#1607 Skim gets as far as loading thumbnails for this document then hangs
Hello,
I'm using the latest version of Skim. I have a document (288k) that I annotated quite extensively with highlighting and embedded notes. Since this morning when I try to bring the document up in Skim (my default PDF viewer) it won't fully load — it only gets as far as displaying the thumbnails, and then it seems to hang; I can't scroll through the thumbnails or load a new document, although I can quit with Ctrl-Q. I am still able to do a Quick Look preview of the document in the Finder and load it into other PDF readers like Adobe Acrobat and Preview, but all of my annotations are gone when I view the document with another viewer. The crazy thing is that I can still see the annotations in the thumbnails when I try to load the document into Skim! I've attached a screenshot illustrating this. I've also attached the troublesome file. Just to note, I did a complete uninstall of Skim using App Cleaner 8 and reinstalled, to no avail.
I would appreciate it if anyone has any ideas for getting Skim to be able to load this document once again. I really want those annotations!
Thanks.
Chris Menzel
Here's the screenshot I failed to attach. Also apologies for randomly setting the Milestone to "Other", the Owner to "Christiaan Hofman" and the Priority to "1". I wasn't sure what to select for those.
Last edit: TXLogic 2026-06-02
I have no idea what is going on. AFAIK there have not been any fundamental changes. Can you make a Sample of Skim when it hangs? Use Activity Monitor, select Skim, show the detail window, and while it hangs click the Sample button.
I'll do that when I get into work, but I remember looking at the process in the Activity Monitor and there was nothing unusual (it was using almost no CPU) so I didn't take a sample.
I meant to ask: when you open the attached in Skim, are you seeing the annotations that can be seen in the JPG I sent of the thumbnails?
Also, what Skim version are you using, and on what OS version? And when (with which Skim version) did this work for you? Are PDFs without notes loading OK for you?
If you only have the problem with a lot of notes, is it possible to attach a version with the notes? You could make a zip archive of the PDF and attach that, this should preserve the notes.
Doh! Sorry, I don't know why I omitted that information. The machine in question (a Mac Mini) is running both the latest version of Tahoe (26.5.1) and the latest version of Skim (1.7.15). Interestingly, though, my MacBook M1 Pro at home is running Tahoe 26.4.1 and Skim1.7.15 and I'm able to bring up the file in question. It has some of the lost annotations but I see in particular that the embedded note on the third page (seen in the thumbnails) is missing. I will try updating the MacBook Pro and will let you know if that makes any difference.
Last edit: TXLogic 2026-06-02
Moreover, is there no crash log or other exception log in the Console app from Skimwhen you try to load this document?
Correct.
So no logs? I don't see that it does not load when there is no exception or something.
And what about a sample?
I saw nothing in the logs. As noted, I'll take a sample when I get into my office.
I'm in my office now. No crash log in Console.app. As noted, I can quit Skim with Ctrl-Q but in all other respects it is unresponsive to keystrokes or mouse gestures. Sample attached. Just to note, I saved out the version of the document I was able to open at home that had preserved some of the annotations and I'm able to open that one in the office. It seems to me that there must be something funky about the mark-ups in the originally attached file, which I assume are somehow stored separately and are able to be ignored by other applications like Preview when I open the problematic file in them. That file still causes the version of Skim here in my office to hang AFTER the thumbnails are all loaded.
I see nothing in the sample, it seems to be just waitingg for something to happen. Perhaps you should start the sample just before opening the file.
And yes, the notes are saved separately in the extended attributes of the file. THey are not preserved in the attached file. Can you please attach a zip of the file, which should preserve them?
Also, could it be that there is a particular type of note that can give problems? Perhaps you can try with a copy of a file to test this out?
OK, I got a sample that I started just before loading the file. I have no idea how to interpret it, of course, but it looks quite different from the other other. The spambot seems to be removing the sample, though. Let me try again.
Last edit: TXLogic 2026-06-02
OK, that worked; the spambot doesn't like the zipped copy of the document. Is there an email address I can send it to?
Last edit: TXLogic 2026-06-02
And you did not answer whether this was just for this file, or perhaps more generally for files with notes, or for any PDF?
I really cannot see anything wrong with the file, and have absolutely no problem loading it. Note even slow, there aren't even that many notes. So I have really no clue about the problem you have. It does look like a bug in PDFKit in 26.5 then, though I cannot pinpoint it to anything to even report it.
And what happens if you embed the notes (in a copy of the file)? You could do that using the skimpdf command line tool using the command:
That worked! I embedded the notes from a copy of the troublesome file (which was still causing Skim to hang) into a clean copy of the original file (with no notes) and the result was a version of the file with the missing notes! And Skim has no problem opening it. Getting those notes back was all I was after but I'm sorry I couldn't help you figure out what the issue was. I will attach the newly created file with the embedded notes; perhaps you'll see something if you do some sort of lower-level comparison of that file with the original troublemaker.
Thanks for your help.
Looks like I forgot to attach the new file with the embedded notes. 🤦♂️ New notes have been added as well.
There's no comparison to make. The embedded notes are just in the PDF, so there are no Skim notes attached (and also not editable in Skim). So this is just opening a PDF without notes in Skim.
The question is still why you aren't able to open a file with Skim notes,something I really don't understand. And you did not answer whether this was a general problem, or just a problem of this particular file.
Sorry, I thought I'd answered that question but I see that I didn't. It is NOT a general problem; I was only experiencing it with this one single file. Oddly, though, now, when I download the file I originally sent you, there are no embedded notes and, weirdest of all, diff reports that the file is are identical to the clean original. I am completely flummoxed — that is the file that was causing Skim to hang and the one I'd used to salvage the original notes thanks to the trick with skimpdf you told me about. Does skimpdf remove the notes from the INFILE and move them to the OUTFILE? I suspect not, so I really do not understand what is happening here. My apologies for the time you spent on this (although, again, your trick with skimpdf was a huge help, so thanks for that).
Last edit: TXLogic 2026-06-03
The Skim notes are attached in the extended attributes, not added to the data content of the file. So diff won't see them, as it will only compare the data. What skimpdf embed does is generate new PDF data that includes the notes, so they become ordinary PDF annotations embedded in the PDF data. The attached Skim notes are not added to the extended attributes, that would duplicate the notes. And the notes won't be editable in Skim, though they will be visible in other PDF viewers. It is the same as Export with embedded notes. See also the FAQ on the Wiki.
Unfortunately I still don't see anything special in the sample, just a window setting just the views.