Re: [Help] Re: [bredelings/BAli-Phy] Test suite error in 4.0-beta7 (Issue #17)]

Étienne Mollier <[email protected]> Wed, 10 Jul 2024 13:29:21 +0200
Newsgroups	gmane.linux.debian.devel.medical
Message-ID	<[email protected]>
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 <[email protected]>
 : :' :  pgp: 8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
 `. `'   sent from /dev/pts/0, please excuse my verbosity
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