Closed edkerk closed 4 months ago
This PR has been automatically tested with GH Actions. Here is the output of the tests:
> Installation type Advanced (via git)
> Installing from location /home/m/actions-runner/_work/RAVEN/RAVEN
> Checking RAVEN release 2.9.0
> You are running the latest RAVEN release
> Checking MATLAB release 2020b
> Checking system architecture glnxa64
> Set RAVEN in MATLAB path Pass
> Save MATLAB path Pass
> Make binaries executable Pass
> Add Java paths for Excel format Pass
> Checking libSBML version 5.20.2
> Checking model import and export
> Import Excel format Pass
> Export Excel format Pass
> Import SBML format Pass
> Export SBML format Pass
> Checking for LP solvers
> glpk Pass
> gurobi Pass
> scip Fail
> cobra Pass
> Set RAVEN solver glpk
> Checking BLAST+ Pass
> Checking DIAMOND Pass
> Checking HMMER Pass
> Checking function uniqueness Pass
*** checkInstallation complete ***
SCIP MEX binary not installed or not functional, some fillGapsLargeTests skipped.
SCIP MEX binary not installed or not functional, some fillGapsSmallTests skipped.
Running blastPlusTests
.
Done blastPlusTests
Running cdhitTests
.
Done cdhitTests
Running checkTasksTests
.
Done checkTasksTests
Running diamondTests
.
Done diamondTests
Running fillGapsLargeTests
.
Done fillGapsLargeTests
Running fillGapsSmallTests
.
Done fillGapsSmallTests
Running hmmerTests
.
Done hmmerTests
Running importExportTests
....
Done importExportTests
Running mafftTests
.
Done mafftTests
Running miriamTests
.
Done miriamTests
Running modelAbilitiesTests
........
Done modelAbilitiesTests
Running modelConversionTests
.
Done modelConversionTests
Running modelCurationTests
.......... ........
Done modelCurationTests
Running modelSortingTests
..
Done modelSortingTests
Running solverTests
..
Error occurred in solverTests/testSCIP and it did not run to completion.
---------
Error ID:
---------
''
--------------
Error Details:
--------------
Error using solverTests>testSCIP (line 77)
SCIP MEX binary not installed or not functional.
..
Done solverTests
Running tinitTests
..........
Done tinitTests
Failure Summary:
Name Failed Incomplete Reason(s)
=====================================================
solverTests/testSCIP X X Errored.
Note: In the case of multiple test runs, this post will be edited.
Main improvements in this PR:
glpk
timeout when running selected large FBA calculationssolveLP
in parallel and COBRA toolbox is not installedgetAllowedBounds
returned inconsistent results when running parallelizationsolveLP
swapping the sign of reported objective function (sol.f
), as already announced with RAVEN release 2.7.12removeMets
also considersmetNotes
field if availablesetParam
error message if incorrect paramType is specifiedcheckInstallation
reports how RAVEN was installed, as described in the WikiInstructions on merging this PR:
develop
as target branch, and will be resolved with a squash-merge.main
as target branch, and will be resolved with a merge commit.