[BioC] load AnnBuilder and install XML

[zhihua li]

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 at med.umich.edu>
>To: zhihua li <lzhtom at hotmail.com>
>CC: bioconductor at 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 at 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