Re: [Rd] exTremes and ismev (PR#13981)

2009-10-05 Thread Uwe Ligges
mzukisi.gw...@gmail.com wrote: Greetings I am attempting to load exTremes and this is what I get... *> utils:::menuInstallPkgs() --- Please select a CRAN mirror for use in this session --- trying URL ' http://cran.uk.r-project.org/bin/windows/contrib/2.9/extRemes_1.60.zip' Content type 'appli

Re: [Rd] suggest enhancement to segments and arrows to facilitate horizontal and vertical segments

2009-10-05 Thread Prof Brian Ripley
This isn't a one-way street, as it means that some erroneous calls will not be detected, and code written to take advantage of this will only work under R >= 2.10.0. I think we should probably insist that one of x1 and y1 is supplied: if both are omitted arrows() would give a warning, but segm

Re: [Rd] R 2.9.2 crashes when sorting latin1-encoded strings

2009-10-05 Thread Prof Brian Ripley
This was a missing PROTECT() in do_order. But I'll echo what Simon Urbanek said: don't do that but rather use the documented ways to re-encode the file as you read it. (Latin-1 used to be needed for collation on Mac OS X as C-level collation in UTF-8 was completely broken -- but we have worke

[Rd] how to document stuff most users don't want to see

2009-10-05 Thread Charles Geyer
The functions metrop and temper in the mcmc package have a debug = FALSE argument that when TRUE adds a lot of debugging information to the returned list. This is absolutely necessary to test the functions, because one generally knows nothing about the simulated distribution except what what one l

Re: [Rd] how to document stuff most users don't want to see

2009-10-05 Thread Duncan Murdoch
On 10/5/2009 1:50 PM, Charles Geyer wrote: The functions metrop and temper in the mcmc package have a debug = FALSE argument that when TRUE adds a lot of debugging information to the returned list. This is absolutely necessary to test the functions, because one generally knows nothing about the

Re: [Rd] how to document stuff most users don't want to see

2009-10-05 Thread William Dunlap
There are several help files in the R sources that describe concepts and not particular R objects. E.g., help(Methods), help(Syntax), and help(regex). They don't have a docType entry and their alias entries do not refer to functions. Perhaps your debugging documentation could go into a similar *.

[Rd] unit testing for R packages?

2009-10-05 Thread Blair Christian
Hi All, I'm interested in putting some unit tests into an R package I'm building. I have seen assorted things such as Runit library, svUnit library, packages with 'tests' directories, etc I grep'd "unit test" through the writing R extensions manual but didn't find anything. Are there any sugges

Re: [Rd] how to document stuff most users don't want to see

2009-10-05 Thread spencerg
There are many arguments in many functions that are rarely used. I prefer to see it all documented in the help pages. If they are not documented in the help pages (and sometimes even if they are), a user who wants them can invent other ways to get similar information with much greater effort,

Re: [Rd] unit testing for R packages?

2009-10-05 Thread Duncan Murdoch
On 10/5/2009 3:01 PM, Blair Christian wrote: Hi All, I'm interested in putting some unit tests into an R package I'm building. I have seen assorted things such as Runit library, svUnit library, packages with 'tests' directories, etc I grep'd "unit test" through the writing R extensions manual

Re: [Rd] unit testing for R packages?

2009-10-05 Thread Seth Falcon
Hi, On Mon, Oct 5, 2009 at 12:01 PM, Blair Christian wrote: > I'm interested in putting some unit tests into an R package I'm > building.  I have seen assorted things such as Runit library, svUnit > library, packages > with 'tests' directories, etc > > I grep'd "unit test" through the writing R e

Re: [Rd] unit testing for R packages?

2009-10-05 Thread Paul Gilbert
Seth I should look at RUnit more carefully sometime, but having had my own system in place from much earlier, I've never made the move. Basically I just use files in the tests/ directory which are run by a makefile in the package directory above. Roughly, this just means that I can run the test

Re: [Rd] unit testing for R packages?

2009-10-05 Thread spencerg
I put unit test in the examples, using "\dontshow" to hide "stopifnot". Many help pages I've written contain code like the following: A <- functionDocumentedHere() B <- manuallyComputedAnswer \dontshow{stopifnot(} all.equal(A, B) \dontshow{)} I think it helps the documentation to incl

[Rd] Wish for stripchart to handle pch %in% 21:25 with bg (PR#13984)

2009-10-05 Thread lobry
Full_Name: Jean Lobry Version: 2.9.0 OS: i386-apple-darwin8.11.1 Submission from: (NULL) (83.197.82.45) Dear R-core, I have posted http://finzi.psych.upenn.edu/Rhelp08/2009-September/212688.html";>this on R-help, and then http://finzi.psych.upenn.edu/R/R-devel/2009-September/054929.html";>that o

[Rd] R's --enable-threads does nothing?; gdb needs -lpthread

2009-10-05 Thread Andrew Piskorski
In the R-2-9-branch (svn revision 49914, 2009-09-24), R's configure script has an "--enable-threads" option. But, does it do anything useful? When I use "--enable-threads=posix", some of the configure output changes slightly, but it seems to have no effect on the actual link commands used when bu

Re: [Rd] unit testing for R packages?

2009-10-05 Thread Duncan Murdoch
On 05/10/2009 4:39 PM, spencerg wrote: I put unit test in the examples, using "\dontshow" to hide "stopifnot". Many help pages I've written contain code like the following: A <- functionDocumentedHere() B <- manuallyComputedAnswer \dontshow{stopifnot(} all.equal(A, B) \dontshow{)} This wi

Re: [Rd] unit testing for R packages?

2009-10-05 Thread spencerg
Hi, Duncan: Thanks for the warning. Can you give me a hint of which release might require this? In particular, will it be R 2.10.0, coming quite soon? Thanks, Spencer Duncan Murdoch wrote: On 05/10/2009 4:39 PM, spencerg wrote: I put unit test in the examples, using "\

Re: [Rd] unit testing for R packages?

2009-10-05 Thread Duncan Murdoch
On 05/10/2009 6:06 PM, spencerg wrote: Hi, Duncan: Thanks for the warning. Can you give me a hint of which release might require this? In particular, will it be R 2.10.0, coming quite soon? The alpha version of 2.10.0 lets this pass, and I can't see changing that now. But 2.11.0

[Rd] str() gives odd looking output on complex vectors that are not purely imaginary (PR#13985)

2009-10-05 Thread richcalaway
Full_Name: Rich Calaway Version: R 2.9.2 OS: Windows Vista Submission from: (NULL) (65.47.30.18) Try this: x <- rnorm(25) y <- rnorm(25)*1i z <- x+y str(z) str(y) When I try this, I see the following: > str(z) cplx [1:25] 0.0102+ 0.9463-1 -1.+ ... > str(y) cplx [1:25] 0+0.0975i 0-1.5060i

[Rd] Characters vs. factors

2009-10-05 Thread hadley wickham
It seems like a recent trend in R has been to make character vectors and factors almost equivalent (apart from the way that factors always remember their original range). There are a few exceptions: * summary.character != summary.factor * table(x, exclude = NULL) != table(factor(x), exclude=NUL

Re: [Rd] unit testing for R packages?

2009-10-05 Thread Philippe Grosjean
Hi, I am the writer of svUnit. My initial goal was to build functions on top of RUnit which is older, and certainly deserves all the credit for core test unit functions. Unfortunately, the way RUnit is working internally did not allowed me to build the extensions I needed. Now, as Seth already t

Re: [Rd] unit testing for R packages?

2009-10-05 Thread hadley wickham
> Now, as Seth already told, there are several functions in svUnit that > ease interactive use of the tests in an R session. What he did not told > is that RUnit has some nice code coverage functions that svUnit does not > have. What are those? I've skimmed through the documentation and couldn't s

Re: [Rd] unit testing for R packages?

2009-10-05 Thread Peter Cowan
On Mon, Oct 5, 2009 at 5:44 PM, hadley wickham wrote: >> Now, as Seth already told, there are several functions in svUnit that >> ease interactive use of the tests in an R session. What he did not told >> is that RUnit has some nice code coverage functions that svUnit does not >> have. > > What ar

Re: [Rd] unit testing for R packages?

2009-10-05 Thread hadley wickham
On Mon, Oct 5, 2009 at 8:48 PM, Peter Cowan wrote: > On Mon, Oct 5, 2009 at 5:44 PM, hadley wickham wrote: >>> Now, as Seth already told, there are several functions in svUnit that >>> ease interactive use of the tests in an R session. What he did not told >>> is that RUnit has some nice code cov

Re: [Rd] unit testing for R packages?

2009-10-05 Thread Peter Cowan
On Mon, Oct 5, 2009 at 7:00 PM, hadley wickham wrote: > On Mon, Oct 5, 2009 at 8:48 PM, Peter Cowan wrote: >> On Mon, Oct 5, 2009 at 5:44 PM, hadley wickham wrote: Now, as Seth already told, there are several functions in svUnit that ease interactive use of the tests in an R session. W

Re: [Rd] Characters vs. factors

2009-10-05 Thread David M Smith
On Mon, Oct 5, 2009 at 4:33 PM, hadley wickham wrote: > It seems like a recent trend in R has been to make character vectors > and factors almost equivalent (apart from the way that factors always > remember their original range). There are a few exceptions: A related issue is that modeling func

Re: [Rd] R's --enable-threads does nothing?; gdb needs -lpthread

2009-10-05 Thread Prof Brian Ripley
On Mon, 5 Oct 2009, Andrew Piskorski wrote: In the R-2-9-branch (svn revision 49914, 2009-09-24), R's configure script has an "--enable-threads" option. But, does it do anything useful? When I use "--enable-threads=posix", some of the configure output changes slightly, but it seems to have no