I have some tools and an R package that together provide a solution to
the problem of updating an R package while it is attached in one or more
running R sessions (whether on the same machine or not.) The technique
is to always create a new directory for the newly installed package, so
that existing installed packages are never overwritten. The tricky part
is to manage this in a way that is transparent to the user, which is
what the package accomplishes. If this is any interest in this I could
make it available; email me privately or respond on the list.
-- Tony Plate
On 4/26/2010 1:05 PM, Kasper Daniel Hansen wrote:
2010/4/26 Christian Brechbühler<brechbueh...@gmail.com>:
On Mon, Apr 26, 2010 at 11:15 AM, Kasper Daniel Hansen
<kasperdanielhan...@gmail.com> wrote:
I am running into a problem with the 00LOCK file and .nfs files. It
seemed to be caused by the following
R is installed on NFS
user A has loaded pkg_A containing a dynamically loaded library
user B (the administrator) runs install.packages("pkg_A")
as the final part of the installation process the 00LOCK directory is
removed
this creates a .nfs file because user A has the dynamic library open
this .nfs file cannot be removed until user A exits R
because of this, 00LOCK cannot be removed, and if the
install.packages call is going to install packages after pkg_A, they
fail
Yup, I've seen that. The program "lsof" can be useful to find which process
has the library open.
User A does not need to exit R; it's enough to detach(package:pkg_A);
library(pkg_A);.
I have now done more careful experimentation with a colleague so I
have more than 1 user, and my earlier description was wrong. I can
reliably trigger this 00LOCK problem if a single user does
library(pkg_A) and then in a separate R session does
install.packages(pkg_A).
I cannot reliable trigger it if
1) the library() and install.packages() were done by the same user,
but on different nodes
2) the library() and install.packages() were done by different users, same node
3) the library() and install.packages() were done by different users,
different nodes
I believe I have run into this problem with 00LOCK when I only had one
R session running (the one doing the install.packages), so I am
beginning to believe that what I seem to run into is a race problem.
But I could of course be wrong.
Kasper
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