similar to: debugging strange segfault

Dear R-devel, Apologies for bothering y'all with this seemingly perennial question. A user reported problem with my most recent version of randomForest (4.4-1), and I was able to reproduce it with his data with R-2.0.0 patched (2004-10-24) on WinXP Pro. The problem is that it crashes R on Windows. However, it does not happen on Linux (tried SUSE ES8 on our Opterons and Quantian on my

Hi! I am trying to install the RMySQL package. The installation stops with the following error message. path to mysql is set. setenv PKG_CPPFLAGS /home/arabidopsis/software/R1.9.1/linux/mysql/include setenv PKG_LIBS /home/arabidopsis/software/R1.9.1/linux/mysql/lib R CMD INSTALL RMySQL_0.5-5.tar.gz #....cut cut. creating src/Makevars ** libs gcc

Dear R-devel, A user reported a strange problem with predict.randomForest in the randomForest package yesterday, and I'm baffled by it. The code at the end of the message produces the error. The problem is that, in predict.randomForest, there's a .Fortran call to "runforest". One of the arguments passed in is "countts", which is a vector of doubles. The error

Dear R-help, I was bitten by the behavior of all() when given logical(0): It is TRUE! (And any(logical(0)) is FALSE.) Wouldn't it be better to return logical(0) in both cases? The problem surfaced because some un-named individual called randomForest(x, y, xtest, ytest,...), and gave y as a two-level factor, but ytest as just numeric vector. I thought I check for that in my code by testing

Hello, I am beginner user of R. I am trying to use GeneNet package. I started by the example on this link: http://strimmerlab.org/software/genenet/download/arabidopsis-net.R However I am getting an error at this line:system("fdp -T svg -o arthdyn.svg arthdyn.dot") # SVG format sh: fdp: command not found I tried to search how to intall the fdp command but could not find explanation. I am

Dear R-devel, Kurt had alerted me to the problem that the randomForest package that I maintain has been failing checks in R-devel. However, I just can't see why or where it's failing. I'd very much appreciate any pointer. The failure occur when running the example code in varImpPlot.Rd: > varImpPlot(mtcars.rf) Error in par(opar) : invalid value specified for graphical parameter

Hi, There is an excellent article at http://www.biomedcentral.com/1471-2105/9/307 by Stroble, et al. describing variable importance in random forests. Does anyone have any suggestions (besides imputation or removal of cases) for how to deal with data that *have* missing data for predictor variables? Below is an excerpt of some code referenced in the article. I have commented out one line and

The following code results in a seg fault. > sessionInfo() R version 2.6.0 Under development (unstable) (2007-06-21 r42013) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C attached base packages: [1] stats graphics

I originally posted this to R-help, but here is probably a better place. I have a rather complex routine which works great in R. Then I bootstrap it. After running a few minutes it typically segfaults, though it happens very randomly. This happens w/ 1.9.0 and 1.9.1 on Fedora1 and a Scyld (RH7.3) system. Traces always point back to routines in src/main/memory.c, though often not the same

If anyone has a few extra CPU cycles to spare, I'd appreciate it if you could verify a problem that I have encountered. Run the code below and tell me if it crashes your R before completion. library(lme4) data(bdf) dump<-sapply( 1:50000, function(i) { fm <- lme(langPOST ~ IQ.ver.cen + avg.IQ.ver.cen, data = bdf, random = ~ IQ.ver.cen | schoolNR); cat("

Dear all, I installed Mandrakelinux 10.1 (community) on my notebook. Before, I used Mandrakelinux 9.1 (and later 10.0 as an update). Now I wanted to compile, as before, R. In the beginning, nothing worked but it seemed to be the problem of GCC 3.4.1 which was shipped with my distribution. After downloading and compiling GCC 3.4.3 everything went smoothly during the compilation of R. The problem

Hi, It's unfortunate that with recent revisions of R 2.13 (this appeared in revision 54640, March 2), 'R CMD build' now removes empty dirs in the package. People might have good reasons for having empty dirs in their packages. For example, in Bioconductor, we have some tools to automatically generate annotation packages and those tools are implemented in software packages that use

I'm a novice with gdb but the following is the result of a segfault problem I've been having with 1.2.0. If there is something else I should do to get more useful information at this point, then someone please let me know. Paul Gilbert ______ [5] /home/mfa5/gilp/zzot : R -d gdb GNU gdb 4.17 Copyright 1998 Free Software Foundation, Inc. GDB is free software, covered by the GNU General

I am new to R and I'd like to use the randomForest package for my thesis (identifying important variables for more detailed analysis with other software). I have found extremely well written and helpful information on the usage of R. Unfortunately it seems to be very difficult to find similarly detailed tutorials for randomForest, and I just can't get it work with the information on

Dear all, Can anybody give me some hint on the following error msg I got with using randomForest? I have two-class classification problem. The data file "sample" is: ---------------------------------------------------------- udomain.edu udomain.hcs hpclass 1 1.0000 1 not 2 NA 2 not 3 NA 0.8 not 4 NA 0.2 hp 5 NA 0.9 hp ------------------------------------------------------------ The

I have some questions about 1. nomenclature, 2. recommended file locations and 3. overall procedure related to creating packages. To the extent that it matters, examples here relate to Windows XP R 2.0.1 beta. The questions are interspersed and prefaced with ***. My understanding is that there are actually 6 forms of a package that one should use in package development: 1.

Hello I'd like to try out some functions in the package randomForest. Therefore, I did install this package. However, it is not possible to load the library, although I have R-Version 2.1.1 (i.e. later than 2.0.0). The commands I used and the Answers/Error from R is as follows: > install.packages("C://Programme//R//rw2011//library//randomForest_4.5-16.zip",

Hello, I've tried to install randomForest on a Ubuntu 8.04 Hardy Heron system. I've repeatedly rec'd the error: > install.packages("randomForest", dependencies = TRUE) ERROR: compiliation failed for package 'randomForest' ** Removing '/home/admuser/R/i486-pc-linux-gnu-library/2.6/randomForest' The downloaded packages are in

This is a question and maybe an announcement. We've been discussing in the group that it would be nice to have a mechanism for something like "inline" C/C++ function calls in R. I do not want to reinvent the wheel, therefore, if something like that already exists, please give me a hint -- I could not find anything. If not, here is a working solution, please criticise so I could

Hi all, I am trying to play around with the randomForest function for classification. I know its performance is great. I am currently using the default options. It has many options. How do I further tweak the options so that I can make its performance even better? What are the options that are mostly used? Thanks a lot! M [[alternative HTML version deleted]]