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

Nicolas Delhomme n|co|@@@de|homme @end|ng |rom umu@@e
Mon Jan 20 10:43:11 CET 2020

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?



> 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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