Bug#1000475: minimac4: autopkgtest regression: *** stack smashing detected ***: terminated

[Paul Gevers]

Source: minimac4
Version: 1.0.2-3
X-Debbugs-CC: debi...@lists.debian.org
Severity: serious
User: debi...@lists.debian.org
Usertags: regression

Dear maintainer(s),

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?

More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation

Paul

[1] https://qa.debian.org/excuses.php?package=minimac4

https://ci.debian.net/data/autopkgtest/testing/amd64/m/minimac4/16920779/log.gz




--------------------------------------------------------------------------------
Minimac4 - Fast Imputation Based on State Space Reduction HMM

--------------------------------------------------------------------------------
(c) 2014 - Sayantan Das, Christian Fuchsberger, David Hinds
Mary Kate Wing, Goncalo Abecasis
Version: 1.0.2;
Built: 2021-11-11 by Reproducible

Command Line Options: Reference Haplotypes : --refHaps
[refPanel.m3vcf.gz], --passOnly,
--rsid, --referenceEstimates [ON],
--mapFile
[docs/geneticMapFile.b38.map.txt.gz]
Target Haplotypes : --haps [targetStudy.vcf.gz]
Output Parameters : --prefix [testRun], --estimate, --nobgzip,
--vcfBuffer [200], --format [GT,DS],
--allTypedSites, --meta, --memUsage
Chunking Parameters : --ChunkLengthMb [20.00], --ChunkOverlapMb
[3.00]
Subset Parameters : --chr [], --start, --end, --window
Approximation Parameters : --minimac3, --probThreshold [0.01],
--diffThreshold [0.01], --topThreshold [0.01]
Other Parameters : --log, --help, --cpus [5], --params
PhoneHome : --noPhoneHome [ON], --phoneHomeThinning [50]


URL = http://genome.sph.umich.edu/wiki/Minimac4
Starting Main Imputation/Estimation Analysis ...
Performing preliminary check on input parameters...

------------------------------------------------------------------------------
PRELIMINARY FILE CHECK

------------------------------------------------------------------------------

Checking GWAS haplotype file : targetStudy.vcf.gz

Gathering variant information ...


ERROR !!! Empty Value for Individual : TA98 at First Marker Most
probably a corrupted VCF file. Please check input VCF file !!! *** stack
smashing detected ***: terminated
Aborted
autopkgtest [07:10:54]: test run-sample-analysis

[Étienne Mollier]

Control: tags -1 moreinfo

Hi Paul,

On Tue, 23 Nov 2021 21:41:25 +0100 Paul Gevers <elb...@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 <emol...@emlwks999.eu>
Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
Sent from /dev/pts/1, please excuse my verbosity.

[Étienne Mollier]

Hi Paul,

Paul Gevers, on 2021-12-08:
> I happen to see this message *now*, as you just closed the bug. Please be
> aware that in the bts the submitter of the bug doesn't see messages to the
> bug report unless they are subscribed (I am not to this bug) or you CC them
> explicitly.
>
> I missed the conversation and thus was not able to help you.

Argh, I'm sorry about that! I'm normally aware of that peculiar
behavior of debbugs, but I happen to trip on the wire from time
to time (probably too often already). Since I found out how to
reproduce the issue pretty quickly after my first message and
confirmed, I did not feel alarmed of your absence of answer.
Looks like I really have to be more prudent when filling my mail
headers.

> Please also read (especially about binNMUs):
> https://wiki.debian.org/Teams/ReleaseTeam/Transitions

Acknowledged, Thanks for the link. I'm sorry for my mess, I see
the binNMUs such as the present minimac4 are done by the release
team, in addition to the other several stages of scheduling,
cleanup, etc. I'm holding my horses to avoid generating further
entropy at the moment, but are there things I should do to put
the situation back on tracks?

In any case, Thank you for your time,
Have a nice day, :)

--
Étienne Mollier <emol...@emlwks999.eu>
Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da

Sent from /dev/pts/2, please excuse my verbosity.