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

[hpages at fhcrc.org]

Hi Philip, Jim, Martin,

I just corrected this in biocLite() and getBioC(). It was a cosmectic
problem only i.e. if you use R 2.6.0 you were (and you are still)
picking up BioC 2.1 (BioC 2.1 packages have an even y in their
version number x.y.z).

Cheers,
H.

Quoting "Groot, Philip de" <philip.degroot at wur.nl>:

> 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
> >>
> >> _______________________________________________
> >> 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
> >
> > _______________________________________________
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> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
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> 
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