zotero crash when adding papers from safari connector

alexcr87

Not sure if this is due to an update (don’t recall installing one recently) but Zotero now crashes when adding papers from the Safari connector.

This morning when first adding a paper I was redirected to a web page asking if I wanted to add a new private key for the connector, and I agreed to that. Behavior going on since then.

Restarting Zotero leads to one subsequent crash, and after the second restart the paper gets added.

alexcr87

Just tested adding the same paper I just added but this time through the "add item by identifier" button, worked fine. So it really seems to be the connector.

alexcr87

anyone else having the same problem?

dstillman

As in Zotero closes completely? Can you post the first 100 or so lines of the crash report?

dstillman

This morning when first adding a paper I was redirected to a web page asking if I wanted to add a new private key for the connector, and I agreed to that. Behavior going on since then.

This appears if the Zotero app isn't open while you try to save and you tell it to save directly to zotero.org instead. Since you have the Zotero app, you don't want to do that.

alexcr87

I think I have found what causes the (intermittent) crashes: the DOI plugin, that I had added recently.

I have a lot of plugins, so either it interferes with another plugin (there’s a DOI lookup when adding items) or with the connector — I wouldn’t know. Weird because adding the item manually ("add item by identifier") works.

I’ve disabled it for now, will test 1-2 days and post the results in this thread (and, subsequently, open a bug report on the DOI plugin github).

alexcr87

Quick question: I tried enabling logging but looks like the log was cleared when restarting Zotero. How do I get access to the crash report you refer to?

And yes, Zotero closes completely. Zotero was opened when adding items.

dstillman

If the app is crashing, macOS generates a crash report. You can view it in Console.

alexcr87

-------------------------------------
Translated Report (Full Report Below)
-------------------------------------

Process: zotero [85554]
Path: /Applications/Zotero.app/Contents/MacOS/zotero
Identifier: org.zotero.zotero-beta
Version: 5.0.97-beta.65+15ae72d14 (5.0.97)
Code Type: X86-64 (Native)
Parent Process: launchd [1]
User ID: 501

Date/Time: 2022-02-08 08:32:27.0354 -0500
OS Version: macOS 12.1 (21C52)
Report Version: 12
Bridge OS Version: 6.1 (19P647)
Anonymous UUID: E4BD3BE4-F0FF-AD2E-6F3E-A5D2F54AA3CB

Sleep/Wake UUID: 63B60AAA-964B-4743-82EC-B0F2281BEFF2

Time Awake Since Boot: 300000 seconds
Time Since Wake: 8629 seconds

System Integrity Protection: enabled

Crashed Thread: 0 Dispatch queue: com.apple.main-thread

Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_PROTECTION_FAILURE at 0x00007ff7b3ce4ff8
Exception Codes: 0x0000000000000002, 0x00007ff7b3ce4ff8
Exception Note: EXC_CORPSE_NOTIFY

Termination Reason: Namespace SIGNAL, Code 11 Segmentation fault: 11
Terminating Process: exc handler [85554]

VM Region Info: 0x7ff7b3ce4ff8 is in 0x7ff7b04e5000-0x7ff7b3ce5000; bytes after start: 58720248 bytes before end: 7
REGION TYPE START - END [ VSIZE] PRT/MAX SHRMOD REGION DETAIL
MALLOC_SMALL 7f8027000000-7f8027800000 [ 8192K] rw-/rwx SM=PRV
GAP OF 0x7788ce5000 BYTES
---> STACK GUARD 7ff7b04e5000-7ff7b3ce5000 [ 56.0M] ---/rwx SM=NUL ... for thread 0
Stack 7ff7b3ce5000-7ff7b44e5000 [ 8192K] rw-/rwx SM=PRV thread 0

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libsystem_pthread.dylib 0x7ff81d38104b ___chkstk_darwin + 55
1 AppKit 0x7ff81feb30cb -[NSView _postFrameChangeNotification] + 304
2 AppKit 0x7ff81feac185 -[NSView setFrameSize:] + 2315
3 AppKit 0x7ff81febcd5c -[NSView setFrame:] + 404
4 AppKit 0x7ff81fecec76 -[NSView resizeWithOldSuperviewSize:] + 697
5 AppKit 0x7ff81fece5ef -[NSView resizeSubviewsWithOldSize:] + 501
6 AppKit 0x7ff81feabef0 -[NSView setFrameSize:] + 1654
7 AppKit 0x7ff81febcd5c -[NSView setFrame:] + 404
8 AppKit 0x7ff81fecec76 -[NSView resizeWithOldSuperviewSize:] + 697
9 AppKit 0x7ff81fece5ef -[NSView resizeSubviewsWithOldSize:] + 501
10 AppKit 0x7ff81feabef0 -[NSView setFrameSize:] + 1654
11 AppKit 0x7ff81fecbfc5 -[NSWindow _oldPlaceWindow:fromServer:] + 882
12 AppKit 0x7ff81feca8f3 -[NSWindow _setFrameCommon:display:fromServer:] + 2696
13 XUL 0x1145d7107 0x11257a000 + 33935623

Thread 1:: Gecko_IOThread
0 libsystem_kernel.dylib 0x7ff81d34d45e kevent + 10
1 XUL 0x112a6caaa 0x11257a000 + 5188266

Thread 2:: Socket Thread
0 libsystem_kernel.dylib 0x7ff81d350e4a __select + 10
1 libnss3.dylib 0x10c1fcaec 0x10c0b3000 + 1350380

Thread 3:: JS Watchdog
0 libsystem_kernel.dylib 0x7ff81d34b506 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x7ff81d385a69 _pthread_cond_wait + 1224

Thread 4:: JS Helper
0 libsystem_kernel.dylib 0x7ff81d34b506 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x7ff81d385a69 _pthread_cond_wait + 1224
2 libmozglue.dylib 0x10bb639dc mozilla::detail::ConditionVariableImpl::wait_for(mozilla::detail::MutexImpl&, mozilla::BaseTimeDuration const&) + 60
3 libsystem_pthread.dylib 0x7ff81d38100f thread_start + 15

Thread 5:: JS Helper
0 libsystem_kernel.dylib 0x7ff81d34b506 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x7ff81d385a69 _pthread_cond_wait + 1224
2 libmozglue.dylib 0x10bb639dc mozilla::detail::ConditionVariableImpl::wait_for(mozilla::detail::MutexImpl&, mozilla::BaseTimeDuration const&) + 60
3 libsystem_pthread.dylib 0x7ff81d38100f thread_start + 15

Thread 6:: JS Helper
0 libsystem_kernel.dylib 0x7ff81d34b506 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x7ff81d385a69 _pthread_cond_wait + 1224
2 libmozglue.dylib 0x10bb639dc mozilla::detail::ConditionVariableImpl::wait_for(mozilla::detail::MutexImpl&, mozilla::BaseTimeDuration const&) + 60
3 libsystem_pthread.dylib 0x7ff81d38100f thread_start + 15

Thread 7:: JS Helper
0 libsystem_kernel.dylib 0x7ff81d34b506 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x7ff81d385a69 _pthread_cond_wait + 1224
2 libmozglue.dylib 0x10bb639dc mozilla::detail::ConditionVariableImpl::wait_for(mozilla::detail::MutexImpl&, mozilla::BaseTimeDuration const&) + 60
3 libsystem_pthread.dylib 0x7ff81d38100f thread_start + 15

Thread 8:: JS Helper
0 libsystem_kernel.dylib 0x7ff81d34b506 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x7ff81d385a69 _pthread_cond_wait + 1224
2 libmozglue.dylib 0x10bb639dc mozilla::detail::ConditionVariableImpl::wait_for(mozilla::detail::MutexImpl&, mozilla::BaseTimeDuration const&) + 60
3 libsystem_pthread.dylib 0x7ff81d38100f thread_start + 15

Thread 9:: JS Helper
0 libsystem_kernel.dylib 0x7ff81d34b506 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x7ff81d385a69 _pthread_cond_wait + 1224
2 libmozglue.dylib 0x10bb639dc mozilla::detail::ConditionVariableImpl::wait_for(mozilla::detail::MutexImpl&, mozilla::BaseTimeDuration const&) + 60
3 libsystem_pthread.dylib 0x7ff81d38100f thread_start + 15

Thread 10:: JS Helper
0 libsystem_kernel.dylib 0x7ff81d34b506 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x7ff81d385a69 _pthread_cond_wait + 1224
2 libmozglue.dylib 0x10bb639dc mozilla::detail::ConditionVariableImpl::wait_for(mozilla::detail::MutexImpl&, mozilla::BaseTimeDuration const&) + 60
3 libsystem_pthread.dylib 0x7ff81d38100f thread_start + 15

dstillman

Are you using an external monitor?

Have you seen this since disabling DOI Manager?

alexcr87

This is interesting ; yes I am using two external monitors.

I have disabled the DOI manager since yesterday, no crash since then. I’ll test some more today ; fingers crossed.

dstillman

@bwiernik: You're popping up a progress window during processing, right? I'm guessing it's some interaction with that and multiple monitors (under some circumstances — clearly not every use of the popup).

bwiernik

Yeah, I pop up a progress window. Any suggestions on troubleshooting this on my end?

dstillman

I'll take a look, but realistically it probably won't be fixed before we update to a newer Mozilla framework after Zotero 6.

mafdz

Commenting to echo that this error is also happening to me, Zotero 6.0.13 on Monterey 12.5.1 on M1 Max, multiple monitors. Disabling the DOI mananger also fixed the issue.

davideagle

Same issue here. Removed the DOI extension fixed the crash issue.