Based on that output, it looks like the problem is related to NCBI:
> GenomeInfoDb:::.test()
Timing stopped at: 80.2 21.16 131.3
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
line 36388 did not have 10 elements
In addition: Warning messages:
1: In getChromInfoFromNCBI(genome, as.Seqinfo = TRUE) :
Assembly Bos_taurus_UMD_3.1.1 is mapped to more than one assembly
(GCF_000003055.5, GCA_000003055.5). The first one was selected.
2: In getChromInfoFromNCBI(genome, as.Seqinfo = TRUE) :
Assembly MusPutFurMale1.0 is mapped to more than one assembly
(GCA_000004665.1, GCA_000239315.1). The first one was selected.
3: In getChromInfoFromNCBI(genome, as.Seqinfo = TRUE) :
Assembly GRCg6a is mapped to more than one assembly (GCA_000002315.5,
GCF_000002315.6). The first one was selected.
RUNIT TEST PROTOCOL -- Mon Jan 25 03:24:07 2021
***********************************************
Number of test functions: 21
Number of errors: 1
Number of failures: 0
1 Test Suite :
GenomeInfoDb RUnit Tests - 21 test functions, 1 error, 0 failures
ERROR in test_seqlevelsStyle_Seqinfo: Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
line 36388 did not have 10 elements
Test files with failing tests
test_seqlevelsStyle.R
test_seqlevelsStyle_Seqinfo
Error in BiocGenerics:::testPackage("GenomeInfoDb") :
unit tests failed for package GenomeInfoDb
Calls: <Anonymous> -> <Anonymous>
Execution halted
I am using R-hub builder and there is a problem with GenomeInfoDb on Windows:
Bioconductor also reports an error: http://bioconductor.org/checkResults/release/bioc-LATEST/GenomeInfoDb/
Based on that output, it looks like the problem is related to NCBI: