[Bioc-devel] Issue importing bigwig files with rtracklayer from Amazon Cloud Drive

Michael Lawrence lawrence.michael at gene.com
Thu May 5 23:24:26 CEST 2016

The URL redirection is something I can try to add. For the other error, you
need to get openssl installed and made visible to pkg-config, so that
rtracklayer finds it during its build process.


On Thu, May 5, 2016 at 2:01 PM, Leonardo Collado Torres <lcollado at jhu.edu>

> Hi Michael,
> I have a use case that is similar to
> https://support.bioconductor.org/p/81267/#82142 and looks to me like
> it might need some changes in rtracklayer to work. That's why I'm
> posting it here this time.
> Basically, I'm trying to use rtracklayer to import a bigwig file over
> the web which is in a different type of url than before. Using
> utils::download.file() with the defaults doesn't work, I have to use
> method = 'curl' and extra = '-L'.
> More specifically, the original url
> http://duffel.rail.bio/recount/DRP000366/bw/DRR000897.bw has an
> effective url
> https://content-na.drive.amazonaws.com/cdproxy/templink/i_aQAPZJkJ9d9lN1NO5DJJtlbpvAdgbNuc1SkqSTHFouFiZq5
> Now, using the second url with utils::download.file() and default
> methods also doesn't work. It does on the browser though.
> As you can see, downloading the file doesn't work out of the box.
> Which I guess that it's not surprising that using rtracklayer I get
> errors like:
> In seqinfo(ranges) :
>   No openssl available in netConnectHttps for
> content-na.drive.amazonaws.com : 443
> You can find further details (code and log file) at
> https://gist.github.com/lcolladotor/c500dd79d49aed1ef33ade5417111453
> Thanks,
> Leo

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