Your message dated Sun, 11 Oct 2026 11:50:07 +0900
with message-id <[email protected]>
and subject line Re: Bug#1111759: r-bioc-genomeinfodb: autopkgtest regression:
sequence names not found in the NCBI assembly
has caused the Debian Bug report #1111759,
regarding r-bioc-genomeinfodb: autopkgtest regression: sequence names not found
in the NCBI assembly
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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1111759: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1111759
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--- Begin Message ---
Source: r-bioc-genomeinfodb
Version: 1.42.3+dfsg-1
Severity: serious
User: [email protected]
Usertags: regression
Dear maintainer(s),
Your package has an autopkgtest, great. However, it fails. Can you
please investigate the situation and fix it? I copied some of the output
at the bottom of this report.
The release team has announced [1] that failing autopkgtest on amd64 and
arm64 are considered RC in testing.
More information about this bug and the reason for filing it can be
found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
Paul
[1] https://lists.debian.org/debian-devel-announce/2019/07/msg00002.html
https://ci.debian.net/packages/r/r-bioc-genomeinfodb/testing/amd64/63135878/
176s RUNIT TEST PROTOCOL -- Wed Aug 13 18:07:16 2025
176s ***********************************************
176s Number of test functions: 22
176s Number of errors: 2
176s Number of failures: 0
176s
176s
176s 1 Test Suite :
176s GenomeInfoDb RUnit Tests - 22 test functions, 2 errors, 0 failures
176s ERROR in test_switching_Seqinfo_between_UCSC_and_NCBI_styles: Error
in .map_UCSC_seqlevels_to_NCBI_seqlevels(UCSC_seqlevels, NCBI_seqlevels, :
176s 'special_mappings' contains sequence names not found in the NCBI
176s assembly
176s ERROR in test_switching_Seqinfo_to_RefSeq_style: Error in
.map_UCSC_seqlevels_to_NCBI_seqlevels(UCSC_seqlevels, NCBI_seqlevels, :
176s 'special_mappings' contains sequence names not found in the NCBI
176s assembly
176s
176s Test files with failing tests
176s
176s test_seqlevelsStyle.R
176s test_switching_Seqinfo_between_UCSC_and_NCBI_styles
176s test_switching_Seqinfo_to_RefSeq_style
176s
176s
176s Error in BiocGenerics:::testPackage("GenomeInfoDb") :
176s unit tests failed for package GenomeInfoDb
176s Calls: <Anonymous> -> <Anonymous>
176s Execution halted
176s autopkgtest [18:07:16]: test pkg-r-autopkgtest:
-----------------------]
OpenPGP_signature.asc
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Version: 1.48.0+dfsg-1
The latest version of the packge passes its tests correctly; therefore I
am closing this bug.
--- End Message ---
