[R-pkg-team] Bug#1111759: r-bioc-genomeinfodb: autopkgtest regression: sequence names not found in the NCBI assembly

[Paul Gevers]

Source: r-bioc-genomeinfodb
Version: 1.42.3+dfsg-1
Severity: serious
User: debian-ci at lists.debian.org
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: 
-----------------------]
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