[Bioc-devel] Data package timeouts

Mike Smith grimbough at gmail.com
Thu Nov 30 10:09:11 CET 2017

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


On 29 November 2017 at 18:56, Michael Love <michaelisaiahlove at gmail.com>

> 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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