No menu bar after El Capitan upgrade - Zotero Standalone

mijalce
After I upgraded to El Capitan, Zotero lost the menubar (with selected and not selected the new option to automatically hide and show menubar).
Also show/hide of the Dock does not function when Zotero is the focus application.
I use the last version of ZS - 4.0.28.6
Thanks
«1
  • dstillman
    I'm not sure what you mean here — I have a menu bar in Standalone on 10.11, and I can hide/show the dock with Cmd-D when Zotero is focused.

    Could you be more precise?
  • mijalce
    I do not have the menu bar, none of the options in the menu are visible. No keyboard shortcut is working. Also,
    - the zoom and minimise button are not present and
    - I cannot resize the Zotero window.

    I reinstalled Zotero and no change.

    Thanks!
  • dstillman
    Can you post a screenshot somewhere (Dropbox, imgur, etc.) and provide a link here?
  • mijalce
    Screenshot, after the Zotero is open
    https://www.dropbox.com/s/hef6ad6i6gzz1p0/Screenshot%202015-10-01%2013.18.28.png?dl=0

    Screenshot, after I move (not resize) Zotero
    https://www.dropbox.com/s/t9p661zh2wphwpi/Screenshot%202015-10-01%2013.20.01.png?dl=0
  • dstillman
    Those screenshots seem to show you not having a title bar — i.e., the bar with the red/yellow/green icons. The menu bar is at the top of the screen with the Apple menu and clock, and that's what can be hidden with the new setting in 10.11.

    I'm not sure why you don't have a title bar, though — you should, and I do, so it's possible that this is due to some other new setting. We can see if anyone else reports it, but you might have to play around and figure out what's different on your system.
  • mijalce
    thanks Dan. Because I can not access the add-ons (no menu bar) can you suggest me how I can disable the add-ons I have, in order to check is some of them causing this. Thank you for the support!
  • yonggeun
    One more person with same issue.

    I also have same issue right after I upgrade my system to OS X 10.11. I downloaded and installed the latest version of zotero ( 4.0.28.6) but still it persists.

    https://www.dropbox.com/s/beqwdc7jg6kykjr/zotero.jpg?dl=0

    :-(
  • mijalce
    @vizualizer:
    do you know which add-ons you have? I have zotxt, Better Bib(La)TeX, zotfile, RTF/ODF-Scan for Zotero, Zotero Scholar Citations
    do you have some applescript?
    I am trying to see will we intersect somewhere, and maybe scope the possible problem.
    @Dan:
    I ran Real time debug with no success. Normal Debug out can be found at https://www.dropbox.com/s/j6l9vgjytbixa4k/Debug%20output.txt?dl=0
  • Awel
    Exact same problem here. Except for the references, mijalce's screenshots could be mine. It happened after I hit the green button to go full screen.
  • mijalce
    I think that the problem might be with Quick Look (qlmange). When I press space I see the Zotero menu bar. I created debug output with iD D668672431.
  • mijalce
    this is the output of Real-time debug

    This file contains debug information

    Testing Quick Look preview with files:
    /Users/-/Library/Application Support/Zotero/Profiles/t1o3fh88.default/zotero/storage/TB4RG5IJ/2012_PHD-Boell-Theorizing_Information_and_Information_Systems.pdf
    2015-10-01 21:42:45.215 qlmanage[2572:165883] *** CFMessagePort: bootstrap_register(): failed 1100 (0x44c) 'Permission denied', port = 0x870b, name = 'com.apple.coredrag'
    See /usr/include/servers/bootstrap_defs.h for the error codes.
    2015-10-01 21:42:45.266 qlmanage[2572:165883] *** CFMessagePort: bootstrap_register(): failed 1100 (0x44c) 'Permission denied', port = 0xaa3f, name = 'com.apple.tsm.portname'
    See /usr/include/servers/bootstrap_defs.h for the error codes.
    2015-10-01 21:42:45.269 qlmanage[2572:165883] *** CFMessagePort: bootstrap_register(): failed 1100 (0x44c) 'Permission denied', port = 0xac27, name = 'com.apple.CFPasteboardClient'
    See /usr/include/servers/bootstrap_defs.h for the error codes.
    2015-10-01 21:42:45.269 qlmanage[2572:165883] void __CFPasteboardSetup() : Failed to allocate communication port for com.apple.CFPasteboardClient; this is likely due to sandbox restrictions
    Permission Error: Copying of text from this document is not allowed.
    Permission Error: Copying of text from this document is not allowed.
    Permission Error: Copying of text from this document is not allowed.
    Permission Error: Copying of text from this document is not allowed.
    Permission Error: Copying of text from this document is not allowed.
    Permission Error: Copying of text from this document is not allowed.
    Permission Error: Copying of text from this document is not allowed.
    Syntax Error: Couldn't read xref table
    Syntax Warning: PDF file is damaged - attempting to reconstruct xref table...
    Syntax Error: Top-level pages object is wrong type (null)
    Syntax Error: Couldn't read page catalog
    Syntax Error: Couldn't read xref table
    Syntax Warning: PDF file is damaged - attempting to reconstruct xref table...
    Syntax Error: Top-level pages object is wrong type (null)
    Syntax Error: Couldn't read page catalog
    Permission Error: Copying of text from this document is not allowed.
    Permission Error: Copying of text from this document is not allowed.
    Permission Error: Copying of text from this document is not allowed.
    Permission Error: Copying of text from this document is not allowed.
    Permission Error: Copying of text from this document is not allowed.
    Permission Error: Copying of text from this document is not allowed.
    Permission Error: Copying of text from this document is not allowed.
    Syntax Error (7629447): Unknown filter 'Crypt'
    Syntax Error (7629447): Unknown filter 'Crypt'
    Permission Error: Copying of text from this document is not allowed.
    Permission Error: Copying of text from this document is not allowed.
    Permission Error: Copying of text from this document is not allowed.
    Permission Error: Copying of text from this document is not allowed.
    Syntax Warning: May not be a PDF file (continuing anyway)
    Syntax Error: Couldn't read xref table
    Syntax Warning: PDF file is damaged - attempting to reconstruct xref table...
    Syntax Error: Couldn't find trailer dictionary
    Syntax Error: Couldn't read xref table
    Syntax Warning: May not be a PDF file (continuing anyway)
    Syntax Error: Couldn't read xref table
    Syntax Warning: PDF file is damaged - attempting to reconstruct xref table...
    Syntax Error: Couldn't find trailer dictionary
    Syntax Error: Couldn't read xref table
    Permission Error: Copying of text from this document is not allowed.
    Permission Error: Copying of text from this document is not allowed.
    Syntax Error: Couldn't read xref table
    Syntax Warning: PDF file is damaged - attempting to reconstruct xref table...
    Syntax Error: Top-level pages object is wrong type (null)
    Syntax Error: Couldn't read page catalog
    Syntax Error: Couldn't read xref table
    Syntax Warning: PDF file is damaged - attempting to reconstruct xref table...
    Syntax Error: Top-level pages object is wrong type (null)
    Syntax Error: Couldn't read page catalog
    Syntax Error: Couldn't read xref table
    Syntax Warning: PDF file is damaged - attempting to reconstruct xref table...
    Syntax Error: Top-level pages object is wrong type (null)
    Syntax Error: Couldn't read page catalog
    Syntax Error: Couldn't read xref table
    Syntax Warning: PDF file is damaged - attempting to reconstruct xref table...
    Syntax Error: Top-level pages object is wrong type (null)
    Syntax Error: Couldn't read page catalog
  • dstillman
    You can clear your add-ons by temporarily moving the 'extensions' directory in your Zotero profile directory out of the way. If that fixes the problem, reinstall them one by one to find the problem.
  • yonggeun
    edited October 1, 2015
    @mijalce

    Hi, These are what I had.

    paper machines
    rtf-odf-scan-for zotero
    zotero scholar citations
    quick look
    zotfile
    zutilo

    I also cleared all the extension files for testing. But it wasn’t helpful.

    I don’t have any applescript so far.

    Before this problem happened I have turned on the auto-hide-menubar function. I am suspicious of this but no evidence. Now the function is turned off.
  • mijalce
    I also removed all the extensions, but the problem is not resolved.
  • dstillman
    edited October 2, 2015
    OK, that's not too surprising — it's far more likely this is caused by some OS X setting that's only enabled on certain machines or some strange interaction with full-screen mode. (Does this happen after a restart, before using full-screen mode?) We'll keep trying to reproduce this.
  • yonggeun
    edited October 2, 2015
    @Dan Stillman

    I hope I can help you reproduce this. The below is all I can say about this bug.

    1. System info
    -1. OS X el capitan,
    -2. Macbook air 2013 mid, i5 1.3Ghz
    -3. No changes with the bug either external display is connected or not.
    -4. Menubar autohiding turned off in OS X. Zotero add-on folder is empty since I erase all the file from the folder after the problem started.


    2. history; actions that I made after OS upgrade.
    -1. OS upgrade

    -2. testing several new functions
    --1. OS level full screen support -> zotero [worked fine]
    ---2. testing java runtime app -> visual thesaurus 3 [unexecutable]
    ---3. download and install Java for OS X 2015-001 from Apple website
    ---4. system restart
    ---5. visual thesaurus 3 works fine.
    ---6. —— [I tested several things again but I cannot remember precisely] ——
    ---7. run zotero to test OS X split view

    --3. Frameless zotero window came out.

    --4. To solve the problem I tried several. all is ineffective.
    ---1. restart system
    ---2. download and install the latest version of zotero (I didn’t erase the old version but just overwrote the new file)
    ---3. clear all the add-ons
    ---4. turn on & off menubar auto hide function and menu bar color.
    ---5. I uninstalled java following this instruction, https://www.java.com/en/download/help/mac_uninstall_java.xml
    -----1. run visual thesaurus 3 again -> still working
    -----2. zotero -> still the problem is same.


    3. Symptoms

    -1. Zotero application window without frame.

    -2. When I click the buggy zotero window, OS X menu bar disappears.

    -3. Resizing the zottero window doesn’t work. But every functions work normally except the disabled window resizing and the frameless window.

    -4. control - F2 is a OS level keyboard shortcut to access the manu bar. But this doesn’t show anything.

    -5. When external display is connected, If you move your mouse focus to another application in display 1, you can see the defective and dimmed menubar of zotero which located display 2.
    --1. https://www.dropbox.com/s/grludqlaf1ak8j3/zotero 2.png?dl=0

    So far this is all I can share.
    Wish you can reproduce the bug.
  • mijalce
    When Zotero is ran in safe mode the menu and title bar are functioning normally with the Menubar autohiding option turned off and on. Thus it might be that something in Zotero that is turned off when in safe mode (but not the apps) is causing the problem when Zotero is running in normal mode.
  • dstillman
    If it doesn't happen in safe mode, that suggests that some other background process on your system — possibly a third-party program — is causing this.
  • yonggeun
    I reboot my mac system in Safe Boot mode and the menubar is still missing.
    But zotero in safe mode works fine.
  • dstillman
    Sorry, I don't understand what you mean. You're saying that safe mode doesn't fix the menu bar and title bar in Zotero for you, as it does for mijalce?
  • yonggeun
    As same as mijalce. zotero works fine in its safe mode.
  • mijalce
    @dan: any suggestion in which direction to explore which third-party can cause this? Thanks!
  • Awel
    An idea maybe... Would any of you be using a window management app, such as divvy? I do. Deleting it did not solve the problem. But I did not enquire any further due to lack of time.

    In any case, If you use a similar app, that might be the source of the problem. If not, I'll continue to happily use it.
  • venturia
    Same problem here. (Zotero with no title bar, 10.11.1). I was running 'magnet', (CrowdCafé) a window manager but disabling this software and a reboot did not solve the issue.
  • mijalce
    I found the solution in other thread in Zotero forums (https://forums.zotero.org/discussion/50859/unable-to-rescale-zotero-after-fullscreenize-it/)
    as it is written there

    go to your Library folder inside your home folder.
    Application Support/Zotero/Profiles/somenumber.default/
    and delete the file xulstore.json

    after doing this everything is back to normal.

    Cheers!
  • adamsmith
    it'd likely be useful if someone could save a copy of the xulstore.json before deleting it and send it to support@zo...ro.org
  • mijalce
    I emailed mine
  • venturia
    Yup! Deleting xulstore.json worked for me too.
  • Awel
    Weird, there's no zotero folder inside my application support folder... Any suggestion? Am I overlooking something? https://www.dropbox.com/s/8ao9sd1lyz66ygk/Screenshot%20.tiff?dl=0
  • mijalce
    in Finder click on Go, press alt (option), Library will be displayed, click on Library, then follow the path
This discussion has been closed.