[Bioc-devel] Data package timeouts

[Mike Smith]

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

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