[Bioc-devel] Data package timeouts

[Sean Davis]

Thanks for the report, Mike.

The problem was (specifically) in parsing a GSEMatrix file using a
filename. This should be fixed in versions 2.46.10 (release) and 2.47.12
(devel).

Sean


On Thu, Nov 30, 2017 at 4:09 AM, Mike Smith <grimbough at gmail.com> wrote:

> Hi Mike,
>
> I was experiencing similar problems with the BeadArrayUseCases vignette,
> where using getGEO() from GEOquery was getting stuck in a (seemingly)
> infinite loop processing a GSE series matrix file.  It looks like both of
> your examples try to do this too, so I suspect it's a similar issue.  I
> think the format of those files has changed recently and it seems to be
> causing a fair few issues with GEOquery.
>
> I temporarily settled a solution by getting querying GEO directly rather
> than using a local file, but it would be nice to get it back working as
> intended.
>
> Mike
>
> On 29 November 2017 at 18:56, Michael Love <michaelisaiahlove at gmail.com>
> wrote:
>
> > I got simultaneous timeout notices for 'airway' and 'parathyroidSE' on
> > both release and devel machines (release was fine leading up to the
> > Bioc release).
> >
> > Not sure what's the issue, I haven't changed these packages in a
> > while. I checked these out and these both build fine and in ~30s on my
> > machine (devel branch).
> >
> > Here are the reports for release:
> >
> > http://bioconductor.org/checkResults/release/data-
> > experiment-LATEST/airway/malbec1-buildsrc.html
> > http://bioconductor.org/checkResults/release/data-experiment-LATEST/
> > parathyroidSE/malbec1-buildsrc.html
> >
> > The vignettes are here:
> >
> > http://bioconductor.org/packages/3.6/data/experiment/
> > vignettes/airway/inst/doc/airway.html
> > http://bioconductor.org/packages/3.6/data/experiment/
> > vignettes/parathyroidSE/inst/doc/parathyroidSE.pdf
> >
> > best,
> > Mike
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
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-- 
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https://seandavi.github.io/
https://twitter.com/seandavis12

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