[Bioc-devel] reacVcf(remoteFile, "hg19", region) fails in VariantAnnotation 1.39.0 (and friends), works with 1.38.0

Paul Shannon p@u|@thurmond@@h@nnon @end|ng |rom gm@||@com
Tue Jul 13 02:46:32 CEST 2021

The problem is described in full here, with 4 lines of code to reproduce.

     https://support.bioconductor.org/p/9138262/ <https://support.bioconductor.org/p/9138262/>

James MacDonald pointed out that my initial analysis is wrong. (Thank you, Jim!)  I claimed this works on macOS, fails on linux, and he shows in the support thread that readVcf(remoteFile) worked find for him on linux.

So maybe, as Jim suggests, there is a problem with the latest version of VariantAnnotation or packages it depends upon:?

Jim’s linux run, and my MacOD run, both used VariantAnnotation_1.38.0, 
My docker (Docker devel) has VariantAnnotation_1.39.0.

However, I installed  1.38.0 on the docker image, and the problem persisted.  Leading me to think that the problem may be one of the packages (zlib, httr?) which VariantAnnotation uses?

One strategy we could employ is to expand the error message to tell us more.  It currently reports

*[E::hts_open_format] Failed to open file
Error in open.BcfFile(BcfFile(file, character(0), ...)) :
  ‘open'  VCF/BCF failed
  filename: https://igv-data.systemsbiology.net/static/ampad/test/chr2.vcf.gz*

Maybe  more information is available at the point of failure which, if reported, might clarify the problem?

 - Paul

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