search for: sblay

Dear R-helpers, I am developing a package named LDehatmap. It depends on the "genetics" package and includes two data files and a demo file. When I'm trying to install it, I get the following messages: * Installing *source* package 'LDheatmap' ... ** R ** data ** demo ** help >>> Building/Updating help pages for package 'LDheatmap' Formats: text html

...on windows, but on Linux (SuSE 64 bit), using OpenMPI, I can't seem to get it to work :( When I do library(Rmpi) I get the warning: mca: base: component_find: unable to open osc pt2pt: file not found (ignored) Interestingly enough all the examples from the snow tutorial ( http://www.sfu.ca/~sblay/R/snow.html) work despite the warning. But then, when I run my app I get mca: base: component_find: unable to open osc pt2pt: file not found (ignored) mca: base: component_find: unable to open osc pt2pt: file not found (ignored) 2 slaves are spawned successfully. 0 failed. *** Process rec...

I wrote an R wrapper function (phylpro) around a C function (Rphylpro). The first time I'm running my function, it runs with no errors. The second time I'm trying to run it, I get an error message with the first argument to .Call garbled. Set up: > dyn.load("Phylpro.so") > source("phylpro.R") > WinHalfWidth<-30 > permReps<-10 > breaks<-c(548,

Hi, I'm new to calling C++/C programs from R and am having some trouble getting started. Following Sigal Blay (Simon Fraser University)'s instructions, I have a .c file called "useC1.c": /* useC1.c */ void useC(int *i) { i[0] = 11; } This produces a .o file : "useC1.o" in a specified directory. I then open R, set the proper directory and:

Is there any way to store the value of warnings but avoid printing them? A simplified example: > out <- c(0.2,0.3,0.4) > var <- c(2,3,4) > outcome <- glm(out ~ var, family=binomial()) Warning message: non-integer #successes in a binomial glm! in: eval(expr, envir, enclos) I don't like the warning printed, but I would like to be able to check it's value after the

Hello R experts, I've been searching for weeks a way to use my quad core xeon to increase speed of a very-very computer-intensive simulation I must do for my works. It seems that most purpose-made packages for R : Snow, Rmpi, snowfall,... are designed for Linux based OS. I do not have access to Linux due to professionnal reasons ... so I must work with windows XP. Do somebody know a way to

Dear R-user, I am trying to use the function 'parLapply' from the 'snow' package which is supposed to work the same wys as 'lapply' but for a parallelized cluster of computers. The function I am trying to call in parallel is 'dudi.pca' (from the 'ade4' package) which performs principal component analyses. When I call this function on a list of

Need way to resize an existing graphics window. This should be applicable across platforms (as part of a package). Context: function1() draws main plot (I'm using grid), function2() adds smaller plot above main plot, but this one can sometimes overflow the original graphics window area. Thanks, Sigal

...not have access to Linux due to > professionnal reasons ... so I must work with windows XP. > > Do somebody know a way to unleash the calculation power of all four cores > under windows XP ? Just tried snow under Windows 2000 and it works. Just follow the examples on http://www.sfu.ca/~sblay/R/snow.html but create a cluster as follow: cl <- makeSOCKcluster(c("localhost", "localhost", "localhost", "localhost")) and you have a cluster of all your four cores. As I don't have a dual or quadcore running windows, I can't confirm that it i...

Version 1.0 of hapassoc now available from CRAN hapassoc is an R package for likelihood inference of trait associations with SNP haplotypes and other attributes using the EM Algorithm. Recent changes include the addition of anova and logLik methods for the class hapassoc, to allow users to perform likelihood ratio tests of haplotype effects. Other changes include bug-fixes and improvements to

Dear R helpers, I need to retrieve several vectors of various types from a call to .C(), but I don't know their length in advance. Is there a way to do this without allocating an excessive amount of memory? If so, an example would be very helpful. S. Blay Department of Statistics and Actuarial Science Simon Fraser University, Vancouver, British Columbia

Dear R helpers, MyPkg passes R CMD check on Linux machines. However, when I 'R CMD check myPkg' on Windows, the libs subdirectory is not being created. If I install the package and then create the libs subdirectory manually and copy the dll files to it, the package seems to work fine (but that's not good enough for submitting it to CRAN). Any advice will be appreciated, Thanks,

Version 1.0 of hapassoc now available from CRAN hapassoc is an R package for likelihood inference of trait associations with SNP haplotypes and other attributes using the EM Algorithm. Recent changes include the addition of anova and logLik methods for the class hapassoc, to allow users to perform likelihood ratio tests of haplotype effects. Other changes include bug-fixes and improvements to

Version 0.2 of the package LDheatmap is now on CRAN. The main function LDheatmap produces a graphical display, as a heat map, of measures of pairwise linkage disequilibria between SNPs. Users may optionally include the physical locations or genetic map distances of each SNP on the plot. The revisions to the package are aimed at improving the user's ability to modify and annotate the

I'm writing a package that successfully calls Java from R using rJava. When R sends my Java function bad data (through .jcall()), I get the error message details (when I run it on a console) and then: Java requested System.exit(1), closing R. Is there a way to call .jcall so that when Java receives bad data, the Java function will exit, but won't take down R with it? Thanks, Sigal

Dear R helpers, MyPkg passes R CMD check on Linux machines. However, when I 'R CMD check myPkg' on Windows, the libs subdirectory is not being created. If I install the package and then create the libs subdirectory manually and copy the dll files to it, the package seems to work fine (but that's not good enough for submitting it to CRAN). Any advice will be appreciated, Thanks,