----- Original Message -----
> From: "Siddhartha Bagaria" <[email protected]>
> To: "Dan Tenenbaum" <[email protected]>
> Cc: "Craig Citro" <[email protected]>, [email protected]
> 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 <[email protected]>
> > wrote:
> >
> > Hi Siddartha,
> >
> > ----- Original Message -----
> >> From: "Siddhartha Bagaria" <[email protected]>
> >> To: [email protected]
> >> Cc: "Craig Citro" <[email protected]>
> >> 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
> >>
> >> _______________________________________________
> >> [email protected] mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
>
_______________________________________________
[email protected] mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
