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jorainer / ensembldb

This is the ensembldb development repository.
https://jorainer.github.io/ensembldb
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ensDbFromGtf does not read uncompressed files: Error in UseMethod("close") #117

Closed egaffo closed 3 years ago

egaffo commented 3 years ago

Reading a GTF in plain text fails with the following error

ensDbFromGtf("Homo_sapiens.GRCh38.97.gtf")
Importing GTF file ... OK
Error in UseMethod("close") :
  no applicable method for 'close' applied to an object of class "character"

No errors when the same file was Gzipped

Tried with ensembldb v2.16.0 and 2.17.0

jorainer commented 3 years ago

can you please provide the output from calling sessionInfo()? I guess there might be an error in a downstream package as ensembldb uses rtracklayer to import gtf files.

jorainer commented 3 years ago

Ah, no, sorry. Indeed, there seems to be a problem in ensembldb. I will fix that. Thanks for reporting!

jorainer commented 3 years ago

versions 2.16.1 and 2.17.1 (will be available through BioC in the next couple of days) should fix this problem.

Closing the issue. Feel free to re-open if necessary.