search for: waltman

...have direct access to the objects' memory space. Onyway, one workaround would be to pass in the whole fooStack object and the index of the elt that you want to modify to the fooModifier fn, but I'd rather not have to pass the whole thing in. Any suggestions? Thanks! Peter Waltman

...used (Mb) gc trigger (Mb) max used (Mb) Ncells 377925 20.2 6819934 364.3 604878 32.4 Vcells 88857341 678.0 240204174 1832.7 90689707 692.0 > output from top is: PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 1199 waltman 17 0 3844m 3.7g 3216 S 0.0 23.6 29:58.74 R Note, the relevant call that invoked my function is: test <- sapply( c(1:10), function(x) get.vars.for.cluster( clusterStack[[x]], opt="rows" ) ) Finally, for fun, I rm()'d all variables with the rm(...

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]]

...ed array and most likely aren't storing the text as ascii, but 4 gigs and up seems a bit excessive. Or is it? For an example, this is the output of top, at the point which R has processed around 5000 genes: PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 4969 waltman 18 0 *6746m 3.4g* 920 D 2.7 88.2 19:09.19 R Is this expected behavior? Can anyone recommend a less memory intensive way to store this data? The relevant code that reads in the file follows: ....code.... lines <- readLines( gzfile( seqs.fname ) )...

...ll result in a trailing space after the "$An.example" - "$An.example* *", requiring that it be deleted before the next term is specified. Any idea how to turn this off? Is this a shell integration issue? Something I'd need to do by compiling my own version? Thanks! Peter Waltman [[alternative HTML version deleted]]

.... I've also played around with eval(), but don't really quite get what that function does since it seems to get into the R internals which I don't entirely understand and I haven't found any great unified documentation on R's handling environment and scoping. Thanks, Peter Waltman

...> gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 377925 20.2 6819934 364.3 604878 32.4 Vcells 88857341 678.0 240204174 1832.7 90689707 692.0 > output from top is: PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 1199 waltman 17 0 3844m 3.7g 3216 S 0.0 23.6 29:58.74 R Note, the relevant call that invoked my function is: test <- sapply( c(1:10), function(x) get.vars.for.cluster( clusterStack[[x]], opt="rows" ) ) Finally, for fun, I rm()'d all variables with the rm( list=ls() ) command,...

...evel of R's memory needs. I see this on both OS's I'm using and both versions of R (v.2.5.x). If I'm doing something wrong in my code below which is causing this issue, please let me know, but it's fairly vanilla code so I'm not sure Thanks, Peter Waltman SessionInfo output: Mac > sessionInfo() R version 2.5.1 (2007-06-27) powerpc-apple-darwin8.9.1 locale: C attached base packages: [1] "stats" "graphics" "grDevices" "utils" "datasets"...

...evel of R's memory needs. I see this on both OS's I'm using and both versions of R (v.2.5.x). If I'm doing something wrong in my code below which is causing this issue, please let me know, but it's fairly vanilla code so I'm not sure Thanks, Peter Waltman SessionInfo output: Mac > sessionInfo() R version 2.5.1 (2007-06-27) powerpc-apple-darwin8.9.1 locale: C attached base packages: [1] "stats" "graphics" "grDevices" "utils" "datasets"...

.... Because Galaxy places the executables within a user-specified directory, we can't hard-code that location if we want these to be general purpose, and would like access to that within the script, themselves, because in some cases, they need to be able to access each other. Thanks, -- Peter Waltman, Ph.D. pwaltman@ucsc.edu 617.347.1876 [[alternative HTML version deleted]]

...mes[1], test$myNames[2]) but that doesn't work either as the myNames members are strings, not the variables themselves (I believe). is it possible to get a listing of the variables themselve, not the names and work off of those? thanks to anyone who can help shed some light on this, Peter Waltman

....2.5.1 on an x86_64, as well as v.2.6.0 on an x686 architecture. I also get similar behavior when I convert the file into a comma-separated file and use read.csv. As a quick workaround I can use scan & strsplit, but thought someone might want to take a look at this problem. Thanks, Peter Waltman p.s. the combination of scan & strsplit I describe above was as follows: my.lines <- scan( "trouble.txt", sep="\n", what='character' ) split.lines <- strsplit( my.lines, "\t" ) num.entries <- sapply( split.lines, length ) after whic...

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(),

...urce locally for each fs with no success (other than not being able to set it back to inherited from base.) Any other thing I can do? Most of the data is either old junk or things I can rip again or download again, but there are some files I can not recover from anywhere else. Thanks, -- Roberto Waltman

Dovecot LDA (deliver) aliases question. I have a multiple virtual domain setup using sendmail, username/domain, password, home directory all stored in mysql,Set-UID/GID for dovecot 'deliver' setup as referenced in Dovecot LDA wiki. Delivery, and POP/IMAP work just fine, serving a mail store in /home/vmail/domain/username type of setup. My problem comes from what may be a

Hi All - I'm running a faily long script that uses rpvm & snowFT to spawn off multiple processes with the 'clusterApplyFT' function. Specifically, what happens is that the head node generates a number of seed clusters that are then spawned off to the pvm cluster (in this case, nodes on a 4 dual-core machine) using clusterApplyFT to apply a function to each seed cluster that

Hi - I'm trying to set up a parallelized batch job that is run under rmpi and managed by sge, using qsub, but it reports that it can't load RMySQL because it can't find the libmysqlclient.so.15 file. Note, when I run R interactively, and manually load the RMySQL library, it works without a hitch, however, when I have qsub launch R, it reports the following error: Error in