[Debian-med-packaging] Bug#1000475: minimac4: autopkgtest regression: *** stack smashing detected ***: terminated

[Étienne Mollier]

Control: tags -1 moreinfo

Hi Paul,

On Tue, 23 Nov 2021 21:41:25 +0100 Paul Gevers <elbrus at debian.org> wrote:
> With a recent upload of minimac4 the autopkgtest of minimac4 fails in 
> testing when that autopkgtest is run with the binary packages of 
> minimac4 from unstable. It passes when run with only packages from 
> testing. In tabular form:
> 
>                         pass            fail
> minimac4               from testing    1.0.2-3
> all others             from testing    from testing
> 
> I copied some of the output at the bottom of this report. Similar to bug 
> #1000413 I think this issue points at ABI breakage. The following in the 
> changelog looks very suspicious:
>     * Rebuild minimac4 against new version of libstatgen
> This is a hint. The test passes in unstable.
> 
> Currently this regression is blocking the migration to testing [1]. Can 
> you please investigate the situation and fix it?

Since the libstatgen has been removed from testing, I had hoped
to reproduce the issue by running the minimac4 version from
sid in bullseye context, but the test passed:

	$ apt source -t sid minimac4
	$ autopkgtest -B minimac4_1.0.2-3.dsc -- schroot bullseye-amd64-sbuild
	[…]
	Get:1 http://[::1]:3142/debian.proxad.net/debian bullseye/main amd64 libstatgen0 amd64 1.0.14-7 [315 kB]
	Get:2 http://[::1]:3142/debian.proxad.net/debian bullseye/main amd64 minimac4 amd64 1.0.2-2 [1354 kB]
	[…]
	 ------------------------------------------------------------------------------
	                              SUMMARY OF ANALYSIS                              
	 ------------------------------------------------------------------------------
	
	 Info file written to                    : testRun.info
	 Imputed VCF information written to      : testRun.dose.vcf.gz
	
	 Time Taken for Reading File             = 1 seconds
	 Time Taken for Re-compression           = 0 seconds
	 Time Taken for Imputation               = 0 seconds
	 Time Taken for Writing File             = 1 seconds
	
	 ------------------------------------------------------------------------------
	                                END OF PROGRAM                                 
	 ------------------------------------------------------------------------------
	
	 Program Successfully Implemented... 
	 
	 Total Run completed in 0 hours, 0 mins, 2 seconds.
	
	 Thank You for using Minimac4 !!! 
	
	autopkgtest [20:52:39]: test run-sample-analysis: -----------------------]
	autopkgtest [20:52:39]: test run-sample-analysis:  - - - - - - - - - - results - - - - - - - - - -
	run-sample-analysis  PASS
	autopkgtest [20:52:39]: @@@@@@@@@@@@@@@@@@@@ summary
	run-sample-analysis  PASS

At first I thought there could have indeed been an ABI breakage,
but the symbols update following gcc-11 made reading the changes
in symbols file a bit confusing.  Do you have any idea what I
could have missed to reproduce the symptom?

Thanks for your work on continuous integration!

Have a good evening,  :)
-- 
Étienne Mollier <emollier at emlwks999.eu>
Fingerprint:  8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
Sent from /dev/pts/1, please excuse my verbosity.
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