similar to: Possible memory leak with large matrices in 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

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 - 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]]

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 - 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()

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

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

hi - sorry for a newbie question, but I've tried to go through the documentation and couldn't find anything that would address my specific need. in a nutshell, I have a txt file containing a data matrix with 10 columns of data. I would like to generate pairwise plots of the data, i.e. 1 column against the other 9. Since this will produce 50 plots, I'd like to do it using a

Hi - I'm reading in a tab delimited file that is causing issues with read.delim. Specifically, for a specific set of lines, the last entry of the line is misread and considered to be the first entry of a new row (which is then padded with 'NA's' ). Specifically: tmp <- read.delim( "trouble.txt", header=F ) produces a data.frame, tmp where if I call tmp[,1],

Looking for help regaining access to encrypted ZFS file systems that stopped accepting the encryption key. I have a file server with a setup as follows: Solaris 11 Express 1010.11/snv_151a 8 x 2-TB disks, each one divided into three equal size partitions, three raidz3 pools built from a "slice" across matching partitions: Disk 1 Disk 8 zpools +--+ +--+ |p1| .. |p1| <-

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(),

The Asterisk Development Team is pleased to announce the release of DAHDI-Linux and DAHDI-Tools version 2.5.0 DAHDI-Linux 2.5.0, DAHDI-Tools 2.5.0 and DAHDI-Linux-Complete 2.5.0+2.5.0 are available for immediate download at: http://downloads.asterisk.org/pub/telephony/dahdi-linux http://downloads.asterisk.org/pub/telephony/dahdi-tools

The Asterisk Development Team is pleased to announce the release of DAHDI-Linux and DAHDI-Tools version 2.5.0 DAHDI-Linux 2.5.0, DAHDI-Tools 2.5.0 and DAHDI-Linux-Complete 2.5.0+2.5.0 are available for immediate download at: http://downloads.asterisk.org/pub/telephony/dahdi-linux http://downloads.asterisk.org/pub/telephony/dahdi-tools

Anyone have problems with getaddrinfo under AIX4.3? I have built 2.5.0 under linux, HP and VPP without too much in the way of problems. However, AIX4.3 version builds OK but doesn't execute getaddrinfo correctly. Any ideas? Terry Raggett ------------- -- +-------------------+----------------------------------+---------------------+ | Terry Raggett | |

Dear list, R 2.5.0 packages for Debian stable (i386 and amd64) are now available from CRAN. The new recommended codetools and rcompgen packages haven't completely made it to Debian yet, but can of course be installed in the standard non-Debian ways. Please consult the README file in the Debian directory, and report problems to me directly or to this list. Best regards, Johannes Ranke --

Attached is a patch for rsync 2.5.0 to fix the "make check" option. The find command was not being passwd the current directory in the hands.test and longdir.test testsuites, which caused them to fail on SunOS 4.X and Solaris 2.X systems. Tom -- Tom L. Schmidt, Manager/SysAdmin Characterization Equipment Micron Technology, Inc. 8000 S. Federal Way P.O. Box 6 Mail Stop 376 Boise,

Hi All, New version 2.5.0 of the IBM_DB gem, the Rails Adapter/Ruby Driver for IBM DB2 and IBM Informix is now available. This release of the gem adds unicode support in the IBM_DB driver for Ruby 1.9. When used with Ruby1.8 the Driver will function in ASCII mode. To know more and get hands with the IBM_DB gem download the latest gem from http://rubygems.org/gems/ibm_db or

This release rolls up a few minor bug fixes since 2.4.0. We now refuse to run on machines with UEFI firmware (on Linux only, patches welcome for other OSes) since it won't work in the general case and you probably have a kernel framebuffer driver running already. We also only attempt to use 24bpp if the alternative would be pseudocolor, but note that since xserver 1.20 24bpp will not work at