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

[Paul Gevers]

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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