Debian Patches

Status for libgoby-java/3.3.1+dfsg2-10

Patch Description Author Forwarded Bugs Origin Last update
protoc.patch Using Debian-packaged protoc compiler Pierre Gruet <> not-needed 2020-08-24
adding_dependencies.patch Adding missing dependencies to the various pom.xml files Pierre Gruet <> yes 2020-10-31
using_jbzip2.patch using the classes of libjbzip2-java as a replacement for Bzip2* Pierre Gruet <> not-needed 2021-08-04
adapting_to_old_fastutil.patch changing some imports linked to fastutil classes Goby 3.3.1 was written for an old fastutil library. Pierre Gruet <> not-needed 2021-08-04
using_GeneratedMessageV3.patch using GeneratedMessageV3 from protobuf to replace GeneratedMessage The protobuf package has changed quite a bit since the version goby 3.3.1
relies on was edited.
Pierre Gruet <> not-needed 2021-08-04
using_commons-cli.patch using classes of commons-cli instead of unpackaged ones Pierre Gruet <> not-needed 2021-07-31
using_correct_SamReader_api.patch using the correct SamReader api Pierre Gruet <> not-needed 2020-11-06
inclusions_in_SplitTranscriptsMode.patch reading class GeneTranscriptRelationships from Goby archive The above-named class is in the archive of Goby and thus does not need to be read elsewhere. Pierre Gruet <> yes 2020-11-02
catch_IOException_LineIterator.patch Catch the IOException launched by close() method of LineIterator Pierre Gruet <> yes 2020-11-03
computing_fisher_pvalue_hypergeom.patch computing p-values by hand as gominer is not packaged in Debian Pierre Gruet <> yes 2021-08-05
exclude_not_runnable_tests.patch modify a few tests when requiring unpackaged tools junitx.framework is not packaged, the test files and, that use it, are deactivated in
We also exclude in this pom, as data files that it
uses are not provided in the source.
Two tests in TestSamRecordParser are skipped for the same reason.
One test in TestConcatAlignmentReader needs a file that does not exist.
The tests in TestIterateSortedAlignment all use a file that does not exist.
One test in TestSkipTo needs to use the network.
One test in TestStatistics is skipped as it expects a Fisher test p-value
greater than 0.05, which seems false after a check with R and also with a
script using libdistlib-java.
Tests in TestDiscoverSequenceVariantsIndelGenotypes and in
TestDiscoverSequenceVariantsMode need genotype.jar or somatic.jar,
which are not in this package nor in a dependency.
Also I removed some tests that fail even in a classic Maven build. Maybe this
is wrong, but anyway they are not run in the classic Maven build and so I am
unsure upstream has kept them up to date. I opened an issue at the link below.
Ignored tests are:
- three tests in TestConcatSortedAlignmentReader;
- all tests in TestIteratedSortedAlignment2;
- one test in TestRealignmentProcessor;
- all tests in TestDiscoverSVMethylationRatesMode;
- five tests in TestDiscoverSequenceVariantsMode;
- three tests in TestLastToCompact;
- one test in TestReformatCompactReadsMode;
- one test in TestSortMode;
- two tests in TestCompareGroupsVCFOutputFormat;
- two tests in MergeIndelFromTest.
Finally, I removed the tests
- in (one test);
- HTSJDKReaderImplTest.testReadingBAM;
- HTSJDKReaderImplTest.testWithPosition;
- HTSJDKReaderImplTest.testWithSlices;
- TestConcatAlignmentReader.testConcatSamBam
which succeed, but need a lot of large data files which I removed when
Pierre Gruet <> yes 2021-08-18
goby_script.patch modifying the launcher script to account for Debian paths Pierre Gruet <> not-needed 2021-08-08
path_of_goby_jar_for_Debian.patch ensuring the correct Debian path of the goby jar will show up This is important for usage messages that are printed when the user invokes
goby with --help.
Pierre Gruet <> not-needed 2021-08-08
jaxb_dependency.patch adding missing jaxb-api dependency in pom Pierre Gruet <> yes 2021-11-23
using_pcre2.patch switching from pcre3 to pcre2 This was tested by running pcreTest (in cpp/src/
successfully. Yet I did not compile the other files.
Pierre Gruet <> yes debian 2021-11-26
omit_test_failing_randomly.patch omit tests that fail randomly Pierre Gruet <> yes 2022-07-03
adding_opens_arg_for_tests.patch adding a --add-opens argument needed to run the tests, starting from OpenJDK17. Pierre Gruet <> no 2022-11-18

All known versions for source package 'libgoby-java'