A belated thanks for this update. Martin
On 03/08/2017 09:53 AM, Welliton Souza wrote:
Martin,
I am using the "Template for Resource Queries"
(http://bioconductor.org/developers/how-to/web-query/). I think the
correct is:
while (N.TRIES > 0L) { # line 5
instead of
while (N.TRIES >= 0L) { # line 5
Because it will run twice when N.TRIES = 1L. At the end of the
loop N.TRIES should be 0 not -1. Or this line will fail.
if (N.TRIES == 0L) { # line 12
Welliton
On Tue, Mar 7, 2017 at 5:15 PM Welliton Souza <well...@gmail.com
<mailto:well...@gmail.com>> wrote:
Thank you Martin for the response, it was very helpful.
I am facing difficulties to write code examples, unit tests and
vignettes for accessing web APIs. I understand that the use of
\dontrun{} is not the best solution for examples. I am using
testthat::skip_on_bioc() to avoid time consuming and internet
connection during execution of unit tests. I also using pre-cached
response data (Rda file) for vignettes because I didn't find a cache
solution for knitr/Rmarkdown. It would be very useful a package that
helps us caching web response data and time consuming results that
can be used in examples, unit tests and vignettes.
Welliton
On Tue, Mar 7, 2017 at 4:49 PM Martin Morgan
<martin.mor...@roswellpark.org
<mailto:martin.mor...@roswellpark.org>> wrote:
On 03/07/2017 02:35 PM, Welliton Souza wrote:
> Thank you Nan Xiao, I think it is a good solution for my case.
I will put
> the definition of host outside the \dontrun{}.
Actually, generally, one doesn't want to work around tests with
hacks,
but either (a) address the underlying problem or (b) justify
what the
current behavior is and live with the warning. Writing \dontrun{}
doesn't help at all -- it might work now, but will suffer from 'bit
rot' in the future; example and vignette code is littered with
examples
like this.
The usual problem with web resources is that the functions that
access
them assume that the resource is reliably available, and that
band width
is infinite. In reality, the web resource is likely to experience
periodic down time, and the band width can be cripplingly slow.
There are a few notes here
http://bioconductor.org/developers/how-to/web-query/
discussing better practice for querying web resources. Avoiding
infinitely querying a web resource and including a time out are two
important steps.
Ideally one would like unit tests that verify that the web
resource is
in fact alive, and that the expected API is available. One would not
necessarily test the entire API, but rely instead on serialized
instances to ensure that one parses the correct information.
With examples, there is a combination of judicious use of web calls
coupled with re-use of data from previous calls. The forthcoming
BiocFileCache (https://github.com/Bioconductor/BiocFileCache)
might be
used to create a temporary cache used during the duration of the
build /
check, limiting the number of unique calls required while still
exposing
substantial functionality in the example pages.
Martin
>
> Welliton
>
> Em ter, 7 de mar de 2017 16:27, Nan Xiao <road2s...@gmail.com
<mailto:road2s...@gmail.com>> escreveu:
>
>> - this check can be bypassed by
>> writing "partially working" examples,
>> for instance:
>>
>> #' token = "foo"
>> #' \dontrun{
>> #' api(..., token)}
>>
>> Best,
>> -Nan
>>
>> On Tue, Mar 7, 2017 at 2:13 PM, Welliton Souza
<well...@gmail.com <mailto:well...@gmail.com>> wrote:
>>
>> Hi Sean,
>>
>> It doesn't require authentication. I've been using this server (
>> http://1kgenomes.ga4gh.org) to provide working examples and
do unit tests
>> but I am not responsible for this server. However the package
was developed
>> to access any server endpoint that use the same API. There
are many web
>> resources to cover, the package takes some time to run all
examples.
>>
>> Welliton
>>
>>
>> Em ter, 7 de mar de 2017 16:03, Sean Davis
<seand...@gmail.com <mailto:seand...@gmail.com>> escreveu:
>>
>> Hi, Welliton.
>>
>> Great question. Just out of curiosity, what are the internet
connection
>> requirements that preclude running examples? Is
authentication required?
>> Or are you connecting to a server that runs only intermittently?
>>
>> Sean
>>
>>
>> On Tue, Mar 7, 2017 at 1:57 PM, Welliton Souza
<well...@gmail.com <mailto:well...@gmail.com>> wrote:
>>
>> Hi,
>>
>> I am developing a package that access web API endpoints. I
wrote the
>> examples within \dontrun{} due to internet connection
requirements.
>> However, the BiocCheck reports that I should provide at least
80 % of
>> running examples. What I should do? The package is mainly
focused on
>> accessing web API and processing response data.
>>
>> Best regards,
>> Welliton Souza
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>
mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>
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>>
>>
>>
>>
>> --
>> https://nanx.me
>>
>
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>
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