[R-SIG-Mac] some errors

[stefano iacus]

On 08/giu/05, at 17:38, Kasper Daniel Hansen wrote:

> Hi
>
> I have recently (some days ago) started working on a Mac, and have  
> a few
> "problems" to report:
>
> So far I have been running R.app under Tiger as well as using R from
> within Emacs
>
> 1) In the "Preferences/Startup" menu, there is a spelling mistake: the
> option "Add $HOME/R/Library" should be "Add $HOME/Library/R" (I  
> guess).
right,

>
> 2) I tried installing Bioconductor binaries using the package menu. I
> can easily install binaries from CRAN. When I pick "bioconductor
> (binaries)" I can retrieve a list of packages from the mirror I am
> using, but when I click on an individal package and choose "Install
> selected", nothing happens. The console output is below. It seems to
> simply retieve the package list and nothing else. The fact that this
> happens only when I do Bioconductor and not CRAN seems to indicate  
> that
> it is a Mac issue? I have installed the packages through other means,
> this is simply a user-report.
>

it's a bug. Use "Specify location" with http://www.bioconductor.org   
as URL, and specify the "binary format".
Then it should work.



> 3) Could it be that R does not read environment variables when started
> on the terminal. On the terminal as well as using ESS (Emacs) I can  
> not
> get .libPaths() to include /Users/kdh/Library/R despite the fact  
> that I
> have exported it from ~/.profile and the variable is set (output  
> below).
> I have also tried using ~/.Renviron
>
> How do people solve the last issue: that of adding the user-dependent
> library, when using ESS/terminal.
>
> The questions might be a bit basic, but still...
>
> Kasper
> ***** Bioconductor install
>
>
> 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 a HTML browser interface to help.
> Type 'q()' to quit R.
>
> trying URL 'http://www.bioconductor.org/bin/macosx/2.1/PACKAGES'
> Content type 'text/plain; charset=ISO-8859-1' length 11224 bytes
> opened URL
> ==================================================
> downloaded 10Kb
>
> trying URL 'http://www.bioconductor.org/bin/macosx/2.1/PACKAGES'
> Content type 'text/plain; charset=ISO-8859-1' length 11224 bytes
> opened URL
> ==================================================
> downloaded 10Kb
>
>
> ******* R_LIBS probelm
>
> north-mesh-wlan-87:~ kdh$ echo $R_LIBS
> /Users/kdh/Library/R/
> north-mesh-wlan-87:~ kdh$ R
>
> R : Copyright 2005, The R Foundation for Statistical Computing
> Version 2.1.0 Patched (2005-05-12), 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.
>
> 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 a HTML browser interface to help.
> Type 'q()' to quit R.
>
>
>> .libPaths()
>>
> [1] "/Library/Frameworks/R.framework/Resources/library"
>
>>
>>
>
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>
>