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SysBioChalmers / RAVEN

The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
http://sysbiochalmers.github.io/RAVEN/
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fix: checkInstallation warning, not error #477

Closed edkerk closed 1 year ago

edkerk commented 1 year ago

Main improvements in this PR:

I hereby confirm that I have:

github-actions[bot] commented 1 year ago

This PR has been automatically tested with GH Actions. Here is the output of the tests:

[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/doc/external/metacyc] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/doc/hpa] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/doc/installation] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/doc/io] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/doc/legacy] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/doc/legacy/core] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/doc/legacy/external] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/doc/pathway] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/doc/plotting] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/doc/solver] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/doc/struct_conversion] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/doc/testing] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/doc/testing/manual_tests] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/doc/testing/unit_tests] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/doc/tutorial] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/external] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/external/kegg] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/external/metacyc] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/hpa] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/installation] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/io] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/legacy] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/legacy/core] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/legacy/external] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/legacy/software] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/legacy/software/xml_toolbox] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/pathway] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/plotting] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/readme] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/GLPKmex] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/WoLFPSORT] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/WoLFPSORT/bin] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/WoLFPSORT/bin/fastafmt] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/WoLFPSORT/bin/pod] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/WoLFPSORT/bin/pod/ja_JP] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/WoLFPSORT/bin/psortModifiedForWolfFiles] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/WoLFPSORT/bin/psortModifiedForWolfFiles/motifLibraries] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/WoLFPSORT/bin/psortModifiedForWolfFiles/psortModules] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/WoLFPSORT/data] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/WoLFPSORT/man] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/WoLFPSORT/man/ja] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/WoLFPSORT/man/ja/man1] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/WoLFPSORT/man/man1] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/apache-poi] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/blast+] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/cd-hit] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/diamond] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/hmmer] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/libSBML] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/m2html] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/m2html/templates] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/m2html/templates/blue] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/mafft] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/mafft/mafft-linux64] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/mafft/mafft-linux64/mafftdir] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/mafft/mafft-linux64/mafftdir/bin] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/mafft/mafft-linux64/mafftdir/libexec] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/mafft/mafft-mac] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/mafft/mafft-mac/mafftdir] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/mafft/mafft-mac/mafftdir/bin] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/software/mafft/mafft-mac/mafftdir/libexec] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/solver] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/struct_conversion] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/testing] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/testing/manual_tests] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/testing/unit_tests] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/testing/unit_tests/tINITtestInfo] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/testing/unit_tests/test_data] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/tutorial] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/.git/logs] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/.git/logs/refs] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/.git/logs/refs/heads] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/.git/logs/refs/remotes] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/.git/logs/refs/remotes/origin] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/.git/refs/remotes] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/.git/refs/remotes/origin] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/.github] 
[Warning: Name is nonexistent or not a directory: /home/m/actions-runner/_work/GECKO/GECKO/RAVEN/.github/workflows] 
 
To get started, type doc.
For product information, visit www.mathworks.com.
 

*** THE RAVEN TOOLBOX ***

 > Installing from location             /home/m/actions-runner/_work/RAVEN/RAVEN
 > Checking RAVEN release               2.8.0
   > 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             5.19.0
 > 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
   > soplex                             Fail
   > cobra                              Pass
 > Set RAVEN solver                     gurobi

 > Checking BLAST+                      Pass
 > Checking DIAMOND                     Pass
 > Checking HMMER                       Pass

 > Checking function uniqueness         Fail
   Duplicate functions in /home/m/crap/Human-GEM/code/GPRs
     getGenesFromGrRules.m
   Resolve conflicting functions to ensure RAVEN functionality

*** checkInstallation complete ***

Running blastPlusTests
.
Done blastPlusTests

Running cdhitTests
.
Done cdhitTests

Running checkTasksTests
PASS: [Gen e[s] from a[s]] Gen e[s] from a[s]
FAIL: [Gen e[s] from a[s]] Gen e[s] from a[s]
.
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/testSoplex and it did not run to completion.
    ---------
    Error ID:
    ---------
    ''
    --------------
    Error Details:
    --------------
    Error using solverTests>testSoplex (line 79)
    SoPlex not installed or cannot be found, test skipped
..
Done solverTests

Running tinitTests
....
New genes added to the model:
G10
G11
G5
G6
G7
G8
G9
No mets ids with prefix "m_" currently exist in the model. The first new id will be "m_0001"
...
New genes added to the model:
G11
G12
G13
G14
No mets ids with prefix "m_" currently exist in the model. The first new id will be "m_0001"
...
Done tinitTests

Failure Summary:

     Name                    Failed  Incomplete  Reason(s)
    =======================================================
     solverTests/testSoplex    X         X       Errored.

Note: In the case of multiple test runs, this post will be edited.