[Bioc-devel] Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed

Paul Shannon p@u|@thurmond@@h@nnon @end|ng |rom gm@||@com
Wed Jun 19 03:48:56 CEST 2019

I see this error today in the macOS release build <https://master.bioconductor.org/checkResults/3.9/bioc-LATEST/trena/celaya2-checksrc.html>:

  ERROR in test_getFootprintsInRegionWithVariants: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed 

On June 8th, in release:

ERROR in /Library/Frameworks/R.framework/Versions/3.6/Resources/library/trena/unitTests/test_HumanDHSFilter.R: 
   there is no package called ‘BSgenome.Hsapiens.UCSC.hg38'

On June 8th, in devel:

Warning in .seqlengths_TwoBitFile(x) :
 mustOpen: Can't open /home/biocbuild/bbs-3.10-bioc/R/library/BSgenome.Hsapiens.UCSC.hg38/extdata/single_sequences.2bit to read: No such file or directory
Timing stopped at: 0.064 0.004 0.069
Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed

If I checked the build report every day, I think I’d see something similar every day.

Wishful thinking tells me that this is not my error, but instead some fluke of the new build system, one which my code happens to trigger.  

The perennial “error” badge at https://bioconductor.org/packages/release/bioc/html/trena.html <https://bioconductor.org/packages/release/bioc/html/trena.html> is a little embarrassing.  

Any advice?

 - Paul

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