Submit BoolNet 2.1.5

id: boolnet
version: 2.1.5
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_BoolNet/91bb1faa2a642f1c94be4a75f85507db47e50551/biosimulators.json
specificationsPatch:
version: 2.1.5
image:
url: ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5
validateImage: true
commitSimulator: true

Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!
The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image and committing your simulator to the BioSimulators registry.
We will discuss any concerns with your submission in this issue.
A complete log of your simulator submission job will be available here. The results of the validation of your tool will also be saved as a JSON file.A link to this file will be available from the "Artifacts" section at the bottom of this page.

The specifications of your simulator is valid!

Summary of tests

Executed 60 test cases

Passed 8 test cases:

cli.CliDescribesSupportedEnvironmentVariablesInline
cli.CliDisplaysHelpInline
cli.CliDisplaysVersionInformationInline
docker_image.DeclaresSupportedEnvironmentVariables
docker_image.DefaultUserIsRoot
docker_image.HasBioContainersLabels
docker_image.HasOciLabels
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling

Failed 14 test cases:

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
results_report.SimulatorGeneratesReportsOfSimulationResults
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

Skipped 38 test cases:

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
sedml.SimulatorSupportsComputeModelChanges
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
sedml.SimulatorSupportsDataSetsWithDifferentShapes
sedml.SimulatorSupportsModelAttributeChanges
sedml.SimulatorSupportsRepeatedTasksWithChanges
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

Failures
combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (3.8 s)
Test that SED documents in nested directories can be executed
Exception:
[Errno 13] Permission denied: 'report.csv'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  subdir/simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: subdir/simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (3.7 s)
Test that SED documents with the same names in nested directories can be executed and their outputs are saved to distinct paths
Exception:
[Errno 13] Permission denied: 'report.csv'

Log:
Found 2 SED-ML documents with 2 models, 2 simulations, 2 tasks, 2 reports, and 0 plots:

  subdir/simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

  subdir__copy/simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: subdir/simulation.sedml ...

Executing SED-ML file 1: subdir__copy/simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 2 SED documents:

  SED documents (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Tasks (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile (3.5 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file.
Exception:
[Errno 13] Permission denied: 'report.csv'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (3.8 s)
Test that when a COMBINE/OMEX archive does not have a defined master file, the simulator executes all SED-ML files.
Exception:
[Errno 13] Permission denied: 'report.csv'

Log:
Found 2 SED-ML documents with 2 models, 2 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

  simulation__copy.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Executing SED-ML file 1: simulation__copy.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 2 SED documents:

  SED documents (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Tasks (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

results_report.SimulatorGeneratesReportsOfSimulationResults (3.6 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file.
Exception:
[Errno 13] Permission denied: 'report.csv'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorProducesLinear2DPlots (3.7 s)
Test that a simulator produces linear 2D plots
Exception:
[Errno 13] Permission denied: 'plot_0.pdf'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:

  simulation.sedml:

    Tasks (1):

      task

    Plots (1):

      plot_0: 5 curves

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorProducesLogarithmic2DPlots (3.7 s)
Test that a simulator produces logarithmic 2D plots
Exception:
[Errno 13] Permission denied: 'plot_0.pdf'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:

  simulation.sedml:

    Tasks (1):

      task

    Plots (1):

      plot_0: 5 curves

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorProducesMultiplePlots (3.8 s)
Test that a simulator produces multiple plots
Exception:
[Errno 13] Permission denied: 'plot_1.pdf'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 2 plots:

  simulation.sedml:

    Tasks (1):

      task

    Plots (2):

      plot_0: 3 curves

      plot_1: 2 curves

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (3.6 s)
Test that that the curated number of output dimensions matches the actual number of output dimensions
Exception:
[Errno 13] Permission denied: 'report.csv'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsAlgorithmParameters (3.4 s)
Test that a simulator supports setting the values of parameters of algorithms
Exception:
[Errno 13] Permission denied: 'report.csv'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports (3.4 s)
Test that a simulator supports the core elements of SED: models, simulations, tasks, data generators for individual variables, and reports
Exception:
[Errno 13] Permission denied: 'report.csv'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsMultipleReportsPerSedDocument (3.5 s)
Test that a simulator supports multiple reports per SED document
Exception:
[Errno 13] Permission denied: 'report_2.csv'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (2):

      report_1: 3 data sets

      report_2: 3 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsMultipleTasksPerSedDocument (3.7 s)
Test that a simulator supports multiple tasks per SED document
Exception:
[Errno 13] Permission denied: 'report.csv'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      task

      task__test_suite_copy

    Reports (2):

      report: 5 data sets

      report__test_suite_copy: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (3.5 s)
Test that a simulator supports time courses with non-zero output start times
Exception:
[Errno 13] Permission denied: 'report.csv'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

Warnings
cli.CliDescribesSupportedEnvironmentVariablesInline (6.8 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports.
Warnings:
The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'

If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

docker_image.DeclaresSupportedEnvironmentVariables (0.8 s)
Test if a Docker image declares the environment variables that is supports
Warnings:
Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

docker_image.HasBioContainersLabels (0.5 s)
Test that a Docker image has BioContainers labels with metadata about the image
Warnings:
The Docker image should have the following BioContainers labels:
  extra.identifiers.biotools

Log:

Skips
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (3.6 s)
Test that simulator logs the execution of COMBINE/OMEX archives
Reason for skip:
[Errno 13] Permission denied: 'report.csv'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (3.5 s)
Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives
Reason for skip:
[Errno 13] Permission denied: 'report.csv'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (3.5 s)
Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives
Reason for skip:
[Errno 13] Permission denied: 'report.csv'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (3.5 s)
Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives
Reason for skip:
[Errno 13] Permission denied: 'report.csv'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000263

Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000263

Log:

published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000088

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000088

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000496

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000496

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019
Format: format_2585
Algorithm: KISAO_0000027
Format: format_2585
Algorithm: KISAO_0000030

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000027, KISAO_0000030

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019
Format: format_2585
Algorithm: KISAO_0000030

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000030

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000027

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000027

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000029

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000029

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000437

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000437

Log:

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (3.7 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1).
Reason for skip:
[Errno 13] Permission denied: 'report.csv'

Log:
Found 1 SED-ML documents with 2 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (3.7 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1) and inherit the changes of the model.
Reason for skip:
[Errno 13] Permission denied: 'report.csv'

Log:
Found 1 SED-ML documents with 2 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorProducesLinear3DPlots (0.0 s)
Test that a simulator produces linear 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

sedml.SimulatorProducesLogarithmic3DPlots (0.0 s)
Test that a simulator produces logarithmic 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (7.0 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements.
Reason for skip:
[Errno 13] Permission denied: 'report.csv'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsComputeModelChanges (7.2 s)
Test that a simulator supports compute model changes
Reason for skip:
[Errno 13] Permission denied: 'report.csv'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (4.0 s)
Test that a simulator supports data generators with different shapes
Reason for skip:
[Errno 13] Permission denied: 'report__copy_2.csv'

Log:
Found 1 SED-ML documents with 1 models, 2 simulations, 2 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      task

      task__copy_2

    Reports (1):

      report__copy_2: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning messages:

R[write to console]: 1:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

R[write to console]: 2:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

R[write to console]: 3: There is no transition and no initial level for gene "egf"! Assuming an input!

R[write to console]: 4: There is no transition and no initial level for gene "tnfa"! Assuming an input!

sedml.SimulatorSupportsDataSetsWithDifferentShapes (4.3 s)
Test that a simulator supports data generators with different shapes
Reason for skip:
[Errno 13] Permission denied: 'report.csv'

Log:
Found 1 SED-ML documents with 1 models, 2 simulations, 2 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      task

      task__copy_2

    Reports (1):

      report: 10 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning messages:

R[write to console]: 1:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

R[write to console]: 2:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

R[write to console]: 3: There is no transition and no initial level for gene "egf"! Assuming an input!

R[write to console]: 4: There is no transition and no initial level for gene "tnfa"! Assuming an input!

sedml.SimulatorSupportsModelAttributeChanges (7.6 s)
Test that a simulator supports changes to the attributes of model elements
Reason for skip:
[Errno 13] Permission denied: 'report.csv'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    No namespace is defined with prefix `qual`

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    No namespace is defined with prefix `qual`

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsRepeatedTasksWithChanges (7.7 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
[Errno 13] Permission denied: 'task_report.csv'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

Found 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (7.9 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
[Errno 13] Permission denied: 'task_report.csv'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

Found 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (3.8 s)
Test that a simulator supports repeated tasks over functional ranges
Reason for skip:
[Errno 13] Permission denied: 'task_report.csv'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (3.7 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
[Errno 13] Permission denied: 'task_report.csv'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (3.7 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
[Errno 13] Permission denied: 'task_report.csv'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (3.7 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
[Errno 13] Permission denied: 'task_report.csv'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (3.7 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
[Errno 13] Permission denied: 'task_report.csv'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (4.0 s)
Test that a simulator supports nested repeated tasks
Reason for skip:
[Errno 13] Permission denied: 'task_report.csv'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 3 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (3):

      __repeated_task_0

      __repeated_task_1

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (3):

    Succeeded: 0

    Skipped: 0

    Failed: 3

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

    Number of poins must be equal to the difference between the output end and start times.

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (3.9 s)
Test that a simulator supports repeated tasks whose sub-tasks have mixed types. Also tests that sub-types executed in order of the values of their order attributes and that reports of the results of repeated tasks handle sub-tasks to produce results of different shapes.
Reason for skip:
[Errno 13] Permission denied: 'task_report.csv'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 3 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (3):

      __repeated_task_0

      __repeated_task_1

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (3):

    Succeeded: 0

    Skipped: 0

    Failed: 3

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

    Number of poins must be equal to the difference between the output end and start times.

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (3.7 s)
Test that a simulator supports repeated tasks over vector ranges
Reason for skip:
[Errno 13] Permission denied: 'task_report.csv'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (3.5 s)
Test that a simulator supports multiple time courses with non-zero initial times
Reason for skip:
[Errno 13] Permission denied: 'report.csv'

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Initial time must be 0.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
-
- The complete log of your validation/submission job, including further information about the failure, is available [here](https://github.com/biosimulators/Biosimulators/actions/runs/739746846). The results of the validation of your image will also be available shortly as a JSON file. A link to this file will be available from the "Artifacts" section at the bottom of [this page](https://github.com/biosimulators/Biosimulators/actions/runs/739746846).

Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!
The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image and committing your simulator to the BioSimulators registry.
We will discuss any concerns with your submission in this issue.
A complete log of your simulator submission job will be available here. The results of the validation of your tool will also be saved as a JSON file.A link to this file will be available from the "Artifacts" section at the bottom of this page.

The specifications of your simulator is valid!

Summary of tests

Executed 60 test cases

Passed 8 test cases:

cli.CliDescribesSupportedEnvironmentVariablesInline
cli.CliDisplaysHelpInline
cli.CliDisplaysVersionInformationInline
docker_image.DeclaresSupportedEnvironmentVariables
docker_image.DefaultUserIsRoot
docker_image.HasBioContainersLabels
docker_image.HasOciLabels
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling

Failed 14 test cases:

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
results_report.SimulatorGeneratesReportsOfSimulationResults
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

Skipped 38 test cases:

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
sedml.SimulatorSupportsComputeModelChanges
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
sedml.SimulatorSupportsDataSetsWithDifferentShapes
sedml.SimulatorSupportsModelAttributeChanges
sedml.SimulatorSupportsRepeatedTasksWithChanges
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

Failures
combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (3.9 s)
Test that SED documents in nested directories can be executed
Exception:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  subdir/simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: subdir/simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (4.0 s)
Test that SED documents with the same names in nested directories can be executed and their outputs are saved to distinct paths
Exception:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 2 SED-ML documents with 2 models, 2 simulations, 2 tasks, 2 reports, and 0 plots:

  subdir/simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

  subdir__copy/simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: subdir/simulation.sedml ...

Executing SED-ML file 1: subdir__copy/simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 2 SED documents:

  SED documents (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Tasks (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile (3.8 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file.
Exception:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (3.9 s)
Test that when a COMBINE/OMEX archive does not have a defined master file, the simulator executes all SED-ML files.
Exception:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 2 SED-ML documents with 2 models, 2 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

  simulation__copy.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Executing SED-ML file 1: simulation__copy.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 2 SED documents:

  SED documents (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Tasks (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

results_report.SimulatorGeneratesReportsOfSimulationResults (3.8 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file.
Exception:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorProducesLinear2DPlots (3.8 s)
Test that a simulator produces linear 2D plots
Exception:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:

  simulation.sedml:

    Tasks (1):

      task

    Plots (1):

      plot_0: 5 curves

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorProducesLogarithmic2DPlots (3.9 s)
Test that a simulator produces logarithmic 2D plots
Exception:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:

  simulation.sedml:

    Tasks (1):

      task

    Plots (1):

      plot_0: 5 curves

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorProducesMultiplePlots (3.9 s)
Test that a simulator produces multiple plots
Exception:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 2 plots:

  simulation.sedml:

    Tasks (1):

      task

    Plots (2):

      plot_0: 3 curves

      plot_1: 2 curves

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (3.7 s)
Test that that the curated number of output dimensions matches the actual number of output dimensions
Exception:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsAlgorithmParameters (3.8 s)
Test that a simulator supports setting the values of parameters of algorithms
Exception:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports (3.8 s)
Test that a simulator supports the core elements of SED: models, simulations, tasks, data generators for individual variables, and reports
Exception:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsMultipleReportsPerSedDocument (3.8 s)
Test that a simulator supports multiple reports per SED document
Exception:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (2):

      report_1: 3 data sets

      report_2: 3 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsMultipleTasksPerSedDocument (4.0 s)
Test that a simulator supports multiple tasks per SED document
Exception:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      task

      task__test_suite_copy

    Reports (2):

      report: 5 data sets

      report__test_suite_copy: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (3.7 s)
Test that a simulator supports time courses with non-zero output start times
Exception:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

Warnings
cli.CliDescribesSupportedEnvironmentVariablesInline (6.6 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports.
Warnings:
The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'

If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

docker_image.DeclaresSupportedEnvironmentVariables (0.9 s)
Test if a Docker image declares the environment variables that is supports
Warnings:
Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

docker_image.HasBioContainersLabels (0.5 s)
Test that a Docker image has BioContainers labels with metadata about the image
Warnings:
The Docker image should have the following BioContainers labels:
  extra.identifiers.biotools

Log:

Skips
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (3.8 s)
Test that simulator logs the execution of COMBINE/OMEX archives
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (3.9 s)
Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (3.8 s)
Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (3.8 s)
Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000263

Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000263

Log:

published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000088

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000088

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000496

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000496

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019
Format: format_2585
Algorithm: KISAO_0000027
Format: format_2585
Algorithm: KISAO_0000030

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000027, KISAO_0000030

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019
Format: format_2585
Algorithm: KISAO_0000030

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000030

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000027

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000027

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000029

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000029

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000437

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000437

Log:

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (3.7 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1).
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 2 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (3.7 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1) and inherit the changes of the model.
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 2 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorProducesLinear3DPlots (0.0 s)
Test that a simulator produces linear 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

sedml.SimulatorProducesLogarithmic3DPlots (0.0 s)
Test that a simulator produces logarithmic 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (7.7 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements.
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsComputeModelChanges (7.9 s)
Test that a simulator supports compute model changes
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (4.4 s)
Test that a simulator supports data generators with different shapes
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 2 simulations, 2 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      task

      task__copy_2

    Reports (1):

      report__copy_2: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning messages:

R[write to console]: 1:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

R[write to console]: 2:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

R[write to console]: 3: There is no transition and no initial level for gene "egf"! Assuming an input!

R[write to console]: 4: There is no transition and no initial level for gene "tnfa"! Assuming an input!

sedml.SimulatorSupportsDataSetsWithDifferentShapes (4.5 s)
Test that a simulator supports data generators with different shapes
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 2 simulations, 2 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      task

      task__copy_2

    Reports (1):

      report: 10 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 1

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning messages:

R[write to console]: 1:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

R[write to console]: 2:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

R[write to console]: 3: There is no transition and no initial level for gene "egf"! Assuming an input!

R[write to console]: 4: There is no transition and no initial level for gene "tnfa"! Assuming an input!

sedml.SimulatorSupportsModelAttributeChanges (8.3 s)
Test that a simulator supports changes to the attributes of model elements
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    No namespace is defined with prefix `qual`

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

  simulation.sedml:

    Tasks (1):

      task

    Reports (1):

      report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Outputs (1):

    Succeeded: 0

    Skipped: 1

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    No namespace is defined with prefix `qual`

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsRepeatedTasksWithChanges (8.5 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

Found 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (8.4 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

Found 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (4.1 s)
Test that a simulator supports repeated tasks over functional ranges
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (4.0 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (4.0 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (4.0 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

  SED documents (1):

    Succeeded: 0

    Skipped: 0

    Failed: 1

  Tasks (2):

    Succeeded: 0

    Skipped: 0

    Failed: 2

  Outputs (2):

    Succeeded: 0

    Skipped: 2

    Failed: 0

The COMBINE/OMEX did not execute successfully:

  The SED document did not execute successfully:

    Number of poins must be equal to the difference between the output end and start times.

    Number of poins must be equal to the difference between the output end and start times.

R[write to console]: Warning message:

R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :

R[write to console]:

R[write to console]:  library ‘/usr/lib/R/site-library’ contains no packages

sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (4.0 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_boolnet/boolnet:2.1.5' could not execute the archive:

  Unknown error

Log:
Found 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

  simulation.sedml:

    Tasks (2):

      __repeated_task_0

      task

    Reports (2):

      __repeated_task_report: 5 data sets

      task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...