[BioC] latest devel GO package not built in R2.0.0

[Dick Beyer]

Hi John,

Thanks very much for your reply.  I tried doing as you suggested, but I get a new error now.  Here is the relevant output:

R : Copyright 2004, The R Foundation for Statistical Computing
Version 2.0.0 beta (2004-09-22), ISBN 3-900051-07-0

> library(reposTools)
Loading required package: tools 
> install.packages2("GO", develOK = TRUE)
Note: You did not specify a download type.  Using a default value of: Win32 
This will be fine for almost all users

[1] "Attempting to download GO from http://www.bioconductor.org/data/metaData-devel/"
[1] "Download complete."
[1] "Installing GO"
Note: Running R version 2.0.0 and package GO was built for R version 1.9.0
  , installing anyway.

[1] "Installation complete"
>From URL:  http://www.bioconductor.org/data/metaData-devel/
         GO version 1.6.2

> library(annaffy)
Loading required package: Biobase 
Welcome to Bioconductor
          Vignettes contain introductory material.  To view,
          simply type: openVignette()
          For details on reading vignettes, see
          the openVignette help page.
Error: package 'GO' required by 'annaffy' could not be found
> local({pkg <- select.list(sort(.packages(all.available = TRUE)))
+ if(nchar(pkg)) library(pkg, character.only=TRUE)})
Error in library(pkg, character.only = TRUE) :
         'GO' is not a valid package -- installed < 2.0.0?

Not usre what to try next.

Thanks very much,
Dick

*******************************************************************************
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
 			Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
*******************************************************************************

On Fri, 24 Sep 2004, John Zhang wrote:

>
>> but it was built in 1.9.0, so I can't load it in 2.0.0beta.  Would someone
> please build GO for R2.0.0?
>
> Now, if you do
>
>> library(reposTools)
>> install.packages2("GO", develOK = TRUE)
>
> you will get the devel GO package built under R 2.0.0. The package still has a
> version number 1.6.2 but the GOTERM environment is a list of lists rather than a
> list of GOTerms objects as it was before (we could not change the version number
> due to a problem with our CVS). The reason for having a list of lists is to save
> space as the data packages are getting bigger and bigger.
>
>>
>> I am trying to use annaffy for the affy mouse4302 chip, but the mouse4302 meta
> data is only for R2.0.0.  So I think I am stuck.
>>
>> Thanks very much,
>> Dick
>> *******************************************************************************
>> Richard P. Beyer, Ph.D.	University of Washington
>> Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
>> Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
>> 			Seattle, WA 98105-6099
>> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
> Jianhua Zhang
> Department of Biostatistics
> Dana-Farber Cancer Institute
> 44 Binney Street
> Boston, MA 02115-6084
>
>