Re: [Rd] Standalone Mathlib, C++ and ISNAN()

2005-01-08 Thread Thomas Lumley
On Sun, 9 Jan 2005, Bill Northcott wrote: Does this mean the changes will be in the current daily builds? I presume the function involved is now in the standalone Rmath build. The function is available for the standalone Rmath library and also linking to R. I'm not sure when the daily snapshot ge

Re: [Rd] p.adjust(s), was "Re: [BioC] limma and p-values"

2005-01-08 Thread Gordon Smyth
Martin, Thanks for this. I was planning to code suggestions for p.adjust() myself today, but you got in before me. I don't think that the new way of handling NAs is quite correct. The trouble is that all of the adjustment methods other than "none" and "bonferonni" are step-down or step-up met

Re: [Rd] Standalone Mathlib, C++ and ISNAN()

2005-01-08 Thread Bill Northcott
On 09/01/2005, at 9:11 AM, Thomas Lumley wrote: The C++ math header undefines isnan, so if isnan is a macro, ISNAN() will not work in C++ code. C99 specifies that isnan is a macro, but in C90 compilers, where it is an extension, isnan is often a function (explaining why the issue didn't come up

[Rd] new("call") problem

2005-01-08 Thread McGehee, Robert
The below looks like the show method has trouble with the default call object (or that there is no default call object). Not sure if this is a bug, design problem, or a difficulty on my part using and extending the call class, but it has caused difficulty for when I want to extend the call class in

Re: [Rd] Standalone Mathlib, C++ and ISNAN()

2005-01-08 Thread Thomas Lumley
A review: The C++ math header undefines isnan, so if isnan is a macro, ISNAN() will not work in C++ code. C99 specifies that isnan is a macro, but in C90 compilers, where it is an extension, isnan is often a function (explaining why the issue didn't come up earlier). For example, isnan is a mac

Re: [Rd] Documentation bug (PR#7483)

2005-01-08 Thread ripley
http://cran.r-project.org is not part of R per se and has its own bug reporting address, [EMAIL PROTECTED] That file was made with makeinfo 4.6, and it is a bug in that version of makeinfo. It is not a problem in the version distributed with R for Windows, for example, made with the current ma

[Rd] Documentation bug (PR#7483)

2005-01-08 Thread tac
Full_Name: Terry A. Cox Version: 2.0.1 OS: Mac OS X Submission from: (NULL) (138.88.250.18) In the file, http://cran.r-project.org/doc/manuals/R-exts.html, several of the headers have incorrect closing tags, e.g., The DESCRIPTION file This creates a problem in standards-compliant web browser

Re: [Rd] p.adjust(s), was "Re: [BioC] limma and p-values"

2005-01-08 Thread Martin Maechler
I've thought more and made experiements with R code versions and just now committed a new version of p.adjust() to R-devel --> https://svn.r-project.org/R/trunk/src/library/stats/R/p.adjust.R which does sensible NA handling by default and *additionally* has an "na.rm" argument (set to FALSE by d

[Rd] Re: [R] Compilation of R code

2005-01-08 Thread Marc Schwartz
On Sat, 2005-01-08 at 07:33 +, Prof Brian Ripley wrote: > On Fri, 7 Jan 2005, Marc Schwartz wrote: > > > On Fri, 2005-01-07 at 16:00 -0800, Sameul M Mwalili wrote: > >> Dear ALL, > >> In order to install the Rice R to C compiler (RCC) you need to patch > >> the R source code. However, the patc

[Rd] p.adjust(s), was "Re: [BioC] limma and p-values"

2005-01-08 Thread Martin Maechler
> "GS" == Gordon K Smyth <[EMAIL PROTECTED]> > on Sat, 8 Jan 2005 01:11:30 +1100 (EST) writes: <.> GS> p.adjust() unfortunately gives incorrect results when GS> 'p' includes NAs. The results from topTable are GS> correct. topTable() takes care to remo

[Rd] cmdscale problem

2005-01-08 Thread Christian Kleiber
Dear R developers, there appears to be a small problem with function cmdscale: for non-Euclidean distance matrices, using option add=FALSE (the default), cmdscale misses the smallest eigenvalue. This affects GOF statistic g.1 (See Mardia, Kent + Bibby (1979): Multivariate Analysis, eq. (14.4.7).

Re: [Rd] as.data.frame.table and the name "Freq"

2005-01-08 Thread Prof Brian Ripley
No sooner said that done. It _is_ nice to see code with a suggested enhancement. On Sat, 8 Jan 2005 [EMAIL PROTECTED] wrote: May I suggest that the method as.data.frame.table not have the name "Freq" hardwired as the response name? This is a problem if "Freq" is already the name of a stimulus fact