[R-SIG-Mac] Can only install packages in my (user) library, even as administrator

[Simon Urbanek]

On Dec 8, 2013, at 10:54 AM, Denis Chabot <chabotd at globetrotter.net> wrote:

> Hi Steve, 
> 
> Le 2013-12-08 à 00:47, Steve Lianoglou <lianoglou.steve at gene.com> a écrit :
> 
>> Hi,
>> 
>> On Wed, Dec 4, 2013 at 8:44 PM, Denis Chabot <chabot.denis at gmail.com> wrote:
>>> Hi,
>>> 
>>> I made 3 changes within a few days of each other and I don’t know which one caused this. I always installed new pacages (and updated existing packages) in the main library on my Mac, not in the library folder of my own account.
>>> 
>>> But after putting a new hard drive in my Mac, updating R to 3.0.2 (from 3.0.1), updating my OS to Mavericks, I can no longer do so, I receive error messages telling me I’d have to use the command line if I insisted in doing it now.
>> 
>> (1) Could you please copy/paste the exact error messages you are
>> getting? Paraphrasing it isn't very helpful.
> 
> The message I get is not written in the console, it is written on top of the Package Installer window of R.app. And it is in French:
> 
> Il n'est actuellement pas possible d'installer des package binaires depuis des dépôts à distance en tant qu'utilisateur root.
> Merci d'utiliser le binaire de R qui provient du CRAN afin d'autoriser aux administrateurs l'installation de packages au niveau système sans passer par l'utilisateur root. Sinon, vous pouvez utiliser R en ligne de commande en tant que root ou installer les packages depuis des fichiers locaux
> 
> If I translate it, it says « It is presently impossible to install binary packages from repositories as user root. Thank you for using R binaries that come from CRAN so that administrators can install packages at the system level without using user root. Otherwise, you can use R on the command line as root to install packages from local files.
> 
> And in the console, this appears:
> 
> Avis dans install.packages(c("mclust"), lib = "/Library/Frameworks/R.framework/Resources/library/",  :
> 'lib = "/Library/Frameworks/R.framework/Resources/library/"' ne peut être ouvert en écriture
>> 
> Would you like to use a personal library instead?  (y/n) 
> 
> so I do not have write access to lib. I am sure the tests you suggest below will confirm it, but I’ve been using R on 3 macs for many years, from an administrator account, and it never happened to me before.
> 
>> 
>> (2)  Can you copy paste the output of the following command from the terminal:
>> 
>> $ ls -ld /Library/Frameworks/R.framework/Resources/library
>> 
>> Mine looks like:
>> 
>> drwxrwxr-x  56 root  admin  1904 Nov 27 11:40
>> /Library/Frameworks/R.framework/Resources/library
>> 
> And mine:
> drwxrwxr-x+ 136 root  wheel  4624 21 nov 14:40 /Library/Frameworks/R.framework/Resources/library
> 

As you can see someone messed with the permissions. To fix that, run

sudo chown -Rh 0:admin /Library/Frameworks/R.framework

in the Terminal (blowing away R and re-installing would also help but the above is less disruptive).

Cheers,
Simon



>> (The leading `$` above is just a delimiter to suggest I am typing at
>> the terminal/bash prompt -- you don't type in `$`)
>> 
>> (3) Please copy/paste the output of the following command from the terminal:
>> 
>> $ groups YOUR_ACCOUNT
> 
> staff everyone localaccounts _appserverusr admin _appserveradm _lpadmin com.apple.sharepoint.group.2 com.apple.sharepoint.group.1 _appstore _lpoperator _developer com.apple.access_screensharing com.apple.access_ssh
> 
>> and the output is:
>> 
>> lianogls domainus com.apple.access_screensharing everyone _appstore
>> netaccounts _appserverusr admin _appserveradm _lpadmin _lpoperator
>> _developer
>> 
>> 
>> Thanks,
>> -steve
>> 
>> -- 
>> Steve Lianoglou
>> Computational Biologist
>> Genentech
> 
> Thanks again Steve, I hope you’ll spot the problem. How it occurred is secondary, though it makes me very curious.
> 
> Denis
> 
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