similar to: install.packages Error

Hi, I had originally posted regarding an error when trying to install package - GenABEL - it has now become clear that R is not able to connect to the net. Below are a couple of things I've tried with the resulting errors I am running R 2.6.2 on Linux e15 X86 How can I fix this? Thank you! 1) download.file("http://www.nytimes.com", destfile<-tempfile()) Error: trying URL

Dear all, since yesterday, I have been experiencing problems with the package GenABEL. When I try to load the package (library(GenABEL)) I get the following error message: Loading required package: MASS Error : .onLoad failed in loadNamespace() for 'GenABEL', details: call: stringSplit[[1]] error: subscript out of bounds Error: package/namespace load failed for ?GenABEL? The funny

Hi all! I am using GenABEL on R for GWAS analysis. I am having a couple of issues: First, I am having a problem reading files (.map, & .ped, size 900Mb, using windows 32-bit) onto R in the "convert.snp.ped" statement. I am thinking this problem is likely due to the large size of the files & my version of R is not able to handle them, since I can read in smaller files.

Hi all! I am desperately trying to figure out the solution to this error, but nothing as of yet is working. As noted in an earlier post I am using GenABEL. In an attempt to read in the phenotype file, in the format .dat, R keeps giving me the error "more columns than column names" I have tried to read in the data without the headers; I have also tried to trim the data to remove any

I've looked through all of the posts about this issue (and there are plenty!) but I am still unable to solve the error. ERROR: cannot allocate vector of size 455 Mb I am using R 2.6.2 - x86_64 on a Linux x86_64 Redhat cluster system. When I log in, based on the specs I provide [qsub -I -X -l arch=x86_64] I am randomly assigned to a x86_64 node. I am using package GenABEL. My data (~ 650,000

Hi, I am using a function 'polygenic' in the package called 'GenABEL'. -------------------------------------------------------------------------------- > h2.gs <- polygenic(b.dbp~age+age2+age3+sex+b.bmi, kin=gs.gkin, data=gs) ------------------------------------------------------------------------------- ## and I got the following error message: Error in svd(X): infinite or

Does anyone use the R library GenABEL? I am using it to calculate SNP interactions. I have a list of 100 SNPs, I need to look at the interaction between each of two SNPs among the list. my question is how to perform this in GenABEL. I want to use the "lm" function, but don't know how to use the SNP information. for example: result <- (lm(y~SNP1+SNP2+SNP1*SNP2)) the problem here

Dear R developers: I am a PHD candidate student in the school of public health of Peking University and my major is genetic epidemiology. I am learning the FAM-MDR algorithm, which is used to detect the gene-gene and gene-environment interactions in the data of pedigree. The codes were written by Tom Cattaert of the University of Liege. The algorithms and the sample datasets are available at

Hi, I'm using kinship2 to calculate heritabilty, but I would like calculate in GenABEL too. I trying the code: > require(kinship2) > require(GenABEL) > pedig = with(Dados, pedigree(id=IID, dadid=PAT, momid=MAT, sex=SEX, famid=FID, missid=0)) > kmat = kinship(pedig) > (mod1 = polygenic(altura ~ SEX + idade, data=Dados, kin=kmat)) Erro em intI(i, n = d[1],

> Dear Sirs , > Today I've downloaded the last release of the R-Program (I an a novel user). I am interested on performing time series analysys (regression,ARIMA,ARCH) to some data-sets, therefore I would like to use some of the packages of R-Contributors (like the tseries one).When I try to install or update packages from CRAN the following text always appear: > > local({a <-

Hi, I've been trying to use the impute2mach function in the GenABEL library. I unfortunately cannot make a working example as when I scale down the files I no longer get an error message. The error message that I get on the full file is: Error in checkSlotAssignment(object, name, value) : assignment of an object of class "NULL" is not valid for slot "data" in an

I'm trying to write a package which uses classes/methods as defined in the `methods' package. I have a single .R file which defines the class and various methods for that class. At the top of the file I have require(methods) and then setClass("myclass", ...) setGeneric("intersect") setMethod("intersect", "myclass", function(x,y) ...) I noticed

The workshop organizing committee of the Southern California Chapter of the American Statistical Association announces the 28th Annual Workshop in Applied Statistics. Professor Colin Cameron from the department of Economics at UC Davis will give a one-day workshop titled "Advances in Count Data Regression." The event will take place on Saturday, March 28, 2009 at UCLA. Details on

======================================================================= Simple CRAN packages which do not compile without modifications (all others do) ======================================================================= -- akima /usr/bin/ld: multiple definitions of symbol _idlc_ -- fracdiff /usr/bin/ld: multiple definitions of symbol _gammfd_ (and others) -- odesolve --

hi, I am from Norway and you'll don't believe me, but a trojan horse in on your pc. I've scanned the network-ports on the internet. (I know, that's illegal) And I have found your pc. Your pc is open on the internet for everybody! Because the smss.exe trojan is running on your system. Check this, open the task manager and try to stop that! You'll see, you can't stop this

Quick question about installing packages on a system where you do not have root access. Suppose a person is using R on a shared system where he cannot write to the installation directory (i.e. /usr/local/lib/R). What general advice would you give regarding where to install packages from CRAN. Should he use the R_LIBS environment variable or maybe .libPaths() in R or .Renviron? Thanks, -roger

Dear R-helpers, I would like to have my students read into R an online Stata dataset: 'http://www.stat.ucla.edu/projects/datasets/risk_project.dta' I was able to read it into R after downloading it and converting it with StatTransfer (http://www.stattransfer.com/). Here is what happens when I use read.dta() as I would use read.table(): > require(foreign) > risk2 <-

I have a few questions about GenABEL, gwaa data. 1) is there a universal way that most GenABEL people use to add more individuals into a 'gwaa' data? For example, I have a 'gwaa' data, but I need to add some dummy parents, for 'gwaa at phdata', it's easy to add these rows, but for 'gwaa at gtdata', I think I need to create SNP data as '0 0 0 0 0.....'

Hi, is it possible, that the current development version for Windows ( http://cran.at.r-project.org/bin/windows/base/R-2.13.0dev-win.exe) is infected by a trojan/virus. My antivir-program (www.avira.com) seems to find a trojan in open.exe at bin\i386. Best regards, Andreas [[alternative HTML version deleted]]

I have build R-1.6.0 on Jaguar (actually on 10.2.2), using gcc 3.1 from Apple, g77 3.1 from fink, ATLAS from fink. It passes all checks OK. I also re-compiled the 233 packages listed below with the same setup. I have NOT tested all these packages in any detail. A tar.gz file with the whole /usr/local/lib/R will be on ftp://gifi.stat.ucla.edu on Tuesday. It will NOT include anything from fink