r-devel@r-project.org discussions for September 2004

10	[Rd] as(object,"list") as(object,"matrix") differences?

Hello! as(object,"list") and as(object,"matrix") behave quite differently if it comes to their attributes. I define two classes. One of them "contains" a "list" the other a "matrix" ...

Wolski
Sep 7, 2004 at 4:17 pm
Sep 10, 2004 at 7:08 pm

8	[Rd] argument srt for mtext(); was: [R] using text on the x axis ticks rather than numbers

[moved to R-devel] The discussions took place on R-devel, hence some people might not have noticed them. Indeed, I think it is possible to provide an srt command (e.g. in half a year for something ...

Uwe Ligges
Sep 8, 2004 at 8:48 am
Sep 8, 2004 at 4:57 pm

6	[Rd] Ordering of values returned by unique

Hi, Is the ordering of the values returned something on what I can rely on, a form of a standard, that a function called unique in R (in futher versions) will return the uniq elements in order of ...

Witold Eryk Wolski
Sep 29, 2004 at 5:17 pm
Sep 29, 2004 at 7:25 pm

6	[Rd] rw2000dev: problems with library(foreign)

I get the following Error in namespaceExport(ns, exports) : undefined exports: write.foreign Error in library(foreign) : package/namespace load failed for 'foreign' with rw2000dev as of (2004-09-17 ...

Kjetil Brinchmann Halvorsen
Sep 24, 2004 at 4:10 pm
Sep 24, 2004 at 8:21 pm

6	[Rd] Namespace problem

Now I try to add some C and Fortan code to my package, so the NAMESPACE file is useDynLib(eha) importFrom(survival, Surv) export(mlreg.fit, risksets) but I get ..... * checking R files for ...

Gb
Sep 19, 2004 at 6:51 pm
Sep 20, 2004 at 6:49 pm

6	[Rd] A couple of issues with colClasses/setAs

Consider this: $ cat test.dat 1 a 2 b Now, we want to read the 2nd column as a factor and ignore the first (since it's just a sequential ID). We can't just put "factor" among the colClasses (would ...

Peter Dalgaard
Sep 8, 2004 at 12:34 am
Sep 8, 2004 at 8:19 pm

5	[Rd] Re: [R] installing on alpha (tru64)

Alexa Dear Martin Maechler, I have tried installing today's Alexa version of R-2.0.0 and have exactly the same problem. I'm reverting to R-devel. Please *never* direct such topics to individuals ...

Martin Maechler
Sep 27, 2004 at 8:39 am
Oct 4, 2004 at 2:59 am

5	[Rd] R-2.0.0 Install problem for package bundle with inter-dependent n amespaces

I have a revised version of the gregmisc package, which I've converted into a package bundle each of which has a namespace: gplots, gmodels, gdata, gtoools. Of course, there are interdependencies ...

Warnes, Gregory R
Sep 17, 2004 at 8:18 pm
Sep 21, 2004 at 8:58 am

5	[Rd] cor() fails with big dataframe

Hello, I have a big dataframe with *NO* na's (9 columns, 293380 rows). # doing memory.limit(size = 1000000000) cor(x) #gives Error in cor(x) : missing observations in cov/cor In addition: Warning ...

Mayeul KAUFFMANN
Sep 16, 2004 at 1:23 am
Sep 16, 2004 at 2:39 pm

5	[Rd] Run up to R 2.0.0 for package maintainers

The major changes for R 2.0.0 are now in place, and we have provided a set of notes for package maintainers at http://developer.r-project.org/200update.txt on both changes needed and new ...

Prof Brian Ripley
Sep 7, 2004 at 10:01 am
Sep 9, 2004 at 7:33 pm

5	[Rd] having trouble building r-devel

Dear R-devel On my Windows 2000 machine, I can build R-patched but not R-devel (since at least 1/9/2004). An error message pops up during the execution of some R code during "make", as below. In ...

Mark Bravington
Sep 8, 2004 at 3:01 am
Sep 8, 2004 at 9:59 am

4	[Rd] Problem with _new_ if class "lm" in object representatio n.

Hi, But "any" rises some other problems well known from S3. One has "any" for "free" in S3. You don't need S4. . But I know how "if" polluted functions look like in S3. They are hard to understand ...

Witold Eryk Wolski
Sep 30, 2004 at 2:35 pm
Oct 11, 2004 at 10:36 am

4	[Rd] Problem with _new_ if class "lm" in object representation.

Hi! Consider this code. setClass("Ctest" ,representation( test="character" ,bla="character" ,mod="lm" ) ) new("Ctest",test="bla") #This produces an error. #Error in validObject(.Object) : Invalid ...

Wolski
Sep 29, 2004 at 7:20 pm
Sep 29, 2004 at 10:23 pm

4	[Rd] checking for _non-existing_ documentation entries.

Hi! I have renamed some functions and deleted others. I have noticed that R CMD check complains only about newly added functions, but documented non-anymore-existing functions seem not to matter. I ...

Wolski
Sep 16, 2004 at 2:23 pm
Sep 21, 2004 at 8:10 am

4	[Rd] Function some()

Dear R-devel list members, Probably not an opportune time for this, given the immanent release of 2.0.0, but I was just reminded (while preparing a lecture) of a function that I find useful and that ...

John Fox
Sep 17, 2004 at 7:10 pm
Sep 17, 2004 at 9:04 pm

4	[Rd] propogation of rounding error for t.tests with unequal sample sizes (PR#7225)

# users would benefit from a warning about the behavior in the # groups.unbalanced case below. A propogation of difference is the variance # calculation is leading to an apparently significant ...

Tucker
Sep 13, 2004 at 8:57 pm
Sep 13, 2004 at 10:49 pm

4	[Rd] package methods different behaviour R1.9.1 patched and R2.0.0

Wolski
Sep 7, 2004 at 9:48 am
Sep 7, 2004 at 7:41 pm

3	[Rd] bug in power.t.test( ) (PR#7245)

Full_Name: Mai Zhou Version: 1.9.1 OS: Win XP Professional Submission from: (NULL) (12.222.227.93) One-sample t test power calculation n = 25 delta = 0.1 sd = 1 sig.level = 1.1 power = 1.088311 ...

Mai
Sep 24, 2004 at 4:53 am
Sep 24, 2004 at 5:12 pm

3	[Rd] Cannot build cluster_1.9,6 under R 2.0.0 beta Sep 21

Doing the normal build process [1] for a first time with a R 2.0.0 snapshot -- the Sep 21 version I uploaded to Debian's 'experimental' section two days ago, ended in failure. The package in question ...

Dirk Eddelbuettel
Sep 24, 2004 at 2:58 am
Sep 24, 2004 at 11:36 am

3	[Rd] Compile error in 2004-09-21 R 1.9.1 Patched

Hi all, I just downloaded the latest R-patched tarball [Version 1.9.1 Patched (2004-09-21)] and ran into an error during compilation. This is on FC2 and the error is as follows: dounzip.c: In ...

Marc Schwartz
Sep 22, 2004 at 1:32 am
Sep 22, 2004 at 12:39 pm

3	[Rd] S4 methods and polymorophism

Hello R Power Users, There is a rather large introduction you may skip to go directly to my question about S4 classes. I am working on some toy code to help me get in through S4 classes. Doing this ...

Eric Lecoutre
Sep 22, 2004 at 10:21 am
Sep 22, 2004 at 11:20 am

3	[Rd] "Namespace dependencies not required" message

I'm still working to add namespace support to some of my packages. I've removed the 'Depends' line from the DESCRIPTION file, and created an appropriate NAMESPACE files. Strangely, whenever I use ...

Warnes, Gregory R
Sep 20, 2004 at 10:05 pm
Sep 21, 2004 at 3:59 pm

3	[Rd] Rcmd problems and questions, lazyloading

Hola! I got past the problems I asked about two days ago, thanks. No I am updating CRAN package asypow (the daily package check on CRAN gave warnings due to .Rd problems, fixed). Now it PASSED Rcmd ...

Kjetil Brinchmann Halvorsen
Sep 18, 2004 at 2:55 am
Sep 19, 2004 at 3:05 pm

3	[Rd] memory allocation questions

Dear R-devel This one seems a bit arcane for R-help. I very often use R to call routines written in Delphi (son of Pascal), doing "persistent" memory allocation within Delphi. That is, I start R and ...

Mark Bravington
Sep 14, 2004 at 1:38 am
Sep 15, 2004 at 12:47 am

3	[Rd] reorder [stats] and reorder.factor [lattice]

I also have a reorder.factor defined in the gregmisc package. It has a slighly different behavior. It allows - sorting the factor level names via 'mixedsort', which sorts mixed numeric/character ...

Warnes, Gregory R
Sep 3, 2004 at 6:36 pm
Sep 14, 2004 at 9:06 am

3	[Rd] Problem with mle in stats4 (R 1.9.1)

Hi! This is a repost of an earlier message (with a clearer example demonstrating the problem I ran into). If you run the mle example in stats4 library(stats4) x <- 0:10 y <- c(26, 17, 13, 12, 20, 5, ...

Daniel Hoppe
Sep 13, 2004 at 6:12 pm
Sep 14, 2004 at 1:13 am

3	[Rd] man page of hist points to truehist, which can't be viewed without loading a library?

rdevel from yesterday, also in 1.9.1 (Debian, -3). The man page of 'hist' (from the graphics package, obtained by "?hist") suggests 'truehist' under "see also", but 'truehist' isn't loaded by default ...

A.J. Rossini
Sep 9, 2004 at 8:07 pm
Sep 9, 2004 at 9:22 pm

3	[Rd] function "apply" and 3D arrays (PR#7221)

Full_Name: jarek tuszynski Version: 1.8.1 OS: windows 2000 Submission from: (NULL) (198.151.13.10) Example code: [,1] [,2] [,3] [1,] 1 1 1 [2,] 1 1 1 [3,] 1 1 1 [4,] 1 1 1 [5,] 1 1 1 [6,] 1 1 1 [7,] ...

Jaroslaw W Tuszynski
Sep 9, 2004 at 8:01 pm
Sep 9, 2004 at 8:33 pm

2	[Rd] problem with R CMD build (PR#7240)

Hello, This may not be a bug--but I'm not sure. I have R 1.91 installed on a machine that's running Windows XP. In Cygwin, when I attempt to use the "build" command it tells me that TMPDIR is set to ...

Sego
Sep 20, 2004 at 10:07 pm
Sep 20, 2004 at 11:37 pm

2	[Rd] Covergence FLAG in glm (PR#7235)

Full_Name: Daniel R Jeske Version: 1.8.1 OS: Windows 2000 Submission from: (NULL) (138.23.228.79) We have just noticed that when you use glm() it seems the logical output 'converged' is always TRUE ...

Daniel Jeske
Sep 18, 2004 at 4:10 am
Sep 18, 2004 at 4:54 pm

2	[Rd] R CMD INSTALL doesn't always clean up (PR#7230)

Full_Name: Eric van Gyzen Version: 1.9.1 OS: FreeBSD Submission from: (NULL) (152.3.22.120) In several cases, "R CMD INSTALL" doesn't remove its temporary directory. It should call "do_cleanup" ...

Vangyzen
Sep 15, 2004 at 7:51 pm
Sep 16, 2004 at 5:11 pm

2	[Rd] Bug in merge() in R-2.0.0 alpha

In some cases, merge() has a problem in R-2.0.0 alpha (2004-09-14): x <- structure(c("a", "b", "2", "0.2-26", "O", "O"), .Dim = c(2, 3), .Dimnames = list(c("1", "2"), c("P", "V", "2"))) y <- ...

Uwe Ligges
Sep 15, 2004 at 4:58 pm
Sep 16, 2004 at 7:50 am

2	[Rd] Rd syntax error detected in CRAN daily checks

Please forgive me if you already received this. I had an e-mail sending glitch this morning. http://cran.r-project.org/src/contrib/checkSummary.html reported an error in Design.trans.Rd * checking Rd ...

Frank E Harrell Jr
Sep 9, 2004 at 6:48 pm
Sep 9, 2004 at 7:34 pm

2	[Rd] Feil i websider (PR#7216)

Warnings about /metno/internweb/fouweb/htdocs/teknisk/verktoy/R/faq.html BAD LINK: http://stat.ethz.ch/R/manual/ BAD LINK: http://nlme.stat.wisc.edu/MEMSS/ BAD LINK: http://stats.mth.uea.ac.uk/Rcgi/ ...

SjekkAlderOgPeker
Sep 8, 2004 at 7:55 am
Sep 8, 2004 at 12:11 pm

2	[Rd] First testing of R-2.0.0 alpha on Gentoo Linux

I just got R-2.0.0 alpha running on my Gentoo Linux system. The only issue I had was that if I do "--with-lapack" in the "configure", "make check" fails very early. Once I removed that option, "make ...

M. Edward Borasky
Sep 7, 2004 at 1:23 am
Sep 7, 2004 at 9:14 am

2	[Rd] Glitch involving difftime and data frame

Error in as.data.frame.default(x[[i]], optional = TRUE) : can't coerce difftime into a data.frame Error in as.data.frame.default(x[[i]], optional = TRUE) : can't coerce difftime into a data.frame ...

Peter Dalgaard
Sep 7, 2004 at 12:17 am
Sep 7, 2004 at 12:54 am

2	[Rd] sunspot data in R 2.0.0

I noticed this in the NEWS: o Datasets 'sunspot.month' and 'sunspot.year' are available separately but not via data(sunspot) (which is used by package lattice to retrieve a dataset 'sunspot'). Now, ...

Deepayan Sarkar
Sep 1, 2004 at 5:18 pm
Sep 1, 2004 at 6:37 pm

1	[Rd] Documentation: Reference Index (.pdf) -- setOldClass (PR#7254)

Apologies for cross postings or manual work caused by resending; the intially sent bug report through the web-interface bounced, however. Full_Name: Bernhard Pfaff Version: 1.9.1 OS: Windows NT ...

Pfaff, Bernhard
Sep 30, 2004 at 12:33 pm
Oct 1, 2004 at 3:55 pm

1	[Rd] fatal error: unable to restor saved data . Rdata (PR#7253)

Full_Name: Yfke Ongena Version: Aqua GUI for R 1.9.1 OS: MAC OS 10.3.5 Submission from: (NULL) (130.37.168.69) R was succesfully installed and worked fine, however, after I closed the session and ...

YP Ongena
Sep 28, 2004 at 11:42 am
Sep 28, 2004 at 11:58 am

1	[Rd] algorithm reference for sample() - Knuth

Thank you for the reference to Knuth. Indeed in vol. 2 he has a

Vadim Ogranovich
Sep 24, 2004 at 11:17 pm
Sep 24, 2004 at 11:36 pm

1	[Rd] algorithm reference for sample()

Hi, Don't know if it belongs to r-devel or r-help, but since I am planning to alter some of R's internal code I am sending it here. The existing implementation of the sample() function, when the ...

Vadim Ogranovich
Sep 24, 2004 at 2:48 am
Sep 24, 2004 at 10:02 am

1	[Rd] browser() is called incidentally (?) somewhere from inside methods::as

Hi, Executing the following code causes the prompt to enter browser() mode. Called from: as(Npatrick1, "list") Browse[1] R : Copyright 2004, The R Foundation for Statistical Computing Version 2.0.0 ...

Wolski
Sep 23, 2004 at 8:00 pm
Sep 24, 2004 at 9:08 am

1	[Rd] noncentrality paramter in power.anova.test (PR#7244)

Full_Name: Version: 1.9.0 OS: Windows XP Submission from: (NULL) (134.126.93.191) I believe the noncentrality parameter, lambda, in power.anova.test is incorrect. The noncentrality paramter is ...

Meyerjp
Sep 23, 2004 at 9:27 pm
Sep 23, 2004 at 10:03 pm

1	[Rd] Rgraphviz compilation error

Hi, I am installing Rgraphviz at Linux Fedora Core 2 with 32 bit AMD athlon with 512 RAM. I have installed graphviz version: graphviz-1.16-1.src.rpm installed already on system. I am doing: $ R CMD ...

Saurin Jani
Sep 22, 2004 at 10:11 pm
Sep 23, 2004 at 6:34 pm

1	[Rd] attaching to position 1

If an attempt is made to attach to position 1, it appears to work (not even a warning) but in fact it doesn't work as many would expect. "search" thinks that it gets placed in position 2, but nothing ...

Patrick Burns
Sep 22, 2004 at 7:30 pm
Sep 23, 2004 at 9:54 am

1	[Rd] Re: R-devel Digest, Vol 19, Issue 20

I met several problems in using R, and I can not find the 5 I used the Tools to create a package in windows, but it seems in the last step, zip command does not work? Is there any good reference ...

Shaogang Qu
Sep 22, 2004 at 4:04 pm
Sep 23, 2004 at 8:11 am

1	[Rd] problem typcasting return of R_ExternalPtrAddr(SEXP s)

In the odesolve routine lsoda(), I allow the function (named func) that calculates the system of differential equations to be defined in a dll that has been dynamically loaded from the file named in ...

Wsetzer
Sep 20, 2004 at 6:10 pm
Sep 20, 2004 at 6:55 pm

1	[Rd] NAMESPACE Warning

I'm trying to learn how to use namespaces, so I have created a small package with two functions. My NAMESPACE file is importFrom(survival, Surv) export(mlreg.fit, risksets) because 'mlreg.fit' uses ...

Gb
Sep 19, 2004 at 5:57 pm
Sep 19, 2004 at 6:03 pm

1	[Rd] R CMD check does not checks for superfluous documentation (PR#7231)

Hi! Due to package maintenance I have removed some functions but forgot to update the coresponding Rd files. If R CMD check is checking for missing documentation entries why it does not check for ...

Wolski
Sep 17, 2004 at 11:14 am
Sep 17, 2004 at 11:38 am

1	[Rd] Problems with Rcmd check in rw2000dev

Hola! I am doing some minimal changes on the package SenSrivastava to make it fit for R2.0.0 (This package passed Rcmd check on earlier versions of R, and are passing the CRAN daily checks!) I am ...

Kjetil Brinchmann Halvorsen
Sep 17, 2004 at 5:35 am
Sep 17, 2004 at 6:23 am

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