[BioC] Building R packages

[Douglas Bates]

On 6/21/05, E Motakis, Mathematics <E.Motakis at bristol.ac.uk> wrote:
> Dear all
> 
> I am trying to build an R package in Windows 2000 that I want to upload in
> Bioconductor. I have created the man and R folders with the appropriate
> files inside and I use the command Rcmd check C:\...\roots to check whether
> the package works properly, but the following problem appears:
> 
> -------------------------------------------------------
> * using log directory 'C:/Program Files/R/rw2001/bin/roots.Rcheck'
> * checking for file 'roots/DESCRIPTION' ... OK
> * checking if this is a source package ... OK
> * checking package directory ... OK
> * checking for portable file names ... OK
> * checking package dependencies ... OK
> * checking index information ... OK
> * checking package subdirectories ... OK
> * checking R files for syntax errors ... OK
> * checking R files for library.dynam ... OK
> * checking S3 generic/method consistency ... WARNING
> Error in .try_quietly({ : Error: Unable to load R code in package 'roots'
> Execution halted
> See section 'Generic functions and methods' of the 'Writing R Extensions'
> manual.
> * checking replacement functions ... WARNING
> Error in .try_quietly({ : Error: Unable to load R code in package 'roots'
> Execution halted
> In R, the argument of a replacement function which corresponds to the right
> hand side must be named 'value'.
> * checking foreign function calls ... WARNING
> Error in .try_quietly({ : Error: Unable to load R code in package 'roots'
> Execution halted
> See section 'System and foreign language interfaces' of the 'Writing R
> Extensions' manual.
> * checking Rd files ... OK
> * checking for missing documentation entries ... ERROR
> Error in .try_quietly({ : Error: Unable to load R code in package 'roots'
> --------------------------------------------------------
> 
> Could someone tell how to correct for the warnings, please?
> 
> Regards,
> Makis

Well the warnings indicate that there is a syntax error in your R
source code.  You will need to source each of the R files in your
package separately to determine where the problem is.  It can be
something as trivial as a missing or an extra comma, which is my
typical error.

I generally do something like

base <- "roots/R"  # change to the proper directory path
nms <- list.files(base, pattern = "\.R$")
for (nm in nms) {print(nm);source(file.path(base,nm))}

That should produce an error message from one of the calls to source()
and it will occur in the file whose name has just been printed.