[Bioc-devel] R CMD CHECK options
----- Original Message -----
From: "Siddhartha Bagaria" <sidb at google.com> To: "Dan Tenenbaum" <dtenenba at fhcrc.org> Cc: "Craig Citro" <craigcitro at google.com>, bioc-devel at r-project.org Sent: Tuesday, May 13, 2014 12:02:37 AM Subject: Re: [Bioc-devel] R CMD CHECK options Hi Dan, thanks. Just to be sure I understand you, are you saying that everyone manually installs all deps before running the checks?
I guess what I am saying is that 1) the BioC build system will automatically install all deps before running checks and 2) once your package is in BioC, all people have to do is biocLite("yourPackage") to get all deps, and 3) before your package is in BioC, I guess you do have to install all deps manually, but 4) if you use biocLite() you don't need to put any repos fanciness in your .Rprofile.
Dan
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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