> I believe you need R 1.7.1beta because there are some bugs in 1.7.0 > http://www.stats.uwo.ca/faculty/murdoch/software/r-devel/rw1071beta. exe Actually, R-1.7.1 was released today so should be available from CRAN. > bioconductor@stat.math.ethz.ch. > [1] "Installing reposTools ..." > Error in upDatePkgs(relLevel, PLATFORM, destdir, method = method) : > Failed to install package reposTools > In addition: Warning messages: > 1: downloaded length 932996 != reported length 5348600 > 2: error 1 in extracting from zip file I have no idea what is going on here, but it looks to me like perhaps the download failed halfway through (the zip file on the server is indeed 5.3MB but the user didn't even get 1MB?) -J

On Wed, 18 Jun 2003, martino barenco wrote: > [1] "Installation complete" > From URL: > http://www.bioconductor.org/repository/release1.2/package/Win32 > Biobase version 1.3.22 Note that it installed Biobase .... getBioC, by default will keep on trucking if it can't get the dependencies. To stop that behaviour, use 'force=FALSE' > So, it seems that Biobase is not installed because genefilter can not be > found. Indeed, when I type: Well, Biobase was installed but genefilter was not, so ... > Error in checkPkgDeps(pkgname) : You can not load package Biobase as > it requires you to have package genefilter which is not currently > installed. Well, there is code in Biobase (not sure if we wantto keep it as such ...) that will not allow Biobase to load unless all of its dependencies are installed. Since genefilter was not installed, it won't load. Now. As to why genefilter was not installed -> I unconvered a problem w/ the Win32 genefilter, I believe that it is fixed but will keep an eye on it in the future. It should be fixed now. -J

I had this problem last night and this morning but I just tried again and its working now. You can run in R install.packages("Biobase",CRAN=getOption("BIOC")) install.packages("genefilter",CRAN=getOption("BIOC")) those were the ones that initially failed for me. Justin http://naturalvariation.org -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of martino barenco Sent: Wednesday, June 18, 2003 3:12 AM To: jgentry@jimmy.harvard.edu; jmacdon@med.umich.edu Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] problems intalling bioconductor on windows NT I updated to R 1.7.1 and it now works better in the sense that something gets downloaded. However, there are still some problems: when I type >getBioC(libName = "exprs") (or libName= <mailto:libname=@all> "all") I get: Running getBioC version 1.2.34.... If you encounter problems, first make sure that you are running the latest version of getBioC() which can be found at: www.bioconductor.org/getBioC.R Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. [1] "Installing reposTools ..." Synching your local package management information ... Package Biobase version 1.3.22 requires package genefilter, would you like to try to install this package? [yes/no] yes Note: No specified download type, defaulting to Win32 Note: Package genefilter not found in any known repository. [1] "Attempting to download Biobase from http://www.bioconductor.org/repository/release1.2/package/Win32" [1] "Download complete." [1] "Installing Biobase" Note: Running R version 1.7.1 and package Biobase was built for R version 1.7.0 , installing anyway. [1] "Installation complete" >From URL: http://www.bioconductor.org/repository/release1.2/package/Win32 Biobase version 1.3.22 Packages that were not updated: annotate geneplotter edd ROC multtest tkWidgets widgetTools So, it seems that Biobase is not installed because genefilter can not be found. Indeed, when I type: >library(affy) I get: Error in checkPkgDeps(pkgname) : You can not load package Biobase as it requires you to have package genefilter which is not currently installed. Error in checkPkgDeps(pkgname) : You can not load package Biobase as it requires you to have package genefilter which is not currently installed. Error in getClass(Class) : "MIAME" is not a defined class Error in library(affy) : .First.lib failed Thank you very much for your precious help. Martino CoMPLEX-University College London >From: Jeff Gentry >To: James MacDonald >CC: m_barenco@hotmail.com, bioconductor@stat.math.ethz.ch >Subject: Re: [BioC] problems intalling bioconductor on windows NT >Date: Mon, 16 Jun 2003 11:29:48 -0400 (EDT) > > > I believe you need R 1.7.1beta because there are some bugs in 1.7.0 > > http://www.stats.uwo.ca/faculty/murdoch/software/r-devel/rw1071bet a.exe > >Actually, R-1.7.1 was released today so should be available from CRAN. > > > bioconductor@stat.math.ethz.ch. > > [1] "Installing reposTools ..." > > Error in upDatePkgs(relLevel, PLATFORM, destdir, method = method) : > > Failed to install package reposTools > > In addition: Warning messages: > > 1: downloaded length 932996 != reported length 5348600 > > 2: error 1 in extracting from zip file > >I have no idea what is going on here, but it looks to me like perhaps the >download failed halfway through (the zip file on the server is indeed >5.3MB but the user didn't even get 1MB?) > >-J > [[alternative HTML version deleted]]