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

[Shepherd, Lori]

With some additional investigation this appears to be a firewall issue as the error was reproducible on other machines.  Work is being done to rectify the issue.

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________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Nicolas Delhomme <nicolas.delhomme using umu.se>
Sent: Monday, January 20, 2020 4:43:11 AM
To: Martin Morgan <mtmorgan.bioc using gmail.com>
Cc: Dan Tenenbaum <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Problem with uncompressing files on tokay1?

Hej Martin and Dan!

First of all, I wish you both a happy new year!

I have made the move to the BiocFileCache, but the build report (3.10 for easyRNASeq) fails as follows:

* creating vignettes ... ERROR
--- re-building ‘simpleRNASeq.Rmd’ using rmarkdown
Quitting from lines 40-41 (./Chapters/01-Introduction.Rmd)
Quitting from lines NA-42 (./Chapters/01-Introduction.Rmd)
Error: processing vignette 'simpleRNASeq.Rmd' failed with diagnostics:
bfcadd() failed; see warnings()

I can’t reproduce it, so it seems to be related to the build system at Bioc?

Thanks,

Nico

> On 25 Nov 2019, at 15:39, 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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