Bug#995020: macaulay2: autopkgtest regression and flaky test: SIGSEGV
I'll go ahead and close this bug. Oops, I put the -done address in Cc instead of To. Trying again... signature.asc Description: PGP signature
Bug#995020: macaulay2: autopkgtest regression and flaky test: SIGSEGV
On Sat 25 Sep 2021 03:32:13 PM EDT, Paul Gevers wrote: Hi Torrance, On 25-09-2021 04:56, Torrance, Douglas wrote: There's a problem though -- this macaulay2 autopkgtest regression is now preventing ntl from migrating to testing! [1] This seems like a chicken and egg situation -- we need it to migrate for the tests to pass, but we need the tests to pass for it to migrate... I must confess that transitions aren't perfectly handled by the migration software (britney) of the release team yet. britney tries to figure which packages should come from unstable and adds them as pinned packages, but hasn't any special notion of transitions. Is there a good solution for this? Not yet. One very hacky idea would be to upload a new macaulay2 package with a very basic autopkgtest that's guaranteed to pass for the time being until everything migrates. Is there a better solution? Yes: * macaulay2 could (temporarily) add *versioned* test dependencies on libsingular4m1 and libflint-2.8.0 (then autopkgtest will do the right thing). * macaulay2 could add *versioned* dependencies on libsingular4m1 and libflint-2.8.0 * I could manually trigger the test with the combination. Let's pick the last option for now and see if it works. That worked! The autopkgtests were all successful, and ntl has migrated to testing [1] (along with the flint and factory binNMU's). I'll go ahead and close this bug. Thanks for all of your help! Doug [1] https://tracker.debian.org/news/1261285/ntl-1151-1-migrated-to-testing/ signature.asc Description: PGP signature
Bug#995020: macaulay2: autopkgtest regression and flaky test: SIGSEGV
Hi Torrance, On 25-09-2021 04:56, Torrance, Douglas wrote: > There's a problem though -- this macaulay2 autopkgtest regression is now > preventing ntl from migrating to testing! [1] This seems like a chicken > and > egg situation -- we need it to migrate for the tests to pass, but we need > the tests to pass for it to migrate... I must confess that transitions aren't perfectly handled by the migration software (britney) of the release team yet. britney tries to figure which packages should come from unstable and adds them as pinned packages, but hasn't any special notion of transitions. > Is there a good solution for this? Not yet. > One very hacky idea would be to upload > a new macaulay2 package with a very basic autopkgtest that's guaranteed to > pass for the time being until everything migrates. Is there a better > solution? Yes: * macaulay2 could (temporarily) add *versioned* test dependencies on libsingular4m1 and libflint-2.8.0 (then autopkgtest will do the right thing). * macaulay2 could add *versioned* dependencies on libsingular4m1 and libflint-2.8.0 * I could manually trigger the test with the combination. Let's pick the last option for now and see if it works. Paul OpenPGP_signature Description: OpenPGP digital signature
Bug#995020: macaulay2: autopkgtest regression and flaky test: SIGSEGV
On Fri 24 Sep 2021 05:15:25 PM EDT, Torrance, Douglas wrote: On Fri 24 Sep 2021 04:40:29 PM EDT, Paul Gevers wrote: Hi Torrance, On 24-09-2021 22:30, Torrance, Douglas wrote: I had noticed this as well. My guess is that it has something to do with the transition of ntl. libntl43 is in testing, and libntl44 recently appeared in unstable. The unstable autopkgtests, using only libntl44, run without issue, e.g., [1], but the testing autopkgtests, which use both, have these segfaults. We even see both soname versions appearing in the stacktrace: But as the transition isn't finished yet, we'd keep both versions of libntl in testing. So, what's loading the old one? Possibly flint and/or singular? Both are dependencies of Macaulay2 which also link against libntl, and both have also already gone through binNMU's for libntl44 in unstable. I'm pretty certain this is the issue. macaulay2 depends on both libsingular4m1 and libflint-2.8.0, which in turn depend on libntl43 (in testing) and libntl44 (in sid after recent binNMU's). Once libntl44 and these two binNMU's migrate, then I think the tests should work again like they do in sid. There's a problem though -- this macaulay2 autopkgtest regression is now preventing ntl from migrating to testing! [1] This seems like a chicken and egg situation -- we need it to migrate for the tests to pass, but we need the tests to pass for it to migrate... Is there a good solution for this? One very hacky idea would be to upload a new macaulay2 package with a very basic autopkgtest that's guaranteed to pass for the time being until everything migrates. Is there a better solution? Cc'ing the Debian Science list for suggestions. Thanks! Doug [1] https://qa.debian.org/excuses.php?package=ntl signature.asc Description: PGP signature
Bug#995020: macaulay2: autopkgtest regression and flaky test: SIGSEGV
On Fri 24 Sep 2021 04:40:29 PM EDT, Paul Gevers wrote: Hi Torrance, On 24-09-2021 22:30, Torrance, Douglas wrote: I had noticed this as well. My guess is that it has something to do with the transition of ntl. libntl43 is in testing, and libntl44 recently appeared in unstable. The unstable autopkgtests, using only libntl44, run without issue, e.g., [1], but the testing autopkgtests, which use both, have these segfaults. We even see both soname versions appearing in the stacktrace: But as the transition isn't finished yet, we'd keep both versions of libntl in testing. So, what's loading the old one? Possibly flint and/or singular? Both are dependencies of Macaulay2 which also link against libntl, and both have also already gone through binNMU's for libntl44 in unstable. 3# NTL::UniqueArray >::~UniqueArray() in /lib/x86_64-linux-gnu/libntl.so.44 4# __cxa_finalize in /lib/x86_64-linux-gnu/libc.so.6 5# 0x7F02080D25B3 in /lib/x86_64-linux-gnu/libntl.so.43 I'm hopeful that once ntl 11.5.1-1 migrates to testing (which is imminent, as today is day 5 of 5), this issue will be resolved. Please don't miss my "flaky" note. That's an RC bug in it's own right. I'm afraid I don't follow. Is this note referring to the previous, unrelated autopkgtest failures? Those particular tests have been reported upstream and are now being skipped. Doug signature.asc Description: PGP signature
Bug#995020: macaulay2: autopkgtest regression and flaky test: SIGSEGV
Hi Torrance, On 24-09-2021 22:30, Torrance, Douglas wrote: > I had noticed this as well. My guess is that it has something to do with > the transition of ntl. libntl43 is in testing, and libntl44 recently > appeared > in unstable. The unstable autopkgtests, using only libntl44, run without > issue, e.g., [1], but the testing autopkgtests, which use both, have these > segfaults. We even see both soname versions appearing in the stacktrace: But as the transition isn't finished yet, we'd keep both versions of libntl in testing. So, what's loading the old one? >> 3# NTL::UniqueArray> NTL::DefaultDeleterPolicy> >::~UniqueArray() in >> /lib/x86_64-linux-gnu/libntl.so.44 >> 4# __cxa_finalize in /lib/x86_64-linux-gnu/libc.so.6 >> 5# 0x7F02080D25B3 in /lib/x86_64-linux-gnu/libntl.so.43 > > I'm hopeful that once ntl 11.5.1-1 migrates to testing (which is > imminent, as > today is day 5 of 5), this issue will be resolved. Please don't miss my "flaky" note. That's an RC bug in it's own right. Paul OpenPGP_signature Description: OpenPGP digital signature
Bug#995020: macaulay2: autopkgtest regression and flaky test: SIGSEGV
On Fri 24 Sep 2021 04:10:40 PM EDT, Paul Gevers wrote: Source: macaulay2 Version: 1.18+ds-4 X-Debbugs-CC: debian...@lists.debian.org Severity: serious User: debian...@lists.debian.org Usertags: regression flaky Dear maintainer(s), With a recent upload of macaulay2 the autopkgtest of macaulay2 fails in testing when that autopkgtest is run with the binary packages of macaulay2 from unstable. It passes when run with only packages from testing. In tabular form: passfail macaulay2 from testing1.18+ds-4 versioned deps [0] from testingfrom unstable all others from testingfrom testing I copied some of the output at the bottom of this report. I noticed that in the past the autopktest regularly fails. As the error is different from the failing log for the old version, I suspect a genuine regression now, but please check that the fixed test isn't flaky. 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=macaulay2 https://ci.debian.net/data/autopkgtest/testing/amd64/m/macaulay2/15490748/log.gz -- /usr/share/doc/Macaulay2/Core/tests/factor.m2:0:1-108:1: error: -- -- factoring over fraction fields -- F=frac(QQ[a]); -- -- i44 : R=F[x,y]; -- -- i45 : assert(#factor(x^2-a^-2*y^2)==3); -- -- i46 : -- -- -- SIGSEGV -- -* stack trace, pid: 3577 -- 0# 0x561FFF048737 in /usr/bin/M2-binary -- 1# 0x561FFF0489EA in /usr/bin/M2-binary -- 2# 0x7F2AE3C76EF0 in /lib/x86_64-linux-gnu/libc.so.6 -- 3# NTL::UniqueArray >::~UniqueArray() in /lib/x86_64-linux-gnu/libntl.so.44 -- 4# __cxa_finalize in /lib/x86_64-linux-gnu/libc.so.6 -- 5# 0x7F2AE34ED5B3 in /lib/x86_64-linux-gnu/libntl.so.43 -- -- end stack trace *- -- /usr/share/doc/Macaulay2/Core/tests/factory.m2:0:1-25:1: error: -- -- o14 : R -- -- i15 : assert( gcd(p,q) == d ) -- -- i16 : -- test deferred, trying to get it to work -- -- factor p -- not implemented yet -- -- -- -- SIGSEGV -- -* stack trace, pid: 3615 -- 0# 0x5612348DA737 in /usr/bin/M2-binary -- 1# 0x5612348DA9EA in /usr/bin/M2-binary -- 2# 0x7FBEA4D64EF0 in /lib/x86_64-linux-gnu/libc.so.6 -- 3# NTL::UniqueArray >::~UniqueArray() in /lib/x86_64-linux-gnu/libntl.so.44 -- 4# __cxa_finalize in /lib/x86_64-linux-gnu/libc.so.6 -- 5# 0x7FBEA45DB5B3 in /lib/x86_64-linux-gnu/libntl.so.43 -- -- end stack trace *- -- /usr/share/doc/Macaulay2/Core/tests/flattenRing.m2:0:1-256:1: error: -- -- i164 : assert( source p === ring J ) -- -- i165 : assert( target q === ring I ) -- -- i166 : assert( source q === ring I ) -- -- i167 : -- -- -- SIGSEGV -- -* stack trace, pid: 3768 -- 0# 0x55599045B737 in /usr/bin/M2-binary -- 1# 0x55599045B9EA in /usr/bin/M2-binary -- 2# 0x7FDC96DC7EF0 in /lib/x86_64-linux-gnu/libc.so.6 -- 3# NTL::UniqueArray >::~UniqueArray() in /lib/x86_64-linux-gnu/libntl.so.44 -- 4# __cxa_finalize in /lib/x86_64-linux-gnu/libc.so.6 -- 5# 0x7FDC9663E5B3 in /lib/x86_64-linux-gnu/libntl.so.43 -- -- end stack trace *- -- /usr/share/doc/Macaulay2/Core/tests/frac.m2:0:1-132:1: error: -- -- o83 : FractionField -- -- i84 : try (1_F/x)^2 -- -- i85 : assert( getNonUnit F === x ) -- -- i86 : -- end -- -- SIGSEGV -- -* stack trace, pid: 3806 -- 0# 0x56275E6BE737 in /usr/bin/M2-binary -- 1# 0x56275E6BE9EA in /usr/bin/M2-binary -- 2# 0x7FC1E5D7BEF0 in /lib/x86_64-linux-gnu/libc.so.6 -- 3# NTL::UniqueArray >::~UniqueArray() in /lib/x86_64-linux-gnu/libntl.so.44 -- 4# __cxa_finalize in /lib/x86_64-linux-gnu/libc.so.6 -- 5# 0x7FC1E55F25B3 in /lib/x86_64-linux-gnu/libntl.so.43 -- -- end stack trace *- -- /usr/share/doc/Macaulay2/Core/tests/galois.m2:0:1-39:1: error: -- o26 = k -- -- o26 : GaloisField -- -- i27 : -- assert( length degree id_(k^1) == 0 ) -- -- i28 : -- end -- -- SIGSEGV -- -* stack trace, pid: 3882 -- 0# 0x558928975737 in /usr/bin/M2-binary -- 1# 0x5589289759EA in /usr/bin/M2-binary -- 2# 0x7F7A7EF02EF0 in /lib/x86_64-linux-gnu/libc.so.6 -- 3# NTL::UniqueArray >::~UniqueArray() in /lib/x86_64-linux-gnu/libntl.so.44 -- 4# __cxa_finalize in /lib/x86_64-linux-gnu/libc.so.6 -- 5# 0x7F7A7E7795B3 in /lib/x86_64-linux-gnu/libntl.so.43 -- -- end stack trace *- -- /usr/share/doc/Macaulay2/Core/tests/galois1.m2:0:1-66:1: error: -- i33 : --assert( p (c*x) == (-t-2)^e * q*r ) -- this behavior has changed (15 June 2014): -- assert( p (c*x) == t*q*r) -- -- i34 : -- -- # Local Variables: -- -- # compile-command: "make -k -C $M2BUILDDIR/Macaulay2/packages/Macaulay2Doc/test
Bug#995020: macaulay2: autopkgtest regression and flaky test: SIGSEGV
Source: macaulay2 Version: 1.18+ds-4 X-Debbugs-CC: debian...@lists.debian.org Severity: serious User: debian...@lists.debian.org Usertags: regression flaky Dear maintainer(s), With a recent upload of macaulay2 the autopkgtest of macaulay2 fails in testing when that autopkgtest is run with the binary packages of macaulay2 from unstable. It passes when run with only packages from testing. In tabular form: passfail macaulay2 from testing1.18+ds-4 versioned deps [0] from testingfrom unstable all others from testingfrom testing I copied some of the output at the bottom of this report. I noticed that in the past the autopktest regularly fails. As the error is different from the failing log for the old version, I suspect a genuine regression now, but please check that the fixed test isn't flaky. 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=macaulay2 https://ci.debian.net/data/autopkgtest/testing/amd64/m/macaulay2/15490748/log.gz -- /usr/share/doc/Macaulay2/Core/tests/factor.m2:0:1-108:1: error: -- -- factoring over fraction fields -- F=frac(QQ[a]); -- -- i44 : R=F[x,y]; -- -- i45 : assert(#factor(x^2-a^-2*y^2)==3); -- -- i46 : -- -- -- SIGSEGV -- -* stack trace, pid: 3577 -- 0# 0x561FFF048737 in /usr/bin/M2-binary -- 1# 0x561FFF0489EA in /usr/bin/M2-binary -- 2# 0x7F2AE3C76EF0 in /lib/x86_64-linux-gnu/libc.so.6 -- 3# NTL::UniqueArray >::~UniqueArray() in /lib/x86_64-linux-gnu/libntl.so.44 -- 4# __cxa_finalize in /lib/x86_64-linux-gnu/libc.so.6 -- 5# 0x7F2AE34ED5B3 in /lib/x86_64-linux-gnu/libntl.so.43 -- -- end stack trace *- -- /usr/share/doc/Macaulay2/Core/tests/factory.m2:0:1-25:1: error: -- -- o14 : R -- -- i15 : assert( gcd(p,q) == d ) -- -- i16 : -- test deferred, trying to get it to work -- -- factor p -- not implemented yet -- -- -- -- SIGSEGV -- -* stack trace, pid: 3615 -- 0# 0x5612348DA737 in /usr/bin/M2-binary -- 1# 0x5612348DA9EA in /usr/bin/M2-binary -- 2# 0x7FBEA4D64EF0 in /lib/x86_64-linux-gnu/libc.so.6 -- 3# NTL::UniqueArray >::~UniqueArray() in /lib/x86_64-linux-gnu/libntl.so.44 -- 4# __cxa_finalize in /lib/x86_64-linux-gnu/libc.so.6 -- 5# 0x7FBEA45DB5B3 in /lib/x86_64-linux-gnu/libntl.so.43 -- -- end stack trace *- -- /usr/share/doc/Macaulay2/Core/tests/flattenRing.m2:0:1-256:1: error: -- -- i164 : assert( source p === ring J ) -- -- i165 : assert( target q === ring I ) -- -- i166 : assert( source q === ring I ) -- -- i167 : -- -- -- SIGSEGV -- -* stack trace, pid: 3768 -- 0# 0x55599045B737 in /usr/bin/M2-binary -- 1# 0x55599045B9EA in /usr/bin/M2-binary -- 2# 0x7FDC96DC7EF0 in /lib/x86_64-linux-gnu/libc.so.6 -- 3# NTL::UniqueArray >::~UniqueArray() in /lib/x86_64-linux-gnu/libntl.so.44 -- 4# __cxa_finalize in /lib/x86_64-linux-gnu/libc.so.6 -- 5# 0x7FDC9663E5B3 in /lib/x86_64-linux-gnu/libntl.so.43 -- -- end stack trace *- -- /usr/share/doc/Macaulay2/Core/tests/frac.m2:0:1-132:1: error: -- -- o83 : FractionField -- -- i84 : try (1_F/x)^2 -- -- i85 : assert( getNonUnit F === x ) -- -- i86 : -- end -- -- SIGSEGV -- -* stack trace, pid: 3806 -- 0# 0x56275E6BE737 in /usr/bin/M2-binary -- 1# 0x56275E6BE9EA in /usr/bin/M2-binary -- 2# 0x7FC1E5D7BEF0 in /lib/x86_64-linux-gnu/libc.so.6 -- 3# NTL::UniqueArray >::~UniqueArray() in /lib/x86_64-linux-gnu/libntl.so.44 -- 4# __cxa_finalize in /lib/x86_64-linux-gnu/libc.so.6 -- 5# 0x7FC1E55F25B3 in /lib/x86_64-linux-gnu/libntl.so.43 -- -- end stack trace *- -- /usr/share/doc/Macaulay2/Core/tests/galois.m2:0:1-39:1: error: -- o26 = k -- -- o26 : GaloisField -- -- i27 : -- assert( length degree id_(k^1) == 0 ) -- -- i28 : -- end -- -- SIGSEGV -- -* stack trace, pid: 3882 -- 0# 0x558928975737 in /usr/bin/M2-binary -- 1# 0x5589289759EA in /usr/bin/M2-binary -- 2# 0x7F7A7EF02EF0 in /lib/x86_64-linux-gnu/libc.so.6 -- 3# NTL::UniqueArray >::~UniqueArray() in /lib/x86_64-linux-gnu/libntl.so.44 -- 4# __cxa_finalize in /lib/x86_64-linux-gnu/libc.so.6 -- 5# 0x7F7A7E7795B3 in /lib/x86_64-linux-gnu/libntl.so.43 -- -- end stack trace *- -- /usr/share/doc/Macaulay2/Core/tests/galois1.m2:0:1-66:1: error: -- i33 : --assert( p (c*x) == (-t-2)^e * q*r ) -- this behavior has changed (15 June 2014): -- assert( p (c*x) == t*q*r) -- -- i34 : -- -- # Local Variables: -- -- # compile-command: "make -k -C $M2BUILDDIR/Macaulay2/packages/Macaulay2Doc/test galois1.out " -- -- # End: -- -- -- -- SIGSEGV -- -*
