[Bioc-devel] Something about time out errors

[Martin Morgan]

On 03/27/2017 12:57 PM, Rainer Johannes wrote:
> Do you have code fetching data from web resources? I also sometimes get timeout errors on ensembldb and I guess it's because in some unit tests I'm fetching data from the ensembl ftp server.
>

Testing web resources is a pretty interesting topic. It doesn't really 
make sense to spend a lot of time downloading a large amount of data, 
but rather to focus the test on the existence of the endpoint, and the 
returned data type. It seems like these tests can be fast and 
light-weight. One approach (for static resources) might ask the web 
server for a last-modified or entity tag (ETag) value, and compare that 
to a manually maintained last-known-good exemplar.

Unit tests for parsing the data into R and processing the data once in R 
are really separate from the web resource, and should probably be 
isolated from tests of the web resource itself.

The approach on this page

   http://bioconductor.org/developers/how-to/web-query/

especially use of timeout(), might be a reasonable way to implement 
this; also BiocFileCache is now available and provides appropriate 
functionality (although looking I see that it doesn't currently support 
time-outs -- but it's better to fix this in the one location rather than 
in many different locations).

Martin

> jo
>
>> On 27 Mar 2017, at 18:37, Martin Morgan <Martin.Morgan at RoswellPark.org> wrote:
>>
>> On 03/27/2017 12:22 PM, Aimin Yan wrote:
>>> I am submitting a R package to bioconductor. but I got time out errors when
>>> I performed R CMD check.
>>>
>>>
>>> Is there a possible way that I can set up time to allow more time for R CMD
>>> check? Or I have to use examples that they do not cost large time.
>>
>> Submitted packages need to conform to package guidelines for space and time
>>
>>  http://bioconductor.org/developers/package-guidelines/#correctness
>>
>> so you'll need to develop realistic examples requiring modest resources.
>>
>> Often long-running examples result from inefficient code, so it is worth-while to profile your code to discover where the most time is spent, and seek efficient implementations for that section of code either through better use of vectorization or more sophisticated algorithms.
>>
>> Martin
>>
>>>
>>>
>>> Thank you for your help
>>>
>>> Aimin
>>>
>>> 	[[alternative HTML version deleted]]
>>>
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>>
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