similar to: snow and different R versions

It would be convenient if, under R-devel r56422, packages that require re-installation because they do not have a NAMESPACE were marked as old.packages, so their lack of functionality can be discovered more easily. > "snow" %in% row.names(old.packages()) [1] FALSE > library(snow) Error in library(snow) : package 'snow' does not have a NAMESPACE and should be

Hello, the package snow is not working on a windows cluster with MPICH2 and Rmpi. There is an error in makeCluster: launch failed: CreateProcess(/usr/bin/env "RPROG="C:\Programme\R\R-2.5.1\bin\R" "OUT=/dev/null" "R_LIBS=" C:/Programme/R/R-2.5.1/library/snow/RMPInode.sh) on 'cl1' failed, error 3 - Das System kann den angegbenen Pfad nicht finden. I

Dear list, i have some problems using the snow package to create a SOCK cluster. The errors just occour irregularly but it seems to me that they occour when I try to create more than one cluster on the same machine via different R instances started via submitting LSF jobs to a cluster. Does anyone have an idea how to solve this or where to start digging for solutions? The error messages

A new version of the 'snow' package for parallel computing in R is available at http://www.stat.uiowa.edu/~luke/R/cluster/snow_0.3-3.tar.gz This substantially revises the way in which worker processes are started to allow snow to be used on Windows and Mac/Windows/Linux combinations. I have successfully used the SOCK version on a standalone Windows machine and combinations of

The command which hangs: I'm hoping there is a simple explanation, but I searched on-line and nothing jumped out. > cl <- makeCluster(type="SOCK",c("localhost"),manual=TRUE) Manually start worker on localhost with C:/PROGRA~1/R/R-214~1.2/bin/Rscript.exe "C:/Program Files/R/R-2.14.2/library/snow/RSOCKnode.R" MASTER=localhost PORT=11944 OUT=/dev/null

Dear users, By running the script below, R crashes systematically at the last command, namely dev.off(), on Windows 7, but not on Windows XP. I therefore don't provide a reproducible example and do not really extract the relevant parts of the script because it has most likely nothing to do with the script itself. I can do it though if you think it might be relevant. R crashes on Windows

Many thanks to Dr Yu for updating Rmpi for R 2.6.0, and for starting to make the changes to support Open MPI. I have just built the updated Debian package of Rmpi (i.e. r-cran-rmpi) under R 2.6.0 but I cannot convince myself yet whether it works or not. Simple tests work. E.g. on my Debian testing box, with Rmpi installed directly using Open Mpi 1.2.3-2 (from Debian) and using 'r' from

Hi, I'm testing affyPara on Debian lenny with R 2.7 from unstable, and the corresponding bioconductor packages from bioconductor.org downloaded using biocLite as per usual. The command cl = makeMPIcluster(k) succeeds, but spawns k R slaves which promptly soak up all available CPU, which is odd since they are not doing anything yet. This looks like a bug to me. Similar behaviour is shown

Hello, I'm training a set of data with Caret package using an elastic net (glmnet). Most of the time train works ok, but when the data set grows in size I get the following error: Error en { : task 1 failed - "arguments imply differing number of rows: 9, 10" and several warnings like this one: 1: In eval(expr, envir, enclos) : model fit failed for Resample01 My call to train

Dear users, I want to set up R to use one R-script directory and one R-library (directory for packages) for many end-users. I try to do this by using one network-share. This works fine as long as we don't use the snowfall package with parallel=TRUE (sfInit(parallel=TRUE, cpus=4, type="SOCK")). When running R with default settings (local library and local script directory)

Hi. I have some problems trying to make cluster via "snow" package and haven't found a solution for my problem in archives and relative topics. I installed ssh server using cygwin and set a password-less SSH Login. In R session after starting ssh service: > system("ssh 10.10.5.15 date") Tue Nov 22 16:22:36 AST 2011 But when I make connection: > con <-

Dear list, I just realized that one of the examples given in the help page to the function makeCluster of the library(snow) has a small syntax error : ## to get started library(snow) ?makeCluster .. will open a halp page containing the command towards the end of the examples : cl <- makeCluster(c(rep(list(macOptions), 2), rep(list(lnxOptions), 2), rep(list(winOptions),

Hi Simon, I'm having trouble with nested parallel workers, specifically, forking inside socket connections. When mclapply is called inside a SOCK, PSOCK or FORK worker I get an error in unserialize(). cl <- makeCluster(1, "SOCK") fun = function(i) { library(parallel) mclapply(1:2, sqrt) } Failure occurs after multiple calls to clusterApply: > clusterApply(cl, 1,

Hi, I am currently building an R package and I am facing a peculiar problem where some of the functions does not work within the package. However, if I source the script the function works. For example, in a method for parallelization of analysis on each chromosome simultaneously I am receiving error at the following position of the code: # this profile the information chromosome wise and

Hi, I'm trying to get a package to pass through "R CMD check --as-cran" and have run into a problem that gives me no idea where to look to fix it. I'm running R version 15.1 on a Windows 7 64-bit machine, with the current set of Rtools. An attempt to check the package dies at the following step: * checking running R code from vignettes ... 'SIBER.Rnw'

On 03/25/2015 07:48 PM, Simon Urbanek wrote: > On Mar 25, 2015, at 3:46 PM, Valerie Obenchain <vobencha at fredhutch.org> wrote: > >> Hi Simon, >> >> I'm having trouble with nested parallel workers, specifically, forking inside socket connections. >> > > You simply can't by definition - when you fork *all* the workers share the same connection

Is my understanding correct that the body() function currently can't return a function's body intact, in order, and as characters ready for editing? My testing and reading of body()'s help indicate that it can not. Here's what I'm seeing. Consider pasting 1+ and a function containing x^2 together to get 1+x^2 As you can see below, body() reports three

An Sweave file, 'test.Rnw': \documentclass{article} \title{Sweave minimal} \author{MK} \begin{document} \maketitle We try Sweave: <<1>>= data(airquality) summary(airquality) x <- airquality[1, 1] @ I try Sexpr: \Sexpr{x} We plot: \begin{center} <<2, fig=TRUE, echo=FALSE >>= boxplot(Ozone ~ Month, data = airquality) @ \end{center} \end{document} I check the

Dear all, I am trying to use the Matrix package to do some calculations on rather large and sparse matrices. An example of such a matrix is given below. mig<-0.2 side<-10 np<-side^2 mig.mat<-matrix(0,np,np) diag(mig.mat[1:(np-side),(side+1):np])<-mig/4 diag(mig.mat[(side+1):np,1:(np-side)])<-mig/4 diag(mig.mat[-np,-1])<-mig/4

Thanks to Luke Tiernay and some experimenting I found out some issues. I don't claim this infomation is complete, but it may be helpful for anyone experimenting with SNOW on Linux: - environment variables PATH and R_SNOW_LIB need to be set on master and slaves. (manually or permanent in ~/.bashrc (adjust your pathnames accordingly). Don't use ~ for home directory, instead specify