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<P>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:</P>
<P>when I type </P>
<P>>getBioC(libName = "exprs") (or <A href="mailto:libName=@all">libName="all</A>")</P>
<P>I get:</P>
<P>Running getBioC version 1.2.34....<BR>If you encounter problems, first make sure that<BR>you are running the latest version of getBioC()<BR>which can be found at: <A href="http://www.bioconductor.org/getBioC.R">www.bioconductor.org/getBioC.R</A></P>
<P>Please direct any concerns or questions to <A href="mailto:bioconductor@stat.math.ethz.ch">bioconductor@stat.math.ethz.ch</A>.</P>
<P>[1] "Installing reposTools ..."</P>
<P>Synching your local package management information ...<BR>Package Biobase version 1.3.22 requires package genefilter, would you like to try to install this package? [yes/no] yes<BR>Note: No specified download type, defaulting to Win32 <BR>Note: Package genefilter not found in any known repository. <BR>[1] "Attempting to download Biobase from <A href="http://www.bioconductor.org/repository/release1.2/package/Win32">http://www.bioconductor.org/repository/release1.2/package/Win32</A>"<BR>[1] "Download complete."<BR>[1] "Installing Biobase"<BR>Note: Running R version 1.7.1 and package Biobase was built for R version 1.7.0<BR> , installing anyway.<BR> <BR>[1] "Installation complete"<BR>From URL: <A href="http://www.bioconductor.org/repository/release1.2/package/Win32">http://www.bioconductor.org/repository/release1.2/package/Win32</A><BR> Biobase version 1.3.22</P>
<P>Packages that were not updated:<BR> annotate<BR> geneplotter<BR> edd<BR> ROC<BR> multtest<BR> tkWidgets<BR> widgetTools</P>
<P>So, it seems that Biobase is not installed because genefilter can not be found. Indeed, when I type:</P>
<P>>library(affy)<BR>I get:</P>
<P>Error in checkPkgDeps(pkgname) : You can not load package Biobase as<BR>it requires you to have package genefilter which is not currently installed.<BR>Error in checkPkgDeps(pkgname) : You can not load package Biobase as<BR>it requires you to have package genefilter which is not currently installed.<BR>Error in getClass(Class) : "MIAME" is not a defined class<BR>Error in library(affy) : .First.lib failed<BR></P>
<P>Thank you very much for your precious help.</P>
<P>Martino</P>
<P>CoMPLEX-University College London<BR><BR></P></DIV>
<DIV></DIV>>From: Jeff Gentry <JGENTRY@JIMMY.HARVARD.EDU>
<DIV></DIV>>To: James MacDonald <JMACDON@MED.UMICH.EDU>
<DIV></DIV>>CC: m_barenco@hotmail.com, bioconductor@stat.math.ethz.ch
<DIV></DIV>>Subject: Re: [BioC] problems intalling bioconductor on windows NT
<DIV></DIV>>Date: Mon, 16 Jun 2003 11:29:48 -0400 (EDT)
<DIV></DIV>>
<DIV></DIV>> > I believe you need R 1.7.1beta because there are some bugs in 1.7.0
<DIV></DIV>> > http://www.stats.uwo.ca/faculty/murdoch/software/r-devel/rw1071beta.exe
<DIV></DIV>>
<DIV></DIV>>Actually, R-1.7.1 was released today so should be available from CRAN.
<DIV></DIV>>
<DIV></DIV>> > bioconductor@stat.math.ethz.ch.
<DIV></DIV>> > [1] "Installing reposTools ..."
<DIV></DIV>> > Error in upDatePkgs(relLevel, PLATFORM, destdir, method = method) :
<DIV></DIV>> > Failed to install package reposTools
<DIV></DIV>> > In addition: Warning messages:
<DIV></DIV>> > 1: downloaded length 932996 != reported length 5348600
<DIV></DIV>> > 2: error 1 in extracting from zip file
<DIV></DIV>>
<DIV></DIV>>I have no idea what is going on here, but it looks to me like perhaps the
<DIV></DIV>>download failed halfway through (the zip file on the server is indeed
<DIV></DIV>>5.3MB but the user didn't even get 1MB?)
<DIV></DIV>>
<DIV></DIV>>-J
<DIV></DIV>>