[Bioc-devel] Data package timeouts

On Thu, Nov 30, 2017 at 6:05 AM, Mike Smith <grimbough at gmail.com> wrote:

Thanks for the speedy response Sean.  I'll switch back to the version
using a file name shortly.

No problem. Let me know if it does not work as expected.

Sean

Cheers,
Mike

On 30 November 2017 at 11:20, Sean Davis <seandavi at 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 <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

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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

--
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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