similar to: R/BioConductor error (PR#7282)

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, I am new to using R and Bioconductor. My first attempt at installing R seemed successful. Then while attempting to getBioC() I had to force quit the R application since I had to attend to something else urgently. When i returned and tried to getBioC, I am getting errors indicating that there is a lock on some files. So i would like to uninstall/remove all R components and Bioconductor

--Apple-Mail-1--963012407 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Hi, I get exactly the same error message as in report no 6920. Furthermore, starting "update Bioconducter" the following message appears (running Mac OS X 10.3.4 (7H63)) : > {library(reposTools);update.packages2(getAllDeps=TRUE)} Synching your local package

Dear list, I face some problems installing gpclib_1.0-1.tar.gz: R-161 R : Copyright 2002, The R Development Core Team Version 1.6.1 (2002-11-01) [...] system("R CMD INSTALL gpclib_1.0-1.tar.gz") WARNING: ignoring environment value of R_HOME ERROR: This R is version 1.5.0 package 'gpclib' depends on R 1.6.1 The same happens with http://www.bioconductor.org/getBioC.R

Hello, I am trying to install R/Bioconductor on a G4 Mac running OS X. I have successfully installed R so that a command window opens, but installation of the downloaded Bioconductor package is giving me trouble. After copying/pasting the Bioconductor installation script in to the window and typing getBioC(), I get the following error message. "Error in getBioC(): R not currently

Hello useRs, I'm trying to install bioconductor on ubuntu edgy eft and R 2.4.0. I have some error messages during installation, in particular for the package "affy" : "Error: package 'affy' required by 'makecdfenv' could not be found" I have tryed to install 'makecdfenv' with the command : getBioC("makecdfenv") But I have this message

Why am I seeing the following in R-devel (sept 2, 2006 build) on opensuse 10.1? I'm sure it is something simple I am missing, but I just don't see it (output below). Thanks, Sean > readLines(url("http://www.bioconductor.org/biocLite.R")) [1] "source(\"http://bioconductor.org/getBioC.R\")" [2] ""

Hi, I have built R (current development version) and BioConductor 1.7 with portland group compiler on a AMD Opteron. When I ran qc assessment on Affymetrix latin square data set, I got the following output, Loading required package: affy Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view,

OK, I really am struggling with this one! Forgive me if I am being stupid.... I am running R 1.7.1 on Suse Linux 8.1. I connect to the internet through a proxy so I have: IAHC-LINUX03:~ # echo $http_proxy wwwcache.bbsrc.ac.uk:8080 IAHC-LINUX03:~ # echo $HTTP_PROXY wwwcache.bbsrc.ac.uk:8080 just in case ;-) SO, i go into R and I get: >

I am receiving the following errors when trying to install gcrma and a number of other Bioconductor packages when the installWithVers flag is set to be TRUE. >source("http://www.bioconductor.org/getBioC.R"); >getBioC("gcrma", installWithVers=T); Running biocinstall version 2.0.7 with R version 2.5.0 Your version of R requires version 2.0 of Bioconductor. Loading

dear all, I try to update my Rversion fro 1.7.1 to 1.8.1 on linux. I have a problem when I try to install pacakges from Bioconductors with : source("http://www.bioconductor.org/getBioC.R") and getBioC(relLevel="release") somme errors append and when I make a library(affy) for example I obtain : > library(affy) Error in setIs("character",

I was trying to install R on a unix server. Because of a firewall i can't install biocLite for working with Bioconductor. With windows it wasn't a problem. I used the option '--internet2' to bypass the firewall. I don't have any idea, how to do it with unix. I tried to set my proxy >Sys.putenv("http_proxy"="http...:8080")

Hi, I am trying to install the BioC package from bioconductor onto a Windows Server 2003 machine. I can connect to bioconductor and when I run the getBioC("affy","release") function it starts to download but then it stops with the following error: Error: unable to create temporary directory 'C:\Program Files\R\R-2.2.1\release\file1eb26e9' The download just ends

Hi everyone, My purpose is to read a .CEL file into R. The .CEL file was created from a .CAB by using DTT software found on Affymetrix website I read the .CEL file in R using ReadAffy as follows: > d2=ReadAffy(widget=T) and I complete the fields as required. It does not complain. For example I could find the description: > description(d2) Experimenter name: BB Laboratory: FFL Contact

Hi Thanks once again for your help, I do appreciate it..... however.... Here is what I get with your test.... (under tcsh - i normally use bash, but I will keep everything the same) users/mwatson> env http_proxy=http://wwwcache.bbsrc.ac.uk:8080/ R >options(internet.info=0) >update.packages() trying URL `http://cran.r-project.org/src/contrib/PACKAGES' unable to connect to

The Bioconductor development team announces release 1.1 of the Bioconductor packages for the analysis of genomic data. Bioconductor is an open source bioinformatics software project based on R. Version 1.1 features: ===================== * All packages from the 1.0 release are included. All current bug fixes have been applied, and most have upgraded and provide enhanced functionality. *

The Bioconductor development team announces release 1.1 of the Bioconductor packages for the analysis of genomic data. Bioconductor is an open source bioinformatics software project based on R. Version 1.1 features: ===================== * All packages from the 1.0 release are included. All current bug fixes have been applied, and most have upgraded and provide enhanced functionality. *

>I just installed bioconductor via getBioC.R but there >is 3 problems: apparently some libraries are missing >and I don't know which one, and even the XML package >add a error message like : >1:Installation of package Rgraphviz had non-zero exit >status in: installPkg(fileName, pkg, pkgVer, type, >lib, repEntry, versForce) >2:Installation of package rhdf5 had non-zero

Hi , there: I used function source to download the package but found > source("http://www.bioconductor.org/getBioC.R") Error in file(file, "r") : unable to open connection In addition: Warning message: unable to resolve 'www.bioconductor.org'. Then I downloaded the packages from CRAN and found > local({a <- CRAN.packages() +

Dear list, I have a lot of troubles installing Rgraphviz. I installed graphviz 2.13 from "graphviz-2.13.20061222.0540.tar" I installed the library Rgraphviz > getBioC("Rgraphviz") Running biocinstall version 2.0.8 with R version 2.5.0 Your version of R requires version 2.0 of Bioconductor. trying URL '