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

Groot, Philip de philip.degroot at wur.nl
Wed Oct 10 16:42:08 CEST 2007


Hello,
 
Thank you for your help! I deleted the R-2.6.0 installation and compiled everything from scratch again. The problem I reported seems to be solved now (I cannot reproduce it any more).
 
Regards,
 
Dr Philip de Groot
Wageningen University

________________________________

From: Martin Morgan [mailto:mtmorgan at fhcrc.org]
Sent: Wed 10-10-2007 16:04
To: James W. MacDonald
Cc: Groot, Philip de; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] biocLite() and getBioC scripts install development packages!



"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
>>
>> _______________________________________________
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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
>
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