similar to: Error when using foreach package for parralelization

Dear list, My name is Juan Fernandez-Tajes and I´m trying to use MALDIquant for analysing MS data from ABI 4700 series, I´ve exported a spot set to T2Dextractor in order to convert in mzXML format. I´ve imported this into R with mqReadMzXml function and have followed the suggested flowchart, however when I´m in the step for peak detections I obtained the following error: peaks <-

Hi there! I have become a big fan of the 'foreach' package allowing me to do a lot of stuff in parallel. For example, evaluating the function f on all elements in a vector x is easily accomplished: foreach(i=1:length(x),.combine=c) %dopar% f(x[i]) Here the .combine=c option tells foreach to combine output using the c()-function. That is, to return it as a vector. Today I discovered the

Hi, I just noticed this article, http://www.howtoforge.net/fully-utilizing-your-x-core-cpu which uses http://code.google.com/p/ppss/ for parralel processing. So, can anyone tell me if parralel processing happens automatically on CentOS, or would I need to use this script as well? We mainly have Dual Core & Dual CPU, Dual Core (i.e. 8 cores) servers and it would be benefitial to know whether

Job Title : Postdoctoral Position in Biostatistics/Bioinformatics Background The joint research unit between bioM?rieux, international leader in in vitro diagnostic, and Hospices Civils de Lyon, second-largest University Hospital Network in France, develops a research program dedicated to the study of injury induced immunosuppression. This program aims at (i) describing and understanding the

Dear expeRts, is it possible to carry out calculations between different foreach() calls? As for nested loops, you want to carry out calcuations not depending on the inner loop only once and not for each iteration of the innermost loop. Cheers, Marius library(foreach) foreach(i=1:3) %:% foreach(j=1:2) %do% { i <- i+1 print(paste(i,j)) } foreach(i=1:3) %:% i

Hi all, Anyone want to help with a native IO.foreach? I''m missing some of the critical logic here. This currently just does a straight BYTE_MAX data read, instead of a line by line data read, and doesn''t deal with lines split between multiple reads. I checked strtok into CVS (for windows-pr) if anyone wants to use that instead of String#split. It''s in

Dear R-List member, tried implement the foreach loop. It works fine, when I'm using %do%, but not when I'm using %dopar%. I always receive one of the following error messages: error in { : task 1 failed - "Objekt 'S3' not found" - could the .export be an solution for this?? Any help is much appreciated! The Code hast the following structure: ########## dft3 =

Dear all, I am converting a large process to a parallel backhend using doMC and foreach. Basically, I havea long list of input graph files and each of them calls soem basic igraph package functions. I am parallelizing the run, in order to save time. All works fine, and each %dopar% call ends with a vector of results that at the end got fed into a data frame and saved as a csv table. When I

Dear R-List member, I have a problem when I'm trying to save two arrays from a foreach-loop. I'm also not sure whether this is possible or just my inexperience. However, this works perferctly fine with a for-loop. Here is an example code - any help is much appreciated!!: ############ n.vpn = 2 n.run= 3 # create to empty matrices sme = matrix(NA,4,n.vpn) test = matrix(NA,4,n.vpn) #

Hi all, I'm currently working on updating an R package to run for loops in parallel to speed up computation time. I'm using the 'foreach' package with a foreach loop. When I run my code inside the loop, I get an error message that a number of the functions aren't recognized (even though the functions have been defined); if I call my R package inside the loop, everything runs

Hi, I've noticed that the usual "break", "next" commands do not work in a foreach loop, is there a nice way to do that? A little more detail: I am using foreach to conduct a very time consuming (may take several days if done sequentially) simulation study. The number of simulations is set to 1000. So the command I am using looks like this simplified version: grandsum

Whas missing the R in the command line: "mpirun -n --hostfile /home/hostfile R --no-save -f rtest.R" Hope this helps mario On 13-Jan-11 22:08, Justin Moriarty wrote: > Hi, > Just wanted to share a working example of doSNOW and foreach for an openMPI cluster. The function eddcmp() is just an example and returns some inocuous warnings. The

I'm trying to use foreach function to do multicore computing in R. Error in FUN(train_adjmt, iter = missedmat[i, 1], iter2 = missedmat[i, : task 1 failed - "?????'predictMatrix'" then I call function A in the console. The problem is I'm calling a function Posdef inside B that is defined in another script file which I source. I had to put predictMatrix in the list

I'm trying to use foreach function to do multicore computing in R. A <-function(....) { foreach(i=1:10) %dopar% { B() }} then I call function A in the console. The problem is I'm calling a function ipredictMatrix inside B that is defined in another script file which I source.However I get the following error: Error in FUN(train_adjmt, iter = missedmat[i, 1], iter2 =

I have this code which is working library("checkpoint") library("gtrendsR") library("doParallel") cl<-makeCluster(4) registerDoParallel(cl) gconnect(usr = "email at gmail.com", psw = "password", verbose = FALSE) names <- c("apple","shit", "android", "rocks") formula <- function(x){ x0 <-

Hi! I have this code which is working formula <- function(x){ return(x) } For( x in names) { x5 <- rbind(x5,formula(x)) } Now, I want to convert this code to parallel processing, so i am using foreach function foreach(x=names, .packages="checkpoint" ,.combine='rbind') %dopar% { x5 <- rbind(x5,formula(x))

Hi useRs, I am running a foreach loop and hoped to get a small message when it hits a multiple of 1000, but it does not work. p <- foreach(i=1:10000, .combine='c') %dopar% { if(i%%1000==0) print(i) sqrt(i) } What is the proper way to do it. Thanks everybody. Stephen B [[alternative HTML version deleted]]

Dear Nik Try the following code loo_predict.mu <- function(model.obj, input.data) { yhat <- foreach(i = 1 : nrow(input.data), .packages="gamlss", .combine = rbind) %dopar% { updated.model.obj <- update(model.obj, data = input.data[-i, ]) predict(updated.model.obj, what = "mu", data = input.data[-i, ], newdata = input.data[i,], type =

What's the best (most concise) way to create the following four defs? D0 = (0, "A") D1 = (1, "B") D2 = (2, "C") D3 = (3, "D") I tried to use list of strings and the foreach construct, but apparently tablegen doesn't allow using identifiers to access array elements. $ cat tbl3.td def StrList { list<string> ls = ["A",

Hi, in R 2.12.1, R CMD check hangs when building a vignette that uses a foreach loop with the doMC parallel backend. This does not happen in R 2.13.1, nor if I use doSEQ instead of doMC. All versions of multicore, doMC and foreach are the same on both my R installations. Has anybody encountered a similar issue? Thank you. Renaud ### UNIVERSITY OF CAPE TOWN This e-mail is subject to the