From Heather.Turner at warwick.ac.uk  Fri May 22 12:13:03 2009
From: Heather.Turner at warwick.ac.uk (Heather Turner)
Date: Fri, 22 May 2009 11:13:03 +0100
Subject: [Rd] install.packages now intentionally references .Rprofile?
In-Reply-To: <6b93d1830905211428h6f5d0e66hdebfb9a3c70984f8@mail.gmail.com>
References: <6ph4ovf1gi0.fsf@gopher4.fhcrc.org>	<alpine.LFD.2.00.0905210715100.30855@gannet.stats.ox.ac.uk>
	<6b93d1830905211428h6f5d0e66hdebfb9a3c70984f8@mail.gmail.com>
Message-ID: <4A167AAF.2040803@warwick.ac.uk>

I had a similar problem when moving to R-2.9.0 as my .Rprofile called
update.packages(). The solution was to use

if(interactive()) {
	utils:::update.packages(ask = FALSE)
}

HTH,

Heather

Mark Kimpel wrote:
> This was my original post, with the code example only slightly modified by
> Martin for clarity. Prior to R-2.9.0, this repeated downloading did not
> occur, the code worked as intended. In fact, if memory serves me correctly,
> it even worked at least during the first 3 months of R-2.0.0 in its
> development stage, before release as a numbered version. Is there a reason
> for that? Is there a work-around? As I mentioned in my original post, the
> code is actually wrapped in a function that checks the date and the date of
> the last update, and proceeds to update package once per week. It was quite
> handy when it was working, hence my desire for a fix for my code.
> 
> Thanks,
> Mark
> ------------------------------------------------------------
> Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
> Indiana University School of Medicine
> 
> 15032 Hunter Court, Westfield, IN  46074
> 
> (317) 490-5129 Work, & Mobile & VoiceMail
> (317) 399-1219  Home
> Skype:  mkimpel
> 
> "The real problem is not whether machines think but whether men do." -- B.
> F. Skinner
> ******************************************************************
> 
> 
> On Thu, May 21, 2009 at 2:17 AM, Prof Brian Ripley <ripley at stats.ox.ac.uk>wrote:
> 
>> On Wed, 20 May 2009, Martin Morgan wrote:
>>
>>  A post on the Bioconductor mailing list
>>>  https://stat.ethz.ch/pipermail/bioconductor/2009-May/027700.html
>>>
>>> suggests that install.packages now references .Rprofile (?), whereas
>>> in R-2-8 it did not. Is this intentional?
>>>
>> Yes.  And in fact it did in earlier versions, to find the default library
>> into which to install.
>>
>>
>>
>>> The example is, in .Rprofile
>>>
>>>  library(utils)
>>>  install.packages("Biobase",
>>>                  repos="http://bioconductor.org/packages/2.4/bioc")
>>>
>>> then starting R from the command line results in repeated downloads
>>> of Biobase
>>>
>>> mtmorgan at mm:~/tmp> R --quiet
>>> trying URL
>>> '
>>> http://bioconductor.org/packages/2.4/bioc/src/contrib/Biobase_2.4.1.tar.gz
>>> '
>>> Content type 'application/x-gzip' length 1973533 bytes (1.9 Mb)
>>> opened URL
>>> ==================================================
>>> downloaded 1.9 Mb
>>>
>>> trying URL
>>> '
>>> http://bioconductor.org/packages/2.4/bioc/src/contrib/Biobase_2.4.1.tar.gz
>>> '
>>> Content type 'application/x-gzip' length 1973533 bytes (1.9 Mb)
>>> opened URL
>>> ==================================================
>>> downloaded 1.9 Mb
>>>
>>> ^C
>>> Execution halted
>>>
>>>  sessionInfo()
>>> R version 2.9.0 Patched (2009-05-20 r48588)
>>> 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=C;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
>>>
>>> Martin
>>> --
>>> Martin Morgan
>>> Computational Biology / Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N.
>>> PO Box 19024 Seattle, WA 98109
>>>
>>> Location: Arnold Building M1 B861
>>> Phone: (206) 667-2793
>>>
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>>
>> --
>> Brian D. Ripley,                  ripley at stats.ox.ac.uk
>> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/<http://www.stats.ox.ac.uk/%7Eripley/>
>> University of Oxford,             Tel:  +44 1865 272861 (self)
>> 1 South Parks Road,                     +44 1865 272866 (PA)
>> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>>
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-devel at r-project.org mailing list
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[Rd] install.packages now intentionally references .Rprofile?
Heather Turner