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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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Installation Problems #152

Open EliKrumholz opened 12 years ago

EliKrumholz commented 12 years ago

I haven't had success installing the lastest Model-SEED-core, the perl Build.pl script gives me the below error. This still creates the Build script after running, but many bin/ functions do not run. I can create models and write to SBML, but I can't read a parsed SBML file or run any FBA. The output from ms-lasterror following a call to mdl-importmodel is below the Build.pl error.

$ perl Build.pl WARNING: the following files are missing in your kit: bin/fbacheckgrowth bin/fbafva bin/mdladdright bin/mdlautocomplete bin/mdlcreatemodel bin/mdlimportmodel bin/mdlloadbiomass bin/mdlloadmodel bin/mdlmakedbmodel bin/mdlprintsbml bin/mdlreconstruction bin/mscreateuser bin/msdeleteuser bin/mslogin bin/mslogout config/Settings.config lib/ModelSEED/editable.pm lib/ModelSEED/FIGMODEL/Biochemistry.pm lib/ModelSEED/FIGMODEL/Compound.pm lib/ModelSEED/ScottTestDB/ModelDB.xml lib/ModelSEEDCore.pm Linux and OSX Installation Instructions.txt MANIFEST.bak ModelDB/ModelDB.sqlite ms/Build.PL ms/Changes ms/ignore.txt ms/lib/ms.pm ms/MANIFEST ms/README ms/t/00-load.t ms/t/boilerplate.t ms/t/manifest.t ms/t/pod-coverage.t ms/t/pod.t README software/mfatoolkit/Windows/glpk.dll software/mfatoolkit/Windows/libltdl3.dll software/mfatoolkit/Windows/MFAToolkitCPLEX.exe software/mfatoolkit/Windows/MFAToolkitNoCPLEX.exe software/mfatoolkit/Windows/SystemParameters.txt software/mfatoolkit/Windows/zlib1.dll Please inform the author.

Checking prerequisites... requires: ! File::Path (2.08_01) is installed, but we need version >= 2.0801 ! perl (5.12.3) is installed, but we need version >= 5.12

ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation

Run 'Build installdeps' to install missing prerequisites.

ERROR: Missing required field 'dist_abstract' for metafile Could not get valid metadata. Error is: Invalid metadata structure. Errors: Missing mandatory field, 'abstract' (abstract) [Validation: 1.4], value is an undefined string (abstract) [Validation: 1.4] at /Library/Perl/Updates/5.12.3/Module/Build/Base.pm line 4568

Could not create MYMETA files Creating new 'Build' script for 'ModelSeedCore' version '0.01'

krum0058:Model-Seed-Core$ bin/ms-lasterror mslasterror Last error printed to file:

/Users/krum0058/gitProjects/ModelSeed/Model-Seed-Core/.errors/error-QDtUV

ModelDriver encountered an unrecoverable error:

""Creating new object failed."" at /Users/krum0058/gitProjects/ModelSeed/Model-Seed-Core/lib/ModelSEED/utilities.pm line 97
    ModelSEED::utilities::ERROR('Creating new object failed.') called at /Users/krum0058/gitProjects/ModelSeed/Model-Seed-Core/lib/PPO/DBObject.pm line 370
    DBObject::set_attributes('ModelSEED::ModelDB::COMPOUND_BIOMASS=HASH(0x10b4617c8)', 'HASH(0x10c88a410)') called at /Users/krum0058/gitProjects/ModelSeed/Model-Seed-Core/lib/PPO/DBObject.pm line 239
    DBObject::create('ModelSEED::ModelDB::COMPOUND_BIOMASS=HASH(0x10b4617c8)', 'HASH(0x10c88a410)') called at /Users/krum0058/gitProjects/ModelSeed/Model-Seed-Core/lib/ModelSEED/FIGMODEL/FIGMODELdatabase.pm line 239
    ModelSEED::FIGMODEL::FIGMODELdatabase::create_object('ModelSEED::FIGMODEL::FIGMODELdatabase=HASH(0x7f892e70b1e8)', 'cpdbof', 'HASH(0x10c88a410)') called at /Users/krum0058/gitProjects/ModelSeed/Model-Seed-Core/lib/ModelSEED/FIGMODEL/FIGMODELreaction.pm line 1408
    ModelSEED::FIGMODEL::FIGMODELreaction::add_biomass_reaction_from_equation('ModelSEED::FIGMODEL::FIGMODELreaction=HASH(0x10c8b87b0)', 'HASH(0x7f892fe62828)') called at /Users/krum0058/gitProjects/ModelSeed/Model-Seed-Core/lib/ModelSEED/FIGMODEL.pm line 3444
    ModelSEED::FIGMODEL::import_model('ModelSEED::FIGMODEL=HASH(0x7f892e70b110)', 'HASH(0x7f892d615450)') called at /Users/krum0058/gitProjects/ModelSeed/Model-Seed-Core/lib/ModelSEED/ModelDriver.pm line 2602
    ModelSEED::ModelDriver::mdlimportmodel('ModelSEED::ModelDriver=HASH(0x7f892e70af18)', 'mdlimportmodel', 'HASH(0x7f892d614fa0)') called at /Users/krum0058/gitProjects/ModelSeed/Model-Seed-Core/lib/ModelSEED/ModelDriver.pl line 131
    main::__ANON__() called at /Library/Perl/5.12/Try/Tiny.pm line 76
    eval {...} called at /Library/Perl/5.12/Try/Tiny.pm line 67
    Try::Tiny::try('CODE(0x7f892d614dc0)', 'Try::Tiny::Catch=REF(0x7f892e70ae88)') called at /Users/krum0058/gitProjects/ModelSeed/Model-Seed-Core/lib/ModelSEED/ModelDriver.pl line 135
    require /Users/krum0058/gitProjects/ModelSeed/Model-Seed-Core/lib/ModelSEED/ModelDriver.pl called at /Users/krum0058/gitProjects/ModelSeed/Model-Seed-Core/config//ModelSEEDbootstrap.pm line 23
    main::run() called at -e line 3

Model-SEED-core revision: 845bde44612c6b7e968e7ff6e0c0e24d27d06123