On 11/30/2017 06:05 AM, Mike Smith wrote:
Thanks for the speedy response Sean. I'll switch back to the version using
a file name shortly.
Is there a use case for BiocFileCache in here -- check if the file is in
the cache bfcquery(), if so, check whether it needs updating
bfcneedsupdate() and perhaps bfcupdate() ? this might make the overall
download process more robust, and would certainly save on build time.
Martin
Cheers,
Mike
On 30 November 2017 at 11:20, Sean Davis <seand...@gmail.com> wrote:
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 <grimbo...@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 <michaelisaiahl...@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
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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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