similar to: Possible memory leak with R v.2.5.0

I'm working with a very large matrix ( 22k rows x 2k cols) of RNA expression data with R v.2.5.0 on a RedHat Enterprise machine, x86_64 architecture. The relevant code is below, but I call a function that takes a cluster of this data ( a list structure that contains a $rows elt which lists the rows (genes ) in the cluster by ID, but not the actual data itself ). The function creates two

Hi - Admittedly, this may not be the most sophisticated memory profiling performed, but when using unix's top command, I'm noticing a notable memory leak when using R with a large matrix that has dimnames set. To allow people to reproduce the problem I'm seeing, I've added a small (< 50 lines) code snippet at the end of this email. I'm seeing this

Hi - Admittedly, this may not be the most sophisticated memory profiling performed, but when using unix's top command, I'm noticing a notable memory leak when using R with a large matrix that has dimnames set. To allow people to reproduce the problem I'm seeing, I've added a small (< 50 lines) code snippet at the end of this email. I'm seeing this

specifically, imagine we have: fooStack <- list() for ( i in 1:5 ) fooStack[[i]] <- list() and we have a function: fooModifier <- function( foo ) { foo$bar <- "bar" } then, if we invoke fooModifier, i.e.: fooModifier( fooStack[[ 1 ]] ) the $bar elt is only set in the scope of the function, and if we use the

Hi - I saw your posting on the R-help mailing list. Were you ever able to get this working? did you end up switching to use the rsge library? I'm trying to do the same, and not having very much luck getting it going. Thanks! Peter Waltman [[alternative HTML version deleted]]

Hi - When I'm trying to read in a text file into a labeled character array, the memory stamp/footprint of R will exceed 4 gigs or more. I've seen this behavior on Mac OS X, Linux for AMD_64 and X86_64., and the R versions are 2.4, 2.4 and 2.2, respectively. So, it would seem that this is platform and R version independant. The file that I'm reading contains the upstream regions

Hi - Not a mission critical issue, but still highly annoying. I just upgraded R to 2.10.0 (the binary for Ubuntu karmic) and the tab completion facility now inserts a space after every completed term (something it didn't do in 2.9.0 or 2.9.2). It wouldn't be an issue so much if it weren't for the fact that it screws up tab-completing the next term, i.e. if I have a list of lists of

Hi - Any help would be greatly appreciated. I'm loading a list variable that's stored in an .RData file and would like attach it. I've used attach( <file_name> ), but that only lets me see the variable that's stored in the file. As the variable name is of the form "comp.x.x", I've tried using attach( ls( pat="comp" ) ), but get an error as ls()

On Fri, Nov 7, 2014 at 11:31 AM, Adrian Chadd <adrian at freebsd.org> wrote: > ... that's .. odd. > > Let's poke the freebsd crypto and network stack people and ask. I > can't imagine why this is a problem anymore and we should default to > it being on. I don't think there's a crypto@ list, though security@ might represent. > The other thing you could

Hi - I'm curious if there is a way to get access to the location of the calling script within R. I found one way of accessing it from this thread, https://stat.ethz.ch/pipermail/r-devel/2008-April/048914.html, which recommends using either: parent.frame(2)$ofile Or FILE <- (function() { attr(body(sys.function()), "srcfile") })()$filename However, those suggestions only

Dear R Helpers, I need help with a slightly unusual situation in which I am trying to select some columns from a data frame. I know how to use the subset statement with column names as in: x=as.data.frame(matrix(c(1,2,3, 1,2,3, 1,2,2, 1,2,2, 1,1,1),ncol=3,byrow=T)) all.cols<-colnames(x) to.keep<-all.cols[1:2] Kept<-subset(x,select=to.keep) Kept

Hi, I have the following table of odds ratios (or), lower limits(ll) and upper limits(ul), which I would like to plot as horizontal lines beginning at the lower limit, ending at the upper limits and with a dot at the odds ratio on an x-axis on a log10 scale. The y axis would be the study sites. >From what I can figure out, it looks like the plotCI function will do everything except give me an

Here is an example barplot that needs some tweaking: library(gplots) ratios <- data.frame(c(0.05,0.10,0.9),c(0.06,0.15,0.76)) rownames(ratios) <- c("T1","T2","T3") colnames(ratios) <- c("A1","A2") ratios <- as.matrix(ratios) myplot <- barplot2(ratios, beside = TRUE,col = c("blue",

Hi - I'm having a really hard time w/understanding R's get function, and would appreciate any help with this. Specifically, I'm using a for loop to call a function. I'd like the function to have access to the variable being incremented in the for-loop, i.e. t.fn <- function() return( get( "i" ) ) t.fn2 <- function() { for ( i in 1:5 ) cat( t.fn(),

Dear R-helpers, I´m in the context of writing a general function for error propagation in R. There are somehow a few questions I would like to ask (discuss), as my statistical knowledge is somewhat restricted. Below is the function I wrote, the questions are marked. Many thanks in advance. propagate <- function(expr, varList, type = c("stat", "raw"), cov = TRUE) {

Hi, Can anyone help me with the following. I have been using R for Monte Carlo simulations and got some results I couldn't explain. Therefor I performed following short test: -------------- mean.sds <- NULL sample.sizes <- 3:30 for(N in sample.sizes){ dum <- NULL for(I in 1:5000){ x <- rnorm(N,0,1) dum <- c(dum,sd(x)) } mean.sds<- c(mean.sds,mean(dum)) }

Does anyone (Hadley??) know if there's a straightforward way in ggplot2 to get data divided by a single factor to plot as a rectangular grid of subplots? So far I've only been able to get such data plotted as a single row or single column of skinny subplots. The code below gives an example implemented with lattice, and my best attempt in ggplot2 cheers Ben Bolker ------------ g=

If I have 3 columns of data, col 1 = Independent Var; cols 2 and 3 are Dep. Vars. I would like to produce a plot with both: col2=f(col1) and col3=f(col1). How do I do this such that I can control line parameters (line type, color, etc). I know that if I stack the data and col2 and col3 are treated as different factor levels, that I can accomplish this, but lose control over the line

For the heck of it I tried upgrading to gcc 3.4.2 (from 3.3.3). It didn't make a difference. So here are the failures for llvm-test. All diffs are against the "native" output. ===================== MultiSource/Applications/sgefa cbe failed differently from jit/llc. First cbe: 84c84 < One-Norm(A) ---------- 8.879153e+02. --- > One-Norm(A) ---------- 8.879156e+02.

On Thu, 9 Sep 2004 20:16:37 -0700 Jeff Cohen <jeffc at jolt-lang.org> wrote: > On Thu, 9 Sep 2004 08:52:10 -0700 > Jeff Cohen <jeffc at jolt-lang.org> wrote: > > > > I haven't got around to this yet but I will. The odds are good the > > > problem is in a BSD system header file so I need to capture the > > > preprocessed source. > > >