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

Régis Ongaro-Carcy reg|@@ong@ro-c@rcy@1 @end|ng |rom u|@v@|@c@
Thu Jul 16 16:26:03 CEST 2020


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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