[BioC] AnnBuilder

[Dick Beyer]

Hi Hua Weng,

I had similar problems in installing AnnBuilder. I have a RedHat EH4 box.  I did three things that worked (as root):
1) Downloaded the libxm12 package from RedHat and
  rpm -Uvh libxm12-devel-2.6.16-6.x86_64.rpm
2) Installed XML
  R CMD INSTALL XML_0.99-6.tar.gz
3) Installed AnnBuilder
  R CMD INSTALL AnnBuilder_1.8.0.tar.gz

Hope that helps,
Dick


Message: 7
Date: Wed, 22 Mar 2006 11:30:37 -0600
From: "Hua Weng" <hweng at biochem.okstate.edu>
Subject: Re: [BioC] AnnBuilder
To: <bioconductor at stat.math.ethz.ch>, "'Ting-Yuan Liu'"
 	<tliu at fhcrc.org>
Message-ID: <1069077431-12231255 at biochem.okstate.edu>
Content-Type: text/plain

Hi, Bioconductor list and Ting-Yuan:



I have problems in using AnnBuilder package.



1)       May I use Windows based R environment to run ABPkgBuilder? I
haven't been successfully run this command. I saw there is a condition
before this command is "if(.Platform$OS != "windows" && interactive())",
Does this mean this command cannot run on windows platform?

2)       I also tried to install AnnBuilder in R2.2.0 on Linux server. But I
haven't been successfully installed it. The problem is before I could
install XML package, it gave me error message "****    You should use a
recent version of libxml2, i.e. 2.6.22 or higher  ****". And when I tried to
install 'libxml2', I got the following error:

    > install.packages("libxml2")

Warning in download.packages(pkgs, destdir = tmpd, available = available,  :

          no package 'libxml2' at the repositories

So I want to ask how I can successfully install 'libxml2' on Linux server?



> sessionInfo()

R version 2.2.0, 2005-10-06, i686-pc-linux-gnu



attached base packages:

[1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"

[7] "base"



3)       I found that UniGene source URL always point to 'Homo sapiens' data
even for the organism other than 'Homo sapiens'. Is that true?



Thanks for your attention!



Hua Weng

Microarray Core Facility

Oklahoma State University

Department of Biochemistry and Molecular Biology

246 Noble Research Center

Stillwater, OK  74078



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Richard P. Beyer, Ph.D.	University of Washington
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