[Debian-med-packaging] Bug#1091575: probabel: FTBFS on i386: dh_auto_test: error: make -j8 check "TESTSUITEFLAGS=-j8 --verbose" VERBOSE=1 returned exit code 2

[Lucas Nussbaum]

Source: probabel
Version: 0.5.0+dfsg-6
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20241228 ftbfs-trixie

Hi,

During a rebuild of all packages in sid, this package failed to build
on i386.

This package currently has binary packages on i386, so this is a regression.

Relevant part (hopefully):
> make[4]: Entering directory '/<<PKGBUILDDIR>>/checks/R-tests'
> XFAIL: run_R_test_palogist.sh
> FAIL: run_R_test_palinear.sh
> XFAIL: run_R_test_pacox.sh
> ===================================================
>    ProbABEL 0.5.0: checks/R-tests/test-suite.log
> ===================================================
> 
> # TOTAL: 3
> # PASS:  0
> # SKIP:  0
> # XFAIL: 2
> # FAIL:  1
> # XPASS: 0
> # ERROR: 0
> 
> .. contents:: :depth: 2
> 
> FAIL: run_R_test_palinear.sh
> ============================
> 
> Checking linear regression...
> Dose: check consistency of names                  OK
> Prob: check consistency of names                  OK
> Check consistency dose <-> prob gtdata            OK
> Running ProbABEL...                               OK
> Error in if (sum(abs(prob.2df.PA[6, 2:3])) == 0) { : 
>   missing value where TRUE/FALSE needed
> Execution halted
> FAIL run_R_test_palinear.sh (exit status: 1)
> 
> XFAIL: run_R_test_palogist.sh
> =============================
> 
> Checking logistic regression...
> Dose: check consistency of names                  OK
> Prob: check consistency of names                  OK
> Check consistency dose <-> prob gtdata            OK
> Running ProbABEL...                               OK
> Comparing R output with ProbABEL output
>  additive (dosages)                               Error: dose.add.PA and dose.add.R are not equal:
>   Component “beta_SNP_addA1”: Mean relative difference: 0.01649978
>   Component “sebeta_SNP_addA1”: Mean relative difference: 0.5609667
> Execution halted
> XFAIL run_R_test_palogist.sh (exit status: 1)
> 
> XFAIL: run_R_test_pacox.sh
> ==========================
> 
> Checking Cox PH regression...
> Loading required package: survival
> Dose: check consistency of names                  OK
> Prob: check consistency of names                  OK
> Check consistency dose <-> prob gtdata            OK
> Running ProbABEL...                               OK
> Comparing R output with ProbABEL output:
>  additive (dosages)                               OK
>  additive (probabilities)                         OK
>  dominant                                         Error: prob.dom.PA and prob.dom.R are not equal:
>   Component “sebeta_SNP_domA1”: 'is.NA' value mismatch: 1 in current 2 in target
>   Component “chi2_SNP_dom”: 'is.NA' value mismatch: 1 in current 2 in target
> Execution halted
> XFAIL run_R_test_pacox.sh (exit status: 1)
> 
> ============================================================================
> Testsuite summary for ProbABEL 0.5.0
> ============================================================================
> # TOTAL: 3
> # PASS:  0
> # SKIP:  0
> # XFAIL: 2
> # FAIL:  1
> # XPASS: 0
> # ERROR: 0
> ============================================================================
> See checks/R-tests/test-suite.log
> Please report to genabel-devel at r-forge.wu-wien.ac.at
> ============================================================================
> make[4]: *** [Makefile:593: test-suite.log] Error 1
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/checks/R-tests'
> make[3]: *** [Makefile:701: check-TESTS] Error 2
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/checks/R-tests'
> make[2]: *** [Makefile:788: check-am] Error 2
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/checks/R-tests'
> make[1]: *** [Makefile:347: check-recursive] Error 1
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> dh_auto_test: error: make -j8 check "TESTSUITEFLAGS=-j8 --verbose" VERBOSE=1 returned exit code 2


The full build log is available from:
http://qa-logs.debian.net/2024/12/28/probabel_0.5.0+dfsg-6_unstable-i386.log

All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20241228;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20241228&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.