[R-pkg-team] Bug#913305: r-bioc-s4vectors breaks multiple autopkgtests

[Andreas Tille]

Currently there is a new BioConductor version released and all r-bioc-*
packages might be in flux and tests temporarily failing.  I'd recommend
to not waste your time on these in the next 1-2 weeks (depending how fast
Dylan will manage the transition.)

Kind regards

    Andreas.

On Fri, Nov 09, 2018 at 12:09:45PM +0100, Paul Gevers wrote:
> Source: r-bioc-s4vectors
> Version: 0.20.0-1
> X-Debbugs-CC: debian-ci at lists.debian.org
> User: debian-ci at lists.debian.org
> Usertags: breaks
> 
> Dear maintainers,
> 
> With a recent upload of r-bioc-s4vectors the autopkgtest of multiple r
> packages, including r-bioc-rsamtools, started to fail in testing when
> that autopkgtest is run with the binary packages of r-bioc-s4vectors
> from unstable. It passes when run with only packages from testing. In
> tabular form:
>                        pass            fail
> r-bioc-s4vectors       from testing    0.20.0-1
> r-bioc-rsamtools       from testing    1.32.3-1
> all others             from testing    from testing
> 
> I copied some of the output at the bottom of this report.
> 
> Currently these regression are contributing to the delay of the
> migration of r-bioc-s4vectors and r-bioc-iranges to testing [1]. Can you
> please investigate the situation? If needed, please change the bug's
> severity. Please align with the reverse dependencies if they all need to
> adapt to new behavior in your package.
> 
> 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=r-bioc-s4vectors
> 
> https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-bioc-rsamtools/1288960/log.gz
> 
> Error in validObject(ans) :
>   invalid class "GRanges" object: 'seqlevels(seqinfo(x))' and
> 'levels(seqnames(x))' are not identical
> In addition: Warning messages:
> 1: no function found corresponding to methods exports from 'XVector'
> for: 'concatenateObjects'
> 2: no function found corresponding to methods exports from
> 'GenomicRanges' for: 'concatenateObjects'
> 3: In .Seqinfo.mergexy(x, y) :
>   Each of the 2 combined objects has sequence levels not in the other:
>   - in 'x': chr1, chr2
>   - in 'y': chr4
>   Make sure to always combine/compare objects based on the same reference
>   genome (use suppressWarnings() to suppress this warning).
> Timing stopped at: 0.02 0 0.019
> Error in validObject(ans) :
>   invalid class "GRanges" object: 'seqlevels(seqinfo(x))' and
> 'levels(seqnames(x))' are not identical
> Timing stopped at: 0.028 0.004 0.033
> Error in validObject(ans) :
>   invalid class "GRanges" object: 'seqlevels(seqinfo(x))' and
> 'levels(seqnames(x))' are not identical
> 
> 
> RUNIT TEST PROTOCOL -- Fri Nov  9 09:11:20 2018
> ***********************************************
> Number of test functions: 20
> Number of errors: 3
> Number of failures: 0
> 
> 
> 1 Test Suite :
> GenomeInfoDb RUnit Tests - 20 test functions, 3 errors, 0 failures
> ERROR in test_Seqinfo_seqlevels_drop_add: Error in validObject(ans) :
>   invalid class "GRanges" object: 'seqlevels(seqinfo(x))' and
> 'levels(seqnames(x))' are not identical
> ERROR in test_Seqinfo_seqlevels_rename: Error in validObject(ans) :
>   invalid class "GRanges" object: 'seqlevels(seqinfo(x))' and
> 'levels(seqnames(x))' are not identical
> ERROR in test_Seqinfo_seqlevels_subset: Error in validObject(ans) :
>   invalid class "GRanges" object: 'seqlevels(seqinfo(x))' and
> 'levels(seqnames(x))' are not identical
> 
> Test files with failing tests
> 
>    test_Seqinfo-class.R
>      test_Seqinfo_seqlevels_drop_add
>      test_Seqinfo_seqlevels_rename
>      test_Seqinfo_seqlevels_subset
> 
> 
> Error in BiocGenerics:::testPackage("GenomeInfoDb") :
>   unit tests failed for package GenomeInfoDb
> In addition: Warning messages:
> 1: 'organism' not found: nothere
> 2: 'organism' not found: nothere
> 3: 'genome' not found: nothere
> 4: 'genome' not found: nothere
> Execution halted
> autopkgtest [09:11:21]: test run-unit-test: -----------------------]
> 




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