Actually I've tried to install XML directly from CRAN. But it failed. > install.packages("XML") trying URL `http://cran.r-project.org/bin/windows/contrib/2.0/PACKAGES' Content type `text/plain; charset=iso-8859-1' length 27110 bytes opened URL downloaded 26Kb Warning message: No package "XML" on CRAN. in: download.packages(pkgs, destdir = tmpd, available = available, I also tried this: > library(reposTools) Loading required package: tools > > install.packages2("XML") Note: You did not specify a download type. Using a default value of: Win32 This will be fine for almost all users Unable to locate the requested package(s) in any known repository As a lot of documentation and mailing responses suggest installing XML directly from CRAN, it seems that the windows version of XML has ever existed in CRAN repository, but later been removed (for copyright issues)? >From: "James W. MacDonald" <jmacdon@med.umich.edu> >To: zhihua li <lzhtom@hotmail.com> >CC: bioconductor@stat.math.ethz.ch >Subject: Re: [BioC] load AnnBuilder and install XML >Date: Thu, 17 Mar 2005 09:32:21 -0500 > >zhihua li wrote: > > Hi netters > > > > I've downloaded and installed AnnBuilder. When I loaded it, I was told > > that the dependent package XML had not been installed. > > According to the manual of AnnBuilder, the XML package can be found in > > CRAN. But I can't find a windows binary there. Instead, I went to > > http://www.omegahat.org/RSXML/index.html and downloaded XML_0.97-0.zip > > there. I used the menu of "install packages from local zip file" and it > > seemed that I've installed XML sucessfully: > > package 'XML' successfully unpacked and MD5 sums checked > > updating HTML package descriptions > > > > But then when I loaded AnnBuilder, I still got: > > > >> library(AnnBuilder) > > > > 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: XML Error in library(pkg, character.only = > > TRUE, logical = TRUE, lib.loc = lib.loc) : 'XML' is not a valid > > package -- installed < 2.0.0? > > > > I'm using R 2.0.1 actually. > > > > Is there something wrong with windows version of XML? > >No, you just did things in an unnecessarily difficult way. > >install.packages("XML") > >will get you what you need. > > > > > > Thanks a lot! > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > >-- >James W. MacDonald >Affymetrix and cDNA Microarray Core >University of Michigan Cancer Center >1500 E. Medical Center Drive >7410 CCGC >Ann Arbor MI 48109 >734-647-5623

Seth Falcon wrote: > "James W. MacDonald" <jmacdon@med.umich.edu> writes: > >>>I'm using R 2.0.1 actually. >>> >>>Is there something wrong with windows version of XML? >> >>No, you just did things in an unnecessarily difficult way. >> >>install.packages("XML") >> >>will get you what you need. > > > With R 2.0.1 that should work because the default is for > install.packages to use the main CRAN site. > > If you use a CRAN mirror, you _might_ not be able to find the Windows > binary XML package. It is a special case I think because it isn't as > easy as other packages to build on Windows. Yep, you are correct. On R-2.0.1 install.packages("XML") doesn't work out of the box. On R-2.1.0, install.packages() finds the correct version at BDR's website. A version that will work with R-2.0.1 can be found here: http://www.stats.ox.ac.uk/pub/RWin/2.0.0/XML_0.97-0.zip Jim > > And to clarify the error message: The binary version you found was > built with an older version of R and so isn't compatible with your R. > > Best, > > + seth > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623