debian Patches
Status for htsjdk/4.1.3+dfsg-2
| Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
|---|---|---|---|---|---|---|
| 10-build.xml.patch | Modifies the upstream build system. | Andreas Tille <tille@debian.org> | not-needed | vendor | 2016-06-29 | |
| 100-fix-java11 | xml.bind has been removed from openjdk 11, add jaxb-api jar file to compilation and classpath | Olivier Sallou <osallou@debian.org> | not-needed | |||
| 13-skip_network_tests | remove network related tests fixing bug 808593 | Olivier Sallou <osallou@debian.org> | not-needed | debian | ||
| 140-skip-testFlushNotSpammed.patch | the test testFlushNotSpammed has been introduced by upstream as an answer to their issue 1497. Yet I am unsure it should be expected to pass in any situation as, in my understanding, it success may depend on when the garbage collector deletes the objects. Anyway, the test is failing with openjdk-17. |
Pierre Gruet <pgt@debian.org> | no | 2022-11-01 | ||
| 150-use-rhino-as-JS-engine.patch | using the rhino JavaScript engine, as nashorn has been removed between openjdk-11 and openjdk-17. | Pierre Gruet <pgt@debian.org> | yes | 2022-11-01 | ||
| 160-mkdirs-before-creating-tempPaths.patch | ensuring directories exist before creating temp files inside, as some tests seem to rely on other ones creating the directories for them | Pierre Gruet <pgt@debian.org> | no | debian | 2023-11-08 | |
| 171-use-org-kordamp-json.patch | adapting code to use Debian package libjson-java instead of the non-free org.json. - Beware, in libjson-java, JSONObject.put returns the added object, not the JSONObject. Calls to put thus cannot be chained. - In JSONArray there is no put method, using add instead. - Error messages are not exactly the same in org.json and libjson-java. - Ignoring default excludes when parsing json string to avoid skipping a field named "class". |
Pierre Gruet <pgt@debian.org> | not-needed | 2024-12-26 | ||
| 190-newest-vcf.patch | deactivating the tests that use newest vcf 4.4, as the comments in the code itself suggest version 4.4 is not handled by htsjdk. Certainly this patch can be removed when some later upstream version gets packaged. |
Pierre Gruet <pgt@debian.org> | not-needed | 2023-12-14 | ||
| 20-fix-version.patch | use debian/changelog as source for version instead of git Also force the name of the root project to avoid it to be copied from the directory name | Vincent Danjean <Vincent.Danjean@ens-lyon.org> | not-needed | |||
| 30-disable-scalatest.patch | Debian repo does not have scalatest dependency, so in the meanwhile, disable scala related tests | Olivier Sallou <osallou@debian.org> | not-needed | |||
| 60-enable-tests | Enable tests using testng | Olivier Sallou <osallou@debian.org> | not-needed | 2018-04-17 | ||
| 70-removesometests-testng.patch | testng below or equal to 6.9.13.4 does nto 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 and a few other testng errors |
Olivier Sallou <osallou@debian.org> | not-needed | |||
| 90-disable-testftp.patch | remove unsupported *tags* and disable ftp tests as require network connection | Olivier Sallou <osallou@debian.org> | not-needed | 2018-09-18 | ||
| 92-disable-testhttp.patch | Skip test requiring http connection Also skipping tests in HtsgetBAMFileReaderTest, which require the network, and adding a test in TestDataProviders as it may need to run methods from HtsgetBAMFileReaderTest. |
Andreas Tille <tille@debian.org> | not-needed | 2021-11-21 |
Showing 1 to 14 of 14 entries
All known versions for source package 'htsjdk'
- 4.1.3+dfsg-2 (sid, trixie)
- 3.0.4+dfsg-2 (bookworm)
- 2.23.0+dfsg-2 (bullseye)