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

Denis Chabot chabotd at globetrotter.net
Sun Dec 8 16:54:29 CET 2013

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

> (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.


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