similar to: benchmarking R installations

I would like to build R and packages with the Intel 10.1 compilers in RHEL4. Using the flags below, I can successfully build R using a vanilla ./configure, but when I install new packages they build with gcc. My sysadmin suggested adding the flags to ./configure as illustrated below, but then the R build blows up with the config tail output that follows far below. It looks like gcc is still being

I am having trouble compiling R-2.6.2 on suse linux x86_64 using the intel compiler. I read section C.2.1 Intel compilers in the R Installation and Administration manual, and put CC=icc CFLAGS="-g -O3 -wd188 -ip" F77=ifort FFLAGS="-g -O3" ICC_LIBS=/opt/intel/cce/10.1.012/lib IFC_LIBS=/opt/intel/fce/10.1.012/lib/ LDFLAGS="-L$ICC_LIBS -L$IFC_LIBS -L/usr/lib64"

Hi, I'm getting the following error: > install.packages() --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... Error in fun(...) : Can't find a usable tk.tcl in the following directories: /usr/share/tcltk/tcl8.4/tk8.4 ./lib/tk8.4 /usr/local/lib/tcltk/tk8.4 /usr/local/share/tcltk/tk8.4 /usr/lib/tcltk/tk8.4 /usr/share/tcltk/tk8.4 ./library

I'm compiling the latest stable build (2.7.0) from source using the Intel Compilers, following the hints in the R-admin guide. I'm using OpenSUSE 10.3 on a Intel Q6600 system. First let me explain a few things I did: 1: Download & Install all the Intel Compilers (as well as the Intel Math Kernel Library) (All defaults) 2: Set up my environment variables in profile.d, using the handy

Hello r-bugs, I am running openSuse 11.0, with my new Intel 8500 (Penryn) C2D, and I want to use icc and ifort. I was able to get a working Goto BLAS, following Dr. Goto's instructions. That seems to work OK with gcc and gfortran. I get about 10% faster computations by using -O3 rather than -O2. I get faster results with Goto BLAS rather than the R BLAS. Now I want to make icc and ifort

Hi Martyn, Thanks for your insight, that seems pretty direct. Unfortunately, I did not compile this version of R (it's on a large supercomputer system and this version of R was installed by the admins). Using "R CMD config", I see the following relevant settings: DYLIB_LD = icc -std=gnu99 DYLIB_LDFLAGS = -shared -openmp LDFLAGS = -L/opt/compilers/intel/cce/9.1.039/lib

I just downloaded R-devel and when loaded it immediately segfaults. I'm not sure how much or what sort of diagnostic info and can provide, but below is my build script, my console output, and the output of uname -r. I am currently dependent on the development version of a package, so I'd like to get R-devel up and running if possible. I am sure there is more info I can provide, but before

I can compile RSPython without difficulty, been when I try to load it, I get the error messages below. Also below are some cryptic warnings I get on R boot (in case these are pertinent) and my sessionInfo(). Any help is appreciated. Thanks, Mark Warning messages: 1: In .updateMethodsInTable(fdef, where, attach) : Couldn't find methods table for "conditional", package

I'm having trouble with a Bioconductor package, an variable expected in an environment does not seem to be there. As part of my investigation of the problem (most likely on my end) I'd like to list the variables contained in an environment. If you have an environment loaded, lets call it "pkgEnv', how does one find what it does contain? Mark

I have a very long list of strings. Each string actually contains multiple values separated by a semi-colon. I need to turn each string into a vector of the values delimited by the semi-colons. I know I can do this very laboriously by using loops, nchar, and substr, but it is terribly slow. Is there a basic R function that handles this situation? If not, is there perhaps a faster way to do it than

I am having trouble getting an install of RCurl to work properly on a Unix server. The steps I have taken are: 1. installed cUrl from source without difficulty 2. installed RCurl from source using the command ~/R_HOME/R-devel/bin/R CMD INSTALL -l ~/R_HOME/R-devel/library ~/RCurl_0.8-0.tar.gz I received no errors during this install 3. when I go back to R and require(RCurl), I get >

I am having trouble getting an install of RCurl to work properly on a Unix server. The steps I have taken are: 1. installed cUrl from source without difficulty 2. installed RCurl from source using the command ~/R_HOME/R-devel/bin/R CMD INSTALL -l ~/R_HOME/R-devel/library ~/RCurl_0.8-0.tar.gz I received no errors during this install 3. when I go back to R and require(RCurl), I get >

Subject pretty much says it all. Wonder if there is there is some code in XML that the new gcc doesn't like? See output below: * Installing *source* package 'XML' ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking

For years I have been using options(error = recover) either in .Rprofile or from within R for debugging purposes. The functionality of this appears to have changed and I can't recover it (no pun intended) using the ?options help page. How can I get the old functionality back, particularly from within .Rprofile? A specific line entry would be appreciated. An example, the help page, and

Subject pretty much says it all. I am running 64-bit Ubuntu 8.04, i.e. Hardy Heron, have openmpi installed, and get the following error message with attempted install of Rmpi. sessionInfo() follows. Mark checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes

I have identical R.profiles and R_HOME directories set up on both my local machine and a remote linux cluster. To keep my libraries and R install separate, I use a site-library on both machines. The first line of my .Rprofile is: '.libPaths(new= "~/R_HOME/site-library") #tell R where site-library is' Until R-2.6.0 this was working fine on both machines, but since I have been

Dear list... In regards to recent upgrade in www.clamav.net to 0.88.3 and... ...as an example I've used this page to create a process where I can create my own clamav programs/stuff/etc... http://qmail.jms1.net/clamav-upgrade.shtml and so I would go to http://crash.fce.vutbr.cz/crash-hat/4/clamav/ and snag the source rpm that Petr made for Fedora 4. He hasn't updated yet (pretty sure

Sorry for the long letter! I have recently started using R. For the start I have tried to repeat examples from Milliken & Johnson "Analysis of Messy Data - Analysis of Covariance", but I can not replicate it in R. The example is chocolate chip experiment. Response variable vas time to dissolve chocolate chip in seconds (time), covariate was time to dissolve butterscotch chip

I am performing many permutations on a data-set with each permutation producing a variable number of results. I thought that the best way to keep track of all this in one object would be with a list ('res.lst'). To address these variable results for each permutation I attempted to construct this list using 'assign'. There is even more nesting than indicated below, but this is a

Just installed the latest R-patched and get the error seen at the end of the output below. Don't know what to make of this but thought I should report it. In general, when installing the latest version of R, should one use R-latest or R-patched? R-latest is stable, but one would assume that R-patched includes the latest bug fixes. Mark mkimpel-m90 ~/R_HOME/R-patched/R-build/bin: ./R R