[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
Lennart C. Karssen
lennart at karssen.org
Mon Jan 6 17:02:04 GMT 2025
Dear Lucas,
Thanks for reporting this bug. Unfortunately, ProbABEL is no longer
actively maintained. I had a quick look at the full build log for i386
and it might be not just a failing test, but something deeper in the
C/C++ code that's considered to be too outdated to modern standards.
I currently don't have the time to dig into this. However, I think a
graceful workaround would be to disable building ProbABEL for the i386
architecture. The main argument for this is the fact that ProbABEL is
used to analyse large genetic datasets, which no researcher would
nowadays do on a 32 bit architecture (and maybe not even in the "old"
days).
In that light, I think it is reasonable to also disable building the
package for all 32 bit architectures like hurd-i386, kfreebsd-i386. It
was nice to have the package for those architectures, but I can't think
of any one using ProbABEL for any serious work on a 32 bit system.
Best,
Lennart.
On 28-12-2024 17:32, Lucas Nussbaum wrote:
> 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.
>
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