[Bioc-devel] R CMD CHECK options

On May 13, 2014, at 10:09 AM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:

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:
source("http://bioconductor.org/biocLite.R")
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:

http://bioconductor.org/packages/release/bioc/html/BiocCheck.html

Dan

Thanks.

Sid