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checkpoint file error

asked 2018-09-24 03:03:33 -0600

rpelicae gravatar image

Hi all,

I'm experiencing an error when I want to add an enzyme to a reaction. In Pathway Tools I move to a reaction frame in my PGDB. Then I click on the reaction frame and select 'Edit --> Create/Add Enzyme'. Depending whether I'm trying to access the enzyme using its protein identifier or gene identifier I get a similar type of error: an older 'checkpoint file' is referred to that involves this enzyme. C:\fakepath\proteincheckpointerror.pngC:\fakepath\genecheckpointerror.png

In each case, If i choose to keep/restore/discard the checkpoint file the result is that Pathway Tools freezes and I can do nothing else than to force it to quit.

I've been trying to find this 'checkpoint file' in the pathway-tools and ptools-local folder. The manual refers to a '.DBNAME-autosave.ckp' file which I'm unable to find. But this seems unrelated since I'm running my PGDB's in file-mode, not MySQL-mode.

System: Mac OSX El Capitan Pathway Tools version: 21.5 Any help would be appreciated to solve this problem, Thank you, Rudy

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answered 2018-09-24 11:52:47 -0600

Suzanne Paley gravatar image

updated 2018-09-24 11:56:13 -0600

The checkpoint file should be in your home directory, and will be named .ptools-enz-editor.ckp. If you can't find it there, start up pathway-tools in -lisp mode, and type the following to the lisp prompt (including the parens):


That should return the full pathname for the file.

As to why pathway-tools is freezing, I would need more information. If you look in the terminal window that came up when you started pathway-tools, do you see any error message? If not, try hitting Ctrl-c in that window to generate a break, and then, once you get a debugger prompt, type

:zoom :count :all

(including the colons, with no space between each colon and the following word) to generate backtrace info, and send that to ptools-support @

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Asked: 2018-09-24 03:03:33 -0600

Seen: 2,945 times

Last updated: Sep 24 '18