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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 6 months ago

tillea commented 11 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 11 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 11 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 11 months ago

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

bredelings commented 11 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 8 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 6 months ago

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

emollier commented 6 months ago

Hi Benjamin,

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

Have a nice day, :) Étienne.

emollier commented 6 months ago

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