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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