9. Development

Miscellaneous items that are useful while developing the code.

Sanity check

In the folder of the development version from GitHub:

R CMD check .

Build from source

In the parent folder of the development version from GitHub:

R CMD build BASiCS

And run then

install.packages('BASiCS_x.x.x.tar.gz', repos=NULL)

on the generated file.

To view pdf manual

The showPDFmanual function below was created by Prof Brian Ripley here

showPDFmanual <- function(package, lib.loc=NULL) 
{ 
     path <- find.package(package, lib.loc) 
     system(paste(shQuote(file.path(R.home("bin"), "R")), 
                  "CMD", "Rd2pdf", 
                  shQuote(path))) 
} 
showPDFmanual("BASiCS")

To install the BioC branch

devtools::install_github("catavallejos/BASiCS", ref = "Devel")

Github install with vignettes

devtools::install_github("catavallejos/BASiCS", ref = "Devel", build_vignettes = TRUE)

To access vignette

browseVignettes("BASiCS")

In BioC

See instructions here, here and here

## Installing R-devel

• Mac OS: http://r.research.att.com