Library becomes damaged when open but idle

EndNote EndNote General
1

I have a strange problem with EndNote X2.  If I have a library open but leave it idle for a while, the “This library appears to be damaged etc” notice appears.  Furthermore, the notice cannot be removed by clicking on OK and I have to go into Task Manager to close the EndNote program and then restart it.  This has become quite a nuisance, even though I am careful now to save the open library every few minutes.  I can’t find any other mention of this problem following an Internet search.  Does anyone know why this might happen and how it can be fixed?

Proinnsias

2

Where does the library live?  It sounds like the program is losing access to the “drive”?

3

A few questions:

  1. Does the problem occur with this specific library or with all library files?  Have you tried using a different EndNote library file to see if the problem reoccurs?  (Which may indicate a possible file corruption.)

  2. What version of Windows are you running?  Has the OS been updated with the latest updates?

  3. Have you run a virus scan on your system?

4

Thanks for the responses.

Yes, it seems that only a single library is affected.  I left a couple of other libraries open for a couple of hours and the error warning about the library being damaged did not appear.  The original problem arose when I was entering notes in the Abstract section of a reference.  After that, even after recovering the library, when I entered additional notes I found they had disappeared the next time I opened the library (or, alternatively, I got the error message about a library being damaged which had the effect of freezing the computer).  I then copied the notes from the Abstract into a Word file and finished taking notes from the document I was reading in that file, but when I then copied the text from the file back into the EndNote reference, the next time I opened the reference all the additional text was gone, but the original section of text which I had copied into Word was left behind!  I then moved the reference to Trash (which caused the EndNote program to crash, but I was able to delete it when I reopened EndNote) and recreated it, but when I copied in the text from the Word file the same thing happened again.  I then created a new reference in a different library and copied in the text with the same result (and when I tried to delete the reference from that library EndNote crashed again, but again worked on the second attempt).  My next ploy was to save the Word file as a text (.txt) file and copy that into EndNote, and it appears to have worked!  At least the entire block of text was still there when I closed and reopened the library, and the error message about the library being damaged has not appeared although I have left the library open for a few hours now.

I’m not sure what all this means, but I will keep my fingers crossed that the problem will not come back.  Incidentally, I am also finding that whenever I close a library before exiting EndNote, when I reopen EndNote it also automatically reopens the library in question.  I have tried this with several libraries with the same result.  I never noticed this before and wonder if it is of any significance.

I am using Windows 7 with automatic updates, and Trend Micro for internet security.

My apologies for this rather rambling account.  Any further contributions will be very welcome.

Proinnsias

5

Not sure about the rest, unless there was some “code” in the text that was crashing endnote, but the new behavior  you noted is controlled by the preferences.  You can edit the preferences>library setting which I think defaults to reopen the last opened library.  The other options available are in the attached gif. 

 

Proinnsias wrote:

 Incidentally, I am also finding that whenever I close a library before exiting EndNote, when I reopen EndNote it also automatically reopens the library in question.  I have tried this with several libraries with the same result.  I never noticed this before and wonder if it is of any significance.

options.gif

6

This might be useful to you. I have had the same problem. After trail and error I found that while the computer (operating Windows 7) was idle a software, ‘iolo’, installed to clean and repair the hard drive came into operation. When I isolated this software to function only on the times I did not need Endnote the problem of the ‘Damaged library’ was solved.

Wyndham

1 Like
7

In short, if you use Dropbox, Google Drive or Sharepoint or another syncing program, that is likely the problem.

A. Move your EndNote database folder away from Dropbox and Google Drive, and back up your data using Endnote Web syncing.

OR

B. Right click on the Dropbox (great) or Google Drive (evil) or Sharepoint (not as evil, Office 365 rocks!) icons and pause syncing while using EndNote. 

More details and a digression:

Jason from Endnote Tech Support explained that the similar problem I have been reporting ever since Endnote 5 (perhaps even 4) is likely related to my using Dropbox and/or Google Drive.  He explained that when you work in Endnote, there are updates made to the various MySQL databases found in the RDB folders with the DATA folder that is created with an identical name to your endnote *.enl file.  These databases end with *.myd or *.myi extensions. 

Even if you don’t have PDF attachments to your records, the various indexes and such are stored there in the /*.DATA/RDB folder.  What happens is that when Dropbox or Google Drive or any other syncing program (such as the www.secondcopy.com program which I highly recommend for periodic backups to removalbe media) syncs the changes on the hard drive to the Dropbox or Google Docs in the Cloud, Endnote may also be simultaneously trying to make a change that requires updating the MySQL file.  This can and does reliably corrupt those files.  So it’s note really your “database” that is corrupt; no need to have a hard attack!

Anyway, for a couple of years now this would happen constantly, and the only explantion I would receive was that I shouldn’t open the databases by clicking on them; use File/Open instead I was told about a year ago.  But it kept happening.  Apparently, however, Endnote figured out just about a year ago what was happening with Dropbox reported that this was happening with MySQL databases in many applications, not just EndNote.  The solution(s) are simple:

A. Move your EndNote database folder away from Dropbox and Google Drive, and back up your data using Endnote Web syncing.

OR

B. Right click on the Dropbox (great) or Google Drive (evil) or Sharepoint (not as evil, Office 365 rocks!) icons and pause syncing while using EndNote. 

P.s. Did I mention Google was evil?  Google Drive will permit pausing, but once you have paused it will no longer respond to right clicking!  I mean, why expect Google to produce a useable application, they rule the universe, why bother with users.  So you end up having to Control/Alf/Delete and stop the process and who knows when it will start again; most likely next time I re-boot.  Google is evil because for instance it first allowed you to have Google Docs but then practically forces you to download it’s substandard application; it wants to own your hard drive you see.