Error importing Agilent QQQ data with Skyline-daily

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Error importing Agilent QQQ data with Skyline-daily Sarah Michaud  2018-11-26
 

Hi Skyline team,

I recently upgraded to the newest Skyline-daily 4.2.1.18329 and am getting an error when importing Agilent 6490/6495 data. Import fails with the following message: "Could not load file or assembly 'pwiz_data_cli.dll' or one of its dependencies. The specified module could not be found."

I'm able to load the data into the same document or a new document with no problems after downgrading to the previous version of Daily.

Thanks,

Sarah

 
 
Brendan MacLean responded:  2018-11-26

Hi Sarah,
That's a pretty basic error. The pwiz_data_cli.dll controls all access to mass spec data formats. If you are getting that error, then you should be totally unable to import any kind of mass spec file (vendor or public format like mzML, mzXML, mz5). I just installed clean on one computer and upgraded another (both development systems, though) and both are able to import older WIFF and Agilent files (and mzML), and you are the first to complain, so at least it seems to be something specific to your machine.

Is there any chance you could download "depends.exe" from here:

http://www.dependencywalker.com/

And then hop onto a Zoom meeting with me to have a look at what is missing on your system that is causing this DLL to fail to even load?

Obviously, we would like to get this fixed quickly. Thanks for reporting it.

--Brendan

 
Brendan MacLean responded:  2018-11-26

In case, I am not available once you have downloaded depends.exe (64-bit), there is a description of how to find your Skyline installation here:

https://skyline.ms/wiki/home/software/Skyline/page.view?name=tip_recover_install

Just search for pwiz_data_cli.dll instead of user.config, check the modified time to make sure you are finding the latest, and then open that file in depends.exe and send me information about the errors you see.

But be aware that not all errors are equal. With a trained eye, I can usually pick out the problem, but there are often many errors that are not important.

Hopefully, we can connect for me to have a look. Of course, you need to get the latest Skyline-daily installer on your computer again to do this.

 
Sarah Michaud responded:  2018-11-26

Hi Brendan,

Sure thing, I've downloaded the "depends.exe". I also realized I didn't copy the full text of the error message I'm getting, if it's helpful.

At 2:49 PM:
Could not load file or assembly 'pwiz_data_cli.dll' or one of its dependencies. The specified module could not be found.
at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache()
at pwiz.Skyline.Model.Results.ChromatogramCache.Build(SrmDocument document, String documentFilePath, ChromatogramCache cacheRecalc, String cachePath, MsDataFileUri msDataFileUri, IProgressStatus status, ILoadMonitor loader, Action`2 complete) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\ChromatogramCache.cs:line 617

Cheers
Sarah

 
Sarah Michaud responded:  2018-11-26

I think it's MSVCP140.DLL? I've attached a screenshot of the errors shown with the Dependency Walker.

We did also try importing data on a different computer in the lab here and got the same failed import message.

 
Brendan MacLean responded:  2018-11-26

Hi Sarah,
Can you try the following to check that conclusion?

The current workaround requires the installation of the Visual Studio 2017 redistributable files as described in this post:
https://social.msdn.microsoft.com/Forums/vstudio/en-US/e653a57a-bc32-4134-87bf-df33058f0531/download-microsoft-visual-c-2017-redistributable?forum=vssetup&prof=required

  1. Go to https://www.visualstudio.com/downloads/
  2. Click Other Tools and Frameworks at the bottom of the page
  3. Click the Download button for "Microsoft Visual C++ Redistributable for Visual Studio 2017"
  4. Run the downloaded installer (and restart your computer if requested)

We were attempting to fix an issue with the Shimadzu DLLs needing the msvc 140 DLLs, but maybe we inadvertently broke the main pwiz_data_cli.dll in the process. I the last Skyline-daily, importing Shimadzu Q-TOF .lcd files required manual installation of the VS 2017 VC redistributables. Now maybe all of PWiz requires this.

It is a one time fix, which will make it impossible for you to test for this on the same machine twice. We are attempting to install what you need with Skyline, but this installs it systemwide so that no matter what Skyline will find it. We just don't want to require this manual step of course. This is just to test that you are right about the source of the problem.

Thanks for helping us debug this.

--Brendan

 
Brendan MacLean responded:  2018-11-26

I think you are right, though. I just looked at my own installation, and it looks like the VC 140 DLLs have simply moved into the Shimadzu subdirectory, rather than the installer placing copies of them both in the root folder and the subdirectory. I will start looking at this.

 
Sarah Michaud responded:  2018-11-26

Hi Brendan,

Installing the Visual Studio 2017 redistributable files worked, no more errors when importing data. Glad the error seems to make sense with what you see as well.

Thanks for the fast replies and help!

Cheers
Sarah