Issue with utilizing MSInspector

support
Issue with utilizing MSInspector edoud  2023-08-25 12:28
 

As I develop targeted assays to share I would like to implement the CPTAC recommendations for assays using the MSinspector external tool - I've downloaded it but am getting an number of errors. I suspect many of the issues are related to it being coded in python 2.7 which is end of life. (Can't get pip installed, can't get pandas installed etc etc). All errors in the attached file. I've been messing around trying to install things in the cmd line and there are just too many issues getting versions for python 2.7.

Do you have any recs or could you give me the contact info for Yin Lu to see if they are planning on updating this tool at all? Thanks!

 
 
Nick Shulman responded:  2023-08-25 13:01

In theory you can post a message on the tool's support board page, and the message will be delivered to the tool authors.
The MSInspector support board page is:
https://skyline.ms/project/home/software/Skyline/tools/Support/MSInspector/begin.view

I will also forward this message to Yin Lu.

I get the same error as you do when I try to install the MSInspector tool from the Tool Store in Skyline:

      File "c:\users\nicksh\appdata\local\temp\easy_install-6ruitk\numpy-1.26.0b1\setup.py", line 53
        raise RuntimeError(f'Cannot parse version {FULLVERSION}')
                                                               ^
    SyntaxError: invalid syntax

I do not know very much about Python so I do not know what can be done about this error.
-- Nick

 
edoud responded:  2023-08-30 07:18

Thanks Nick - I am completely clueless with Python and tried my best to get around these errors to no avail. I had hoped the Msinspector tool might save me time/effort on making some figures, but perhaps not. Guess we will see if Yin Lu has any thoughts/suggestions.

Best,
Emma

 
jehan mohammadnazri40720 responded:  2025-05-05 10:09

Hi,

I am also having issues with running MSInspector and Python 2.7 that was downloaded through MSInspector. Was the issue resolved? Please let me know.

Thanks,
Jehan

 
edoud responded:  2025-05-05 10:20

Hi Jehan,
I was never able to get MSInspector to work on recent versions of skyline (lots of different overlapping issues with versions of python etc). Yin Lu emailed me that he is in the process of an update to MS Inspector though!

From the man himself:
"I'm Yin Lu. The author of MSInspector. I went over the error you posted. I think the main issue is about Python 2.7 and its package pandas.

You were able to install Python 2.7 and its package Jinja2. But you failed to install pandas-0.21.0.tar.gz because it's required package numpy>=1.9.0 couldn't get installed. The default most recent numpy-1.26.0 is not available for Python 2.7 now. I think once package numpy>=1.9.0 gets installed, the issue can get resolved.

There is a python package file numpy-1.13.1+mkl-cp27-cp27m-win_amd64.whl
https://www.silx.org/pub/wheelhouse/numpy-1.13.1%2Bmkl-cp27-cp27m-win_amd64.whl
After you download it, in the command line console, go to the directory where the file numpy-1.13.1+mkl-cp27-cp27m-win_amd64.whl is located and run the command line "pip install numpy-1.13.1+mkl-cp27-cp27m-win_amd64.whl"
You can manually install the package to Python.
Then try to install MSInscpector again. And pandas-0.21.0.tar.gz should get installed.

In addition, we developed the Python 3 version of MSInspector. I will upload it to Skyline in the following two to three weeks, once I test its installation and running in some other new environments. I will let you know after it's updated, and you can try that accordingly."

That was this February - so hopefully the python 3 version will be uploaded very soon!

 
jehan mohammadnazri40720 responded:  2025-05-05 11:38

Hi Emma,

Thanks for getting back and sharing Yin Lu's response! Glad to hear a new version will be out. Hope it will be uploaded soon.

Do I have this right, you are still not able to use MSInspector, even with Yin Lu's recommendation to download numpy> =1.13.1? I tried following his instructions but I still could not get it to work.

Jehan

 
edoud responded:  2025-05-05 11:53

Correct, I've personally never successfully used MSInspector. I'm hoping for the new version!