I have identical R.profiles and R_HOME directories set up on both my local machine and a remote linux cluster. To keep my libraries and R install separate, I use a site-library on both machines. The first line of my .Rprofile is: '.libPaths(new= "~/R_HOME/site-library") #tell R where site-library is' Until R-2.6.0 this was working fine on both machines, but since I have been unable to upgrade packages on the remote machine. Every attempt at upgrade results in a directory '00LOCK' being place in the site-directory and then the upgrade fails. This has happened with R-2.6.0, 2.6.1, and now with R-devel (2.7.0). If I have this setup incorrectly I am puzzled as to why it works with my local machine and why it worked with versions of R prior to 2.6.0. Ideas? Thanks, Mark -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 204-4202 Home (no voice mail please) mwkimpel<at>gmail<dot>com
Mark W Kimpel wrote:> I have identical R.profiles and R_HOME directories set up on both my > local machine and a remote linux cluster. To keep my libraries and R > install separate, I use a site-library on both machines. > > The first line of my .Rprofile is: > '.libPaths(new= "~/R_HOME/site-library") #tell R where site-library is' > > Until R-2.6.0 this was working fine on both machines, but since I have > been unable to upgrade packages on the remote machine. Every attempt at > upgrade results in a directory '00LOCK' being place in the > site-directory and then the upgrade fails.This directory gets placed there and then removed when the upgrade is finished, to prevent two processes from trying to simultaneously update the directory. If you terminated an upgrade in an unexpected way, say by dropping your connection, then the file will be left and you need to manually remove it before you try to upgrade again. If you have removed it, and it keeps re-appearing, it is a sign of something else going wrong (usually outside of R). Paul> > This has happened with R-2.6.0, 2.6.1, and now with R-devel (2.7.0). > > If I have this setup incorrectly I am puzzled as to why it works with my > local machine and why it worked with versions of R prior to 2.6.0. > > Ideas? > Thanks, > Mark >=================================================================================== La version fran?aise suit le texte anglais. ------------------------------------------------------------------------------------ This email may contain privileged and/or confidential in...{{dropped:26}}
I'm still having problems with this 00LOCK error. Tonight I recompiled
R-devel from scratch, created a new site-library directory after moving
the old one to scratch storage, and tried reinstalling my packages. 13
out of 290 packages successfully reinstalled and, once again, 00LOCK has
appeared.
I tried to hack around this by installing packages one at a time, each
time looking for 00LOCK and, if present, unlinking it recursively. This
fails, although I can unlink other packages with identical permissions
from within R. Outside of R, in the bash shell, I can rm -r 00LOCK
without any problems. What follows is just some output demonstrating this.
Why does unlink not work for this one particular directory?
Mark
x <- unlink("00LOCK", recursive = TRUE)
> x
[1] 1 # unlink fails
> dir()
[1] "00LOCK" "acepack"
[3] "affxparser" "affyio"
[5] "AffymetrixDataTestFiles" "akima"
[7] "amap" "aws"
[9] "Biobase" "hapmap100kxba"
[11] "kernlab" "plasmodiumanophelescdf"
[13] "R.css" "som"
[15] "stjudem" "xlahomology"
> ?unlink
> y <- unlink(x = "00LOCK", recursive = TRUE)
> y
[1] 1
> y <- unlink(x = "acepack", recursive = TRUE)
> y
[1] 0 #u unlink succeeds
From the command line:
ls -al
drwxr-xr-x 3 mkimpel psych 4096 2007-12-11 23:13 00LOCK
drwxr-xr-x 13 mkimpel psych 4096 2007-12-11 23:12 affxparser
drwxr-xr-x 10 mkimpel psych 4096 2007-12-11 23:12 affyio
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, & Mobile & VoiceMail
(317) 204-4202 Home (no voice mail please)
mwkimpel<at>gmail<dot>com