macOS Sierra

:open_mouth: Note to self: make a copy of the Documents folder (with a different name) before downloading Sierra.

What a crock. I cannot express how much I loathe iCloud. Thank you, Lit&Lat, for using Dropbox with the iOS app. Thank you, thank you, thank you!

If you’ve got a Time Machine backup, you shouldn’t have to worry; at worst you can just restore the entire Documents folder from that. Also, it’s fairly easy to avoid turning that feature on during the upgrade. Apple didn’t try to trick me into using some vaguely described “space saving” feature or anything.

This is tremendously helpful information and thank you for passing it on to all of us. And expressed so clearly. Sounds like knowledge learned through personal experience, and for that you have my sympathies. But you’ve saved many of us a lot of heartache and lost data.

I’m glad the info was of help! Through some poking around, I found out that my issue from the Scrivener end of things was due to the fact that Apple hadn’t counted on those of us who use multiple computers actually setting up the Desktop & Documents feature on all those computers (even though the entire premise of this feature is being able to access all of your desktop and documents files from any of your computers). If you enable this feature on multiple computers, it decides one of those computers is the primary and renames your Desktop and Documents folders on the other computer(s) and saves those as sub-folders within the primary folder, renaming them to reflect the name of the computer from which they were taken. Which then confuses Scrivener because, of course, the folder no longer has the same name. So just to be clear, this is most definitely an Apple issue and not a Scrivener one.

Interesting article written by a Scrivener user who would have lost all of his documents, including those in Dropbox, but for having backups. Useful read, especially about the default switch on of the iCloud Drive and Optimize Mac Storage features in Sierra:

9 to 5 Mac Opinion: Correction, Sierra’s storage management tools are a complete disaster … nightmare/

For everyone who was aware of what quite likely would happen when Documents In The Cloud get activated—though maybe not to the actual extent—and therefore did not tick the little box of death from the start, Apple added some extra and not-so-easy to evade hassles.

For example, the font-aliasing problem that makes the majority of the smaller system fonts difficult to read on non-retina displays, first introduced with Yosemite and fixed in El Capitan, made a celebrated return in Sierra.

Also not good, but rather not Apple’s fault I guess, is that LibreOffice does not run under Sierra at all. So Scrivener users relying on the Open Document Text as an output format should think twice about switching to Sierra at the present state of things.

I’m not sure if this is the right place to put it, but anyway:

[size=150]By no means do install the 10.12.2 Beta 16C32F![/size]

Apple did change something with PDF display again and this time it is really horrendous. DEVONthink Pro Office immediately crashes every time when you select a PDF in the item list. Scrivener takes its time, but it does inevitably crash too. So does PDF Expert.

So be smarter than me.

This is very helpful information. Thank you.

One note in the “little box of death” is that I would recommend reading the article I gave a link to above.

The “gotcha” discussed in that article is that even if you know enough to not activate the feature when updating to Sierra (depending on how you have your documents and Dropbox setup, or preference to use another cloud service for your files), once you have moved to Sierra, when you then update to a newer version of the OS, Sierra will automatically activate the feature for you without informing you that it has done this. As described in the article, this led a very knowledgeable Mac user who writes about its OS for a living to get caught out and have his MacBook Air “bricked” and all his Dropbox files deleted on all his Macs.

Would also recommend reading discussions of other Sierra issues before deciding to update from El Capitan, especially with respect to its handling of PDFs, which, as you’ve shared with us, seems to be a continuing problem. For anyone who relies on PDFs for their research materials, the problems Sierra is causing with being able to view and work with existing PDFs is a big issue.

I have to say, I updated my MBP to 10.12 before this thread started and I presume I set it not to use Documents in the Cloud—as you can do things like that later, I generally don’t do it immediately—but, for various reasons I didn’t boot it up until 10.12.1 came out. But when I upgraded, once again, I was asked if I wanted to use Documents in the Cloud, and said “No”, so I haven’t been caught by that problem.

But thanks all the same for this thread. I won’t upgrade my other machines until the PDF and other bugs are sorted out, but even then, I won’t be using Documents in the Cloud.

I don’t put all my files in my documents folder anyway, many of them are in the Dropbox folder or Cubby folders which are outside the documents folder, and they will stay outside the documents folder.

FYI, For those where PDFs are an important part of the research workflow, the latest Devonthink release (2.9.7 version largely focused since 2.9.2 on fixing known issues created by OSX 10.12 because of the revised (described by some as broken) Apple PDFKit) here are the items listed that still have not been able to been fixed:

Known issues still present with version 2.9.7(copied from the manual):

  • "The PDF sidebar doesn’t support reordering pages with drag-and-drop due to PDFKit bugs.
  • Flickering while resizing or moving PDF annotations, again due to PDFKit bugs.
  • Encrypted PDF documents can’t be unlocked; guess it: PDFKit bugs.
  • Note PDF annotations can’t be opened or expanded. No kidding, it’s PDFKit."

Here is the link to the information: … .pdf#page8

Worth also noting is the number of fixes and workarounds that have been required to get a PDF Workflow back to a semi-functioning state since the OS 10.12 update.

When I installed Sierra I didn’t set up Document Sync. Thank goodness. It just didn’t sound like something I needed.

Just an FYI on further problems with the latest versions and betas of Sierra and how it handles PDFs. The link is from the DevonThink Forum where they are on about their 6th update, mostly related to PDF issues created in Sierra, with new problems created with each new Sierra update. … =2&t=23403

“It Just Works” seems, very unfortunately, a catch phrase that these days catches you out rather than delivering on its promise.

Yeah sierra screwed up pdfkit pretty bad. See Michael Tsai’s blog for a compendium of the problems.

Curious about whether there is a sense that the latest version of OSX Sierra 10.12.4 has resolved any of these problems, or if it is still causing the same type of problems with PDFs, including damaging existing annotations.

From what I can see on the DevonThink forum, the problems remain, but the conversations are dated.

So wondering if people have just given up on Apple resolving these issues with Sierra, or if version 12.4 did fix these issues.

At the moment still working with OSX 10.11 because PDFs and the annotations included are such a critical part of my work and writing. Wondering if it’s time to move to 10.12, or still worth holding with what I know works.

Any current experiences and knowledge would be appreciated.

You’re probably already familiar with this, but it’s the best, reasonably up-to-date round-up that I’ve seen. (With thousands of pdf’s in DevonThink and elsewhere, many “scansnapped”, I’m particularly cautious and have so far stayed with 10.11.)

Hugh, very useful link thanks!!! Personally I’ve not had too many problems with Sierra, I use Bookends for PDF notes and annotation management and the problems with PDFKit mostly affected Jon the developer rather than me. But YMMV…

Very useful, Hugh. Thank you.

As it happens, I’ve been using PDFPen Pro for years. Some long time ago I posted a request with Smile for Chinese OCR, but they said it was uneconomic for them; I didn’t realise that Smile use a proprietary engine, and have always just been very happy using PDFPen Pro. But when I received their reply, I found ‘PDF OCR X Community Edition’, a free app on the App Store, which presumably does use PDFkit, and which let me OCR individual pages in Chinese—they have an “Enterprise Edition” (at £28.99) which will apparently handle multiple page PDFs, but the free version was good enough for me—so I didn’t pursue it further with Smile. All that said, I have not upgraded PDFPen Pro from version 7.x as I no longer need it so much, but having read the article, I might revise that decision.

On the other hand, I have not yet needed to display PDFs in Scrivener, and have been assuming that the current reported problems under Sierra will be eliminated with the release of the 64-bit v. 3. I have a licence for Devon Think Pro, but have never found a need to learn and use it, although I do keep an up-do-date installation DMG; I don’t know if that is 64-bit or still 32-bit. As for Bookends, although I am a great fan and always keep it updated, my use has solely been with references to printed books and I haven’t any experience of it in relation to PDFs.


Nope, the problems with PDFKit affect 64bit apps so S3 won’t be immune. As the tidbits article mentions (and was my personal experience with Bookends), developers have work arounds for most of the bugs and so end users have mostly not seen too many effects (features were disabled for a while etc).

Why did Apple decided to release the rewritten PDFKit in such a terrible, broken state. I assume they are not going to revert like they did for DNS a couple of releases ago, they would have done so already…

Nevertheless, I did upgrade to Sierra when it was released and I had no issues I wasn’t suffering from previous releases. But it was also the most underwhelming release of macOS ever since I switched (I’ve used Siri about 5 times, tabs was the only useful addition I can think of, universal clipboard never worked for me).

I think that for me it’s simply a matter of trust. Many of my PDFs are OCR’d newspaper cuttings. Before I trust Sierra I should like to see some evidence that Apple, with its very recent history of Preview deleting OCR layers, has the expertise to get its previous PDFkit functionality 100 per cent restored without introducing new bugs, as at least one recent update appears to have done. However, for hold-outs like me, that desire is likely to collide with convenience as developers release updates that only work on Sierra and beyond…

Rather like you, Mark, I didn’t make much use of DevonThink. Till quite recently: the release of DT To Go 2, an iOS version of the application that includes much more reliable sync-ing, has made the software more useful to me, though increased its complexity slightly. (And the promise of a not-too-far-distant substantial increase in the automatic actions that the software can undertake, in filing, for example, is also attractive.)

I have it too, and if I upgrade to Sierra will probably make greater use of it. I also like PDF Expert, for its greater wealth of annotational tools on iOS. I’m not sure whether PDF Expert uses PDFkit.

Hugh, just tried your link, but did not work. If you have an updated link, would appreciate it, as would be very interested in this discussion.

FYI, the Administrator of the DT forum and developer of that app recommends skipping Sierra as 10.13 will soon be released, and hopefully of more value and less bug prone than 10.12 and with a full PDF fix. Hopefully…