R help - Feb 2006 - Errors using update.packages()

When trying to update packages after the sysadmin updated R on my unix box 
I got errors on some packages. For example for chron:

* DONE (chron)
mkdir: cannot create directory `/usr/lib/R/library/00LOCK': Permission 
denied
ERROR: failed to lock directory '/usr/lib/R/library' for modifying

I got similar messages for spatial and cluster and warnings for other 
packages. Finally I got:

Warning messages:
1: number of rows of result
 	is not a multiple of vector length (arg 1) in: cbind(1, pkgs, lib)
2: number of rows of result
 	is not a multiple of vector length (arg 2) in: cbind(1, 
update[found, , drop = FALSE], file = files)
3: installation of package 'chron' had non-zero exit status in: 
install.packages(update[, "Package"], instlib, contriburl =
contriburl,
4: installation of package 'VR' had non-zero exit status in: 
install.packages(update[, "Package"], instlib, contriburl =
contriburl,
5: installation of package 'dse' had non-zero exit status in: 
install.packages(update[, "Package"], instlib, contriburl =
contriburl,
6: installation of package 'mgcv' had non-zero exit status in: 
install.packages(update[, "Package"], instlib, contriburl =
contriburl,
7: installation of package 'nlme' had non-zero exit status in: 
install.packages(update[, "Package"], instlib, contriburl =
contriburl,
8: installation of package 'survival' had non-zero exit status in: 
install.packages(update[, "Package"], instlib, contriburl =
contriburl,
9: cannot create HTML package index in: 
tools:::unix.packages.html(.Library)
>From Sys.info():
                              sysname                              release
                              "Linux"              
"2.6.15-1.1831_FC4smp"
>From the startup:
Version 2.2.1  (2005-12-20 r36812)

I don't have root privileges but am installing in my private library:
stat71/dscott10> echo $R_LIBS
/home/staff/dscott/Computing/R/Rprivatelib

Any suggestions?

David Scott



_________________________________________________________________
David Scott	Department of Statistics, Tamaki Campus
 		The University of Auckland, PB 92019
 		Auckland	NEW ZEALAND
Phone: +64 9 373 7599 ext 86830		Fax: +64 9 373 7000
Email:	d.scott at auckland.ac.nz


Graduate Officer, Department of Statistics

David Scott <d.scott at auckland.ac.nz> writes:
> When trying to update packages after the sysadmin updated R on my unix box 
> I got errors on some packages. For example for chron:
> 
> * DONE (chron)
> mkdir: cannot create directory `/usr/lib/R/library/00LOCK': Permission 
> denied
...
> >From the startup:
> Version 2.2.1  (2005-12-20 r36812)
> 
> I don't have root privileges but am installing in my private library:
> stat71/dscott10> echo $R_LIBS
> /home/staff/dscott/Computing/R/Rprivatelib
> 
> Any suggestions?
update.packages tries to update all available packages, including the
system ones. Try
update.packages("/home/staff/dscott/Computing/R/Rprivatelib")
 

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