Re: [Help] Re: [bredelings/BAli-Phy] Test suite error in 4.0-beta7 (Issue #17)]
Hi again, Étienne Mollier, on 2024-07-10: > 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. Actually, the CI kicked in and reported a different set of test failures[1]. I'm not sure what's up. Does this ring a bell? [1]: https://salsa.debian.org/med-team/bali-phy/-/jobs/5952519 Have a nice day, :) -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/0, please excuse my verbosity `-on air: Saga - (Goodbye) Once Upon A Time signature.asc Description: PGP signature
Re: [Help] Re: [bredelings/BAli-Phy] Test suite error in 4.0-beta7 (Issue #17)]
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 '/<>/obj-x86_64-linux-gnu/src/bali-phy/bali-phy' '/<>/obj-x86_64-linux-gnu/../examples/5S-rRNA/48-muscle.fasta' --iter=3 '--package-path=/<>/obj-x86_64-linux-gnu/src/builtins:/<>' --- 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 '/<>/obj-x86_64-linux-gnu/src/bali-phy/bali-phy' '/<>/obj-x86_64-linux-gnu/../examples/5S-rRNA/5d-muscle.fasta' --iter=200 '--package-path=/<>/obj-x86_64-linux-gnu/src/builtins:/<>' -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 '/<>/obj-x86_64-linux-gnu/src/bali-phy/bali-phy' '/<>/obj-x86_64-linux-gnu/../examples/5S-rRNA/5d-muscle.fasta' --iter=50 '--package-path=/<>/obj-x86_64-linux-gnu/src/builtins:/<>' --- 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 '
Re: [Help] Re: [bredelings/BAli-Phy] Test suite error in 4.0-beta7 (Issue #17)]
I should note that the new version now has a dependency on libcereal-dev for serialization. -BenRI 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. -BenRI On 5/30/24 1:31 AM, Andreas Tille wrote: Am Wed, May 29, 2024 at 09:39:01AM +0200 schrieb Étienne Mollier: I'm having a look at BAli-Phy 4.0 beta 13 and after a few adjustments, I see the test suite is passing alright. I pushed my changes on salsa and am preparing an experimental upload. Thanks a lot Andreas.
Re: [Help] Re: [bredelings/BAli-Phy] Test suite error in 4.0-beta7 (Issue #17)]
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. -BenRI On 5/30/24 1:31 AM, Andreas Tille wrote: Am Wed, May 29, 2024 at 09:39:01AM +0200 schrieb Étienne Mollier: I'm having a look at BAli-Phy 4.0 beta 13 and after a few adjustments, I see the test suite is passing alright. I pushed my changes on salsa and am preparing an experimental upload. Thanks a lot Andreas.
Re: [Help] Re: [bredelings/BAli-Phy] Test suite error in 4.0-beta7 (Issue #17)]
Am Wed, May 29, 2024 at 09:39:01AM +0200 schrieb Étienne Mollier: > I'm having a look at BAli-Phy 4.0 beta 13 and after a few > adjustments, I see the test suite is passing alright. I pushed > my changes on salsa and am preparing an experimental upload. Thanks a lot Andreas. -- https://fam-tille.de
Re: [Help] Re: [bredelings/BAli-Phy] Test suite error in 4.0-beta7 (Issue #17)]
Hi Andreas, > From: Benjamin Redelings >> Would you be able to build beta13 for experimental? Andreas Tille, on 2024-05-28: > can anybody check bali-phy? I'm having a look at BAli-Phy 4.0 beta 13 and after a few adjustments, I see the test suite is passing alright. I pushed my changes on salsa and am preparing an experimental upload. Have a nice day, :) -- .''`. Étienne Mollier : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/1, please excuse my verbosity `-on air: Virtual Symmetry - Message From Eternity signature.asc Description: PGP signature
[Help] Re: [bredelings/BAli-Phy] Test suite error in 4.0-beta7 (Issue #17)]
Hi, can anybody check bali-phy? Kind regards Andreas. - Weitergeleitete Nachricht von Benjamin Redelings - Date: Tue, 28 May 2024 05:42:45 -0700 From: Benjamin Redelings To: bredelings/BAli-Phy Cc: Andreas Tille , Author Subject: Re: [bredelings/BAli-Phy] Test suite error in 4.0-beta7 (Issue #17) Hi Andreas, Would you be able to build beta13 for experimental? -BenRI -- Reply to this email directly or view it on GitHub: https://github.com/bredelings/BAli-Phy/issues/17#issuecomment-2135124799 You are receiving this because you authored the thread. Message ID: - Ende weitergeleitete Nachricht - -- https://fam-tille.de
