[Bioc-devel] Data package timeouts

[Martin Morgan]

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 <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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>>
>>
>>
>> --
>> 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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> 
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