[Bioc-devel] Data package timeouts

[Sean Davis]

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
>>> >
>>> > _______________________________________________
>>> > 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
>>
>
>


-- 
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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