Submit VCell 7.4.0.49 #583

vcdaemon · 2022-07-13T15:10:17Z

id: vcell
version: 7.4.0.49
specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.4.0.49/biosimulators.json
specificationsPatch:
version: 7.4.0.49
image:
url: ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49
digest: "sha256:77b54d81ed53508052e7eda09feb51c710d57758334a132bba70f4e762e54148"
validateImage: true
commitSimulator: true

biosimulators-daemon · 2022-07-13T15:16:14Z

Thank you @vcdaemon 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 for 90 days 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 for 90 days from the "Artifacts" section at the bottom of this page.

biosimulators-daemon · 2022-07-13T15:16:17Z

The specifications of your simulator is valid!

biosimulators-daemon · 2022-07-13T15:22:40Z

Summary of tests

Executed 74 test cases
Passed 7 test cases:
- cli.CliDescribesSupportedEnvironmentVariablesInline
- cli.CliDisplaysHelpInline
- cli.CliDisplaysVersionInformationInline
- docker_image.DeclaresSupportedEnvironmentVariables
- docker_image.DefaultUserIsRoot
- docker_image.HasBioContainersLabels
- docker_image.HasOciLabels
Failed 26 test cases:
- combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
- combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
- combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
- combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
- docker_image.SingularityImageExecutesSimulationsSuccessfully
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- 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-Fehlberg
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
- 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:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength
- results_report.SimulatorGeneratesReportsOfSimulationResults
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Skipped 41 test cases:
- published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
- published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
- published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
- published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
- published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
- published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
- 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-discrete-SSA
- published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
- published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
- published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
- published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
- published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- sedml.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic3DPlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- 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.SimulatorSupportsSubstitutingAlgorithms
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

biosimulators-daemon · 2022-07-13T15:22:41Z

Failures

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (2.0 s)

Test that SED documents in nested directories can be executed

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:21:01 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (1.9 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/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:21:03 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile (1.9 s)

Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file.

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:21:05 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (1.9 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/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:21:07 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

docker_image.SingularityImageExecutesSimulationsSuccessfully (2.9 s)

Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives

Exception:

The Docker image could not be successfully executed as a Singularity image:
  Jul 13, 2022 3:20:51 PM java.util.prefs.FileSystemPreferences$1 run
  INFO: Created user preferences directory.
  15:20:51 [main] WARN  cbit.vcell.resource.PropertyLoader - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory
  Encountered fatal IOException while creating CLIUtils; killing VCell.
  java.io.IOException: Cannot run program "python": error=2, No such file or directory
  	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)
  	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)
  	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)
  	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)
  	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)
  	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)
  	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)
  Caused by: java.io.IOException: error=2, No such file or directory
  	at java.lang.UNIXProcess.forkAndExec(Native Method)
  	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)
  	at java.lang.ProcessImpl.start(ProcessImpl.java:134)
  	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)
  	... 6 more

Log: None

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (2.0 s)

Test that simulator logs the execution of COMBINE/OMEX archives

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:22:17 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (2.0 s)

Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:22:19 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (2.0 s)

Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:22:21 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (2.2 s)

Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:22:24 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (1.9 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:22:26 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (1.9 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000086

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:22:28 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (1.9 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:22:29 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (1.9 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:22:31 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (1.9 s)

Required model formats and simulation algorithms for SED tasks:

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

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:22:37 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (1.9 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:22:33 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (1.9 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000027

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:22:35 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

published_project.SimulatorCanExecutePublishedProject:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength (1.8 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9000
Algorithm: KISAO_0000019

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:22:39 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

results_report.SimulatorGeneratesReportsOfSimulationResults (2.0 s)

Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file.

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:22:15 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

sedml.SimulatorProducesLinear2DPlots (1.9 s)

Test that a simulator produces linear 2D plots

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:21:13 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

sedml.SimulatorProducesLogarithmic2DPlots (1.9 s)

Test that a simulator produces logarithmic 2D plots

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:21:15 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

sedml.SimulatorProducesMultiplePlots (2.0 s)

Test that a simulator produces multiple plots

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:21:17 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

sedml.SimulatorSupportsAlgorithmParameters (1.9 s)

Test that a simulator supports setting the values of parameters of algorithms

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:21:23 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports (1.9 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/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:21:37 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

sedml.SimulatorSupportsMultipleReportsPerSedDocument (1.9 s)

Test that a simulator supports multiple reports per SED document

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:21:39 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

sedml.SimulatorSupportsMultipleTasksPerSedDocument (1.9 s)

Test that a simulator supports multiple tasks per SED document

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:21:41 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (2.1 s)

Test that a simulator supports time courses with non-zero output start times

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:22:13 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

biosimulators-daemon · 2022-07-13T15:22:42Z

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.9 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'
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

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: None

cli.CliDisplaysHelpInline (2.3 s)

Test that a command-line interface provides inline help.

Warnings:

Command-line interface should support the `-h` option for displaying help inline.

The command-line interface displayed the following when executed with `-h`:

  usage: VCell [-h | -v] [-q] -i <input> -o <outputDir> [-t <milliseconds>]
               [-c]  [-vcml | -sbml] [-hasDataOnly] [-makeLogsOnly]
               [-nonSpatialOnly] [-keepTempFiles] [-exactMatchOnly]
               [-forceLogFiles]
  
  BioSimulators-compliant command-line interface to the VCell simulation
  program <http://vcell.org>.
  
  optional arguments:
  
   -c,--convert           Converts OMEX Archives to either sbml or vcml
                          format, attempting sbml first then vcml unless
                          otherwise specificed by flags. Requires -i and -o
                          flags.
   -exactMatchOnly        Run the model solver only if it's an exact kisao
                          match.
   -forceLogFiles         Generates log files ordinarily run only for batch
                          execution
   -h,--help              show this help message and exit
   -hasDataOnly           Export the sims that have been previously run and
                          have results on the VCell server.
   -i,--input <arg>       Path to OMEX/COMBINE Archive which contains one or
                          more SED-ML encoded simulation experiments, or
                          VCML file
   -keepTempFiles         Keep simulation results for debugging.
   -makeLogsOnly          Rather than creating the omex files, just make the
                          logs.
   -nonSpatialOnly        Export only non-spatial simulations.
   -o,--outputDir <arg>   Directory to save outputs or the converted OMEX
                          Archive from VCML file
   -q,--quiet             Suppress all console output [NOT CURRENTLY
                          IMPLIMENTED]
   -sbml                  Specifies conversion of OMEX Archive to sbml
                          format.
   -t,--timeout <arg>     Specifices a timeout duration.
   -v,--version           Show program's version number and exit
   -vcml                  Specifies conversion of OMEX Archive to vcml
                          format.

Command-line interface should support the `--help` option for displaying help inline.

The command-line interface displayed the following when executed with `--help`:

  usage: VCell [-h | -v] [-q] -i <input> -o <outputDir> [-t <milliseconds>]
               [-c]  [-vcml | -sbml] [-hasDataOnly] [-makeLogsOnly]
               [-nonSpatialOnly] [-keepTempFiles] [-exactMatchOnly]
               [-forceLogFiles]
  
  BioSimulators-compliant command-line interface to the VCell simulation
  program <http://vcell.org>.
  
  optional arguments:
  
   -c,--convert           Converts OMEX Archives to either sbml or vcml
                          format, attempting sbml first then vcml unless
                          otherwise specificed by flags. Requires -i and -o
                          flags.
   -exactMatchOnly        Run the model solver only if it's an exact kisao
                          match.
   -forceLogFiles         Generates log files ordinarily run only for batch
                          execution
   -h,--help              show this help message and exit
   -hasDataOnly           Export the sims that have been previously run and
                          have results on the VCell server.
   -i,--input <arg>       Path to OMEX/COMBINE Archive which contains one or
                          more SED-ML encoded simulation experiments, or
                          VCML file
   -keepTempFiles         Keep simulation results for debugging.
   -makeLogsOnly          Rather than creating the omex files, just make the
                          logs.
   -nonSpatialOnly        Export only non-spatial simulations.
   -o,--outputDir <arg>   Directory to save outputs or the converted OMEX
                          Archive from VCML file
   -q,--quiet             Suppress all console output [NOT CURRENTLY
                          IMPLIMENTED]
   -sbml                  Specifies conversion of OMEX Archive to sbml
                          format.
   -t,--timeout <arg>     Specifices a timeout duration.
   -v,--version           Show program's version number and exit
   -vcml                  Specifies conversion of OMEX Archive to vcml
                          format.

Log: None

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:
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

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: None

docker_image.HasBioContainersLabels (0.7 s)

Test that a Docker image has BioContainers labels with metadata about the image

Warnings:

Docker images are encouraged to have the following BioContainers labels:
  extra.identifiers.biotools

Log: None

biosimulators-daemon · 2022-07-13T15:22:43Z

Skips

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: None

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: None

published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (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: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000030

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000030

Log: None

published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9012
Algorithm: KISAO_0000669

Reason for skip:

Case requires model formats format_9012 and simulation algorithms KISAO_0000669

Log: None

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: None

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_000019

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_000019

Log: None

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: None

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: None

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: None

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: None

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: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000449

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000449

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9001
Algorithm: KISAO_0000057

Reason for skip:

Case requires model formats format_9001 and simulation algorithms KISAO_0000057

Log: None

published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9010
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log: None

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (1.9 s)

Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1).

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:21:09 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (1.9 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/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:21:11 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

sedml.SimulatorProducesLinear3DPlots (0.3 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: None

sedml.SimulatorProducesLogarithmic3DPlots (0.3 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: None

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.3 s)

Test that that the curated number of output dimensions matches the actual number of output dimensions

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (3.8 s)

Test that a simulator supports model changes that involve adding, replacing, and removing model elements.

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:21:19 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

Jul 13, 2022 3:21:21 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

sedml.SimulatorSupportsComputeModelChanges (3.8 s)

Test that a simulator supports compute model changes

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:21:25 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

Jul 13, 2022 3:21:27 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (1.9 s)

Test that a simulator supports data generators with different shapes

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:21:29 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

sedml.SimulatorSupportsDataSetsWithDifferentShapes (1.9 s)

Test that a simulator supports data generators with different shapes

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:21:31 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

sedml.SimulatorSupportsModelAttributeChanges (4.0 s)

Test that a simulator supports changes to the attributes of model elements

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:21:33 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

Jul 13, 2022 3:21:35 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

sedml.SimulatorSupportsRepeatedTasksWithChanges (3.8 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:21:43 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

Jul 13, 2022 3:21:45 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (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/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:21:47 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

Jul 13, 2022 3:21:49 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (2.0 s)

Test that a simulator supports repeated tasks over functional ranges

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:21:51 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (2.1 s)

Test that a simulator supports repeated tasks over uniform ranges

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:21:53 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (2.0 s)

Test that a simulator supports repeated tasks over uniform ranges

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:21:55 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (2.0 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:21:57 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (2.1 s)

Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:21:59 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (2.0 s)

Test that a simulator supports nested repeated tasks

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:22:01 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (2.0 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:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:22:03 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (2.0 s)

Test that a simulator supports repeated tasks over vector ranges

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:22:05 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

sedml.SimulatorSupportsSubstitutingAlgorithms (4.0 s)

Check that a simulator can substitute algorithms that it doesn't implement with similar algorithms when the algorithm substitution policy is less restrictive than :obj:AlgorithmSubstitutionPolicy.SAME_METHOD. Also check that a simulator ignores unsupported algorithm parameters when the algorithm substitution policy is less restrictive than :obj:AlgorithmSubstitutionPolicy.NONE.

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:22:07 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

Jul 13, 2022 3:22:09 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (2.0 s)

Test that a simulator supports multiple time courses with non-zero initial times

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.4.0.49' could not execute the archive:

  Unknown error

Log:

Jul 13, 2022 3:22:11 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

Encountered fatal IOException while creating CLIUtils; killing VCell.

java.io.IOException: Cannot run program "python": error=2, No such file or directory

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)

	at org.vcell.cli.CLIUtils.instantiatePythonProcess(CLIUtils.java:989)

	at org.vcell.cli.CLIUtils.getCLIUtils(CLIUtils.java:183)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:149)

	at org.vcell.cli.CLIStandalone.wrappedExecSingleOmex(CLIStandalone.java:521)

	at org.vcell.cli.CLIStandalone.singleMode(CLIStandalone.java:514)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:46)

Caused by: java.io.IOException: error=2, No such file or directory

	at java.lang.UNIXProcess.forkAndExec(Native Method)

	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)

	at java.lang.ProcessImpl.start(ProcessImpl.java:134)

	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)

	... 6 more

biosimulators-daemon · 2022-07-13T15:22:44Z

- 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 for 90 days [here](https://github.com/biosimulators/Biosimulators/actions/runs/2664415161). 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/2664415161).

moraru · 2022-08-29T22:08:53Z

Superseded by #587

vcdaemon added the Validate/submit simulator Validate a simulation tool or request its submission to the BioSimulators registry label Jul 13, 2022

biosimulators-daemon added the Invalid This doesn't seem right label Jul 13, 2022

moraru closed this as completed Aug 29, 2022

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Submit VCell 7.4.0.49 #583

Submit VCell 7.4.0.49 #583

vcdaemon commented Jul 13, 2022

biosimulators-daemon commented Jul 13, 2022

biosimulators-daemon commented Jul 13, 2022

biosimulators-daemon commented Jul 13, 2022

biosimulators-daemon commented Jul 13, 2022

biosimulators-daemon commented Jul 13, 2022

biosimulators-daemon commented Jul 13, 2022

biosimulators-daemon commented Jul 13, 2022

moraru commented Aug 29, 2022

Submit VCell 7.4.0.49 #583

Submit VCell 7.4.0.49 #583

Comments

vcdaemon commented Jul 13, 2022

biosimulators-daemon commented Jul 13, 2022

biosimulators-daemon commented Jul 13, 2022

biosimulators-daemon commented Jul 13, 2022

Summary of tests

biosimulators-daemon commented Jul 13, 2022

Failures

biosimulators-daemon commented Jul 13, 2022

Warnings

biosimulators-daemon commented Jul 13, 2022

Skips

biosimulators-daemon commented Jul 13, 2022

moraru commented Aug 29, 2022