1641488960: Insert button causes libreoffice crash

nodice
I don't know why this started happening, but now every time I try to insert a citation, libreoffice (4.0.2 on Ubuntu 13.04) eats up all the memory on my computer and crashes. I opened the document from the command line and this is what was printed out when it crashed:

#
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x00007f2f488a185e, pid=3213, tid=139840698943232
#
# JRE version: 7.0_25-b30
# Java VM: OpenJDK 64-Bit Server VM (23.7-b01 mixed mode linux-amd64 compressed oops)
# Problematic frame:
#
  • adamsmith
    In LO, under
    Tools--> Options --> LibreOffice--> Advanced
    what exactly do you see under Java options?
  • nodice
    "use a java runtime environment" is checked.

    Two options for 'java runtime environmentes (JRE) already installed:'
    Sun microsystems Inc, version 1.6.0_27
    Oracle corporation 1.7.0_25

    location: /usr/lib/jvm/java-7-openjdk-amd64/jre

    Two options for 'optional (unstable) options', both unchecked.
  • nodice
    Also, when this occurs and I close firefox, it stays running in the background until I kill it.
  • adamsmith
    Try selecting the Oracle 1.7 version unless that's already the case.
  • nodice
    Sorry, I should have mentioned that Oracle 1.7 is selected.
  • adamsmith
    That also occurs in a fresh document?
    Simon will probably have to look at this.
    It's certainly not a general issue, I have things running without problems on the same set-up.
  • nodice
    No, it does not occur with a fresh document. I would really like to avoid having to re-write and re-cite my entire document, though. Is there a way to get more useful error output, so that I can see where it's choking?
  • adamsmith
    I would really like to avoid having to re-write and re-cite my entire document, though.
    obviously. Let's see if Simon has an idea. He wrote the plugin.
  • nodice
    Yes, thank you!
  • nodice
    I have isolated the problem to a single citation that I created. Trying to enter a citation after the first appearance of this "bad" citation causes the crash.

    The only unusal thing about this citation is that I created it through the "new item" (journal article) button and entered the data myself, since it is for a submitted but unpublished article.

    Please let me know what other information about this would be most useful to you.
  • nodice
    Never mind, it is not that citation. It is a very specific location in the document. If I try to insert a citation just before this location, everything is fine. If I move the cursor one character to the right and then try to insert, everything crashes.
  • adamsmith
    Odd. Anything peculiar about that location?
    We've had prior reports of problems with citations inserted in tables.
  • nodice
    Nothing that I can tell. No hidden characters. I can confirm that it is from the location i mentioned to the end of the paragraph, which is about 4 sentences.
  • nodice
    If I copy this paragraph to a new document, I can add citations with no problem.

    I should mention that I am using the "bookmarks" option, as I need to work with it as a .doc file.
  • nodice
    OK, there was a frame next to the text in this paragraph that contained a figure. When I removed the frame, things started working again in this paragraph.
  • Simon
    Did the JRE print a frame, or was that the whole message? I doubt that the JVM should be segfaulting in the first place, but without more output I have absolutely no idea what would have caused this.

    Also, it looks like have your Zotero data directory in your Dropbox, which could corrupt your Zotero database. (See this ZotPad KB article or numerous forum threads.)
  • nodice
    The JRE did not print a frame. I do have 6 'hs_err_pid' log files from various crashes while I was trying to figure this out.

    As I mentioned in an earlier post, it has something to do with a frame that contained an image, as removing it seemed to help.

    However, even after this, zotero did not keep track of entries correctly and would put citations back that I had previously deleted.

    I resorted to recreating the file and adding new citations from scatch.

    When using "bookmarks", it seems difficult to tell when you have actually deleted a citation, as opposed to zotero thinking you have just "modified" it. In the latter case, it seems the citation sticks around but is invisible. This might have been causing some of the trouble, as well.
  • adamsmith
    as a work-aroundish solution, would it be possible for you to just write in Reference marks and .odt and only convert to bookmarks/doc when sending this, or are you going back&forth all the time?
  • nodice
    It's the classic "I run Linux and use libreoffice but my PI runs windows and uses Word" situation. .docs are readible by both, so this seems to make the most sense.
  • adamsmith
    right, but whether switching back&forth is a major hassle depends on how often you send the document. If you're doing this all the time, you do want to stay with bookmarks of course, but if you just send a version every couple of weeks or so, just switching those to bookmarks is easy.
  • nodice
    OK, now editing an ODT document with ReferenceMarks. Tried to edit a citation in the paragraph next to the frame I mentioned earlier, and watched as LibreOffice took up all the memory (8 GB) on my computer before crashing.

    Again, Firefox does not crash, but I need to restart it to use zotero when I re-open the document. However, when I close Firefox, the process does not stop, and I need to 'killall firefox' before launching a new instance.

    I removed the frame by cutting and pasting into a different document and now I can edit the citation just fine.
  • nodice
    Another interesting point is that only one of the two frames in my document causes this problem.
  • kaimouse
    "When using "bookmarks", it seems difficult to tell when you have actually deleted a citation, as opposed to zotero thinking you have just "modified" it. In the latter case, it seems the citation sticks around but is invisible. This might have been causing some of the trouble, as well."

    I have been having this same issue. Deleted a reference that didn't disappear from my bibliography yet remained invisible in text, throwing the numbering (vancouver style) all out. Additionally, cutting and pasting text with citations appeared to lose the link to zotero and wouldn't update. Luckily I am using dropbox and could look at an earlier version of the document to check which references the numbers were supposed to correspond to as I had forgotten.

    I'm in exactly the same situation - ubuntu/libre at home, win/word at work and uni so stored in bookmarks. Switching to referencemarks fixes this problem, though is not ideal.
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