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
13-skip_network_tests remove network related tests fixing bug 808593 Olivier Sallou <osallou@debian.org> not-needed debian
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
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
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

All known versions for source package 'htsjdk'

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