search for: repostools

...12407 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 management information ... Packages which have been added/updated: sm sma wavethresh Note: reposTools can not access /Library/Frameworks/R.framework/Resources/library. This will not affect your R session unless you wish to...

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 t...

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...

...ny concerns or questions to bioconductor@stat.math.ethz.ch. You are downloading all of the Bioconductor packages and any dependencies. Depending on your system this will be about 90-95 packages and be roughly 200MB in size. Are you sure that you want to do this? [y/n] y Loading required package: reposTools Error in library(package, character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts, : 'reposTools' is not a valid package -- installed < 2.0.0?

...ion 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 which cannot install the reposTools (same error message). I was suggested to try above unusal install method as reposTools from bioconductor is using it. Then I was suggested to report this error here. In general our R-161 installation (Linux/i686) works well. Also running 'R CMD INSTALL ...' in a common shell is ok. Only a...

...For details on reading vignettes, see the openVignette help page. > > >Loading required package: affyio >Loading required package: affydata >Loading required package: Biobase >Loading required package: gcrma >Loading required package: matchprobes >Loading required package: reposTools >Loading required package: simpleaffy >Loading required package: genefilter >Loading required package: survival >Loading required package: splines >Welcome to 'affyQCReport' V 1.6-1 >Further information available at: www.bifix.org > mailto: craig.parman at bifix....

...fy Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Loading required package: reposTools Welcome to 'simpleaffy' V 2.1.3 Produced by The Paterson Institute for Cancer Research and funded by CANCER RESEARCH UK. http://bioinformatics.picr.man.ac.uk/simpleaffy mailto: microarray at picr.man.ac.uk...

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

...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

...new package that provides classes & tools to handle graph objects in R. * hexbin: A new package which includes binning functions, in particular hexagonal bins for graphing * marrayTools: A new package with miscellaneous functions use in the functional genomics core facility in UCB * reposTools: A new package that provides tools for dealing with file repositories, which allow users to easily install, update and distribute packages, vignettes and other files. * tkWidgets: vExplorer, a powerful tool designed to allow users to interact with vignette documentation in a hands on mann...

...new package that provides classes & tools to handle graph objects in R. * hexbin: A new package which includes binning functions, in particular hexagonal bins for graphing * marrayTools: A new package with miscellaneous functions use in the functional genomics core facility in UCB * reposTools: A new package that provides tools for dealing with file repositories, which allow users to easily install, update and distribute packages, vignettes and other files. * tkWidgets: vExplorer, a powerful tool designed to allow users to interact with vignette documentation in a hands on mann...

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