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

[Leonardo Collado Torres]

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