On Dec 8, 2013, at 10:54 AM, Denis Chabot <[email protected]> wrote:
> Hi Steve, > > Le 2013-12-08 à 00:47, Steve Lianoglou <[email protected]> a écrit : > >> Hi, >> >> On Wed, Dec 4, 2013 at 8:44 PM, Denis Chabot <[email protected]> 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 > > _______________________________________________ > R-SIG-Mac mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
