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This repository has been archived by the owner on Aug 10, 2021. It is now read-only.
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:
""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
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
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