From hpages at fhcrc.org  Sat Jun 10 04:01:50 2006
From: hpages at fhcrc.org (Herve Pages)
Date: Fri, 09 Jun 2006 19:01:50 -0700
Subject: [Rd] install.packages() does not warn when 'lib' arg is missing
 on Linux or Windows
In-Reply-To: <A1531EF1-302A-4E49-B18B-831F19F65BA2@r-project.org>
References: <448875CA.60901@fhcrc.org>
	<A1531EF1-302A-4E49-B18B-831F19F65BA2@r-project.org>
Message-ID: <448A280E.5090003@fhcrc.org>

Simon Urbanek wrote:
> On Jun 8, 2006, at 9:08 PM, Herve Pages wrote:
>
>> Man page for 'install.packages' says that if the 'lib' arg is missing,
>> then it "defaults to '.libPaths()[1]' with a warning".
>
> Where are you quoting from? I read (R 2.3.1):

Hi Simon,

I was quoting from the description of the 'lib' argument (among all 
functions
described on this man page, the 'install.packages' function is the only 
one to
have a 'lib' arg):

    lib: character vector giving the library directories where to
         install the packages.  Recycled as needed.  If missing,
         defaults to '.libPaths()[1]' with a warning.

I forgot to check the "Details" section for the 'install.packages' function
where the description is indeed correct. Sorry!

>> On my Mac OS X system:
>>
>>> .libPaths()
>>     [1] "/Users/biocbuild/Library/R/Library"
>
> ^^ - this is your custom setting, it is not the default
>
>>     [2] "/Library/Frameworks/R.Framework/Versions/2.3/Resources/ 
>> library"
>>
>
> The default on OS X is
>
> > .libPaths()
> [1] "/Library/Frameworks/R.framework/Resources/library"
> >
>
> in the shell and
>
> > .libPaths()
> [1] "/Library/Frameworks/R.framework/Versions/2.3/Resources/library"
> >
Yep right. Since it was the first time I was installing R-2.3.1 (from 
the CRAN
.dmg file, I choosed to install all components, including the R GUI) I 
was assuming
that my settings would have been the defaults but they were not :-/
I didn;t know about the Library/Preferences/org.R-project.R.plist file but a
real Mac OS X user showed it to me and reset my settings to the defaults.
Sorry for the trouble...

Best,

H.

-- 
------------------------
Herv? Pag?s
E-mail: hpages at fhcrc.org
 Phone: (206) 667-5791
   Fax: (206) 667-1319



[Rd] install.packages() does not warn when 'lib' arg is missing on Linux or Windows
Herve Pages