

Thank you very much for the email. It works fine now.


________________________________
 From: James W. MacDonald <jmacdon@uw.edu>

Cc: "bioconductor@r-project.org" <bioconductor@r-project.org> 
Sent: Wednesday, January 16, 2013 10:13 AM
Subject: Re: [BioC] ‘AnnotationForge’ is not available for Linux system??

Hi Capricy Gao,

On 1/16/2013 10:58 AM, capricy gao wrote:
> I am trying to install AnnotationForge package on my linux system and got the following message:
>
> ____________________
>
>> source("http://bioconductor.org/biocLite.R")
>> biocLite("AnnotationForge")
> BioC_mirror: http://bioconductor.org
> Using R version 2.15, BiocInstaller version 1.4.9.
> Installing package(s) 'AnnotationForge'
> Warning messages:
> 1: package â€˜AnnotationForgeâ€™ is not available (for R version 2.15.1)
> 2: installed directory not writable, cannot update packages 'AnnotationDbi',
> Â  'Biobase', 'Biostrings', 'Cairo', 'DNAcopy', 'GenomeGraphs', 'Hmisc',
> Â  'IRanges', 'RColorBrewer', 'RCurl', 'RSQLite', 'SKAT', 'XML', 'affy',
> Â  'affyio', 'annotate', 'biomaRt', 'bitops', 'caTools', 'colorspace', 'digest',
> Â  'doMC', 'fastcluster', 'flexmix', 'foreach', 'fpc', 'gcrma', 'gdata',
> Â  'genefilter', 'ggplot2', 'gplots', 'gtools', 'h5r', 'igraph', 'iterators',
> Â  'lumi', 'mclust', 'methylumi', 'modeltools', 'multcomp', 'multicore',
> Â  'mvtnorm', 'plotrix', 'plyr', 'preprocessCore', 'proto', 'reshape2',
> Â  'scatterplot3d', 'stringr', 'xtable', 'KernSmooth', 'MASS', 'Matrix', 'boot',
> Â  'class', 'cluster', 'codetools', 'foreign', 'lattice', 'mgcv', 'nlme',
> Â  'nnet', 'rpart', 'spatial', 'survival'
> ------------------------------------------------
>
> All other packages such as edgeR, DESeq... are fine. This is the first time I met this kind of problem...
>
> Anybody could help me out? Thanks.

You are using BiocInstaller version 1.4.9, which implies that you are 
installing BioC version 2.10. This version didn't have AnnotationForge. 
If you want to upgrade, then follow the instructions on the install page 
of the BioC website:

|source("http://bioconductor.org/biocLite.R")
biocLite("BiocUpgrade")

Best,

Jim
|


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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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