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 Unfortunately, ProbABEL is no longer actively maintained.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for i386 and it might be not just a failing test, but something deeper in the C/C++ code that's considered to be too outdated to modern standards.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: lu...@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-de...@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 2The 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=lu...@debian.org or: https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20241228&fusertaguser=lu...@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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