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bredelings / BAli-Phy

Bayesian co-estimation of phylogenies and multiple alignments via MCMC
http://www.bali-phy.org/
GNU General Public License v2.0
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Test suite error in 4.0-beta7 #17

Closed tillea closed 1 month ago

tillea commented 7 months ago

Hi, I tried to package 4.0-beta7 for Debian. In our CI you can find a full build log which contains an error in one test:

5/37 bali-phy 5d -A 200             FAIL             10.83s   killed by signal 11 SIGSEGV
>>> ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=129 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /builds/med-team/bali-phy/debian/output/source_dir/obj-x86_64-linux-gnu/src/bali-phy/bali-phy /builds/med-team/bali-phy/debian/output/source_dir/obj-x86_64-linux-gnu/../examples/5S-rRNA/5d.fasta --iter=200 --package-path=/builds/med-team/bali-phy/debian/output/source_dir/obj-x86_64-linux-gnu/src/builtins:/builds/med-team/bali-phy/debian/output/source_dir -Inone

Please let me know if you need further information. Kind regards, Andreas.

bredelings commented 7 months ago

Hi Andreas,

Thanks! I am traveling overseas right now and my internet access is limited, so I might not be able to fully investigate this until I get back on Dec 31.

I'm not quite sure why that test would crash. The current development version doesn't seem to crash when I enable the address sanitizer, so I tagged as 4.0-beta8. Does that work?

-BenRI

tillea commented 7 months ago

Hi Ben, have a nice travel - but I do not have good news for you. The tagged 4.0-beta8 fails as well. I'm not in a hurry - just wanted to report this before you might tag the final release. Kind regards, Andreas.

bredelings commented 7 months ago

I was able to reproduce the bug and figure out where it is coming from.

bredelings commented 6 months ago

I've fixed the testsuite error on the master branch. I'm planning to do a new beta9 release at the end of January, which would include the fix. I'm aiming to do the 4.0 release around Jun.

bredelings commented 3 months ago

Hi Andreas, I finally did a beta9 release, so the issue should be fixed. Would you be able to build beta9 for experimental? -BenRI

bredelings commented 1 month ago

Hi Andreas, Would you be able to build beta13 for experimental? -BenRI

emollier commented 1 month ago

Hi Benjamin,

I confirm the issue is resolved on Debian end too with beta13. Thanks!

Have a nice day, :) Étienne.

emollier commented 1 month ago

I forgot to mention the package is upload to Debian experimental for further tests.