Zotero/Rstudio Interaction leading to OO crash

SalishSea

My everyday work environment is OO3.2, Ubuntu 10.04-64AMD, Firefox 3.1.6, R (statistical software 2.13) and an IDE for working with R called Rstudio. Rstudio and Zotero are not playing nicely together.

I have reported this interaction to Rstudio here:

http://support.rstudio.org/help/discussions/problems/572-crashes

and dmesg logs, Rstudio logs etc. are available there.

Note that Zotero consists of two plugins - one for firefox, and an extension to OO that allows communication between OO and the Zotero sql database. FIrefox seems to survive these crashes, but I loose OO and R - have to kill Rstudio from the command line.


The following lines from the Rstudio log suggest that Rstudio and Zotero are not playing nicely together:

02 Jun 2011 16:47:27 [rsession-rob] ERROR system error 1 (Operation not permitted) [path=/home/rob/.zoteroIntegrationPipe]; OCCURRED AT: uintmax_t core::FilePath::size() const /home/ubuntu/rstudio/src/cpp/core/FilePath.cpp:297; LOGGED FROM: uintmax_t core::FilePath::size() const /home/ubuntu/rstudio/src/cpp/core/FilePath.cpp:297
02 Jun 2011 16:47:27 [rsession-rob] ERROR system error 1 (Operation not permitted) [path=/home/rob/.zoteroIntegrationPipe]; OCCURRED AT: uintmax_t core::FilePath::size() const /home/ubuntu/rstudio/src/cpp/core/FilePath.cpp:297; LOGGED FROM: uintmax_t core::FilePath::size() const /home/ubuntu/rstudio/src/cpp/core/FilePath.cpp:297
02 Jun 2011 16:47:27 [rsession-rob] ERROR system error 1 (Operation not permitted) [path=/home/rob/.zoteroIntegrationPipe]; OCCURRED AT: uintmax_t core::FilePath::size() const /home/ubuntu/rstudio/src/cpp/core/FilePath.cpp:297; LOGGED FROM: uintmax_t core::FilePath::size() const /home/ubuntu/rstudio/src/cpp/core/FilePath.cpp:297
02 Jun 2011 16:47:27 [rsession-rob] ERROR system error 1 (Operation not permitted) [path=/home/rob/.zoteroIntegrationPipe]; OCCURRED AT: uintmax_t core::FilePath::size() const /home/ubuntu/rstudio/src/cpp/core/FilePath.cpp:297; LOGGED FROM: uintmax_t core::FilePath::size() const /home/ubuntu/rstudio/src/cpp/core/FilePath.cpp:297



Many thanks!

Rob

adamsmith

that thread on the r-studio forums is listed as "private or deleted"

Also - what exactly are you doing when that happens? Does it happen on start-up? When trying to insert a citation into Ooo?

SalishSea

Oops...

You are right. Rstudio staff will have to unlock it. I'd expect that done within an hour. They are very responsive - just like Zotero!


R

SalishSea

Rstudio forum post now public.

SalishSea

Adam,

Typically I am running regressions of large datasets (10^8 bytes), >500K observations in Rstudio. (That's my life!) I have 4Gigs of RAM, and I typically am working with <3.

OO just dies, closes the process, and starts up again in recovery model. Rstudio's attention goes elsewhere, and eventually I have to kill it from the command line. FF seems OK.

One time I lost my X server, but I have not been able (or trying) to replicate that.

adamsmith

this just doesn't sound like Zotero has any part in actually creating the crash. Have you tried replicating this with Firefox closed? Just because a Zotero error is picked up by the r-studio log it doesn't actually have to be connected.

SalishSea

Fair enough, but it is an obvious place to look. Without a replicable example, I can't imagine that we can trace this down, so I'll close this for now, pending someone else reporting trouble with these great tools.

Thanks,

adamsmith

well as I said - if you can replicate this with FF closed you'd be able to definitely exclude Zotero as a possible culprit. If this doesn't replicate with FF closed the next step would be to try to see if it replicates with Zotero disabled and FF open etc.