Source: r-bioc-s4vectors
Version: 0.20.0-1
X-Debbugs-CC: debian-ci@lists.debian.org
User: debian-ci@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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