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

[Paul Shannon]

Thanks, Martin.   Your hunch was right, the problem was in our sever.  We had some expired ssl certificates on the nginx server which dispatched to Flask.

The irregular behavior we saw - where readVcf worked in some settings, and failed in others - is apparently due to different ssl stringencies in different operating systems, including across different versions of linux.

I should have known better than to pin this on VariantAnnotation and Rsamtools.

 - Paul



> On Jul 13, 2021, at 3:33 AM, Martin Morgan <mtmorgan.bioc using gmail.com> wrote:
> 
> This 'worked for me' on my macOS and on the Bioconductor docker image after BiocManager::install("VariantAnnotation")
> 
> The relevant packages are Rsamtools and Rhtslib, but these have gone through very little change.
> 
> The shortest way to get to the call is through Rsamtools
> 
>  url = "https://igv-data.systemsbiology.net/static/ampad/test/chr2.vcf.gz"
>  b = open(BcfFile(url))
> 
> This goes immediately into C code and (the quite old now) htslib. I looked at the C code briefly, and there is no easy way to extract more information about the reason for failure.
> 
> I don't really have any great insight to offer here; superficially it sounds like the server is sometimes rejecting connections, and these have happened to line up with OS.
> 
> Martin Morgan
> 
> On 7/12/21, 8:46 PM, "Bioc-devel on behalf of Paul Shannon" <bioc-devel-bounces using r-project.org on behalf of paul.thurmond.shannon using gmail.com> wrote:
> 
>    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
>     https://igv-data.systemsbiology.net/static/ampad/test/chr2.vcf.gz
>    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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