Another synchronisation error

Recently, when synchronising Zotero with the circular green arrow, a red 'pling' appears indicating an error. Some problem about deleting empty folders. I checked the database integrity which reports no corruption.

I set an error log and repeated the sync: this is the error ID which was copied to the clipoard:


Could one of the development team help with this please? My local copy of Zotero doesn't update to changes made earlier in the day at work.
  • Win error 145 during operation removeEmptyDir on file C:\Users\[…]\Zotero\storage\FZRAQXI4 (The directory is not empty.
    This (and many similar errors) would likely be caused by either 1) running security software that's preventing Zotero from making changes to files within its own data directory or 2) having your data directory, or the 'storage' directory within it, symlinked/aliased to somewhere else.
  • Many thanks for the advice, and sorry for the delay in replying.

    Yes, I had indeed synced the storage of PDF attachments to a local server, which mysteriously has become empty. Not sure how this happened, but I changed the Zotero sync options to 'absolute paths' and selected the default, in the hope that this would direct the sync towards default storage on C:\users\me\... etc, where the Zotero folders are (and does have PDFs in). However after trying a sync, a further error came up. Logging error reporting gave a debug ID:

    Dbug ID: D252370998

    I could see Zotero trying to update some of the attachments, but didn't succeed. The attachments are present in the on-line library and can be downloaded/opened, so I followed the instructions on the Zotero knowledge base: 'files not syncing' and did the following:

    ...go to the Sync → Reset pane of the Zotero preferences on Computer B, choose Reset File Sync History...

    Ran the sync again with logging on; still the same problems and this is the debug ID:

    Dbug ID: D1425537598
  • Yes, I had indeed synced the storage of PDF attachments to a local server, which mysteriously has become empty. Not sure how this happened, but I changed the Zotero sync options to 'absolute paths' and selected the default
    If you're referring to the Linked Files Base Directory, this wouldn't have anything to do with that. A symlink/alias is a technical filesystem thing and has no relation to linked files. Linked files aren't stored in the data directory and don't sync, so they're irrelevant here.

    What I said above still applies.
  • Thanks - understood re the Linked Files Base Directory; it's blank now anyway.

    The Zotero Data Directory is set to the default of C:/user/'me'/Zotero (with 'me' being the true username). This is the local system drive.

    I have excluded the entire 'Zotero' folder from BitDefender.

    Restarted the computer, tried to sync again, and still no luck.

    Debug ID: D2025382223

    Have I missed something in your original reply above?

  • I can't tell you what the problem is on your system — just that something is still preventing Zotero from making changes to files in the data directory. It could potentially also be a permissions problem within that directory. It could also happen if you have PDF files open locally that were changed elsewhere and need to be redownloaded, though that's less likely given that it's happening for many files.
  • OK I could not find a reason for the mis-synchronisations; had already checked the permissions for the Zotero folder and all access was appropriate.

    Anyway I managed to solve it the long way round. There were only about 10 PDF files, 7 of them in one collection, that weren't synchronising with the web version; so I went through the Debug ID report and noted the storage folder names. Then:
    1. Copied each of the PDFs (or opened and resaved the ones that couldn't be copied!) from their storage folder back out to disk somewhere else.
    2. Then went to Zotero desktop and deleted the attachment from the reference.
    3. Then emptied the Zotero desktop bin.
    4. Then reattached each of the PDFs back onto the references.
    5. Finally did a re-sync, and no errors came up.
    6. Checked the web version and all attachments were in place.
    6. Went through the whole collection in Zotero desktop and removed any non-essential duplicate PDFs for the same reference. My impression was that there were more than usual, so possibly occurred as a result of mis-synchronisations.

    Thanks for the assistance; hopefully all will remain good now.
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