Zotero/Rstudio Interaction leading to OO crash

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
  • 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?
  • 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
  • Rstudio forum post now public.
  • 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.
  • 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.
  • 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,
  • 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.
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