[Rd] Default subset and concatenation operators for namedList

2012-01-24 Thread Renaud Gaujoux
Hi, in R version 2.14.1 (2011-12-22), is it wanted that the class namedList does not overloads the '[' and 'c' operators: showMethods('c', class='namedList') showMethods('[', class='namedList') This means that if one creates a class that inherits from namedList, one has to define these opera

[Rd] Last Call: Who says this is not a bug in delete.response()?

2012-01-24 Thread Paul Johnson
On January 5, I posted here concerning this issue (https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14767), and I have not heard any answers from people who think this is not a bug, or a simple accident in the delete.response function. The output from delete.response on a terms object alters t

Re: [Rd] Sweave driver extension

2012-01-24 Thread Yihui Xie
Maybe this is a my personal taste: I do not like pseudo R code in the form <> inside a chunk, and I'm curious about why you do not use real R functions to do the job. coxme <- function(formula, data, subset, blah blah ){ coxme_check_arguments(...) coxme_build(...) coxme_compute(...) coxme

Re: [Rd] factor S4 class is NA when as.character method exists

2012-01-24 Thread John Chambers
On 1/24/12 9:35 AM, Prof Brian Ripley wrote: On 24/01/2012 17:17, William Dunlap wrote: Here is code that does make factor() work on a new class like yours. It uses Sv3 methods. Which is necessary as unique() is an S3 generic in the base namespace, and creating some other function named 'un

Re: [Rd] Failure to get compactPDF to compact a pdf file

2012-01-24 Thread John Maindonald
Quoting from the R-2.14.1 help page for compactPDF: " This by default makes use of 'qpdf', available from http://qpdf.sourceforge.net/> (including as a Windows binary) and included with the CRAN Mac OS X distribution of R. If 'gs_cmd' is non-empty, GhostScript will used instead. " The def

Re: [Rd] R-devel now triggers nags on notes from vignettes

2012-01-24 Thread Henrik Bengtsson
On Tue, Jan 24, 2012 at 8:42 AM, Michael Friendly wrote: > I recently submitted a minor update to a CRAN package that passed all CRAN > checks > ~ two weeks ago. > > Now, I get the response below from the CRAN-check-daemon > > R-devel reports > > * checking installed files from ‘inst/doc’ ... NOTE

[Rd] Sweave driver extension

2012-01-24 Thread Terry Therneau
Almost all of the coxme package and an increasing amount of the survival package are now written in noweb, i.e., .Rnw files. It would be nice to process these using the Sweave function + a special driver, which I can do using a modified version of Sweave. The primary change is to allow the follow

Re: [Rd] factor S4 class is NA when as.character method exists

2012-01-24 Thread Prof Brian Ripley
On 24/01/2012 17:17, William Dunlap wrote: Here is code that does make factor() work on a new class like yours. It uses Sv3 methods. Which is necessary as unique() is an S3 generic in the base namespace, and creating some other function named 'unique' elsewhere (which is what setGeneric does

Re: [Rd] factor S4 class is NA when as.character method exists

2012-01-24 Thread William Dunlap
Here is code that does make factor() work on a new class like yours. It uses Sv3 methods. > setClass("foo", contains="numeric") [1] "foo" > as.character.foo <- function(x) paste("x=",x@.Data,sep="") > unique.foo <- function(x, ...) structure(NextMethod("unique"), class=class(x)) > someF

Re: [Rd] Rnw file generated strange symbols in pdf file

2012-01-24 Thread Ben Bolker
Zhu Wang ccmckids.org> writes: > I found my Rnw file generated strange symbols in pdf file. > For instance, on page 4 of the following file, > > http://cran.r-project.org/web/packages/cts/vignettes/kf.pdf > you can see Belcher et~al on line 2, and Figure~1 on line 5. The > symbol ~ should not

[Rd] R-devel now triggers nags on notes from vignettes

2012-01-24 Thread Michael Friendly
I recently submitted a minor update to a CRAN package that passed all CRAN checks ~ two weeks ago. Now, I get the response below from the CRAN-check-daemon R-devel reports * checking installed files from ‘inst/doc’ ... NOTE The following files are already in R: ‘jss.cls’ Please remove them fro

[Rd] Rnw file generated strange symbols in pdf file

2012-01-24 Thread Zhu Wang
Hello, I found my Rnw file generated strange symbols in pdf file. For instance, on page 4 of the following file, http://cran.r-project.org/web/packages/cts/vignettes/kf.pdf you can see Belcher et~al on line 2, and Figure~1 on line 5. The symbol ~ should not appear in the pdf file although t

Re: [Rd] Failure to get compactPDF to compact a pdf file

2012-01-24 Thread Prof Brian Ripley
On 24/01/2012 08:30, John Maindonald wrote: I am failing to get compactPDF to make any change to a pdf file that, a/c to the message from the CRAN upload site, can be very substantially compacted. Any ideas what may be wrong? AFAICS you are quoting a message from R-devel, which tries to find '

[Rd] Failure to get compactPDF to compact a pdf file

2012-01-24 Thread John Maindonald
I am failing to get compactPDF to make any change to a pdf file that, a/c to the message from the CRAN upload site, can be very substantially compacted. Any ideas what may be wrong? I have also tried recreating the pdf file. I also tried R CMD build --resave-data --compact-vignettes DAAG The da