similar to: Suspected memory leak with R v.2.5.x and large matrices with dimnames set

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

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]]

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 - 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()

I've got a covariance matrix that I'd like to index using the dimnames: > vcov1 n0 x0 s n1 n2 n0 82.43824759 1.839505e-02 -4.975196e-01 2.882394e+03 -2.615986e-01 x0 0.01839505 6.134010e-03 -7.695922e-04 -6.373946e+01 6.086321e-03 s -0.49751964 -7.695922e-04 9.638943e-03 3.406594e+02 -3.173671e-02 n1 2882.39407745

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 - 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(),

I have downloaded and built rsync 2.6.0 on our HP ProLiant DL380-G3 servers (2 Hyperthread processors, 4 GB RAM, 840 GB Hard Disk, etc. etc.) running Red Hat 8 with the latest errata kernel (2.4.20-28smp) and updates from HP for RH8. rsync is run in daemon mode from xinetd. When doing transfers the machine requesting the transfer starts to run out of memory. After every rsync transfer there

Is it expected behavior for gc() to return shrinking values as it gets called multiple times? Here's what I've got: > gc() used (Mb) gc trigger (Mb) Ncells 221754 6.0 467875 12.5 Vcells 3760209 28.7 14880310 113.6 > gc() used (Mb) gc trigger (Mb) Ncells 221760 6.0 467875 12.5 Vcells 3016206 23.1 11904247 90.9 > gc() used (Mb) gc

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| <-

Full_Name: Ashley Ford Version: 1.4.0 OS: Windows NT4 Submission from: (NULL) (146.80.9.20) I am suffering from a memory leak in read.table in the new precompiled windows 1.4. it works fine in 1.3 Create a 90000 line file of 7 variables eg perl -e '$e=exp(1);for($i=0;$i<90000;$i++){printf "%d".(" %f"x6)."\n", $i,$i*$e,3,4,5,6,7,8,9}' > n90000 R :

Hi, when doing as.double() on an object that is already a double, the object seems to be copied internally, doubling the memory requirement. See example below. Same for as.character() etc. Is this intended? Example: % R --vanilla > x <- double(1e7) > gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 234019 6.3 467875 12.5 350000 9.4 Vcells 10103774 77.1

Hi guys, the SUPER codec by Erightsoft http://www.erightsoft.net/SUPER.html contains lots of GPL and LGPL code: mplayer, ffmpeg, x264, musepack, theora, which they admit and give credit for. Still, their product is proprietary, and they insist on it. I tried to get the source through their forum, but they of course won't give it: http://www.erightsoft.net/Supforum.html I'll forward

What is the canonical link to Reference of "ServerAliveInterval"? Background: I want to write an answer at serverfault (Q-A Site). I want to avoid copy+pasting. I would like to lead the new comer to the canonical reference. Regards, Thomas G?ttler -- Thomas Guettler http://www.thomas-guettler.de/

On (05/17/19 15:13), Sergey Senozhatsky wrote: > 5.1.0-next-20190517 > > I'm looking at quite a lot of kmemleak reports coming from > drm/nouveau/core/memory, all of which are: > > unreferenced object 0xffff8deec27c4ac0 (size 16): > comm "Web Content", pid 5309, jiffies 4309675011 (age 68.076s) > hex dump (first 16 bytes): > 00 00

On (05/17/19 15:13), Sergey Senozhatsky wrote: > ... but most likely it's utterly wrong. > JFI, I removed kmemleak annotation and added the following thing: @@ -360,6 +360,7 @@ gp100_vmm_valid(struct nvkm_vmm *vmm, void *argv, u32 argc, return -EINVAL; } + kfree(map->tags); ret = nvkm_memory_tags_get(memory,

JohnG <mcsjgs@cox.net> wrote: > I run OS X 10.3.7 on a PowerMac MDD G4 on a cable broadband connection. > I have reason to think my system has been tampered with. Security > features in Mac OS X have been left unlocked (Preference Pane - Users) OSX is substantially different from FreeBSD (even without netinfo) despite having some of the same source code. I doubt you'll find