Bioconductor / GenomeInfoDb

Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
https://bioconductor.org/packages/GenomeInfoDb
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Windows build error #20

Closed igordot closed 2 years ago

igordot commented 3 years ago

I am using R-hub builder and there is a problem with GenomeInfoDb on Windows:

Error: package 'GenomeInfoDb' required by 'GenomicRanges' could not be found

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:

> 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
hpages commented 2 years ago

Looks like this was an intermittent issue that disappeared a long time ago.