On 28/08/2008 10:46 AM, Marie Pierre Sylvestre wrote:
Dear R users,I am currently writing a R package and to do so I am following the guidelines in manual 'Writing R extensions'. In Section 3.1, it is suggested to tidy up the code using a file containing the following: options(keep.source = FALSE) source("myfuns..R") dump(ls(all = TRUE), file = new.myfuns.R") I have done this for my own packages and although it runs, I get several warnings of the type: Warning message: In dump(ls(all = TRUE), file = "PermAlgo.R") : deparse may be incomplete I am clueless as to what this means. Even if I try to tidy only one function from my code, I get the warning. E.g. the file lala.R contains only this: partialHazards <- function(t, v, covArray, betas){ exp( covArray[v,t,] %*% betas ) } the file tidylala.R contains: options(keep.source = FALSE) source("lala.R") dump(ls(all = TRUE), file = "newlala.R") On Linux I run:R --vanilla < tidylala.RThen I obtain: Warning message: In dump(ls(all = TRUE), file = "newlala.R") : deparse may be incomplete The file newlala.R looks like this: `partialHazards` <- function (t, v, covArray, betas) { exp(covArray[v, t, ] %*% betas) } What does the warning mean? Can I simply ignore it?
I've now taken a look, and this really was a bug. source() was partially ignoring options(keep.source = FALSE), and this confused dump(). I've fixed it in R-patched.
I've also clarified the advice about tidying up code, by adding a warning that following it will delete all of your comments. I think you're better off writing it in a tidy way in the first place, or using a smart editor to reformat it. R retains enough information to write a code prettifier that preserves comments, but I don't know of one.
Duncan Murdoch ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
