Bug#909530: Please help debugging (Was: Bug#909530: t-coffee: autopkgtest regression)
Hi Liubov, thanks a lot for your patch. I've tested it and uploaded the package. Happy that you persist in the team Andreas. -- http://fam-tille.de
Bug#909530: Please help debugging (Was: Bug#909530: t-coffee: autopkgtest regression)
Control: tags -1 help Hi, On Fri, Sep 28, 2018 at 02:38:19PM +0200, Andreas Tille wrote: > > Strange. I'm able to reproduce this here even on my local machine in a > > shell where I did some `unset HOME`. I wonder why this error was not > > produced with version 11.00.8cbe486-6 before. Anyway, now since the > > issue can be easily reproduced I'll find a fix soonish. > > While that is now really fixed[1] the other issues seem to be caused > by something else. This is really only happening in the package in > unstable. Back to gdb ... :-( I've tried to track down the issue using gdb + fprintf[2] to fix the coredump issue. Unfortunately I did not finalised and will not have any time for the next seven days. Any help would be welcome Andreas. > [1] > https://salsa.debian.org/med-team/t-coffee/commit/9cffa995e4603e396054062c6f3dbff1568bf243 [2] https://salsa.debian.org/med-team/t-coffee/blob/master/debian/patches/debug.patch -- http://fam-tille.de
Bug#909530: t-coffee: autopkgtest regression
Hi again, On Fri, Sep 28, 2018 at 12:12:58PM +0200, Andreas Tille wrote: > > also for me) I ran t_coffee: > > root@autopkgtest-lxc-vfquea:/tmp/autopkgtest-lxc.3n021a13/downtmp/build.S6P/src# > > t_coffee > > ERROR: Could not set a HOME directory. > > Set any of the following environement variables to some suitable > > location: HOME, HOME_4_TCOFFEE, TMP or TEMP [FATAL:T-COFFEE] > > Segmentation fault > > Strange. I'm able to reproduce this here even on my local machine in a > shell where I did some `unset HOME`. I wonder why this error was not > produced with version 11.00.8cbe486-6 before. Anyway, now since the > issue can be easily reproduced I'll find a fix soonish. While that is now really fixed[1] the other issues seem to be caused by something else. This is really only happening in the package in unstable. Back to gdb ... :-( > > Paul > > PS: also there is a typo in the error message: > > environement -> environment > > Will be fixed as well. Is also fixed in[1]. Kind regards Andreas. [1] https://salsa.debian.org/med-team/t-coffee/commit/9cffa995e4603e396054062c6f3dbff1568bf243 -- http://fam-tille.de
Bug#909530: t-coffee: autopkgtest regression
Hi Paul, On Thu, Sep 27, 2018 at 02:05:19PM +0200, Paul Gevers wrote: > > I ran autopkgtest locally with the --shell option. After it failed (yes, > also for me) I ran t_coffee: > root@autopkgtest-lxc-vfquea:/tmp/autopkgtest-lxc.3n021a13/downtmp/build.S6P/src# > t_coffee > ERROR: Could not set a HOME directory. > Set any of the following environement variables to some suitable > location: HOME, HOME_4_TCOFFEE, TMP or TEMP [FATAL:T-COFFEE] > Segmentation fault Strange. I'm able to reproduce this here even on my local machine in a shell where I did some `unset HOME`. I wonder why this error was not produced with version 11.00.8cbe486-6 before. Anyway, now since the issue can be easily reproduced I'll find a fix soonish. > Paul > PS: also there is a typo in the error message: > environement -> environment Will be fixed as well. Thanks a lot for all your QA work Andreas. -- http://fam-tille.de
Bug#909530: t-coffee: autopkgtest regression
Hi Andreas, On 24-09-18 22:05, Andreas Tille wrote: > I admit I have no clue why this fails. I've build the package with > autopkg hook in pbuilder successfully and the unit test also runs > on my local machine. > > I suspect that using a more modern compiler than that was used for the > recent package compared to the previous with successful tests had > uncovered some hidden issue but it only happens under certain > circumstances. > > Any idea why the test fails on ci infrastructure is welcome. I ran autopkgtest locally with the --shell option. After it failed (yes, also for me) I ran t_coffee: root@autopkgtest-lxc-vfquea:/tmp/autopkgtest-lxc.3n021a13/downtmp/build.S6P/src# t_coffee ERROR: Could not set a HOME directory. Set any of the following environement variables to some suitable location: HOME, HOME_4_TCOFFEE, TMP or TEMP [FATAL:T-COFFEE] Segmentation fault Paul PS: also there is a typo in the error message: environement -> environment signature.asc Description: OpenPGP digital signature
Bug#909530: t-coffee: autopkgtest regression
Control: tags -1 unreproducible Control: tags -1 help On Mon, Sep 24, 2018 at 09:12:16PM +0200, Paul Gevers wrote: > > https://ci.debian.net/data/autopkgtest/testing/amd64/t/t-coffee/1045746/log.gz > > # Command Line: t_coffee sample_seq1.fasta [PROGRAM:T-COFFEE] > > # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 1242 ppid 1131 > #CL: t_coffee sample_seq1.fasta I admit I have no clue why this fails. I've build the package with autopkg hook in pbuilder successfully and the unit test also runs on my local machine. I suspect that using a more modern compiler than that was used for the recent package compared to the previous with successful tests had uncovered some hidden issue but it only happens under certain circumstances. Any idea why the test fails on ci infrastructure is welcome. Kind regards Andreas. -- http://fam-tille.de
Bug#909530: t-coffee: autopkgtest regression
Source: t-coffee Version: 11.00.8cbe486-7 X-Debbugs-CC: debian...@lists.debian.org User: debian...@lists.debian.org Usertags: regression Dear maintainers, With a recent upload of t-coffee the autopkgtest of t-coffee fails in testing when that autopkgtest is run with the binary packages of t-coffee from unstable. It passes when run with only packages from testing. In tabular form: passfail t-coffee from testing11.00.8cbe486-7 all others from testingfrom testing I copied some of the output at the bottom of this report. Currently this regression is contributing to the delay of the migration to testing [1]. Can you please investigate the situation and fix it? If needed, please change the bug's severity. 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=t-coffee https://ci.debian.net/data/autopkgtest/testing/amd64/t/t-coffee/1045746/log.gz # Command Line: t_coffee sample_seq1.fasta [PROGRAM:T-COFFEE] # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 1242 ppid 1131 #CL: t_coffee sample_seq1.fasta signature.asc Description: OpenPGP digital signature
