[BioC] AnnBuilder

[Ting-Yuan Liu]

Hi Hua,

Yes, you could run AnnBuilder in Windows system.  That is not what I 
usually do, but I tried and succeed.  However, my R in the windows 
machine is "built from source" (see section 3.1 of the manual "R 
Installation and Administration") and it might be a little different from 
your R (which is built from the binary installer, I guess.)  Someone 
reported to me that it is unable to run AnnBuilder in the Windows system, 
but it did work in my machine.  Therefore, you can try first to see if you 
can build annotation packages from the binary-installed R.  If not, you 
should switch to the source-installed R.  

HTH,
Ting-Yuan
______________________________________
Ting-Yuan Liu
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
Seattle, WA, USA
______________________________________

On Wed, 22 Mar 2006, Hua Weng wrote:

> 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
> 
>  
> 
>