[Bioc-devel] R CMD CHECK options

Dan Tenenbaum dtenenba at fhcrc.org
Tue May 13 06:39:13 CEST 2014

Hi Siddartha,

----- Original Message -----
> From: "Siddhartha Bagaria" <sidb at google.com>
> To: bioc-devel at r-project.org
> Cc: "Craig Citro" <craigcitro at google.com>
> Sent: Monday, May 12, 2014 9:00:04 PM
> Subject: [Bioc-devel] R CMD CHECK options
> Hello!
> This is my first time posting to the community. I am working on a new
> Bioconductor package for the Google Genomics API. I tried to search
> but could not find the options and environment variables I should use
> for R CMD CHECK before submission to Bioconductor. I have
> dependencies
> on packages from both CRAN and Bioconductor so I will also need to
> set
> multiple repository locations. Currently, I was planning to use
> setOption("repos"=c(CRAN="..",bioc="..")) in my .Rprofile, but I want
> to confirm if this is standard practice in the community for running
> checks during development.

If you use biocLite() it will automatically install CRAN and Bioconductor dependencies for packages.

For example:
biocLite("IRanges") # installs IRanges and its CRAN and Bioconductor dependencies

Note that when submitting to Bioconductor we also run the additional checks found in the BiocCheck package:



> Thanks.
> Sid
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