similar to: understanding dump.frames; typo;

Dear all, As the object of this mail suggests, the methods package is not loaded by default in R2.13 when using Rscript whereas it is loaded when using an interactive session. An example with the metafor package : library(metafor) example(addpoly.rma) this works in an interaction R shell, but put it in a .R file and use it with Rscript, it won't work until you added library(methods)

Dear List, I'm having trouble running a .bat file which calls an R-Script via the command line (using "Rscript"). I put the following line in a file called "test.bat": Rscript --vanilla test.R Then I tried to launch "test.bat" via Windows' CMD (I plan to make this a scheduled Windows task). The actual R-script ("test.R") is executed just fine

Dear R-Experts, I seem to be dealing with a so called "headless" problem in R. I wrote a quite extensive program that generates a Bayesian network from a query protein's Phylogenetic Tree and subsequently uses a message passing algorithm to infer the most likely annotation for the query leaf in the tree using the other leaves known -and proven- protein function annotations. The

Rscript eats up the last argument when reporting the command it runs: $ Rscript --verbose "/tmp/test.R" one two three running '/usr/local/lib/R-devel/lib/R/bin/R --slave --no-restore --file=/tmp/test.R --args one two' With the patch below, I get the following: $ Rscript --verbose "/tmp/test.R" one two three running '/usr/local/lib/R-devel/lib/R/bin/R --slave

All, I'd like to automatically output text from R to HTML. In doing this I've run into trouble with non-ascii characters, as my browser (and presumably others) does not render such characters correctly. For example, the 'fancy' single quotes associated with summary.lm are multi-byte characters on my platform. This particular problem is solved by options(useFancyQuotes=FALSE).

Hi, I'm trying to create a package that contains reference class definitions from which users can create reference objects, but there seems to be something awry. My toy example creates an empty package via package.skeleton('TestClass') to which I add the following R code: TestClass <- setRefClass('TestClass',fields=c('name')) Unfortunately my R console output

I've been trying to get some code to run on a 64-bit FreeBSD machine running R : Copyright 2006, The R Foundation for Statistical Computing Version 2.3.0 (2006-04-24) ISBN 3-900051-07-0 and keep getting a core dump with the following results: *** caught segfault *** address 0x0, cause 'unknown' Traceback: 1: .Call("R_point_in_polygon_sp", as.numeric(point.x),

>>>>> nospam at altfeld-im de <nospam at altfeld-im.de> >>>>> on Sun, 13 Nov 2016 13:11:38 +0100 writes: > Dear R friends, to allow post-mortem debugging In my > Rscript based batch jobs I use > tryCatch( <R expression>, error = function(e) { > dump.frames(to.file = TRUE) }) > to write the called frames into a

Hello. I am having a problem directing the results of xYplot in the Hmisc package to a file. First I'll give you my sessionInfo and then my data and code, afterwhich I'll describe my problem. > sessionInfo() R version 2.4.1 Patched (2007-02-26 r40806) i686-pc-linux-gnu locale:

Dear Luke and others, I have many R versions on my machine and want to start a particular one when snow builds its cluster. (The same version I start snow from.) It seems that everything is set up correctly in defaultClusterOptions: > mget(ls(defaultClusterOptions), defaultClusterOptions) $homogeneous [1] TRUE $manual [1] FALSE $master nodename "maya.unil.ch" $outfile [1]

Dear R, Usually when I want to read pdf help for R functions under Linux, I do the following steps > help("par",help_type="pdf") > system(paste(getOption("pdfviewer"),"par.pdf")) which works well. First question, can I let "help" to save the pdf file to a different place other than current working directory? Now I want to write a small

/Hello. SUMMARY: $ BOOM=$'\xFF' LC_ALL=en_US.UTF-8 Rscript --vanilla -e "Sys.getenv()" Error in substring(x, m + 1L) : invalid multibyte string at '<ff>' $ BOOM=$'\xFF' LC_ALL=en_US.UTF-8 Rscript --vanilla -e "Sys.getenv('BOOM')" [1] "\xff" BACKGROUND: I launch R through an Son of Grid Engine (SGE) scheduler, where the R

> From: Abhijit Dasgupta <adasgupta@araastat.com> > Date: October 31, 2010 1:30:02 AM EDT > To: Matt Shotwell <shotwelm@musc.edu> > Subject: Re: [R] ForestPlot or similar > > I just did something very similar using ggplot's pointrange geom. In the following, I'm plotting hazard ratios, for which the nominal value is 1 and not 0. x has 5 columns: drug, hr,

Dear R friends, to allow post-mortem debugging In my Rscript based batch jobs I use tryCatch( <R expression>, error = function(e) { dump.frames(to.file = TRUE) }) to write the called frames into a dump file. This is similar to the method recommended in the "Writing R extensions" manual in section 4.2 Debugging R code (page 96):

Dear all I've just tried the brand new 'grdevice' option in Sweave but couldn't make it work. When I declare \SweaveOpts{grdevice=pdf} or \SweaveOpts{grdevice=cairo_pdf} trying to plot something simple <<fig=T, echo=T>>= plot(1:10,1:10,main='Some title') @ would result in an Sweave error: 18:16:47.299: 1 : term verbatim 18:16:47.308: 2 : echo term verbatim

I have had the following problem with R 2.10, 2.13.1, and 2.13.2, running on Ubuntu linux 10.04, xubuntu 11.10, and a version of Redhat (I think 5). rnorm.sobol is producing impossible random values, and occasionally the routine crashes. Here are samples of the output and the crash message. library(fOptions) Zs <- rnorm.sobol(50, dimension=1) produces this: [,1] [1,]

Hi, I was wondering if someone in the mailing list has any insight into this segfault error that I consistently find when running a script containing heatmap() in R 2.8.1 and 2.8.0 on a Linux 64-bit machine. Some points: 1. This occurs when running heatmap(). 2. Interestingly, if I source() the script or copy and paste the script in its entirety, this error occurs. However, if I run the

>>>>> nospam at altfeld-im de <nospam at altfeld-im.de> >>>>> on Tue, 15 Nov 2016 01:15:46 +0100 writes: > Martin, thanks for the good news and sorry for wasting your (and others > time) by not doing my homework and query bugzilla first (lesson learned! > ). > > I have tested the new implementation from R-devel and observe a semantic >

Hi all, I found that the two different versions of "survival" packages, namely 2.36-5 vs. 2.36-8 or later, give different results for coxph function. Please see below and the data is attached. The second one was done on Linux, but Windows gave the same results. Could you please let me know which one I should trust? Thanks, ...Tao #####============================ R2.13.0,

>From "Writing R Extensions": "Only ASCII characters (and the control characters tab, formfeed, LF and CR) should be used in code files." So I am afraid you cannot use ?m. Gabor On Mon, Feb 18, 2019 at 3:36 PM I?aki Ucar <iucar at fedoraproject.org> wrote: > > Hi, > > We found a (to our eyes) strange behaviour that might be a bug. First > a little