[Bioc-devel] Problem with uncompressing files on tokay1?

Mike Smith gr|mbough @end|ng |rom gm@||@com
Mon Nov 25 16:15:44 CET 2019

Could this be another instance where you need to specify mode = "wb" when
you call download.file()?  I've seen many examples of Windows downloads
being corrupted because it uses mode = "w" by default.

Presumably BiocFileCache would both handle this correctly and save multiple
downloads, so it's a double win.

On Mon, 25 Nov 2019 at 15:40, Martin Morgan <mtmorgan.bioc using gmail.com> wrote:

> Thanks this seems like a problem with large file size on Windows, probably
> in Rhtslib.
> It might be better practice and more reliable to use BiocFileCache for
> downloads, e.g.,
> url = "
> ftp://ftp.plantgenie.org/Tutorials/RnaSeqTutorial/data/star/unitTest/213.1_subset_sortmerna_trimmomatic_sorted.bam.bai
> "
> BiocFileCache::bfcrpath(rnames = url)
> which downloads (once) and returns the path to the cached file.
> Martin
> On 11/25/19, 8:24 AM, "Bioc-devel on behalf of Nicolas Delhomme" <
> bioc-devel-bounces using r-project.org on behalf of nicolas.delhomme using umu.se>
> wrote:
>     Hej!
>     The easyRNASeq package is not building on tokay1, with what seems to
> be a file decompression issue?
> https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/easyRNASeq/tokay1-buildsrc.html
>     It works fine on the other OSs.
>     The error is triggered while downloading a small dataset during the
> vignette creation. I use `download.file` as the function to fetch the data,
> so it should be cross-platform compatible. I have no easy access to a
> windows machine, so I can’t easily reproduce the problem. Any insight into
> what could be the reason would be much appreciated :-)
>     The easy solution would be to turn off the evaluation of that section
> of the vignette, but I’d rather not as it is a good test of the complete
> functionality of the package (something that would feel ill-fitted as a
> unit test).
>     Thanks in advance,
>     Nico
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