This is a follow-up to an old thread with kind of solution to the
00LOCK problem on NFS.
I have made a patch to install.packages to accept a new argument
locktype = c("lock", "no-lock", "pkglock")
which is passed to R CMD INSTALL. This addition might have
independent interest aside from the NFS problem, as it exposes
functionality from R CMD INSTALL to install.packages and the very
convenient update.packages. Patches are at
http://www.biostat.jhsph.edu/~khansen/packages2.R-patch
http://www.biostat.jhsph.edu/~khansen/install.packages.Rd-patch
(patches to files in the utils package) and both
R-devel (R version 2.12.0 Under development (unstable) (2010-05-17 r52025))
and
R-2.11 (R version 2.11.0 Patched (2010-05-17 r52025))
passed make check-all with these two patches applied. I thought about
adding a note describing my findings below to the details section, but
decided against it.
Regarding the 00LOCK problem. In my testing, using the patches above
and setting locktype = "pkglock", makes it possible to deal with the
NFS problem. Specifically, I have not been able to make
update.packages() fail midway, due to a un-removable 00LOCK file
(which is not too surprising, as I now have a per-package lock).
However, sometimes (but far less frequently than before), a
00LOCK-pkgname directory remains after update/install.packages.
Sometimes this 00LOCK-pkgname directory does not contain any .nfs*
files (!?) and sometimes it does. For this reason, I still precede any
install/update.packages with a check for the existence of a
00LOCK-pkgname directory and an attempt to remove it.
The difference between using locktype = "pkglock" and not is
specifically that without, it was possible for update.packages to fail
midway even though there were no 00LOCK* files at the start of the
update process.
Originally I hypothesized that the presence of the .nfs* files in the
00LOCK directory had to do with synchronization issues between the
file server and the compute node. In order to approach this I tried
to insert a
system("sleep 10")
at the beginning of
do_cleanup
in
tools/R/install.R
but that did not work.
Since the pkglock approach described above seems to solve this issue
for me, I have not pursued the synchronization issue further.
Kasper
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
