similar to: Can´t start help and update on Mac (PR#6920

reposTools is part of Bioconductor not R. Please use the correct bug repository. Note that PR#6920 does not mention any `error message' whatsoever (nor does it claim to): the message quoted help.start() Making links in per-session dir ... If /usr/bin/open is already running, it is *not* restarted, and you must switch to its window. Otherwise, be patient ... is the standard

Hi I am running R 2.0 on Suse Linux 8.2. I get an error message when loading a library: "Incorrect permissions to edit the package database, /usr/lib/R/library/liblisting.Rda: save.locLib(locLibList, curLib)" However, when I look at that file, the user I am running R as has r and w permissions on it.... So firstly - any ideas why I get this error message? And secondly, does it

Full_Name: H Deshmukh Version: 2.0 OS: 2000 Submission from: (NULL) (129.174.206.239) Can somebody tell me what is it that i am doing wrong,i was not sure whether to post BioConductor error here or not. Thanks >source("http://www.bioconductor.org/getBioC.R") > getBioC(libName = "all") Running getBioC version 1.2.65.... If you encounter problems, first make sure that

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

Full_Name: Dr. Hans A. Kestler Version: 1.8.1. OS: Linux, Win, Mac OSX Submission from: (NULL) (134.60.73.116) The code below produces after a different number of iterations i the following error: Error in optim(par = rep(0.5, length(edges)), loglik, method = "L-BFGS-B", : non-finite value supplied by optim This was reproducible on different machines (Mac G4 OSX, AMD Opteron

Dear List, I tested the example in the reposTools vignette: library(reposTools); Loading required package: tools genRepos("Test Repository", "http://biowww.dfci.harvard.edu/~jgentry/","newRepos"); Error in rep.int(colnames(x), nr) : unimplemented type 'NULL' in 'rep' Could someone help me out with this one? I'd appreciate all help.... I am

Full_Name: Hans Kestler Version: 2.2.0 OS: 10.4.3 Submission from: (NULL) (84.156.184.101) > sam1.out<-sam(raw1[,2:23],raw1.cl,B=0,rand=124) We're doing 319770 complete permutations Error: cannot allocate vector of size 575586 Kb R(572,0xa000ed68) malloc: *** vm_allocate(size=589402112) failed (error code=3) R(572,0xa000ed68) malloc: *** error: can't allocate region

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,

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

Hi, I want to automatically fit variograms to a large number of different sample data sets, and call the funtion "likfit" (in package geoR) from within a for-loop. "likfit" does again call "optim". After ssuccessfully fitting variograms to some of the data sets, the procedure crashes and I get the error message: Error in optim(par = ini, fn = negloglik.GRF,

Hi, is it possible to generate differently colored error bars in one plot? Thx in advance, Heinrich [[alternative HTML version deleted]]

...unless its me missing something... > help.search("prompt", agrep=F) Error: couldn't find function ".class1" > traceback() 12: initialize(value, ...) 11: initialize(value, ...) 10: new("ObjectsWithPackage", value, package = pkg) 9: metaNameUndo(unique(these), prefix = "M", searchForm = searchForm) 8: methods:::getGenerics(ns) 7:

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

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. *

Sorry to ask a (probably) dumb question, but I am trying to install XML package on Windows XP, R 2.0.1, and I get the error: "This application has failed to start because libxml2.dll was not found. Re-installing the application may fix this problem" > library(XML) Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library

Hi How do I install "gregmisc" packages? I did- % sudo R > install.packages("gregmisc") . . > barplot2() but, Error: couldn't find function "barplot2" -- atuya Mac OSX 10.2.6 R 1.7.1

Dear R folks, One of the fantastic new tools in R is `Sweave'. I have tested it so much that I know it works and produces fine documentation, and with (GNU) Emacs/ESS it is nice to work with, too. I started to have a look at including some Swoven (is that a strong verb?) documentation with my R package, but it seems that there is no model to copy among those packages that I have installed in

Hi, I been trying to install bioconducter into R using the script on the bioconductor home page. However, I get this error message: > source("http://www.bioconductor.org/biocLite.R") Error in file(file, "r", encoding = encoding) : unable to open connection In addition: Warning message: unable to connect to 'www.bioconductor.org' on port 80. It is maybe

I'm sorry if the answer to my problem is buried in the archives. I have limited experience with R and I couldn't find a solution to my particular problem. I am running Mac OS X Aqua GUI v1.01 on a new G5 running os 10.3.8 with a 1.8Ghz processor and 1GB of sdram. I just downloaded bioconducter a week ago and I'm trying to cluster a matrix I created with a simulation with