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Help with fatal error: The slot PROCESS is unbound...

asked 2017-07-27 15:32:06 -0500

anonymous user

Anonymous

Hi, I am using Pathway Tools v 21 on a Mac OS 10.9.5 as it is embedded in the MetaPathways (https://github.com/hallamlab/metapathways2/wiki (https://github.com/hallamlab/metapath...)) pipeline. For some reason, on a subset of my samples, I get some version of the following error in the pathologic.log file when trying to build PGDBs:

batch-pathologic: 26-Jul-2017 14:40:47 Fatal error: The slot PROCESS is unbound in the object #<ecocyc @="" #x1042f6c362=""> of class #<standard-class ecocyc="">. Evaluation stack:

; Autoloading for DISASSEMBLE: ; Fast loading from bundle private/disasm.fasl. ; Fast loading from bundle code/x/disx86-64.fasl. ->(TPL::ZOOM-COMMAND :FROM-READ-EVAL-PRINT-LOOP NIL ...) (SYS::..RUNTIME-OPERATION "applyn" :UNKNOWN-ARGS) (TPL:DO-COMMAND "zoom" :FROM-READ-EVAL-PRINT-LOOP ...)

For each of the samples that building a PGDB fails on the error is the same but the ECOCYC @ #[insert number here] differs. As I am a new user to both programs, I am not sure how to troubleshoot this issue. As far as the MetaPathways developers can tell it is not an issue with MP, but rather something with Pathway Tools and/or my data. Any idea how I can resolve this issue?

Thank you so much. colleen

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answered 2017-07-31 16:13:49 -0500

ptools-admin gravatar image

updated 2017-07-31 16:16:06 -0500

Two things:

1) Your version of Mac OSX is quite old. It's possible there could be some issue with the libraries not being compatible with v21.0.

2) Have you tried to use it in interactive mode instead of batch mode? Batch mode does not provide much in terms of debugging capability. If you try running the same thing in interactive mode, we can provide you some more debugging help. For this type of issue, it maybe better to submit your debugging information via the ptools-support email list.

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Asked: 2017-07-27 15:32:06 -0500

Seen: 27 times

Last updated: Jul 31