search for: jmacdon

...' or 'recommended' or 'defunct-base' must already be known to R. See the information on DESCRIPTION files in section 'Creating R packages' of the 'Writing R Extensions' manual. Execution halted ERROR: installing package DESCRIPTION failed ** Removing '/Users/jmacdon/R-devel/library/rcompgen' The downloaded packages are in /private/tmp/Rtmpb0Refs/downloaded_packages Updating HTML index of packages in '.Library' Warning message: In install.packages("rcompgen", type = "source") : installation of package 'rcompgen' had...

Hi all, Most of the analyses I do are short little once-and-done type things that are easily encapsulated in a .Rnw file. However, I sometimes end up with projects that take an extended amount of time. Usually these projects are not easily encapsulated in an .Rnw file, so I have been using a single .R file with lots of comments. The problem with this approach is keeping track of what you have

I have 2GB installed on my windows XP box running R 1.9.0, and after performing a prune.tree(intree,newdata), I get an out of memory error within R, but it says the maximum allowed is 1024gb (1/2 of what I have!) Can R not use more than 1GB on an XP box? I noticed I had ~600mb left over after R conked out, so clearly I had more memory... What about virtual memory? --j -- Jonathan Greenberg

Hi,   I need to generate a heatmap on a square matrix and wouldn't want to reorder the columns and the rows on the heatmap display.    I have used the options Rowv=NULL and Colv=NULL but doesn't seem to work. Following is a snippet of the heatmap function i am using. args <- commandArgs(); inputfile <- args[2] imgfile   <- args[3] bitmap(imgfile, height=15, width=15, res=100,

Hi dear R-listers, I'm trying to fit a 3-level model using lme in R. My sample size is about 2965 and 3 factors: year (5 levels), ssize (4 levels), condition (2 levels). When I issue the following command: > lme(var~year*ssize*condition,random=~ssize+condition|subject,data=smp,method ="ML") I got the following error: Error in logLik.lmeStructInt(lmeSt, lmePars) :

...ot;stats" "graphics" "grDevices" "utils" "datasets" "methods" [7] "base" other attached packages: rae230a "1.16.0" > On Jun 11, 2007, at 11:27 PM, Seth Falcon wrote: > "James W. MacDonald" <jmacdon at med.umich.edu> writes: > >> Hi Oleg, >> >> Oleg Sklyar wrote: >>> Hi, >>> >>> anybody has an idea as for the following error, the example is >>> actually >>> from the GO package examples. Thanks, Oleg >>> >>&gt...

On Solaris when my package is built, I get the following result: creating vignettes ...Segmentation Fault - core dumped OK My question isn't why I get a segfault, but why does build return an OK after such an inauspicious event? Is build only supposed to error out if something more central to the package is off? R CMD check does issue a warning that the vignette is missing, so maybe that

The function knn.cv in the class package doesn't have error checking to ensure that the length of the classlabel argument is equal to the number of rows in the test set. If the classlabel is short, the result is often a segfault. > library(class) > dat <- matrix(rnorm(1000), nrow=10) > cl <- c(rep(1,5), rep(2,5)) > cl2 <- c(rep(1,5), rep(2,4)) > knn.cv(dat, cl) [1] 2

> R.version.string [1] "R version 2.1.0, 2005-03-17" I don't see anything in either https://svn.r-project.org/R/trunk/NEWS or in the Changes file for R-2.1.0 about changes in package.skeleton() (nor in the help page), but when I run this function, all the .Rd files produced are of the data format even if all I have in my .GlobalEnv are functions. A trivial example is to run the

Hi, Could someone point me to the relevant documentation that covers what should be in the DESCRIPTION file for packages that have functions imported via the NAMESPACE file? I have read the R Extensions manual, but I cannot find where it covers the DESCRIPTION file vis a vis importing from a namespace. An example: I have a package foo that uses two functions x and y from package bar. Both

If one wants to unload compiled code for a package containing a namespace, my understanding is that .onUnload() should be used, with a call to library.dynam.unload(). This is used in e.g., the stats and methods packages, but it appears to me that the compiled code is not being unloaded when the package is detached(). Am I misunderstanding something? Best, Jim > search() [1]

Full_Name: Lixin Han Version: 2.4.0 OS: Windows 2000 Submission from: (NULL) (155.94.110.222) A character vector c('a','b') is supplied to rm(). As a result, 'c' is deleted unintentionally. > a <- 1:5 > b <- 'abc' > c <- letters > ls() [1] "a" "b" "c" > rm(c('a','b')) > ls() character(0)

I have used heatmap to visualize my microarray data. I have a matrix of M-values. I do the following. #The distance between the columns. sampdist <- dist(t(matrix[,]), method="euclidean") sclus <- hclust(sampdist, method="average") #The distance between the rows. genedist <- dist(matrix[,], method="euclidean") gclus <- hclust(genedist,

...hz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. ------------------------------ Message: 95 Date: Wed, 08 Jul 2009 16:08:32 -0400 From: "James W. MacDonald" <jmacdon@med.umich.edu> Subject: Re: [R] heatmap.2: question regarding the "raw z-score" To: "Chrysanthi A." <chrysain@gmail.com> Cc: r-help@r-project.org Message-ID: <4A54FCC0.2000905@med.umich.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Chrysanth...

...ction! I don't know if anyone has done a >> package, for this type of analysis but with over 2000 packages  >> floating >> around you might get lucky. ------------------------------ Message: 25 Date: Mon, 30 Mar 2009 10:15:43 -0400 From: "James W. MacDonald" <jmacdon@med.umich.edu> Subject: Re: [R] PLS package loading error! To: mienad <mienad@gmail.com> Cc: r-help@r-project.org Message-ID: <49D0D40F.4060402@med.umich.edu> Content-Type: text/plain; charset=UTF-8; format=flowed Hi Damien, How did you install the package? Usually this error pops...

Aren't the headers usually in the devel package (e.g., fftw-devel-2.1.5-0.dag.rh73.i386.rpm)? You might try installing the devel package too. HTH Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Rick Bilonick <rab at nauticom.net> 10/07/03 03:39PM

Note that package.descripton() is deprecated in R-1.9.0. You have to use packageDescription() instead. Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Sundar Dorai-Raj <sundar.dorai-raj at PDF.COM> 03/30/04 10:51AM >>> You can access this from

I don't know of a good tutorial, but I find that looking at ?par is usually good for answering most graphing questions. To resize axes, look at xlim and ylim under ?par. As for changing the axes, you can suppress the axes using e.g., for the x-axis xaxt="n" in your plotting function call, and then add your own axis using the axis() function (see ?axis). HTH, Jim James W.

As far as I know, the following should work. Can anybody tell me if/where I am going wrong? > packageDescription("KEGG", field="Version") [1] "1.6.4" > require(KEGG, version="1.6.4") Loading required package: KEGG [1] FALSE Warning message: There is no package called 'KEGG', version 1.6.4 in: library(package, character.only = TRUE, logical

Hi, I don't use Windows as my primary OS anymore, so didn't notice this until recently. In R-2.10.0 under Windows useFancyQuotes is FALSE by default, but this doesn't seem to affect the rendering of (text) help pages. This is not a problem if I run via the Rgui or Rterm (via DOS prompt), as the help pages are rendered in a popup window that understands directional quotes.