EndNote X8 Keeps Crashing on Mac

After having the exact same issue on both Endnote 7 and updated 8.2 constantly crashing on my MacBook Pro (OS Sierra 10.12.6) and being completely unworkable as I’m writing my thesis, I have discovered the following:

    • Issues arose after MPB operating system El Capitan 10.11 (I.e., if your OS is this or earlier, you should be fine) due to Apple changing their PDFkit.
    • In my Endnote Library, this has resulted in some of my pdfs being duplicated in the “PDF” folder in the .Data file of my Library. (I.e., more than one of the sub folders contained the same pdf for a given reference in my Endnote Library). 
    • If you only use Endnote as a citation manager and not as a reference manager, then you can just move the “PDF” folder from the .Data folder to somewhere else. This will stabalize Endnote, but you will have to access all your pdfs manually by searching for them in the moved “PDF” folder.

Here is the fix I did (564 references, with 311 pdfs):

  1. SAVE A COPY OF YOUR LIBRARY!!! (put the backup in a safe place). It is easy to screw up how your library talks to the attached pdfs, so make sure you have an original untouched backup somewhere.
  2. Close Endnote if you have it open
  3. Open the .Data folder of your library, make a copy of the “PDF” folder to a temporary different location, like your desktop.
  4. Now create a new empty folder and name it “PDF_temporary_fixing” on your desktop. 
  5. You now have two folders on your desktop, the copied “PDF” folder, and the “PDF_temporary_fixing”
  6. In this copied “PDF” folder that you have moved to your desktop, move all of the pdfs out of their sub folders and into the “PDF_temporary_fixing”. There are shortcuts that you can google on how to do this quickly instead of moving one-by-one if you have a ton of pdfs.
  7. Now you should have just a list of pdf files on your “PDF_temporary_fixing” folder. By doing this, you will be able to identify  any duplicates of pdfs because they will have the same name (write these down). You would have a much harder time doing this if you have to go through the sub folders one-by-one.
  8. You can now delete the copied PDF folder, as you have now identified your duplicates.
  9. Go back into your .Data folder of your Library, and into your “PDF” folder that you have there, and search within that “PDF” folder for the identified pdf duplicates. Write down the folder number that the duplicates (both/all copies) are in. For example: for pdf “Smith-2016.pdf” you could have one duplicate in folder “3907727203” and another in folder “2442186214”. It is also worth it to look at each pdf in adobe to see if one has any highlights/comments that you may have made, so you know which one to keep. I also made note of which file was older/bigger to help me decide which one I would keep.
  10. By this step you should have a list of all your duplicates, their folders, and an idea of which ones you would like to keep.
  11. Now you get to go into the “PDF” folder in the .Data folder and delete the folders with duplicates!
  12. You’re not quite done yet, you now have to open Endnote and make sure that the references which had multiple .pdfs are still talking to the remaining .pdf in the “PDF” folder in the .Data folder. Search for each reference and click on it to see if it still opens the reference. If they all do, great! You’re done and can also delete your “PDF_temporary_fixing” folder. If not, then keep going.
  13. For any references that aren’t opening their pdfs, you have to re-attach them manually.
  14. Close Endnote
  15. Go into the “PDF” folder in the .Data folder, and move  the folders with the references you want to attach completely out of the “PDF” folder and onto your desktop.
  16. Open Endnote, and search for each reference that you need to re-attach. Drag their associated pdf onto the reference in Endnote to attach manually. Do this for each reference.
  17. You can now delete the moved folders on your desktop, as Endnote automatically creates a new copy in the “PDF” folder.

By doing the above my Endnote significantly stabilized. I found 6 duplicated references out of 311, so hopefully this is more of a sporadic occurence. I also would recommend manually attaching pdfs to imported references instead of getting Endnote to find and attach the pdfs for you. Don’t forget to create back-ups of your library regularly if something goes wrong.

I hope this works for other people! It’s labour-intensive but salvaged my thesis, library, and prevented me from having to run Endnote in Bootcamp or Parallels Desktop.

**UPDATE #1** after one week of regular daily use, the software remains stabilized. I am curious if others have tried and had any sucess using my posted fix?

**UPDATE #2** stburrow highlights an aspect of this problem that I haven’t encountered, being the use of Smart Groups, because I have not used them in my libraries. Therefore it appears that my fix will not work if the library utilizes Smart Groups.

hope someone can help it too

I am having the same exact problems. I am so frustrated. Has anyone figured out how to fix endnote so we can actually use it on our Macpro laptops? Thanks

I have been monitoring this thread since my posting three weeks ago.  I decided to try a few fixes, all without success.  Owing to my present status (writing dissertation, full-time) I don’t have the luxury of waiting for Clarivate to fix EN 8.2.  I have exported my EN library to SonnySoftware’s Bookends program.  Maybe some of this troubleshooting will help somebody else figure something out for Endnote, but I doubt it:

Following up on the suggestions by K-Jacob that duplicate pdf’s in the EN library tend to destabilize the program, I removed about 215 duplicates from my 6000+ record EN library.  When I tried to use some functionality in EN that used to work (smart groups) the program crashed multiple times.  Not a confidence builder for EN 8.2.

Next I tried using the EN ‘Recover Library…’ function in the ‘Tools’ menu.  After I entered the name of the recovered library, EN began indexing the pdf files in the recovered library.  Usually after getting through indexing about 15 pdf files the program crashed.  Later I deleted all the pdf files from the library copy that I was trying to recover, and the ‘Recover Library…’ function was able to complete whatever it does to fix a corrupted EN library.  Clearly the program was having some problems with some of my pdf files, but when I tried using the smart groups function within my recovered library, sans pdf files, the EN 8.2 program still crashed.

I think that there are multiple bugs contributing to the instability of EndNote 8.2 on the Mac.  As prior posters have noted (and I also was told by Clarivate support) Clarivate blames Apple for changes it made to the OS X pdf tool kit since the El Capitan release.  Perhaps that is true to some extent, but to my thinking it is the software vendor’s responsibility to adjust to changes in the operating systems that it sells products for.  El Capitan has been out for over two years, which seems to me plenty of time to develop and issue an update to EndNote that addresses whatever changes in Sierra and High Hierra occured.  When I contacted Clarivate about my problems with EndNote X8.2 three weeks ago, they advised me to reinstall everything on my computer under El Capitan and complain to Apple for them to fix OS X.  That suggestion is patently absurd.  I am not going to break my computer’s ability to interact with my other Apple devices (iPad, iPhone, etc.) because Clarivate is trying to shame Apple into changing their operating system.  I expect Apple doesn’t care a toss over how well one program (EndNote) functions on their products.  I could be wrong about Clarivate and/or Apple, and maybe patches are just about to be released.  Unfortunately I have work to get finished over the next thirty days, and I am not going to gamble on loading up my dissertation with EndNote citation codes if I can’t trust EndNote to run without crashing.  I don’t need the headache of watching EndNote freeze/crash while trying to finish my final dissertation copy.  All of this situation is a shame.  EndNote wasn’t the fanciest software for managing research literature, but I had developed a lot of workarounds for functionalities that were missing or that I had issues with.  Now I am going to have to start over with Bookends, which in itself is a headache but in the long run it is a headache I can deal with.  People and institutions depend on programs like EndNote.  I don’t appreciate getting caught in the middle of a staring match between Apple and Clarivate, waiting to see who blinks first.

Bien évidemment, je rencontre le même problème

La qualité n’est pas le fort de Thomson Reuters

Je déconseille fortement ce logiciel et encourage tout un chacun à utiliser Zotero

I’ve also found that Endnote crashes whenever I try to create a smart group.

Obviously, this isn’t a new problem.

Neither would it logically have anything to do with MacOS or pdfs. Clearly, the Endnote program has a serious bug.

Time to lift your game Clarivate!

Just adding to the chorus. Endnote seems unusuable on 10.13.3, incredibly slow, now crashing endlessly. Can only imagine if I were trying to do a dissertation with this, I’d defenstrate either myself or the computer. 

Really wanted that Word integration…

So. Here I am struggling with the same problems… Do you guys have feedback on Zotero? EndNote is simply unusable… 

Thanks

EDIT: how long do you think it will take before they fix all of this?

Last Fall I decided to take the plunge and buy a big-screen iPad Pro with iPencil for reading and annotating papers.  Although I was in the throes of writing my dissertation (I still am), I anticipated starting a new project in another academic department at my university, with a new stream of literature to read.  I was somewhat relieved to see that Clarivate (Formerly Thomson Reuters) had quietly removed some of the more objectionable barriers of their iPad EndNote application and that I could finally get some use from it on the iPad.  Later, when I took up my dissertation writing again in early January, I learned of the ‘problems’ with EndNote X8 after I updated my computers to OS X 10.13 High Sierra over the holidays.  Before that OS X update everything worked OK for me with EndNote.  The OS X upgrade necessitated a Microsoft Office 2016 update and following that update everything concerning EndNote unraveled for me.

Usually when a piece of software becomes unreliable on the Mac I assume that it is something that I am doing wrong, but I soon found out that EndNote X8 was an exception.  After failing in my attempt to reverse my upgrade of EndNote X8 back to X7 (my university would not give me a new install code to downgrade EndNote), I tried calling Clarivate to work with them, but the attitude that I got was that EndNote X8’s instability is the fault of Apple and Clarivate is blameless.  Clarivate support’s advice was for me to complain to Apple that they need to fix their OS X pdf kit and downgrade my computer to OS X El Capitan until Apple fixes High Sierra.  Working a new full-time research job, commuting 90 miles per day, and trying to finish a PhD dissertation made that suggestion impractical for me.  Even if I had the time, I wasn’t about to roll back my computer to an old OS because Clarivate either will not or cannot fix their program.

Earlier I looked at Zotero and Mendeley when I got my new iPad Pro.  Both programs’ reliance upon a paid subscription to a web server for file synchronization between the Mac and iPad was off-putting to me.  I had been through that sort of setup previously with Sente and I didn’t like it.  In my opinion, it should be possible to sychronize a Macintosh to an iPad through local wireless without having to buy a subscription (Mekentosj Papers 2 could do it).  Also, it was my impression that Zotero wasn’t especially well-suited to science-related work (I am in chemistry) but rather it is more humanities-focused.  However, that may just be bias on my part.  I really didn’t do much with Mendeley since it appeared to me to just be more of the same (similar to Zotero).

I really wanted to like EndNote Mac because my institution (Virginia Tech) licenses it for all of us and it has been a de-facto standard in the academic community for ages.  However, the EndNote Mac program changes at a glacial pace and as recent experiences prove, not always for the better.  If their telephone support response to me that Apple will have to change OS X is representative of the Clarivate’s position, then EndNote X8 Mac may not get ‘fixed’ until the next version of OS X gets released next Fall.  I base this guess on the assumption that, by then, even Clarivate will get the message then that Apple is not going to rewrite their pdf kit just to accomodate one recalcitrant software developer.  Unfortunately I cannot wait that long.  I have to write now.

I would strongly recommend that you try BookEnds as an alternative to EndNote X8.  It is a paid-app but it works very similarly to EndNote (that is, when EndNote used to work reliably).  I occasionally fire up EndNote X8 on my computer to see if there is a ‘patch’ update and I occasionally check responses to my postings here, but there is nothing.  I have found it necessary to move on/

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That worked for me, too, thank you soooooo much! (What worked is the suggestion to copy the whole document and paste it into a fresh new document)

Came across a very simple solution after seeing some quite complex solutions on here as to why Endnote was super dooper slow and crashing basically every time I edited a single reference on my mac having just instaled it today (and I’m running an old version of OS - Yosemite 10.10.5 and current version of Endnote X8.2).

Don’t open Endnote directly aside from when you are only doing stuff in it/first time when you need to when installing it,etc - instead make sure Endnote is closed, then go to Word and click on the Endnote tab and click on “go to Endnote” button to open it instead. Ensures only one copy of Endnote is open. If you have Endnote open and then use word Endnote tab for citations it’ll open a second copy without you realising.

Haven’t been running it for long after doing this but in the space of a few hours of frustrating repetitive freezing and either closing itself or me having to force close Endnote suddenly I can actually use it and (touch wood) no further issues so far. 

K-Jacob I tried to do what you suggested but have no PDF folder (guess as haven’t put any PDFs into Endnote). Found a much simpler solution which is that Word opens a second copy of Endnote if you happen to have Endnote open already which makes it go super slow and crash constantly -so closing all copies of Endnote and then then just using the “go to endnote” button in Word as the only way of opening it and seems to have fixed the problem completely.

And the crashing problem was alive and well with my older OS version (Yosemite).

Wow, I’ve had the same problem here and it’s a bit disconcerting to see this issue persist for longer than a year. And frustrating when this occurs during large projects with set deadlines!

Is it more stable to use the online version? Otherwise, I’m going to need to find a better solution.

Some specific pdfs seem to be more toxic and routinely cause crashes. I just tried to add the same pdf to 2 different libraries. Other pdfs were OK but one caused repeated crashes.

well said man keep up the good work

Had the same experience with Clarivate advising me that it was an apple problem with their pdf toolkit and incompatability with annotated pdf’s in OSX High Sierra.

Clarivate advised me to either role back to an earlier version of OSX or only use libraries without pdfs. Both are not really viable options, especially when using shared libraries on multi author projects. Can’t understand why Clarivate can’t simply patch Endnote to remove or prevent the pdfthumbnail rendering of pdfs when used with High Sierra which seems to be the cause of all the crashes.

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Here is my error report. I can not open the Endnote, even with updated version X8.2, which said improving the compatibility with High Sierra.  It seems the problem is related to the PDFs. I do not know how to solve it. I tried to put the documents in the totally new folder, but this does not work for me. 

Process: EndNote X8 [7832]
Path: /Applications/EndNote X8/EndNote X8.app/Contents/MacOS/EndNote X8
Identifier: com.ThomsonResearchSoft.EndNote
Version: 18.2.0.13302 (2017.18.2.0.13302)
Code Type: X86 (Native)
Parent Process: ??? [1]
Responsible: EndNote X8 [7832]
User ID: 501086115

Date/Time: 2018-06-07 09:42:17.339 -0700
OS Version: Mac OS X 10.13.5 (17F77)
Report Version: 12
Anonymous UUID: 88F396C0-80E3-295A-B349-C5F5805FC11D

Sleep/Wake UUID: BD3433B2-9F7E-45D3-9344-E3E6F3F9EE25

Time Awake Since Boot: 18000 seconds
Time Since Wake: 4400 seconds

System Integrity Protection: enabled

Crashed Thread: 2 Dispatch queue: PDFThumbnailRenderingController_SharedThumbnailOperationQueue (QOS: UNSPECIFIED)

Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x0000000050000020
Exception Note: EXC_CORPSE_NOTIFY

Termination Signal: Segmentation fault: 11
Termination Reason: Namespace SIGNAL, Code 0xb
Terminating Process: exc handler [0]

Here is my error report. I can not open the Endnote even with X8.2, which has feature of improving the compatibility with High Sierra. I tried to move the files to a new fold, but this does not work for me. It seems the error is related to the PDFS. Totally do not know how to solve this problem. 

Process: EndNote X8 [7832]
Path: /Applications/EndNote X8/EndNote X8.app/Contents/MacOS/EndNote X8
Identifier: com.ThomsonResearchSoft.EndNote
Version: 18.2.0.13302 (2017.18.2.0.13302)
Code Type: X86 (Native)
Parent Process: ??? [1]
Responsible: EndNote X8 [7832]
User ID: 501086115

Date/Time: 2018-06-07 09:42:17.339 -0700
OS Version: Mac OS X 10.13.5 (17F77)
Report Version: 12
Anonymous UUID: 88F396C0-80E3-295A-B349-C5F5805FC11D

Sleep/Wake UUID: BD3433B2-9F7E-45D3-9344-E3E6F3F9EE25

Time Awake Since Boot: 18000 seconds
Time Since Wake: 4400 seconds

System Integrity Protection: enabled

Crashed Thread: 2 Dispatch queue: PDFThumbnailRenderingController_SharedThumbnailOperationQueue (QOS: UNSPECIFIED)

Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x0000000050000020
Exception Note: EXC_CORPSE_NOTIFY

Termination Signal: Segmentation fault: 11
Termination Reason: Namespace SIGNAL, Code 0xb
Terminating Process: exc handler [0]

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I’ve had the problem of Endnote X8 crashing under 10.13 for awhile, but it was seemingly “random”. It crashed this morning, and now I cannot open Endnote at all without it crashing immediately (I don’t even see the splash page).

This is more than an inconvenience! My professional life revolves around accessing my Endnote library.

@stburrow

I am also uttelry annoyed at Clarivate for the stance they take on a MAJOR crashing bug that basically renders EndNote X8 useless on a Mac running macOS10.13.

Yes, it’s true that Apple has a PDF Kit software issue. But Clarivate could easily code a workaround. I run constantly into reproducible crashes when simply clicking a record in the database that has an attached PDF. But if this PDF is not previewed or displayed in the main window, there is no reason to necessitate EndNote to access that PDF file at that moment and thus running into the system bug. If Clarivate cannot recode that, than either they are simply unwilling, or Endnote’s code is a big mess anyway.

One cannot even get rid of PDFs because for removing an attachment you would need to be able to select a record first - and you cannot, if that action crashes the app.

It seems that only certain PDFs cause the crashes at 100% “success rate”. Not a single word from Clarivate to maybe tell us what the distinguishing properties of “offending” PDFs are. it does not have to do with contained markings, as some other posts hinted.

I might also switch back to Bookends. How to move my 2500 heavily-PDFed references? I dunno yet.

If X9 does not fix the issue, I will leave Endnote and make sure that I tell all students NOT to get this app ever. If X9 fixes the issue, I do expect a free upgrade as X8 never was a working product. (Did I hear somebody laugh? :-/ )