r-devel@r-project.org discussions for October 2008

24	[Rd] why is \alias{anRpackage} not mandatory?

Dear R developers, if one uses package.skeleton() to create a new package, then a file anRpackage.Rd with the following entries is prepared: \name{anRpackage-package} \alias{anRpackage-package} ...

Thomas Petzoldt
Oct 6, 2008 at 9:46 am
Oct 10, 2008 at 6:26 am

14	[Rd] R 2.8.0 qqnorm produces error with object of class zoo?

Dear list-reader, by running the following script: library(zoo) sessionInfo() search() packageDescription("zoo") data(EuStockMarkets) dax <- as.zoo(EuStockMarkets[1:10, "DAX"]) daxr <- diff(log(dax)) ...

Pfaff, Bernhard Dr.
Oct 22, 2008 at 10:36 am
Nov 3, 2008 at 2:08 pm

11	[Rd] * buffer overflow detected *: /usr/lib64/R/bin/exec/R terminated on R 2.6.2 to 2.8.0: logging a bug?

Dear friends, there is a serious problem with RODBC on R from 2.6.2 to 2.8.0 on a postgresql 8.3 database. Let's say we define an empty dsn called "test", with user "postgres" and password "none". We ...

Corrado
Oct 31, 2008 at 11:17 am
Nov 7, 2008 at 11:32 am

10	[Rd] dos-style line endings in .Rbuildignore result in files not being excluded

I was trying, on a Linux system, to get a .Rbuildignore file to work. After far too long, I found the problem was the <CR <NL line endings in the .Rbuildignore file -- I had originally created it on ...

Tony Plate
Oct 14, 2008 at 5:10 am
Oct 16, 2008 at 4:54 am

7	[Rd] [R-sig-Debian] problem with update.packages (PR#13161)

Confirmed in plain R using the same package built this morning from last night's tarball from Denmark: Running update.packages() yields: --- Please select a CRAN mirror for use in this session --- ...

Edd
Oct 14, 2008 at 12:40 am
Oct 14, 2008 at 12:40 pm

6	[Rd] conditionally import a namespace?

Dear R-devel, I have a problem defining the dependencies for a package. My package (latticist, not yet released) "Suggests" RGtk2, but specifically does not require it. If RGtk2 is available, the ...

Felix Andrews
Oct 30, 2008 at 6:40 am
Oct 31, 2008 at 7:09 am

6	[Rd] RFC: Kerning, postscript() and pdf()

Ei-ji Nakama has pointed out (from another Japanese user, I believe) that postscript() and pdf() have not been handling kerning correctly, and this is a request for opinions about how we should ...

Prof Brian Ripley
Oct 12, 2008 at 3:36 pm
Oct 17, 2008 at 11:38 am

6	[Rd] relative path to source files in vignette

Hi, this may be slightly off-topic, but as you are the experts: we have written a small vignette, in which we want to refer to .R, .Rd source files by means of relative paths. More specifically, we ...

Peter Ruckdeschel
Oct 10, 2008 at 6:19 pm
Oct 14, 2008 at 4:03 pm

6	[Rd] Attributes of top level environments clobbered (was Re: [R] possible bug in function 'var' in R 2.7.2?)

The bug discussed in the following year-old post suggested that the problem of clobbering attributes of top level environment objects would be fixed for 2.7 but its still in R version 2.7.2 ...

Gabor Grothendieck
Oct 3, 2008 at 3:08 pm
Oct 4, 2008 at 3:58 pm

5	[Rd] Problems with Sweave and pdf.options(encoding="ISOLatin7") (PR#13234)

Hi, Sweave for some reason does not respect encoding setting in pdf.options. Everything is OK with ps.options. Thus when using non-default encoding for graphs, resulting graphics eps file is correct, ...

Zemlys
Oct 31, 2008 at 9:35 am
Nov 19, 2008 at 6:33 pm

5	[Rd] Dynamic linking to binary code from other packages??

Dear R-devel, I am writing a package that needs some C++ functions from an external SDK (Affymetrix fusion). The same functions are already compiled into another package (affxparser). Can I ...

Charles Danko
Oct 25, 2008 at 8:05 pm
Nov 13, 2008 at 7:42 pm

4	[Rd] gfortran optimization problems

Colleagues, I have a routine in package labdsv that calls a FORTRAN subroutine. Recently, I was informed that it sometimes gives different results on a PC and Mac, and that the PC version is clearly ...

Dave Roberts
Oct 24, 2008 at 10:53 pm
Nov 13, 2008 at 6:35 pm

4	[Rd] Can't open files containing russian letters in path (PR#13195)

Full_Name: Arkady Sherman Version: 2.8.0 OS: Windows XP sp3 ntfs file system Submission from: (NULL) (158.195.166.129) Freshly installed version 2.7.2 works well, but 2.8.0 can't open files with ...

Asherman
Oct 22, 2008 at 9:10 pm
Nov 4, 2008 at 5:48 pm

4	[Rd] using yscrollcommand in tkcanvas crashes R (PR#13231)

Full_Name: Sundar Dorai-Raj Version: 2.8.0 OS: Windows Submission from: (NULL) (76.220.41.126) The following code crashes R: library(tcltk) tt <- tktoplevel() tc <- tkcanvas(tt, yscrollcommand = ...

Sundar Dorai-Raj
Oct 30, 2008 at 5:10 am
Oct 30, 2008 at 7:59 pm

4	[Rd] writting null (\000 or ^@) to an external text file without the new warning

I have some functions that write an external text file for postprocessing by another program. Some instructions to the other program need to be indicated by null values (\000 or ^@). The function ...

Greg Snow
Oct 28, 2008 at 6:23 pm
Oct 28, 2008 at 10:09 pm

4	[Rd] Errors in R CMD check for R 2.8.0

useR's, I get these 2 errors when I run "R CMD check" on my package, and I cannot figure out how to get around them. Does anyone have any ideas? If it is of any help, I use Windows XP. ... * checking ...

Dxc13
Oct 24, 2008 at 1:52 pm
Oct 28, 2008 at 11:12 am

4	[Rd] 0 ^ NaN == Inf, why?

In R, 0 ^ NaN yields Inf. I would have expected NaN or perhaps 0. Is this behaviour intended? R version 2.8.0 (2008-10-20) i386-pc-mingw32 locale: LC_COLLATE=English_United ...

Stephen Milborrow
Oct 25, 2008 at 2:59 pm
Oct 27, 2008 at 1:31 pm

4	[Rd] changed behaviour of 'get' in 2.8.0: request for unchange

There is an unannounced and non-backwards-compatible change to the behaviour of 'get' in R2.8.0. 'get'ting a missing value now causes an error, whereas hitherto it's just returned a "missing" ...

Mark Bravington
Oct 24, 2008 at 3:07 am
Oct 26, 2008 at 7:38 pm

4	[Rd] normalizePath bug (PR#13199)

Full_Name: Joseph Haykov Version: 2.8.0 OS: Windows Submission from: (NULL) (216.189.177.202) normalizePath("C:\\DOCUME~1\\JOSEPH~1\\LOCALS~1\\Temp\\RtmpolZ4Vy\\file72ae2cd6.txt") returns ...

Joe
Oct 23, 2008 at 2:45 pm
Oct 23, 2008 at 6:32 pm

4	[Rd] Possible GPL Violation

Hi All, I was cruising around today, and came across a company (ZumaStat) that adds additional statistics functionality to SPSS. http://www.zumastat.com/robust_statistics.htm "ZumaStat provides a ...

Ian Fellows
Oct 22, 2008 at 8:48 pm
Oct 22, 2008 at 10:48 pm

4	[Rd] splinefun gives incorrect derivs when extrapolating to the left (PR#13132)

This is a low priority bug that has been around for a while, but I came across it again while alpha testing 2.8. The resulting function for splinefun gives incorrect deriv values when x is less than ...

Greg Snow
Oct 6, 2008 at 5:50 pm
Oct 12, 2008 at 12:19 pm

3	[Rd] 2.8.0 release bugs (PR#13210)

Dear colleagues, Using the last release 2.8.0 I had (for the first time since working with R) the difficulties in transmission of some Central European letters (��) from R editor to the console ...

Janek Musek
Oct 27, 2008 at 7:30 pm
Nov 6, 2008 at 3:39 pm

3	[Rd] A question about the API mkchar()

Hi guys, I've got a question about the API mkchar(). I have met some difficulty in parsing utf-8 string to mkchar() in R-2.7.0. I was intending to parse an utf-8 string str_jan (some Japanese ...

Fán Lóng
Oct 28, 2008 at 10:26 am
Nov 3, 2008 at 9:07 pm

3	[Rd] Wrong behavior of lines.survfit for conf.int="only" (PR#13180)

I downloaded the source for survival and I think I found the bug. I have not tried to build the package with this change to test it, but just defining the function with this change seems to work. The ...

Diggsb
Oct 20, 2008 at 3:55 pm
Oct 20, 2008 at 6:02 pm

3	[Rd] solve cdf for noncentrality (PR#11527)

Full_Name: Jerry W. Lewis Version: 2.7.0 OS: Windows XP Professional Submission from: (NULL) (198.180.131.16) If you are saying that there is no need to solve for the noncentrality parameter, please ...

Jerry Lewis
Oct 9, 2008 at 5:20 pm
Oct 14, 2008 at 1:50 pm

3	[Rd] Thin spaces

Hi all, I'm looking at providing some nicer number formatting features for axes in ggplot2. One thing I would like to do is use thin spaces to separate digits, like you can in latex. I realise I can ...

Hadley wickham
Oct 12, 2008 at 2:24 am
Oct 12, 2008 at 2:43 pm

3	[Rd] Can DESCRIPTION Maintainer: field contain general URL instead of only email address?

Our firm would like to route support requests through a website instead of using email. However R will refuse to install a package if DESCRIPTION's Maintainer field does not have a valid email adress ...

William Dunlap
Oct 3, 2008 at 6:01 pm
Oct 3, 2008 at 9:49 pm

3	[Rd] R CMD install runs out of memory

$ R CMD install ggplot2 ... scale-usage-d1 text html latex scale_brewer text html latex example perl(90227) malloc: *** mmap(size14880000) failed (error code) *** error: can't allocate region *** ...

Hadley wickham
Oct 3, 2008 at 2:14 pm
Oct 3, 2008 at 3:59 pm

2	[Rd] problems installing rJava with R-2.8.0

Dear R-developers, I am having trouble installing rJava on R 2.8.0 / debian etch. What goes wrong? I am happy for every advice. Best, Christian Warning in install.packages("rJava") : argument 'lib' ...

Christian Kohler
Oct 29, 2008 at 3:51 pm
Nov 9, 2008 at 7:35 pm

2	[Rd] Small modification of zip.file.extract in utils?

Dear list, I needed to extract a zip-archive, and found zip.file.extract in utils. My only problem was the use of tempdir(), since I wanted to permanently extract the archive at a fixed location for ...

Jon Olav Skoien
Oct 30, 2008 at 7:08 pm
Nov 1, 2008 at 11:09 am

2	[Rd] R books: self-serving question

thought someone here might know: how would I go about nominating my book (Ecological Models and Data in R, Princeton University Press 2008) for inclusion in the R books page ... ? I can supply ...

Ben Bolker
Oct 29, 2008 at 10:09 pm
Oct 30, 2008 at 1:28 am

2	[Rd] S4 object does not commute? (PR#13209)

Hello all, It appears that for the simplest of S4 objects, z+1 does not equal 1+z. Presumably this is a bug, as 1+z seems to make a malformed object (at least malformed as an input to str). Thanks, ...

Robert McGehee
Oct 27, 2008 at 4:25 pm
Oct 28, 2008 at 3:50 pm

2	[Rd] HAVE_BZLIB_H not set

When building 2.8.0 this morning for Fedora, I noticed that it was building the included bzlib2 source and using it rather than the system bzip2 libraries and headers. I tracked down the reason to ...

Tom "spot" Callaway
Oct 26, 2008 at 4:02 pm
Oct 27, 2008 at 10:19 am

2	[Rd] write.csv(..., col.names = FALSE) (PR#13202)

Full_Name: Stefan Albrecht Version: 2.7.2 (and 2.8.0) OS: Windows NT Submission from: (NULL) (194.127.8.17) Dear R Debug-Team, in write.csv() it is not possible to set both row.names = FALSE, ...

Stefan Albrecht
Oct 24, 2008 at 12:30 pm
Oct 27, 2008 at 8:18 am

2	[Rd] unlist change the ordered type

Hi the list, unlist respect the all the atomic type except orderd (it change of ordered into factor) : ### integer class(unlist(list(1:5,1:3))) #[1] "integer" ### numeric class(unlist(list(1.2,3.5))) ...

Christophe Genolini
Oct 24, 2008 at 9:15 pm
Oct 26, 2008 at 6:35 pm

2	[Rd] Possible uninstall problem on windows.

I just uninstalled R 2.7.2 on Windows XP after having installed R 2.8.0 The uninstaller removed the String values HKEY_LOCAL_MACHINE\SOFTWARE\R-core\R\Current Version ...

Erich Neuwirth
Oct 26, 2008 at 1:50 pm
Oct 26, 2008 at 2:47 pm

2	[Rd] Getting the panel location of a xyplot matrix using a mouse click in a GDCanvas

Hi: I would like to find out the panel of a xyplot matrix where a mouse clicked. I know this functionality is already bundled in trellis.focus but I can't use it because I am coding a stand alone ...

Daniel Kornhauser
Oct 23, 2008 at 7:26 pm
Oct 24, 2008 at 4:58 pm

2	[Rd] R CMD INSTALL problem

Dear list members, I've run into a problem with R CMD INSTALL under Windows Vista and R 2.8.0: --------- snip ----------- C:\Users\John Fox\workspace c:\R\R-2.8.0\bin\R CMD INSTALL car installing to ...

John Fox
Oct 21, 2008 at 10:23 pm
Oct 22, 2008 at 12:21 am

2	[Rd] R CMD build on Vista

Hello, I have R 2.7.2 and RTools 2.8 on a vista pro computer. On my computer R CMD build changes the file names : all capital letters are transformed into lowercase letters (for instance the ...

Ollivier TARAMASCO
Oct 19, 2008 at 4:56 pm
Oct 20, 2008 at 1:37 pm

2	[Rd] Minor feature request: Let 'R CMD co*nfig' tell me where the INCLDIR is

On Debian / Ubuntu / ... we have [1] edd at ron:~ R CMD config --cppflags -I/usr/share/R/include edd at ron:~ but I seem to have no way to learn 'just' the /usr/share/R/include part from R CMD ...

Dirk Eddelbuettel
Oct 17, 2008 at 1:45 am
Oct 18, 2008 at 3:29 pm

2	[Rd] error installing gtools (PR#13168)

Full_Name: Ebi Hal Version: R-2.7.2-1 OS: Fedora core 9 Submission from: (NULL) (129.215.170.238) I tried to install gplots by running R install.packages("gplots") but the process failed while ...

Ebihallo
Oct 15, 2008 at 1:30 pm
Oct 15, 2008 at 5:50 pm

2	[Rd] defines in Rmath.h and R_NO_REMAP

Hi, I'm programming with R 2.7.2 and had some trouble including Rmath.h for its random variates generation routines: Although I define R_NO_REMAP (which works fine for Rinternals.h stuff), Rmath.h ...

Daniel Sabanés Bové
Oct 11, 2008 at 7:41 pm
Oct 13, 2008 at 12:09 pm

2	[Rd] match() (PR#13135)

Full_Name: Willa Chen Version: 2.7.2 OS: Window XP Submission from: (NULL) (128.122.182.70) The match function does not return value properly. See an example below. [1] 35

Wchen
Oct 6, 2008 at 10:05 pm
Oct 11, 2008 at 7:25 pm

2	[Rd] Installing ROracle in windows.. Pls help

I have installed R 2.7.2 in windows, now i am trying to install R oracle... I am using Oracle 10g. i have downloaded the Roracle 0.5-9 sources, and i am trying to compile it using Vc++, i found from ...

Rita. A
Oct 10, 2008 at 6:07 am
Oct 10, 2008 at 11:14 am

2	[Rd] A strange behaviour of file.path in Windows? (PR#13119)

Full_Name: Enrico Pegoraro Version: 2.7.2 OS: Windows (Vista or Xp PRO) Italian Submission from: (NULL) (87.4.189.202) If you send these lines of code: outdir="c:/pippo" ...

Pego Enrico
Oct 3, 2008 at 8:05 am
Oct 3, 2008 at 11:02 am

2	[Rd] Memory crash

Hello, I get a segfault when running glmmboot in my own package glmmML. Has happened many time before, but this time I get no hint of where in my C functions the error might be. I give the output ...

Göran Broström
Oct 3, 2008 at 9:32 am
Oct 3, 2008 at 10:52 am

1	[Rd] row.names(data.frame(matrixWithDimnames)) depends on first rowname being "" or not. (PR#13230)

Full_Name: Bill Dunlap Version: R version 2.9.0 Under development (unstable) (2008-10-29 r46795) OS: Linux Submission from: (NULL) (76.28.245.14) When data.frame() is given a matrix with rownames, ...

Wdunlap
Oct 30, 2008 at 4:00 am
Nov 3, 2008 at 12:41 pm

1	[Rd] [BUG] [PATCH] R-2.8.0 failes to build without X support due to a typo (PR#13233)

Full_Name: Andrew Version: 2.8.0 OS: Linux-2.6.x Submission from: (NULL) (78.107.248.171) R-2.8.0 failes to build without X support due to a typo in the source code. The following patch fixes this ...

Bircoph
Oct 31, 2008 at 12:10 am
Oct 31, 2008 at 9:48 am

1	[Rd] Fixing an only one coefficient in an ARIMA model

Good afternoon, I would like fitting an ARIMA model without the first coefficient. For example, I want to fit an AR(3) like this : y[t]=a[1]*y[t-1]+a[2]*y[t-2]+a[3]*y[t-3], where a[1]=0. How can I ...

Yohann MOREAU
Oct 28, 2008 at 1:10 pm
Oct 30, 2008 at 4:23 pm

1	[Rd] pairwise.wilcox.test for paired samples

Dear R Core, pairwise.wilcox.test does not handle "paired = TRUE" correctly; e.g. set.seed(13) x <- rnorm(20) g <- c(rep(1, 10), rep(2, 10)) wilcox.test(x ~ g)$p.value # 0.075 pairwise.wilcox.test(x, ...

Matthias Kohl
Oct 25, 2008 at 2:19 pm
Oct 25, 2008 at 5:32 pm

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