similar to: calling MPI parallel C code from R

A few years ago I used the following to compile a shared object that I wanted to call from R and it worked just fine. R CMD SHLIB -o ~/my_C/R.shared.so/cocite.mat.so cocite.mat.c Now when it is executed?I receive the following error message: make: *** No rule to make target `cocite.mat.o', needed by `/home/mkimpel/my_C/R.shared.so/cocite.mat.so'. Stop. I've consulted R CMD SHLIB

I have been working with my sysAdmin to get R-devel up and running with 64-bit compilation on our PowerPC cluster. We've got the base install to compile with the following flags: LDFLAGS=-m64 FFLAGS="-m64 -mpowerpc64" FCFLAGS="-m64 -mpowerpc64" CFLAGS="-m64 -mpowerpc64" ../configure --prefix='/N/hd03/mkimpel/BigRed/R_HOME/R-devel/R-build'

Switched back to R-devel tonight after using R-2.6.1 for awhile and when I updated my devel packages Matrix installation failed. Not critical for me but thought I should report it. I am using Ubuntu Gusty AMD64 OS. Tail of install output and sessionInfo follows. Mark Loading required package: methods Loading required package: lattice Attaching package: 'Matrix' The

I am experiencing an OOLOCK error when attempting to update packages to my site-library. I have an identical setup on my local Linux machine, but this problem on the remote Linux machine (PPC cluster) started about 3 weeks ago and is present whether I used R-devel or R-2.6.0 or R-2.5.1. Also, of course I manually remove the 00LOCK folder after each failed attempt. Below is my error output,

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 >

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

Martin, Well, thanks for jumping in! We need all the help we can get ;) I changed the execute bit as you suggested and recompiled, no luck, still the same error message. Below is the output you wanted me to look at, its a bit beyond me so I include both a brief grep summary and then the whole enchilada. I do note that my output is different from yours, but I'm not sure how to interpret. I

Martin, Well, thanks for jumping in! We need all the help we can get ;) I changed the execute bit as you suggested and recompiled, no luck, still the same error message. Below is the output you wanted me to look at, its a bit beyond me so I include both a brief grep summary and then the whole enchilada. I do note that my output is different from yours, but I'm not sure how to interpret. I

I'm doing some work on a potential patch to the Bioconductor package Rgraphviz and have some questions on code that is contained in engine.c. In particular, I am developing some custom shapes using polygon and need to make sure that, with rendering, the line connecting the centers of two polygons stops at the border of each polygon. The polygons can be transparent, so the option of just

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 that I'd like to subset based on a logical value within each element. Example below. I'd like to get just those list elements for further study whose $sig.cor slot is TRUE. In this example, I'd only want element [[2]]. Should be simple, I know. How can I do this? Thanks, Mark > gene.pair.tf.lst [[1]] [[1]]$gene.pair [1] "Lgals1:Pxmp2"

I am doing some work the Rgraphviz, a Bioconductor package, but since my question is of a more general nature, thought I would send to this list in hopes that a graph theory expert could answer my question. I wish to do some statistics on node-node relationships. In particular, I want to see if two connected nodes share a common property. I believe that the more "connected" the two

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

I'm running Mclust 3.0 in R-2.7.0 and have run into a situation where the optimal number of clusters, 12, seems to be greater than the number of colors available to Mclust. The code below, which demonstrates errors, does not if the max no of clusters is set at 10. sessionInfo, after a restart of R and loading of packages, follows the output. Is this a known problem with Mclust? Can I

Some time ago I had difficulty installing RBGL with Ubuntu Hardy on R-2.7.0 and the problem was attributed to an with BGL. I got some very helpful advice and posted a script to fix the problem by hacking the RGBL source code: dateTue, Jan 15, 2008 at 2:16 PMsubjectRe: [R-sig-Debian] trouble installing building packages from source using R 2.6.0 on Ubuntu Gutsy AMD64mailing

I have used merge regularly and thought I understood how it worked, but I must not. I have two dataframes with identical colnames from two different experiments, TL01 and LC01. Each dataframe has a column named "Entrez.Gene", which I have converted to "as.character" just to make sure merge is not looking at factor levels. Because I have done some filtering, the Entrez.Gene

I am getting some unexpected results from some functions of igraph and it is possible that I am misinterpreting the vertex numbers. Eg., the max betweenness measure seems to be from a vertex that is not connected to a single other vertex. Below if my code snippet: require(igraph) my.graph <- graph.adjacency(adjmatrix = my.adj.matrix, mode=c("undirected")) most.between.vert <-

After some struggling with the data format, non-standard in BioConductor, I have gotten cor.balance in package CORREP to work. My desire was to obtain maximum-likelihood p-values from the same data object using cor.LRtest, but it appears that this function wants something different, which I can't figure out from the documentation. Briefly, my dataset consists of 36 samples from 12

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