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problem installing packages from terminal

5 messages · Federico Calboli, Simon Urbanek, stefano iacus

Federico Calboli
# 
Hi All,

I tried to install Hmisc from source, but I had errors due to  
permission issues (I enabled root form my box). I tried to install  
from the terminal after su-ing to root, but I get the following:

 > install.packages("locfit")
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... Error in fun(...) : no display name and  
no $DISPLAY environment variable
Error: .onLoad failed in 'loadNamespace' for 'tcltk'

The same command in Debian Linux opens a tcl/tk widget... How can I  
install stuff from the terminal? I'd rather not log out and log in  
again as root to install stuff that needs g77... (I did for Hmisc,  
and worked like a charm). BTW, I installed all the .dmg packages that  
were bundled with R.app.

Cheers,

Federico


Federico C. F. Calboli
Department of Epidemiology and Public Health
Imperial College, St. Mary's Campus
Norfolk Place, London W2 1PG

Tel +44 (0)20 75941602   Fax +44 (0)20 75943193

f.calboli [.a.t] imperial.ac.uk
f.calboli [.a.t] gmail.com
Simon Urbanek
# 
Hi Federico,
On Jun 4, 2005, at 2:18 PM, Federico Calboli wrote:

            

      
      
      
    

        
Are you sure? Please look at the output more closely.  Hmisc usually  
fails due to compiler problems, not permission issues. If you are  
using R binary from CRAN, you don't need to use root for  
installation, any user with admin privileges will do. The last  
warning about permissions on .css can be safely discarded and has  
nothing to do with the success/failure of a package installation.

Furthermore R.app checks permissions before installation, so it would  
ask for authorization if there were any permission issues.

Finally, you can use R.app to install as root as well - if you want  
to force installation as root, click on the "lock" icon in the tool  
bar, the installation will then be performed as root (but usually  
this is not necessary, see above).

            

      
      
      
    

        
You didn't select CRAN mirror. You should either set it globally or  
supply the url to install.packages. Also note that the default on  
CRAN OS X is binary installation, so what you probably want is rather  
install.packages("Hmisc",repos="http://cran.us.r- 
project.org/",type="source") - of course replace with your mirror of  
choice.

            

      
      
      
    

        
You don't need to - in fact it's not recommended to enable the root  
user on OS X and it's completely unnecessary, because you should be  
using sudo with the same effect without potentially hazardous side- 
effects of enabling root.

Cheers,
Simon

  
  


  


      

    

    

      
      

        


  

        

      Federico Calboli
    

    

      
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Hi Simon, 

Thanks for the very comprehensive explanation... I am new to OSX and to
a number of things done the R.app way.

            

      
      
      
    

        
I am a Linux user at work (and I sysadmin for myself as well), and the
more Linux/Unix like in behaviour I can make OSX the better. The fact
that I have administrative privileges is something I find pretty weird.

Cheers,

Federico

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      stefano iacus
    

    

      
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On 04/giu/05, at 20:18, Federico Calboli wrote:

        

            

      
      
      
    

        
the binaries of R for Mac OS X assumes X11 tcltk. You need to start  
the X11 server and either set the DISPLAY var to :0 if you use R from  
the command line. R.app sets the DISPLAY var for you.

Unless you build an aqua version of the tcltk R package (i.e. you  
configure R to use Aqua TclTk headers) you always need to have a X11  
window server running (like on Linux, I would say).

stefano

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
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On Jun 4, 2005, at 3:32 PM, Federico Calboli wrote:

        

            

      
      
      
    

        
What do you mean? This may be just a terminology issue. On OS X  
"administrators" (i.e. users with administrative privileges - or as  
System Preferences call it "users that are allowed to administer this  
computer") are users that can sudo to get root privileges. They are  
also members of the "admin" group. Other than that, they are ordinary  
users, so if you login as one, you (and any program you run) can do  
as little harm as any other regular user. Only if you sudo (either on  
the command line or using Security framework) you get the effective  
permissions of a root. As with any system, you should think twice  
before giving someone admin access ;).

The advantage of this security concept (which you can use on any unix  
system) as opposed to actually logging in as root is that you run  
only very specific tasks with root privileges, thus reducing the  
possibility of damaging the system. This is why root is disabled by  
default on OS X - to make it more secure.
Another nice security aspect is that SF authentication changes only  
euid, therefore it is still possible to trace which user is actually  
using the root privileges.

BTW: A side note on the original topic: if you install a package  
manually as root, it will change its permissions inside the  
framework, so you won't be able to update it as admin user anymore -  
you'll always have to do it as root from that point on. Another  
reason to not do that ;).

Cheers,
Simon