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List:       bioc-devel
Subject:    [Bioc-devel] BioC Release 2.0 REMINDER
From:       maechler () stat ! math ! ethz ! ch (Martin Maechler)
Date:       2007-04-10 15:28:26
Message-ID: 17947.44314.610199.59524 () stat ! math ! ethz ! ch
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Thank you guys,

embarassingly the R-alpha version I was using was basically
broken __ blush __
  having stemmed from a mix of R-2.4.1-alpha and R-2.5.0-alpha...
__ blush __


[ "Of course",  my  pkgType is "source" ].

Martin

>>>>> "Vince" == Vincent Carey 525-2265 <stvjc at channing.harvard.edu>
>>>>>     on Tue, 10 Apr 2007 10:00:35 -0400 (EDT) writes:

    Vince> i can't reproduce it on macosx using 2.5.0 svn rev
    Vince> 41107 as long as I use type="source" biocLite works.

    Vince> R 2.6 on linux worked also (but with the TEMPORARY
    Vince> message)

    Vince> --- Vince Carey, PhD Assoc. Prof Med (Biostatistics)
    Vince> Harvard Medical School Channing Laboratory - ph
    Vince> 6175252265 fa 6177311541 181 Longwood Ave Boston MA
    Vince> 02115 USA stvjc at channing.harvard.edu

    Vince> On Tue, 10 Apr 2007, Seth Falcon wrote:

    >> Hi Martin,
    >> 
    >> Martin Maechler <maechler at stat.math.ethz.ch> writes: > I
    >> wonder however, why
    >> >
    >> > biocLite(.)  or biocinstalll(.)
    >> 
    >> biocinstall is an implementation detail (perhaps we
    >> should hide it better) and should never be called
    >> directly.
    >> 
    >> > do only partially work for me.  > I get
    >> >
    >> > Running biocinstall version 2.0.3 with R version 2.5.0
    >> (currently in alpha) > Your version of R requires version
    >> 2.0 of Bioconductor (currently in alpha too).  > 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" > Please wait...
    >> >
    >> > Warning: unable to access index for repository
    >> http://bioconductor.org/packages/2.0/bioc/src/contrib >
    >> Warning: unable to access index for repository
    >> http://bioconductor.org/packages/2.0/data/annotation/src/contrib
    >> > ...............
    >> >
    >> > and in the end nothing is installed.  > Maybe you need
    >> to update the index file there, > or was I supposed not
    >> to use biocinstall() for alpha/beta > testing ?
    >> 
    >> Can you verify that you can connect to the
    >> bioconductor.org website?  biocLite worked for me on the
    >> 8th (from Switzerland, even) and seems to be working for
    >> me this morning in Seattle.
    >> 
    >> It would also help to know what getOption("pkgType") says
    >> for you.
    >> 
    >> Can others confirm difficulty using biocLite?
    >> 
    >> Best,
    >> 
    >> + seth
    >> 
    >> --
    >> Seth Falcon | Computational Biology | Fred Hutchinson
    >> Cancer Research Center http://bioconductor.org
    >> 
    >> _______________________________________________
    >> Bioc-devel at stat.math.ethz.ch mailing list
    >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
    >>


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