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Originally Posted by kovidgoyal
Maybe be the metadata reading code is doing this? IIRC the Cybook uses the metadata plugins?
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Yep. For some reason it only affects the PDF metadata reader... I'm not sure why but I believe it has something to do with pyPdf's PdfFileReader object. I've committed a fix to my branch. The fix will prevent this from cropping up in other metadata readers as well.
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Originally Posted by pthwaite
As far as I am aware, no files are or should I say, were open?
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When you get an error about not being able to unmount a device it's because there is a file on the device that is open. Just like when you open a file in a text editor. Every app on your system opens a lot of tiles. lsof (OS X/Linux/*nix only) shows a list of every file in use (open) by every running app. The issue was Calibre is opening all PDF files on the device to read the metadata and then not closing them when finished.