[Bioc-devel] Package submission with strong external dependency during build/check [take 2]

[Martin Morgan]

This set up is not possible in Bioconductor.

I suggest that you explore the use of 'mocks' so that your code thinks, during testing and examples, that it is querying an elasticsearch server, but is actually checking that it can send the appropriate message / interpret the expected response -- you're testing your R code, not the elasticsearch implementation.

There is some more information at

  https://books.ropensci.org/http-testing/

but perhaps others have experience with this approach?

Martin Morgan


On 7/16/20, 10:26 AM, "Bioc-devel on behalf of Régis Ongaro-Carcy" <bioc-devel-bounces using r-project.org on behalf of regis.ongaro-carcy.1 using ulaval.ca> wrote:

    Hello Bioconductor,

    I would like to submit my software package to Bioconductor and I have some questions.

    My package strongly depends on ElasticSearch (ES, https://www.elastic.co/elasticsearch) as database and search engine. It sends data to, and retrieves data from ES. 
    Thus, a big part of the build/check is based on the fact that there is an empty ES available for building/checking the examples, manual, vignettes and tests.

    The only thing actually required on the R-side is two variables in the env to target ES IP address and port (user/pwd optionally). I mainly use the docker version of ES on my computer so that is fairly easy to run and interact with it.

    So, my questions are: is it possible to run a disposable container alongside the Bioconductor build/check system run? Do some packages already implemented it?

    The container should be discarded afterward. This setup works fine on my computer and I am wondering how it could be achieved on Bioconductor's side and if there is another easier/more efficient/more suitable solution. I am hitting the time limit on travis when checking tests without longtests, so a ES container with longtests would also be needed.

    Best regards,
    Régis Ongaro

    P.S.: many thanks Martin Morgan, I spent some time trying to find the right option in the university MS outlook to turn the html default mail into plain text. Hoping it will work this time.
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