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

Shepherd, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Fri Jan 24 13:01:46 CET 2020

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.

Get Outlook for Android<https://aka.ms/ghei36>

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?



> 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
>    _______________________________________________
>    Bioc-devel using r-project.org mailing list
>    https://stat.ethz.ch/mailman/listinfo/bioc-devel

Bioc-devel using r-project.org mailing list

This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
	[[alternative HTML version deleted]]

More information about the Bioc-devel mailing list