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I'm having the same issue. When plugging in my iPhone 5S, I get the following message:
calibre, version 2.3.0
ERROR: Error: Error communicating with device
database disk image is malformed
Traceback (most recent call last):
File "site-packages/calibre/gui2/device.py", line 87, in run
File "site-packages/calibre/gui2/device.py", line 502, in _books
File "/var/folders/jg/kkbm2yds11lb_r4ycy01psxr0000gn/T/calibre_2.3.0_tmp_S5wqQG/JdXgpa_ios_local_db/Marvin_overlays.py", line 310, in books
DatabaseError: database disk image is malformed
I'm using an iPhone 5S running 7.1.2
The version of Marvin I'm using is 2.7.5
The computer I'm using is a MacBook Air running 10.9.4
The Calibre version is 2.3
Plugins are iOS reader applications 1.4.3 & Marvin XD 1.2.4
I have 2778 books in Calibre
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