Re: [Rd] dependencies on system packages

2011-02-03 Thread Simon Urbanek
Jeroen, On Feb 3, 2011, at 9:31 PM, Jeroen Ooms wrote: > > Many R packages depend on some unix libraries that are not part of most > default installations. I often spend a significant amount of time figuring > out where to get the appropriate libraries for compiling these packages, > after they

[Rd] dependencies on system packages

2011-02-03 Thread Jeroen Ooms
Many R packages depend on some unix libraries that are not part of most default installations. I often spend a significant amount of time figuring out where to get the appropriate libraries for compiling these packages, after they give some vague error of something missing. I was wondering why the

Re: [Rd] Creating a reference class object from a class definition in a package fails

2011-02-03 Thread John Chambers
Yes, as noted in my previous mail, which crossed yours. If you included the TestClass in a code_file= in the package skeleton, the default NAMESPACE file from package.skeleton() will do that for you: exportPattern("^[[:alpha:]]+") exportClasses( "TestClass" It's certainly true that _if_

Re: [Rd] Creating a reference class object from a class definition in a package fails

2011-02-03 Thread John Chambers
You don't say, but my guess is you created the package without a namespace. For reasons that are not too clear at the moment, the namespace seems to be needed. At any rate, replicating your experiment with the argument namespace=TRUE to package.skeleton() worked: > require(TestClass2) Loadin

[Rd] keep.source when semicolons separate statements on the one line; PS

2011-02-03 Thread John Maindonald
I forgot to add the sessionInfo() information: > sessionInfo() R version 2.12.1 Patched (2011-01-22 r54081) Platform: x86_64-pc-mingw32/x64 (64-bit) . . . The following is 'semicolon.Rnw' > \SweaveOpts{engine=R, keep.source=TRUE} > > <>= > library(SMIR); data(bronchit); library(KernSmooth) > @

[Rd] keep.source when semicolons separate statements on the one line

2011-02-03 Thread John Maindonald
The following is 'semicolon.Rnw' > \SweaveOpts{engine=R, keep.source=TRUE} > > <>= > library(SMIR); data(bronchit); library(KernSmooth) > @ % > > Code for panel A is > <>= > <> > @ % Sweave("semicolon") yields the following 'semicolon.tex' > Code for panel A is > \begin{Schunk} > \begin{Sinput

Re: [Rd] Creating a reference class object from a class definition in a package fails

2011-02-03 Thread Jeffrey Horner
Apparently reference classes must be declared in the NAMESPACE file via an S4 declaration. If I place the following in the NAMESPACE file all is well: exportClasses(TestClass) export(TestClass) Jeff On Wed, Feb 2, 2011 at 9:25 PM, Jeffrey Horner wrote: > Hi, > > I'm trying to create a package

Re: [Rd] S3 method for S4 object

2011-02-03 Thread Martin Morgan
On 02/03/2011 09:29 AM, Paul Gilbert wrote: > I am trying to extend an S3 method to work with an S4 object as well > as the S3 objects it works with, but UseMethod does not seem to > recognize the S4 class and dispatches to the default method. Is this > to be expected or should I be looking for an

[Rd] S3 method for S4 object

2011-02-03 Thread Paul Gilbert
I am trying to extend an S3 method to work with an S4 object as well as the S3 objects it works with, but UseMethod does not seem to recognize the S4 class and dispatches to the default method. Is this to be expected or should I be looking for an error in my code? If it is not an error in my c

[Rd] Minor typo in files2.Rd (Manipulaton)

2011-02-03 Thread Rainer Stuetz
There is a minor typo in the title section of 'files2.Rd': ~/R/r-devel> svn diff Index: src/library/base/man/files2.Rd === --- src/library/base/man/files2.Rd (revision 54213) +++ src/library/base/man/files2.Rd (working copy)

[Rd] bug in codetools/R CMD check?

2011-02-03 Thread Hin-Tak Leung
Hi Mr Tierney, I have noticed an error message from R 1.12.x's CMD check for a while (apparently prof Ripley completely rewrote CMD check in R 1.12+) e.g.: http://bioconductor.org/checkResults/2.7/bioc-LATEST/snpMatrix/lamb2-checksrc.html * checking R code for possible problems