similar to: ESS does not recognize installed libraries

Hello. By way of background, I am running out of memory when attempting to normalize the data from 160 affymetrix microarrays using justRMA (from the affy package). This is despite making 6 gigabytes of swap space available on our sgi irix machine (which has 2 gigabytes of ram). I have seen in various discussions statements such as "you will need at least 6 gigabytes of memory to normalize

Basically, the `Detail' section of ?tune says it all: Details: As performance measure, the classification error is used for classification, and the mean squared error for regression. ... Andy > From: Tae-Hoon Chung > > Hi, all; > > Basically, the subject contains the all information I need to know. > In e1071 library, there are functions to tune parameters.

Hi, all; Our group is planning to develop a web-based analysis package with R. I have some questions. (1) Can we use R as a daemon-like way such that, after invoking R and making it run in a kind of background mode, just put some R script into R using some pipe-like mechanism and retrieve the result out of it? (2) If this is possible, then how can we do it? If this is not possible, then what

Hi, all; I got an unusual error while using mclust library 2.1-7 on R 2.0.1. When I tried to run Mclust(rnorm(100)), I got segmentation fault error. Does anyone know what causes this problem? I came across the same problem even when I tried to run the example shown in Mclust help using iris data. Thanks in advance, Tae-Hoon Chung -------------------------------------------------- Tae-Hoon Chung

Hi, All; I have a question. In R, what is the best way to make R idle for a while and try something again later? For example, suppose there is an R job which accesses a file that may be shared with other active jobs. So when the file is being accessed by other job, your job will not be able to access the file and your job will crash because of that. To avoid this, you want your job to try to

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Hi, All; When I generate a "special" paper postscript image larger than "a4" or "letter" using R, I can only see one-page portion of all image, of course. What will be the simple solution for this? Is there any way I can set the bounding box information on the image? Or any other suggestions? Thanks in advance; Tae-Hoon Chung

Hi, All; Suppose I have a class 'dat' such that setClass('dat', representation (.version='character', x='numeric', y='numeric')). If I want to make a method that changes the .version slot of 'dat' class in a way like set.version(d) <- '0.2' when d is an object of 'dat' class, how can I do this? Thanks in advance. Tae-Hoon

Is there any requirement for TclTk support for R? When I tried to call the tcltk library, it failed with the following message: > library(tcltk) Error in firstlib(which.lib.loc, package) : Tcl/Tk support is not available on this system Error in library(tcltk) : .First.lib failed for 'tcltk' The system information is as follows: Linux osirus.tgen.org 2.6.9-42.0.10.ELsmp #1

Happy new year to all; A few days ago, I posted similar problem. At that time, I found out that our R program had been 32-bit compiled, not 64-bit compiled. So the R program has been re-installed in 64-bit and run the same job, reading in 150 Affymetrix U133A v2 CEL files and perform dChip processing. However, the memory problem happened again. Since the amount of physical memory is 64GB, I think

Hi, All; I tried to use library mclust in 64-bit compiled R 2.0.1 but failed. Installation went smoothly without any warning or error. However, when I tried to use them with the following simple code, it crashed. Library(mclust) Dat <- c(rnorm(20, mean=0, sd=0.2), rnorm(30, mean=1, sd=0.2)) Ind <- Mclust(dat, 1, 5)$classification cbind(Dat, Ind) The error message was:

I'm trying to select a subset of a dataframe while dropping some factors. While the dataset gets smaller all Factor levels remain and I need to get rid of them. Strangely enough, I am almost certain that the same code on the same data worked OK earlier today - and it is not the first time that I'm not able to replicate earlier results with this command (I know, I might just be going

Hi, all; I know there has been a lot of discussions on memory usage in R. However, I have some odd situation here. Basically, I have a rare opportunity to run R in a system with 64GB memory without any limit on memory usage for any person or process. However, I encountered the memory problem error message like this: Error: cannot allocate vector of size 594075 Kb I got this error message while

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Running R2.4.0 on Apple Mac OS X 10.4.8, in Emacs ESS mode, and also R.app. In an attempt to learn a bit more about a particular method (geneNames in package affy) I invoked getMethods("geneNames") which produced geneNames methods, but not the one in affy (output below). I had to know the signature (AffyBatch) in order to find the method > getMethod("geneNames",

I have run into a problem loading a just saved R object using R-devel. I have been saving and loading this particular type of R object for a long while and never ran into this problem. I save, then immediately reload (to test save) and get "ReadItem: unnknown type 65". This error is reproducible after logout from server and restart of emacs and R. Below is my output and

I have run into a problem loading a just saved R object using R-devel. I have been saving and loading this particular type of R object for a long while and never ran into this problem. I save, then immediately reload (to test save) and get "ReadItem: unnknown type 65". This error is reproducible after logout from server and restart of emacs and R. Below is my output and

I am getting the following error in my script. I am very very new to R and have obtained this script from another person. #read file in (dummy data) starburst.plot<-function(affy.fold, affy.FDR)(ifelse( ((affy.fold) >=0), -1*log10(affy.FDR), 1*log10(affy.FDR))) starburst.plot<-function(meth.fold, meth.FDR)(ifelse( ((meth.fold) >=0), -1*log10(meth.FDR), 1*log10(affy.FDR))) At my next

Hello, I am trying to install affy package in R as follow: >R CMD INSTALL -l lib ~/rstuffs/affy_1.4.32.tar.gz Then I get an error at the end: Warning message: There is no package called 'Biobase' in: library(package, character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts, [1] "ProgressBarText" [1]

Hi, I decided to upgrade to 1.8 today... :-) Anyway, we are writing our own package that is dependent on a bioconductor library - 'affy'. I've checked and when I fire up R, library(affy) behaves as expected... so it all seems to be installed and OK... In the DESCRIPTION file in my package source I have the line: Depends: affy When I run R CMD check simpleaffy I get to: ... *