[Bioc-devel] R CMD CHECK options

[Siddhartha Bagaria]

Hi Dan, thanks. Just to be sure I understand you, are you saying that
everyone manually installs all deps before running the checks?

Sent from my mobile device.

> 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
>>
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>>