similar to: Problems installing R

Neither biocLite nor the GUI menus can install packages on my system. Here is relevant output: > version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 11.1 year 2010 month 05 day 31 svn rev 52157 language R version.string R version 2.11.1 (2010-05-31) > source("http://bioconductor.org/biocLite.R") BioC_mirror =

Dear R-help Hi, I'm Won. I try to do microarray normalization by R. I use justRMA function within affy package, got error about segment fault. I don't know why it happen. I attached error below. Please help me. Thank you. Cheers, Won ======================= OS : Redhat linux Cpu : intel xeon X5570 Memory : 26Gb & OS : Ubuntu Cpu : intel q6600 Memory : 8Gb

Hi, I am trying to install Bioconductor onto R version 2.7.0 for Windows. I installed R, then followed the instructions on http://www.bioconductor.org/download, which state that you should type the following: source("http://bioconductor.org/biocLite.R") biocLite() When I do that, I get the following error: Running biocinstall version 2.2.9 with R version 2.7.0 Your version of R

Hi together, we received a question about the bioconductor package, maybe anybody could help the guy and I will deliver the message over our forum to him. If this way is allowed ... Regards Knut Here the question: Hello, I have installed R on a linux machine. I have then installed the biocLite.R package from bioconductor. I wanted to install a few other packages - hgu133plus2cdf, rma . I

Hi again, I have been playing around with the order of loading packages, and as far as I can tell, there's nothing specific with affycoretools that's causing my Rgui to crash (i.e., shuts down and the Microsoft 'please send error report' box pops up). Instead, it has something to do with the order & type of packages that are loaded that add items to the menu bar by

hi all, Am new to R. I am having problems installing Bioconductor package in R on fedora core 4 running on AMD64 bit machine. this is the error message I get : gcc -shared -L/usr/local/lib -o affyPLM.so avg_log.o biweight.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o LESN.o lm.o lm_threestep.o log_avg.o matrix_functions.o

Hello, I want to use expresso for preprocessing the hgu133a-spikein data from affycompII. But there is an error: > library(affy) > path <- "z:/Microarray/hgu133a-spikein/rawdata" > celFile <- list.celfiles(path=path,full.names=TRUE); > affyBatch <- ReadAffy(filenames=celFile[1:6]); > eset1 <-

Dear All, I am trying to build a package for a set of functions. I am able to build the package and its working fine. When I check it with R CMD check I get a following warning : no visible global function definition for ‘biocLite’ I have used biocLite to load a user defined library from within a function if that library is not pre-installed

Dear people, I'm new here, so this is my first try. I have ubuntu 9.04 installed with R 2.8 (which surprises me because I realized that the last version R 2.9 is available but in the Synaptic Package Manager 2.8 appears as the last one). I have also graphviz 2.20.2. I have been trying to install Rgraphviz either from R running "biocLite("Rgraphviz")" and from the shell

I am getting the following error in my script. I am very very new to R and have obtained this script from another person. #read file in (dummy data) starburst.plot<-function(affy.fold, affy.FDR)(ifelse( ((affy.fold) >=0), -1*log10(affy.FDR), 1*log10(affy.FDR))) starburst.plot<-function(meth.fold, meth.FDR)(ifelse( ((meth.fold) >=0), -1*log10(meth.FDR), 1*log10(affy.FDR))) At my next

Hello, I am trying to install affy package in R as follow: >R CMD INSTALL -l lib ~/rstuffs/affy_1.4.32.tar.gz Then I get an error at the end: Warning message: There is no package called 'Biobase' in: library(package, character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts, [1] "ProgressBarText" [1]

Hi, I decided to upgrade to 1.8 today... :-) Anyway, we are writing our own package that is dependent on a bioconductor library - 'affy'. I've checked and when I fire up R, library(affy) behaves as expected... so it all seems to be installed and OK... In the DESCRIPTION file in my package source I have the line: Depends: affy When I run R CMD check simpleaffy I get to: ... *

Hello all, I am trying to make a genome association plot for p-values related to SNPs and was fortunate to find that R contains a package that produces Manhattan plots which is what's preferred for my current project. The function mhtplot() is found in the 'gap' package which I installed in R 2.11.1 on Windows. I thought I'd test out the function first with the examples they

I have run into a problem loading a just saved R object using R-devel. I have been saving and loading this particular type of R object for a long while and never ran into this problem. I save, then immediately reload (to test save) and get "ReadItem: unnknown type 65". This error is reproducible after logout from server and restart of emacs and R. Below is my output and

I have run into a problem loading a just saved R object using R-devel. I have been saving and loading this particular type of R object for a long while and never ran into this problem. I save, then immediately reload (to test save) and get "ReadItem: unnknown type 65". This error is reproducible after logout from server and restart of emacs and R. Below is my output and

Hi, I have been using the prcomp function to perform PCA on my example microarray data, (stored in metric text files) which looks like this: 1a 1b 1c 1d 1e 1f ...................................................4r 4s 4t g1 1.2705 1.2766 ...........................................................2.0298 g2 0.1631

Hi R-ers, I am struggling with my x-axis in a association plot. What I would like is to place the labels of the x-axis between the tick markers and normally the labels are printed at the place where the tick marker is placed. I don???t want to move the tick marker (it gives the switch between one chromosome and the next) but I just want to put the chromosome number in between the

Hi, all. Something strange happened to my ESS. I use Mac OS X. When R is used in stand alone mode, it recognizes external libraries like "affy", "e1071" etc. However, when R is invoked through ESS in Emacs, it produces errors like: Error in library(affy) : There is no package called 'affy' Interestingly, I remember I successfully used these libraries through ESS in

Dear list, I?m using R embedded in another program (coded in tcl/tk) under Windows Vista. In this context I don?t launch Rgui.exe but rather Rtem.exe. Now I have a problem finding libraries not specifically installed as administrator (and which are not in the path ?program files? but in Contacts\Documents of the current user). To be precise, the user launching my tcl/tk program can?t find

Hi Matt Your method is the easiest way for me to install the 64-bit R. I followed the directions on your web site and then did the following: R --arch=x86_64 source("http://bioconductor.org/biocLite.R") biocLite(type = "source",lib = "/Library/Frameworks/R.framework/Versions/2.8/Resources/RLib64") I got many errors and warnings which I copied to the attached file.