Re: [Rd] S4: what to put in initialize, validity and constructor?

2008-05-03 Thread Oleg Sklyar
[EMAIL PROTECTED] wrote: Do not change initialize! As I sat, this is a toy example. In my real example, initialize does a lot of things like calculation of quality indice (b is not the scare of a, but B1, B2 and B3 are the the within matrix of A after imputation with 3 differents methods

[Rd] zero variance in part of a glm (PR#11355)

2008-05-03 Thread m . crawley
In this real example (below), all four of the replicates in one treatment combination had zero failures, and this produced a very high standard error in the summary.lm. =20 Just adding one failure to one of the replicates produced a well-behaved standard error. =20 I don't know if this is a bug, bu

[Rd] Using option na.rm=True in function SD does not work for matrix with complete columns of NAs (PR#11364)

2008-05-03 Thread m . tschiedel
Dear R-developers, =20 according to the "what's new"-section in version R 2.7.0, there has been = a change in the working of co[rv] and so also in sd and var. =20 I am afraid, that the use of function sd with option "na.rm=3DT" has not = been changed appropriately. So the following problem exists w

[Rd] Quartz doesn't display x-axis properly until a window resize (PR#11368)

2008-05-03 Thread luis . lopezoliveros
Full_Name: Luis Lopez-Oliveros Version: 2.7.0 OS: Mac OS X 10.5.2 Submission from: (NULL) (71.176.115.32) In R 2.7.0 for Mac OS X, Quartz plots are drawn a little bit off-screen. What happens is that the plots appear to be displayed a little below than where they should be in the Quartz window, c

Re: [Rd] zero variance in part of a glm (PR#11355)

2008-05-03 Thread Charles C. Berry
NOT a bug. The estimate of the probability of mi is precisely 1.0 for one cell in your setup. The information contributed by that cell has a factor of p*(1-p) in it, which works out to zero. The bad behavior of asymptotic methods for binary regressions in such settings is well known. H

[Rd] error with R-patched (2008-05-02 r45591)

2008-05-03 Thread Mark Kimpel
Just installed the latest R-patched and get the error seen at the end of the output below. Don't know what to make of this but thought I should report it. In general, when installing the latest version of R, should one use R-latest or R-patched? R-latest is stable, but one would assume that R-patch

Re: [Rd] error with R-patched (2008-05-02 r45591)

2008-05-03 Thread Prof Brian Ripley
On Sat, 3 May 2008, Mark Kimpel wrote: Just installed the latest R-patched and get the error seen at the end of the output below. Don't know what to make of this but thought I should report it. Nor do we. You have something incorrect in your startup files, but we don't have those. In gene

[Rd] texi2dvi instead of pdflatex in R2.7.0? and related bioc 2.2 builds

2008-05-03 Thread Oleg Sklyar
Dear lists: I am somewhat puzzled by the use of texi2dvi/pdflatex in R2.7.0. When building EBImage (bioconductor) with 2.7.0 I get the same error both in Windows and Linux, which reads the following: ** building package indices ... * DONE (EBImage) * creating vignettes ... ERROR /usr/bin/texi

[Rd] R CMD check: small tests suggestion

2008-05-03 Thread hadley wickham
It would be nice if R CMD check ran any file in the tests directory that has "one of the extensions .R, .S, .q, .r, or .s" - i.e. it should match the files processed in the R directory. Hadley -- http://had.co.nz/ __ R-devel@r-project.org mailing list

Re: [Rd] error with R-patched (2008-05-02 r45591)

2008-05-03 Thread Mark Kimpel
I have found the cause of the problem I am having with R-patched. In my .Rprofile I have a function that loads a bunch of my own functions, one of which contains the character "(R)". No other version of R I have used since writing this function ~2 yrs. ago has had a problem reading in this characte

Re: [Rd] R CMD check: small tests suggestion

2008-05-03 Thread Prof Brian Ripley
On Sat, 3 May 2008, hadley wickham wrote: It would be nice if R CMD check ran any file in the tests directory that has "one of the extensions .R, .S, .q, .r, or .s" - i.e. it should match the files processed in the R directory. Whereas what it is documented in 'Writing R Extensions' is to use

Re: [Rd] error with R-patched (2008-05-02 r45591)

2008-05-03 Thread Prof Brian Ripley
From the NEWS file for R-patchd: BUG FIXES o The parser sometimes accepted invalid quoted strings in a UTF-8 locale. This is likely to be the issue, but we still don't have a reproducible example (see the posting guide). On Sat, 3 May 2008, Mark Kimpel wrote: I have found t