similar to: segfault when using data.table package in conjunction with foreach

Dear all, please could you advise me on the following : I've written a R script that reads 3 arguments from the command line, i.e. : " args <- commandArgs(TRUE) TUMOR <- args[1] GERMLINE <- args[2] CHR <- args[3] ". when I submit the R script to a PBS HPC scheduler, I do the following (below), but ... I am getting an error message. (I am not posting the error message,

Hi, The problem is most likely, you need to call a R CMD BATCH with your arguments and the R-script inside of a shell script that you submit to your qsub. Unfortunately we don't use qsub anymore so can't test it, but it should be as follows: R-script eg. test.R: > ##First read in the arguments listed at the command line > args=(commandArgs(TRUE)) > > ##args is now a list of

This sounds like an operating system specific question, in that "submit the R script to a PBS HPC scheduler" would be the kind of action that would run R with very different environment variables and possibly different access credentials than your usual interactive terminal. A thorough reading of the "Installation and Administration Guide" and some study of your HPC

I have a dataframe in the general format: chr1 0.5 chr1 0 chr1 0.75 chr2 0 chr2 0 chr3 1 chr3 1 chr3 0.5 chr7 0.75 chr9 1 chr9 1 chr22 0.5 chr22 0.5 where the first column is the chromosome location and the second column is some value. What I'd like to do is have a histogram created for each chr location (i.e. a separate histogram for chr1, chr2, chr3, chr7, chr9, and chr22). I am just

Hello I have a data frame and one of its columns is as follows: Col chr1:71310034 chr14:23354088 chr15:37759058 chr22:18262638 chrUn:31337214 chr10_random:4369261 chrUn:3545097 I would like to get rid of colon (:) and replace this column with two new columns containing the terms on each side of the colon. The new columns should look as follows: Col_a Col_b chr1

Hello, I'm trying to install KEGGSOAP with bioconductor but i'm facing this problem: /> biocLite("KEGGSOAP") BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.4. Installing package(s) 'KEGGSOAP' trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/KEGGSOAP_1.30.0.tar.gz' Content type

I have a data.frame with all character columns, I would like to convert the last two columns into numeric.> x[1:5, ] chrN start end 1 chr1 71310034 71310064 2 chr14 23354088 23354118 3 chr14 71310034 71310064 4 chr15 37759058 37759088 5 chr22 18262638 18262668 > apply(x, 2, FUN = mode) chrN start end

I am running R 3.5.1 on ubuntu 18.04, installed via apt. When I run R from the bash prompt, I get (reinstalling r-base doesn't help) > devtools::install_github("goranbrostrom/eha", build_vignettes = TRUE) *** caught segfault *** address 0x68456, cause 'memory not mapped' Traceback: 1: dyn.load(file, DLLpath = DLLpath, ...) 2: library.dynam(lib, package,

Greetings, I am new to R, but trying to put in the time to learn. I have read the R manual and several other introductory texts; however, there is nothing like actually putting it into practice. So here is my problem, and its more of a learning exercise for myself than anything else, but I'm stuck and getting extremely frustrated that I can't figure it out. I'm trying to make a

Hello, I try to install pbdMPI. Compilation successful, but load fails with segfault. Is anyone can help me? R version 3.0.0 pbdMPI version 0.1-6 Intel compiler version 13.1.1 OpenMPI version 1.6.4-1 CPU Intel x86_64 # R CMD INSTALL pbdMPI_0.1-6.tar.gz .. .... checking for gcc... icc -std=gnu99 checking whether the C compiler works... yes checking for C compiler default output file name...

Hi, I downloaded 2.8.1 and tried to compile it using gcc 3.4.6. (simple install, just ./configure, make, make check, make install) I found that it compiled and went through the tests fine. The foreign library, however, that seems to be segfaulting on me (see output below). I did see an old posting about a similar problem, but there was no resolution. Have other people experienced this at all?

R Help List: Just curious if anyone has successfully built R on a SPARC platform running Sun Solaris 10 using the latest Sun Studio 12 set of compilers. If so, I would be interested in the compile flags that you used. I have tried several different builds of version 2.5.1, 2.6.0, and 2.6.1 using various different compile flags and I am able to compile and check, but for whatever reason, the

I have an lapply function call that I want to parallelize. Below is a very simplified version of the code: url_base <- "https://cloud.r-project.org/src/contrib/" files <- c("A3_1.0.0.tar.gz", "ABC.RAP_0.9.0.tar.gz") res <- parallel::mclapply(files, function(s) download.file(paste0(url_base, s), s)) Instead of download a couple of files in parallel, I get a

I have an R program I am attempting to use to generate some SVGs. I've been using the cairoDevice library. When running a session not connected to an X session (like if I'm sshed in), attempting "library(cairoDevice)" causes: *** caught segfault *** address 0x8, cause 'memory not mapped' Traceback: 1: .C("R_gtk_setEventHandler", PACKAGE =

Dear R List, I encountered a serious problem regarding the registration of ".C" when following the documentation "Writing R Extensions" that leads to a segmentation fault (tested on windows and mac os x). The registration mechanism for ".C" routines via R_registerRoutines and the R_CMethodDef structure has been enhanced recently with the addition of two fields, one

Hi Emil, First, thanks for the response. As you mentioned, a lot of times tryCatch does the work, as you can return a value. However, sometimes it is useful to assign several variables when an error occurs. You could do it with <<-, but I prefer to reduce it's usage unless completely necessary. I guess that the attachment was missed in the moderation. Here it is the function:

Hi, I'm using R-2.12 on a linux 64bit machine. When I run a chunk of code inside a foreach() %do% { ...} or %dopar% {...} (with doMC backend) I keep getting a segfault. Running the *same* code within lapply(something, function(x) ... ) doesn't result in any segfaults. I'll paste the output below, but I'm not sure it would be helpful. I'm more curious how to go about smoking

Hello all, (Thank for your reply) I have a web-application in Apache Tomcat, when i start R in this application, I used packe RSJava Code ROmegahatInterpreter interp; String [] rargs = {"--no-save"}; REvaluator e; interp = new ROmegahatInterpreter ( ROmegahatInterpreter.fixArgs(rargs),false ); e =new REvaluator (); Errors ================ R version 2.10.1 (2009-12-14)

I got the following after running succesfully through this loop 28 million times... the loop opens text files in a directory and inserts line by line into a database... *** caught segfault *** address 0xc0000010, cause 'memory not mapped' Traceback: 1: .getGeneric(f, where, package) 2: getGeneric("coerce", where = where) 3: as(obj, "integer") 4:

Hello, Please keep this on the list, always cc r-help. One of the files in your attachment is empty: y <- read.csv(file.choose("GT.csv")) Error in read.table(file = file, header = header, sep = sep, quote = quote,? : ? no lines available in input Rui Barradas ? Citando Chaitanya Ganne <Chaitanya.Ganne at jefferson.edu>: > Thank you so much for your input. > > I am