Siddharta,

The development process I use, which as far as I know is the canonical
"Right Way" (tm) is:

(Build with no vignettes -this is often skipped)
Install and test code or use devtools (repeat many times)
Final install
Build
Check

So basically, you should have already successfully installed the package
(which will grab its dependencies) before running check. This makes sense
because if you don't have the package installed you can't have been testing
it. R CMD check is intended to be a final test, not an intermediate one.

Hope that helps
~G


On Tue, May 13, 2014 at 7:30 AM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:

>
>
> ----- Original Message -----
> > From: "Siddhartha Bagaria" <sidb@google.com>
> > To: "Dan Tenenbaum" <dtenenba@fhcrc.org>
> > Cc: "Craig Citro" <craigcitro@google.com>, bioc-devel@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@fhcrc.org>
> > > wrote:
> > >
> > > Hi Siddartha,
> > >
> > > ----- Original Message -----
> > >> From: "Siddhartha Bagaria" <sidb@google.com>
> > >> To: bioc-devel@r-project.org
> > >> Cc: "Craig Citro" <craigcitro@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
> > >>
> > >> _______________________________________________
> > >> Bioc-devel@r-project.org mailing list
> > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >>
> >
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
Computational Biologist
Genentech Research

	[[alternative HTML version deleted]]

