Re: [R] Tidying up code - Warning message: deparse may be incomplete
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.R Then 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.
Re: [R] Tidying up code - Warning message: deparse may be incomplete
DM == Duncan Murdoch [EMAIL PROTECTED] on Fri, 29 Aug 2008 08:36:12 -0400 writes: DM 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.R Then 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? DM I've now taken a look, and this really was a bug. source() was DM partially ignoring options(keep.source = FALSE), and this confused DM dump(). I've fixed it in R-patched. DM I've also clarified the advice about tidying up code, by adding a DM warning that following it will delete all of your comments. I think DM you're better off writing it in a tidy way in the first place, or using DM a smart editor to reformat it. R retains enough information to write a DM code prettifier that preserves comments, but I don't know of one. I strongly agree with your last paragraph, and I have always thought that we should recommend using R-aware editors rather than dump() nowadays ... but then I thought that I've been biased at all times, being a co-developer of ESS, authoring its M-x ess-fix-miscellaneous (and more), and also the author of a (non public) Emacs lisp file called 'R-stylepolice.el' as early as in 1999. Martin Maechler DM 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.
Re: [R] Tidying up code - Warning message: deparse may be incomplete
Martin Maechler wrote: I strongly agree with your last paragraph, and I have always thought that we should recommend using R-aware editors rather than dump() nowadays ... but then I thought that I've been biased at all times, being a co-developer of ESS, authoring its M-x ess-fix-miscellaneous (and more), and also the author of a (non public) Emacs lisp file called 'R-stylepolice.el' as early as in 1999. BTW: Has there been any progress on turning the highlighting _off_ in iESS and transcript mode? The highlighted for and in make me crazy... -- O__ Peter Dalgaard Ă˜ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ 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.
[R] Tidying up code - Warning message: deparse may be incomplete
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.R Then 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? thanks, MP __ 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.
Re: [R] Tidying up code - Warning message: deparse may be incomplete
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.R Then 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? The warning means that you may have lost some information, i.e. sourcing newlala.R won't produce the same thing as sourcing lala.R. I think in your case, there's no loss, so it's a bug, but I don't have time to track down why you're getting it. 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.