Crashed during a save and corrupted my file

Crashed during a save and corrupted my file Asger  2019-01-15

Dear MacCoss Lab,

I was using Skyline (64-bit) on a Windows 10 Pro on a small molecules data set with about 68 transitions and 200 samples.
Usually I dont encounter any problems even with bigger data sets, but Skyline have crashed a couple of times so I have adopted a habit of saving a lot, however this time Skyline crashed as I was saving and corrupted my files (Document, Chromatogram data, View and SKYL file), resulting in the error:

Failure opening
Exception has been thrown by the target of an invocation.

Is there any hope for recovering my data?


Brendan MacLean responded:  2019-01-15

Hi Asger,
Well, that looks like the XML is truncated, but can you provide the .sky file by putting it and any auxiliary files, like the .skyd and libraries into a ZIP file and posting the ZIP to:

We will have a look. This is a highly unexpected result for a crash in Skyline, because Skyline saves to a temporary file and only renames it to being the current file once the save is complete. So, in theory, it shouldn't be possible to end up with a truncated file like this because of a problem in saving or a crash. I would expect that to result in a truncated temporary file with the prefix ~SKY but not your .sky file being truncated.

But, if you can share the file we will have a look and see what the current state is.

Sorry for the problem and for the crashes, which we would love to fix if you can give us any help in reproducing them.


Asger responded:  2019-01-15

Hi Brendan,

Feel free to have a look I have uploaded the files under the name 15.01.19 ANDIS_Missing_AWR


Nick Shulman responded:  2019-01-15
Hi, Asger,

It turns out that the only file which got corrupted was the audit log.
The audit log is a new feature in Skyline version 4.2, where the actions that you take to modify your document are remembered in a file with the filename extension ".skyl" which is saved next to your .sky file.

If you delete the file "ANDIS_Missing_AWR.skyl" then Skyline will be able to open up your Skyline document ("") without any error.

It looks like we must have made a mistake in the way that we write out the audit log, which made it possible for a partial file to be written to the final location. We will try to fix this problem, and also make it so that failure to read the audit log does not prevent you from opening your document.
-- Nick
Asger responded:  2019-01-16
Worked like a charm, Thanks a lot :)