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ModelSEED / Model-SEED-core

The Model SEED is a tool for building, curating, and analyzing gonome-scale metabolic models. Visit the Model SEED homepage for installation instructions and full feature documentation.
http://bionet.mcs.anl.gov/index.php/Model_SEED_Homepage
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Error during installation on Rob Edward's machine #56

Closed cshenry closed 13 years ago

cshenry commented 13 years ago

The error appears to be a commented out } at the end of processReactionWithMFAToolkit

If I correct that, the error I now get is ""Unable to find database configuration for ModelDB USERS"" at /data/ModelSeed/lib/ModelSEED/FIGMODEL.pm line 134

Rob

linsalrob commented 13 years ago

Fresh pull tonight, running ms-config load Mysettings:

Use of uninitialized value in concatenation (.) or string at /data/ModelSeed/bin/../lib/ModelSEED/ModelSEEDScripts/ms-config.pl line 117. Use of uninitialized value in concatenation (.) or string at /data/ModelSeed/bin/../lib/ModelSEED/ModelSEEDScripts/ms-config.pl line 151. [: 4: unexpected operator g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD -DLINUX -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM -I/usr/include -o /data/ModelSeed/software/mfatoolkit/Linux/mfatoolkit /data/ModelSeed/software/mfatoolkit/Source/driver.o /data/ModelSeed/software/mfatoolkit/Source/MFAProblem.o /data/ModelSeed/software/mfatoolkit/Source/CPLEXapiEMPTY.o /data/ModelSeed/software/mfatoolkit/Source/SCIPapi.o /data/ModelSeed/software/mfatoolkit/Source/GLPKapi.o /data/ModelSeed/software/mfatoolkit/Source/LINDOapiEMPTY.o /data/ModelSeed/software/mfatoolkit/Source/SolverInterface.o /data/ModelSeed/software/mfatoolkit/Source/Species.o /data/ModelSeed/software/mfatoolkit/Source/Data.o /data/ModelSeed/software/mfatoolkit/Source/InterfaceFunctions.o /data/ModelSeed/software/mfatoolkit/Source/Identity.o /data/ModelSeed/software/mfatoolkit/Source/Reaction.o /data/ModelSeed/software/mfatoolkit/Source/GlobalFunctions.o /data/ModelSeed/software/mfatoolkit/Source/AtomCPP.o /data/ModelSeed/software/mfatoolkit/Source/UtilityFunctions.o /data/ModelSeed/software/mfatoolkit/Source/AtomType.o /data/ModelSeed/software/mfatoolkit/Source/Gene.o /data/ModelSeed/software/mfatoolkit/Source/GeneInterval.o /data/ModelSeed/software/mfatoolkit/Source/stringDB.o -L/usr/lib -lglpk ""Unable to find database configuration for ModelDB USERS"" at /data/ModelSeed/lib/ModelSEED/FIGMODEL.pm line 136 ModelSEED::FIGMODEL::FIGMODELERROR('Unable to find database configuration for ModelDB USERS') called at /data/ModelSeed/lib/ModelSEED/FIGMODEL/FIGMODELdatabase.pm line 158 ModelSEED::FIGMODEL::FIGMODELdatabase::get_object_manager('ModelSEED::FIGMODEL::FIGMODELdatabase=HASH(0x30888d8)', 'user') called at /data/ModelSeed/lib/ModelSEED/FIGMODEL/FIGMODELdatabase.pm line 272 ModelSEED::FIGMODEL::FIGMODELdatabase::sudo_get_objects('ModelSEED::FIGMODEL::FIGMODELdatabase=HASH(0x30888d8)', 'user', 'HASH(0x3088c80)') called at /data/ModelSeed/lib/ModelSEED/FIGMODEL/FIGMODELdatabase.pm line 298 ModelSEED::FIGMODEL::FIGMODELdatabase::get_objects('ModelSEED::FIGMODEL::FIGMODELdatabase=HASH(0x30888d8)', 'user', 'HASH(0x3088c80)') called at /data/ModelSeed/lib/ModelSEED/FIGMODEL/FIGMODELdatabase.pm line 249 ModelSEED::FIGMODEL::FIGMODELdatabase::get_object('ModelSEED::FIGMODEL::FIGMODELdatabase=HASH(0x30888d8)', 'user', 'HASH(0x3088c80)') called at /data/ModelSeed/bin/../lib/ModelSEED/ModelSEEDScripts/ms-config.pl line 376

devoid commented 13 years ago

Can you attach your Mysettings.conf file? Removing any username/password pairs if they are present. I'm thinking you have something like:

[Optional]
dataDirectory=

When you want to either define it or comment it out.

devoid commented 13 years ago

I'm closing this issue since it appears to be a configuration problem. @linsalrob Are you Rob Edwards? If you are still experiencing problems, check the last comment regarding the dataDirectory option. If that doesn't fix it for you, feel free to reopen the issue, posting most of the configuration here.