Hi Benjamin, On 6/20/24 11:16 PM, Benjamin Redelings wrote: > Thanks a lot from me as well! I see the 4.0-beta13 version in > experimental now. > > I noticed that some of the tests for 4.0-beta13 passed, but some timed > out.: > > https://salsa.debian.org/med-team/bali-phy/-/jobs/5786155 > > I have released a 4.0-beta14 that decreases startup times, so that the > tests run more quickly. Hopefully this will prevent timeouts in future > packaged versions. Thanks for revising the test suite to get tests to pass in a reasonable timespan; sorry it took me some time to get to it as I had busy schedule in the past few weeks. I ran the test suite during the build on 4.0-beta14 and caught a few failures: Summary of Failures: 33/37 bali-phy 48 +A 3 FAIL 0.33s exit status 1 34/37 bali-phy 5d -A 200 FAIL 0.33s exit status 1 35/37 bali-phy 5d +A 50 FAIL 0.55s exit status 1 37/37 bali-phy testsuite FAIL 28.58s exit status 1 Ok: 33 Expected Fail: 0 Fail: 4 Unexpected Pass: 0 Skipped: 0 Timeout: 0 Here are the detailed test output for 33, 34 and 35: =================================== 33/37 ==================================== test: bali-phy 48 +A 3 start time: 10:07:08 duration: 0.33s result: exit status 1 command: ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=37 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/bali-phy/bali-phy' '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/../examples/5S-rRNA/48-muscle.fasta' --iter=3 '--package-path=/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/builtins:/<<PKGBUILDDIR>>' ----------------------------------- stderr ----------------------------------- Created directory "48-muscle-1" for output files. bali-phy: Error! In module 'Text.Show': Can't add alias 'Data.List.dmelem_11304' -> 'Data.Foldable.dmelem_11304' in module 'Text.Show' because 'Data.Foldable.dmelem_11304' is neither declared nor imported. ============================================================================== =================================== 34/37 ==================================== test: bali-phy 5d -A 200 start time: 10:07:08 duration: 0.33s result: exit status 1 command: ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=228 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/bali-phy/bali-phy' '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/../examples/5S-rRNA/5d-muscle.fasta' --iter=200 '--package-path=/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/builtins:/<<PKGBUILDDIR>>' -Inone ----------------------------------- stderr ----------------------------------- Created directory "5d-muscle-2" for output files. bali-phy: Error! In module 'Text.Show': Can't add alias 'Data.List.dmelem_11304' -> 'Data.Foldable.dmelem_11304' in module 'Text.Show' because 'Data.Foldable.dmelem_11304' is neither declared nor imported. ============================================================================== =================================== 35/37 ==================================== test: bali-phy 5d +A 50 start time: 10:07:08 duration: 0.55s result: exit status 1 command: ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=173 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/bali-phy/bali-phy' '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/../examples/5S-rRNA/5d-muscle.fasta' --iter=50 '--package-path=/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/builtins:/<<PKGBUILDDIR>>' ----------------------------------- stderr ----------------------------------- Created directory "5d-muscle-1" for output files. bali-phy: Error! In module 'Bio.Alignment.Class': Can't add alias 'Prelude.dmenumFromThenTo_3345' -> 'Compiler.Enum.dmenumFromThenTo_3345' in module 'Bio.Alignment.Class' because 'Compiler.Enum.dmenumFromThenTo_3345' is neither declared nor imported. ============================================================================== The test 37 is affected by many more cases of "Can't add alias": FAIL! (116 unexpected failures, 2 expected failures, 155 tests total) Full log would probably be better suited in your issue tracker than in a mailing list. Let me know if you need it. I tried to trip Salsa CI so it produces an independent build and a build log to point to, but it doesn't look to be operating right now. Have a nice day, :) -- .''`. Étienne Mollier <emollier@debian.org> : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/0, please excuse my verbosity `-
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