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rcavalcante / annotatr

Package Homepage: http://bioconductor.org/packages/devel/bioc/html/annotatr.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=annotatr.
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failed to load resource #42

Closed mbassalbioinformatics closed 3 years ago

mbassalbioinformatics commented 3 years ago

Hi im using annotatr v1.14 off bioconductor and when attempting to run

build_annotations(genome = 'hg38', annotations = "hg38_enhancers_fantom")

I get the following message 

snapshotDate(): 2020-04-27
loading from cache
Error: failed to load resource
  name: AH14150
  title: hg19ToHg38.over.chain.gz
  reason: error in evaluating the argument 'con' in selecting a method for function 'import': invalid class “ChainFile” object: undefined class for slot "resource" ("characterORconnection")

Im surprised this is failing since just last week on the same machine the same command worked fine.... suggestions please?

mbassalbioinformatics commented 3 years ago

For some reason, updating annotatr to 1.16 and rtracklayer to the latest versions fixes the problem. The update has to be done manually though, so dl the source and install from tar.gz

rcavalcante commented 3 years ago

Just wanted to comment and say I'm glad you resolved the issue.

If my memory serves, there was some breaking change to UCSC resources between versions of Bioconductor that had to be fixed (I can't remember which ones exactly, but they're likely related to the version you had and updated to). I think that might have been the issue.

Anyhow, thanks for using annotatr.