Well, the error seems clear: your R session has too many files open.
Now most OSes do have limited tables of files per process, but the
numbers are not small: on Mac OS I believe it is 256 (that's what bash
reports on mine): 1024 is a common value for other Unixen.
You could try closeAllConnections(), in case that helps enough to let
you shutdown the session (but R allows only 128 connections, so that
is not the main cause here).
Have you any idea what you might be doing that opens hundreds of
files (at a lower level than R). Are you actually using those spatial
packages (it might be one of those)?
It is possible to raise the limit on the number of open files (in
bash, ulimit -n), but this is not advisable unless you need it.
On Fri, 20 Mar 2009, Roland Kaiser wrote:
Hi!
I'm using the R GUI with joy ever since, despite some occasional
misbehaviour. However, the last days I have noticed some errors
that really waste a considerable amount of time.
I'm sorry, I can't come up with a reproducible example,
but I try to explain how the error was raised in my case.
During testing of code I subsequently executed
lines by cmd + return.
After several times suddenly the working directory
in the GUI shows <deleted> instead of the path.
Maybe I did some strange key combination here,
but in the past I did never deleted the path by accident?
The console then states:
2009-03-20 10:06:08.537 R[620] Cannot load Interface Builder file
'/System/Library/Frameworks/AppKit.framework/Resources/German.lproj/NSAlertPanel.nib'
I am not able to save any open files, but can copy
and paste to TextEdit to prevent loss.
Funny to see what sessionInfo() tells invoked after.
sessionInfo()
Fehler in gzfile(file, "rb") : kann Verbindung nicht öffnen
Zusätzlich: Warning message:
In gzfile(file, "rb") :
kann komprimierte Datei
'/Users/roli/Library/R/2.8/library/maptools/Meta/package.rds' nicht öffnen.
Grund evtl. 'Too many open files'
when q() the session console prints again
… too many open files … and quits.
SessionInfo after restart and reloading packages and data
GUI version is Mac OS X GUI rev. 5372 for R 2.8.x
sessionInfo()
R version 2.8.1 (2008-12-22)
i386-apple-darwin8.11.1
locale:
de_AT.UTF-8/de_AT.UTF-8/C/C/de_AT.UTF-8/de_AT.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] maptools_0.7-16 foreign_0.8-29 spatstat_1.14-9 deldir_0.0-7
[5] gpclib_1.4-2 mgcv_1.4-1.1 rgdal_0.6-7 sp_0.9-32
loaded via a namespace (and not attached):
[1] grid_2.8.1 lattice_0.17-17
Any Ideas what will cause that crash?
Is a matter of my system locale (German in this case).
No.
--
Brian D. Ripley, [email protected]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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