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.b...@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-boun...@r-project.org on behalf of
> paul.thurmond.shan...@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
>
>
>
>
>
> [[alternative HTML version deleted]]
>
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