[BioC] biocLite() and getBioC scripts install development packages!

[James W. MacDonald]

Hi Philip,

Groot, Philip de wrote:
> Hello list,
>  
> I encountered the following problem while trying to install the latest bioconductor 2.1 release: both biocLite() and getBioC() detect that the latest R-release 2.6.0 is a development version (which is NOT the case; I double checked it!). As a result, bioconductor development libraries are being installed, which will fail due to dependency problems (wrong versions of the different required libraries etc).
>  
> Please fix this!
>  
> Regards,
>  
> Dr Philip de Groot
> Wageningen University
>  
> Screendump:
>  
> R version 2.6.0 (2007-10-03)
> Copyright (C) 2007 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>   Natural language support but running in an English locale
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>  
>> source("http://bioconductor.org/biocLite.R")
>> biocLite()
> Running biocinstall version 2.1.7 with R version 2.6.0 (under development)

The only 'problem' here is that the (under development) part of this 
message needs to be removed.

> Your version of R requires version 2.1 of Bioconductor.

If you read this line ^^^^^ you will note that it states it is 
installing version 2.1, which was released on Monday (and hence is _not_ 
the development version).

Best,

Jim


> Will install the following packages:
>  [1] "affy"         "affydata"     "affyPLM"      "annaffy"      "annotate"
>  [6] "Biobase"      "Biostrings"   "DynDoc"       "gcrma"        "genefilter"
> [11] "geneplotter"  "hgu95av2"     "limma"        "marray"       "matchprobes"
> [16] "multtest"     "ROC"          "vsn"          "xtable"       "affyQCReport"
> Please wait...
>  
> 
>> sessionInfo()
> R version 2.6.0 (2007-10-03)
> x86_64-unknown-linux-gnu
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> loaded via a namespace (and not attached):
> [1] rcompgen_0.1-15 tools_2.6.0
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623