Your message dated Sat, 24 Nov 2018 13:21:21 +0000
with message-id <[email protected]>
and subject line Bug#913305: fixed in r-bioc-s4vectors 0.20.1-2
has caused the Debian Bug report #913305,
regarding r-bioc-s4vectors breaks multiple autopkgtests
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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913305: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=913305
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: r-bioc-s4vectors
Version: 0.20.0-1
X-Debbugs-CC: [email protected]
User: [email protected]
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: -----------------------]
signature.asc
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: r-bioc-s4vectors
Source-Version: 0.20.1-2
We believe that the bug you reported is fixed in the latest version of
r-bioc-s4vectors, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Dylan Aïssi <[email protected]> (supplier of updated r-bioc-s4vectors package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sat, 24 Nov 2018 13:52:03 +0100
Source: r-bioc-s4vectors
Binary: r-bioc-s4vectors
Architecture: source
Version: 0.20.1-2
Distribution: unstable
Urgency: medium
Maintainer: Debian R Packages Maintainers <[email protected]>
Changed-By: Dylan Aïssi <[email protected]>
Description:
r-bioc-s4vectors - BioConductor S4 implementation of vectors and lists
Closes: 913305
Changes:
r-bioc-s4vectors (0.20.1-2) unstable; urgency=medium
.
* Team upload.
* Bump version of broken packages. (Closes: #913305)
Breaks: r-bioc-genomicalignments (<< 1.18~)
r-bioc-iranges (<< 2.16~)
r-bioc-shortread (<< 1.40~)
r-bioc-variantannotation (<< 1.28~)
Checksums-Sha1:
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9db2102775352504efbf0169ff69d5a8e620eb32 4308
r-bioc-s4vectors_0.20.1-2.debian.tar.xz
6cb9825a97c9c3efe84a634f793b785de08a06f7 9551
r-bioc-s4vectors_0.20.1-2_amd64.buildinfo
Checksums-Sha256:
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r-bioc-s4vectors_0.20.1-2.dsc
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r-bioc-s4vectors_0.20.1-2.debian.tar.xz
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r-bioc-s4vectors_0.20.1-2_amd64.buildinfo
Files:
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r-bioc-s4vectors_0.20.1-2.dsc
0bfd27c38a45e375fb063657cd3d5971 4308 gnu-r optional
r-bioc-s4vectors_0.20.1-2.debian.tar.xz
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r-bioc-s4vectors_0.20.1-2_amd64.buildinfo
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