[Bioc-devel] Guidelines for shiny packages

Dan Tenenbaum dtenenba at fhcrc.org
Mon Sep 29 21:56:38 CEST 2014

----- Original Message -----
> From: "Thomas Dybdal Pedersen" <thomasp85 at gmail.com>
> To: bioc-devel at r-project.org
> Sent: Monday, September 29, 2014 12:49:16 PM
> Subject: [Bioc-devel] Guidelines for shiny packages
> Hi All
> I’m in the process of getting package submitted to Bioconductor. The
> package is a pure shiny package and this has led to some -
> especially one question. For those not familiar with shiny apps, the
> code that makes these work resides in their own .R files outside of
> the R directory in a package. 

Actually, the code for a shiny app can be in a package. The runApp() function can be called with a list instead of a directory, where the list contains named items "ui" and "server". See the example in ?runApp. 
We prefer this approach as it fits better into the package framework and allows better code reuse. 

> Consequently they are not ‘build’ and
> whatever is in there is not part of the package namespace. The
> functionality of my GUI requires several packages, but for the
> reasons given above they are not imported into the package
> namespace. Still they are needed for the package to function
> properly. The main question is thus: How to state this hard
> dependency in the DESCRIPTION file without getting knocked on the
> head for not importing your dependencies during check and BiocCheck?

See above. If you call runApp() as described above then you handle package dependencies the same way you would in a regular package.


> Another related question/proposal is: Based on the interest in Shiny
> at BioC 2014 it seems as we should anticipate a lot of shiny based
> packages. As one of the core principles of the Bioconductor project
> is to promote good coding style and high quality packages I was
> wondering whether it would make sense to begin working on a set of
> guidelines for developing shiny based GUIs, as their structure and
> style differs a lot from standard R packages. Just a suggestion -
> I’ll happily join such an effort…

> best
> Thomas
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

More information about the Bioc-devel mailing list