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

[Martin Morgan]

"James W. MacDonald" <jmacdon at med.umich.edu> writes:

> 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).
  
but maybe you have dependency problems anyway? Have you tried
following the 'install - how-to' link on the Bioconductor web page,
and 'Update packages' at the bottom of the page

> source('http://bioconductor.org/biocLite.R')
> update.packages(repos=biocinstallRepos(), ask=FALSE)

Martin

>> 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
>> 
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> -- 
> 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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor