htsjdk and picard-tools test issues are gradle related. After some deeper tests and discussions with debian-java team, it appears the errors faced in testing (after the patches I proposed on testng) are related to the gradle version on debian. Someone in java team should upgrade to an upper release I tested manually with success (though 1 test failed for picard-tools and should be investigated later on, but other tests are fine, and issue is not build related).
New release should fix the issue. In the meanwhile, to avoid packages removal, I suggest to apply my proposed patches and to disable testing. Once gradle is upgraded in repo, then we could go for test reactivation. I can update code and upload both if everyone agrees with this strategy. Only point is to not forget to follow gradle upgrade and which packages should be updated to reintegrate tests. Could lower severity of those 2 bugs to keep track of the issue. Olivier -- gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
