Last updated on 2026-11-08 13:54:28 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.0 | 485.90 | 62.74 | 548.64 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.1.0 | 329.63 | 49.33 | 378.96 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.1.0 | 362.00 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.0 | 402.00 | 49.61 | 451.61 | OK | |
| r-devel-windows-x86_64 | 0.1.0 | 783.00 | 231.00 | 1014.00 | OK | |
| r-patched-linux-x86_64 | 0.1.0 | OK | ||||
| r-release-linux-x86_64 | 0.1.0 | 468.04 | 50.76 | 518.80 | OK | |
| r-release-macos-arm64 | 0.1.0 | 110.00 | -16.00 | 94.00 | ERROR | |
| r-release-macos-x86_64 | 0.1.0 | 335.00 | 358.00 | 693.00 | ERROR | |
| r-release-windows-x86_64 | 0.1.0 | 770.00 | 180.00 | 950.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.0 | ERROR | ||||
| r-oldrel-macos-x86_64 | 0.1.0 | 327.00 | 429.00 | 756.00 | ERROR | |
| r-oldrel-windows-x86_64 | 0.1.0 | 474.00 | 193.00 | 667.00 | OK |
Version: 0.1.0
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(r2sbml)
>
> test_check("r2sbml")
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
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Number of ODEs - 4
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Number of ODEs - 4
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Conversion completed.
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Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 4
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Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
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Number of ODEs - 5
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Number of ODEs - 5
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Number of ODEs - 5
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Number of ODEs - 3
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Number of ODEs - 3
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Number of ODEs - 5
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Number of ODEs - 5
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Number of ODEs - 4
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Number of ODEs - 4
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Number of ODEs - 4
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Number of ODEs - 1
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Number of ODEs - 4
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Number of ODEs - 1
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Number of ODEs - 2
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Number of ODEs - 1
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Number of ODEs - 1
Conversion completed.
Number of ODEs - 3
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Number of ODEs - 1
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Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
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Number of ODEs - 2
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Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
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Number of ODEs - 2
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Number of ODEs - 2
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Number of ODEs - 2
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Number of ODEs - 2
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Number of ODEs - 1
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Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
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Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 1
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Number of ODEs - 1
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Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
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Number of ODEs - 1
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Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Renamed p to p_: the name is reserved in Julia.
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Renamed p to p_: the name is reserved in Julia.
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Unable to perform conversion due to the following:
line 9: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-initial-values-132.R
Unable to perform conversion due to the following:
line 9: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-initial-values-146.R
Unable to perform conversion due to the following:
line 9: (20902 [Error]) The value of a <rateRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.4
The <rateRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-initial-values-154.R
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
filename: /Volumes/Builds/packages/sonoma-arm64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
error(s): 0
File: /Volumes/Builds/packages/sonoma-arm64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
filename: /Volumes/Builds/packages/sonoma-arm64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlassignmentrules.xml
error(s): 0
File: /Volumes/Builds/packages/sonoma-arm64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlassignmentrules.xml (Level 3, version 2)
filename: /Volumes/Temp/tmp/Rtmp8AMRuP/file1f604029de0d.xml
error(s): 0
File: /Volumes/Temp/tmp/Rtmp8AMRuP/file1f604029de0d.xml (Level 3, version 2)
filename: /Volumes/Builds/packages/sonoma-arm64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
error(s): 0
File: /Volumes/Builds/packages/sonoma-arm64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
Conversion completed.
Number of ODEs - 4
filename: /Volumes/Builds/packages/sonoma-arm64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
error(s): 0
File: /Volumes/Builds/packages/sonoma-arm64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
filename: /Volumes/Temp/tmp/Rtmp8AMRuP/file1f607b5d2225.xml
error(s): 0
File: /Volumes/Temp/tmp/Rtmp8AMRuP/file1f607b5d2225.xml (Level 3, version 2)
filename: /Volumes/Temp/tmp/Rtmp8AMRuP/file1f604a8cacb6.xml
error(s): 0
File: /Volumes/Temp/tmp/Rtmp8AMRuP/file1f604a8cacb6.xml (Level 3, version 2)
filename: /Volumes/Builds/packages/sonoma-arm64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
error(s): 0
File: /Volumes/Builds/packages/sonoma-arm64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
filename: /Volumes/Builds/packages/sonoma-arm64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
error(s): 0
File: /Volumes/Builds/packages/sonoma-arm64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
filename: /Volumes/Builds/packages/sonoma-arm64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlfunctiondefinition.xml
error(s): 0
File: /Volumes/Builds/packages/sonoma-arm64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlfunctiondefinition.xml (Level 3, version 2)
filename: /Volumes/Temp/tmp/Rtmp8AMRuP/file1f605f4bf6d3.xml
error(s): 1
Encountered the following SBML errors:
line 1: (01035 [Error]) Main XML content is empty.
filename: /Volumes/Temp/tmp/Rtmp8AMRuP/file1f605f4bf6d3.xml
error(s): 1
Encountered the following SBML errors:
line 1: (01035 [Error]) Main XML content is empty.
Encountered the following SBML errors:
line 1: (01035 [Error]) Main XML content is empty.
Encountered the following SBML errors:
line 1: (01035 [Error]) Main XML content is empty.
filename: /Volumes/Builds/packages/sonoma-arm64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
error(s): 0
File: /Volumes/Builds/packages/sonoma-arm64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 1
Unable to perform conversion due to the following:
line 1: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'r2sbml_J0_A_reactants' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-reaction-terms-78.R
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 0
Renamed p to p_: the name is reserved in Julia.
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Renamed t to t_: the name is reserved in nlmixr2.
Conversion completed.
Number of ODEs - 2
Renamed t to t_: the name is reserved in MATLAB.
Conversion completed.
Number of ODEs - 2
Renamed t to t_: the name is reserved in Julia.
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Unable to perform conversion due to the following:
line 14: (20801 [Error]) The value of 'symbol' in an <initialAssignment> definition must be the identifier of an existing <compartment>, <species>, or <parameter> defined in the model or <speciesReference> in Level 3, or in Level 3 Version 2, any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.8
The <initialAssignment> with symbol 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 14: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 14: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 14: (20801 [Error]) The value of 'symbol' in an <initialAssignment> definition must be the identifier of an existing <compartment>, <species>, or <parameter> defined in the model or <speciesReference> in Level 3, or in Level 3 Version 2, any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.8
The <initialAssignment> with symbol 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 15: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 15: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 15: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 1: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'r2sbml_J0_A_reactants' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 6
Conversion completed.
Number of ODEs - 18
[ FAIL 12 | WARN 0 | SKIP 9 | PASS 928 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On CRAN (9): 'test-algebraic-solved.R:80:5', 'test-convert.R:536:5',
'test-convert.R:614:5', 'test-names.R:104:5', 'test-outputs.R:88:5',
'test-sbml-test-suite.R:40:5', 'test-spelling.R:233:5',
'test-spelling.R:394:5', 'test-spelling.R:461:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-initial-values.R:132:9'): a rule-set stoichiometry reaches the generated derivative ──
<Rcpp::exception/C++Error/error/condition>
Error: Conversion failed.
Backtrace:
▆
1. ├─testthat::expect_no_warning(convertReactions(sbml, out, format = "R")) at test-initial-values.R:132:9
2. │ └─testthat:::expect_no_(...)
3. │ └─testthat:::quasi_capture(enquo(object), NULL, capture)
4. │ ├─testthat (local) .capture(...)
5. │ │ ├─base::withRestarts(...)
6. │ │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
7. │ │ │ └─base (local) doWithOneRestart(return(expr), restart)
8. │ │ └─base::withCallingHandlers(...)
9. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
10. └─r2sbml::convertReactions(sbml, out, format = "R")
── Error ('test-initial-values.R:146:9'): a rule-set stoichiometry reproduces its analytic solution ──
<Rcpp::exception/C++Error/error/condition>
Error: Conversion failed.
Backtrace:
▆
1. └─r2sbml (local) solve_r(stoich_cases[[nm]]$model(), times) at test-initial-values.R:146:9
2. └─r2sbml::convertReactions(sbml, out, format = "R") at test-initial-values.R:30:5
── Error ('test-initial-values.R:154:5'): a rate-rule stoichiometry is integrated from its declared value ──
<Rcpp::exception/C++Error/error/condition>
Error: Conversion failed.
Backtrace:
▆
1. └─r2sbml::convertReactions(sbml, out, format = "R") at test-initial-values.R:154:5
── Error ('test-reaction-terms.R:78:5'): repeated references whose stoichiometry is assigned add too ──
<Rcpp::exception/C++Error/error/condition>
Error: Conversion failed.
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-reaction-terms.R:78:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─r2sbml (local) solve_r(m, times)
5. └─r2sbml (local) source_r(sbml) at test-reaction-terms.R:35:5
6. └─r2sbml::convertReactions(sbml, out, format = "R") at test-reaction-terms.R:29:5
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 00969 ─────────
case 00969: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 00970 ─────────
case 00970: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 00971 ─────────
case 00971: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 01102 ─────────
case 01102: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 01104 ─────────
case 01104: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 01105 ─────────
case 01105: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 01107 ─────────
case 01107: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 01434 ─────────
case 01434: error: convertReactions: Conversion failed.
[ FAIL 12 | WARN 0 | SKIP 9 | PASS 928 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-macos-arm64
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [10s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(r2sbml)
>
> test_check("r2sbml")
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Renamed p to p_: the name is reserved in Julia.
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Renamed p to p_: the name is reserved in Julia.
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Unable to perform conversion due to the following:
line 9: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-initial-values-132.R
Unable to perform conversion due to the following:
line 9: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-initial-values-146.R
Unable to perform conversion due to the following:
line 9: (20902 [Error]) The value of a <rateRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.4
The <rateRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-initial-values-154.R
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
filename: /Volumes/Builds/packages/big-sur-x86_64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
error(s): 0
File: /Volumes/Builds/packages/big-sur-x86_64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
filename: /Volumes/Builds/packages/big-sur-x86_64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlassignmentrules.xml
error(s): 0
File: /Volumes/Builds/packages/big-sur-x86_64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlassignmentrules.xml (Level 3, version 2)
filename: /Volumes/Temp/tmp/RtmpUfCHH3/file1867568d85d59.xml
error(s): 0
File: /Volumes/Temp/tmp/RtmpUfCHH3/file1867568d85d59.xml (Level 3, version 2)
filename: /Volumes/Builds/packages/big-sur-x86_64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
error(s): 0
File: /Volumes/Builds/packages/big-sur-x86_64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
Conversion completed.
Number of ODEs - 4
filename: /Volumes/Builds/packages/big-sur-x86_64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
error(s): 0
File: /Volumes/Builds/packages/big-sur-x86_64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
filename: /Volumes/Temp/tmp/RtmpUfCHH3/file18675788cf74b.xml
error(s): 0
File: /Volumes/Temp/tmp/RtmpUfCHH3/file18675788cf74b.xml (Level 3, version 2)
filename: /Volumes/Temp/tmp/RtmpUfCHH3/file186752757b85f.xml
error(s): 0
File: /Volumes/Temp/tmp/RtmpUfCHH3/file186752757b85f.xml (Level 3, version 2)
filename: /Volumes/Builds/packages/big-sur-x86_64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
error(s): 0
File: /Volumes/Builds/packages/big-sur-x86_64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
filename: /Volumes/Builds/packages/big-sur-x86_64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
error(s): 0
File: /Volumes/Builds/packages/big-sur-x86_64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
filename: /Volumes/Builds/packages/big-sur-x86_64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlfunctiondefinition.xml
error(s): 0
File: /Volumes/Builds/packages/big-sur-x86_64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlfunctiondefinition.xml (Level 3, version 2)
filename: /Volumes/Temp/tmp/RtmpUfCHH3/file18675b9a3c3a.xml
error(s): 1
Encountered the following SBML errors:
line 1: (01035 [Error]) Main XML content is empty.
filename: /Volumes/Temp/tmp/RtmpUfCHH3/file18675b9a3c3a.xml
error(s): 1
Encountered the following SBML errors:
line 1: (01035 [Error]) Main XML content is empty.
Encountered the following SBML errors:
line 1: (01035 [Error]) Main XML content is empty.
Encountered the following SBML errors:
line 1: (01035 [Error]) Main XML content is empty.
filename: /Volumes/Builds/packages/big-sur-x86_64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
error(s): 0
File: /Volumes/Builds/packages/big-sur-x86_64/results/4.6/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 1
Unable to perform conversion due to the following:
line 1: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'r2sbml_J0_A_reactants' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-reaction-terms-78.R
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 0
Renamed p to p_: the name is reserved in Julia.
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Renamed t to t_: the name is reserved in nlmixr2.
Conversion completed.
Number of ODEs - 2
Renamed t to t_: the name is reserved in MATLAB.
Conversion completed.
Number of ODEs - 2
Renamed t to t_: the name is reserved in Julia.
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Unable to perform conversion due to the following:
line 14: (20801 [Error]) The value of 'symbol' in an <initialAssignment> definition must be the identifier of an existing <compartment>, <species>, or <parameter> defined in the model or <speciesReference> in Level 3, or in Level 3 Version 2, any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.8
The <initialAssignment> with symbol 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 14: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 14: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 14: (20801 [Error]) The value of 'symbol' in an <initialAssignment> definition must be the identifier of an existing <compartment>, <species>, or <parameter> defined in the model or <speciesReference> in Level 3, or in Level 3 Version 2, any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.8
The <initialAssignment> with symbol 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 15: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 15: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 15: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 1: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'r2sbml_J0_A_reactants' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 6
Conversion completed.
Number of ODEs - 18
[ FAIL 12 | WARN 0 | SKIP 9 | PASS 928 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On CRAN (9): 'test-algebraic-solved.R:80:5', 'test-convert.R:536:5',
'test-convert.R:614:5', 'test-names.R:104:5', 'test-outputs.R:88:5',
'test-sbml-test-suite.R:40:5', 'test-spelling.R:233:5',
'test-spelling.R:394:5', 'test-spelling.R:461:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-initial-values.R:132:9'): a rule-set stoichiometry reaches the generated derivative ──
<Rcpp::exception/C++Error/error/condition>
Error: Conversion failed.
Backtrace:
▆
1. ├─testthat::expect_no_warning(convertReactions(sbml, out, format = "R")) at test-initial-values.R:132:9
2. │ └─testthat:::expect_no_(...)
3. │ └─testthat:::quasi_capture(enquo(object), NULL, capture)
4. │ ├─testthat (local) .capture(...)
5. │ │ ├─base::withRestarts(...)
6. │ │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
7. │ │ │ └─base (local) doWithOneRestart(return(expr), restart)
8. │ │ └─base::withCallingHandlers(...)
9. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
10. └─r2sbml::convertReactions(sbml, out, format = "R")
── Error ('test-initial-values.R:146:9'): a rule-set stoichiometry reproduces its analytic solution ──
<Rcpp::exception/C++Error/error/condition>
Error: Conversion failed.
Backtrace:
▆
1. └─r2sbml (local) solve_r(stoich_cases[[nm]]$model(), times) at test-initial-values.R:146:9
2. └─r2sbml::convertReactions(sbml, out, format = "R") at test-initial-values.R:30:5
── Error ('test-initial-values.R:154:5'): a rate-rule stoichiometry is integrated from its declared value ──
<Rcpp::exception/C++Error/error/condition>
Error: Conversion failed.
Backtrace:
▆
1. └─r2sbml::convertReactions(sbml, out, format = "R") at test-initial-values.R:154:5
── Error ('test-reaction-terms.R:78:5'): repeated references whose stoichiometry is assigned add too ──
<Rcpp::exception/C++Error/error/condition>
Error: Conversion failed.
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-reaction-terms.R:78:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─r2sbml (local) solve_r(m, times)
5. └─r2sbml (local) source_r(sbml) at test-reaction-terms.R:35:5
6. └─r2sbml::convertReactions(sbml, out, format = "R") at test-reaction-terms.R:29:5
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 00969 ─────────
case 00969: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 00970 ─────────
case 00970: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 00971 ─────────
case 00971: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 01102 ─────────
case 01102: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 01104 ─────────
case 01104: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 01105 ─────────
case 01105: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 01107 ─────────
case 01107: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 01434 ─────────
case 01434: error: convertReactions: Conversion failed.
[ FAIL 12 | WARN 0 | SKIP 9 | PASS 928 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-macos-x86_64
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(r2sbml)
>
> test_check("r2sbml")
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Renamed p to p_: the name is reserved in Julia.
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Renamed p to p_: the name is reserved in Julia.
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Unable to perform conversion due to the following:
line 9: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-initial-values-132.R
Unable to perform conversion due to the following:
line 9: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-initial-values-146.R
Unable to perform conversion due to the following:
line 9: (20902 [Error]) The value of a <rateRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.4
The <rateRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-initial-values-154.R
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
filename: /Volumes/Builds/packages/big-sur-arm64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
error(s): 0
File: /Volumes/Builds/packages/big-sur-arm64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
filename: /Volumes/Builds/packages/big-sur-arm64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlassignmentrules.xml
error(s): 0
File: /Volumes/Builds/packages/big-sur-arm64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlassignmentrules.xml (Level 3, version 2)
filename: /Volumes/Temp/tmp/Rtmpdt0I0T/file70a35a00ed44.xml
error(s): 0
File: /Volumes/Temp/tmp/Rtmpdt0I0T/file70a35a00ed44.xml (Level 3, version 2)
filename: /Volumes/Builds/packages/big-sur-arm64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
error(s): 0
File: /Volumes/Builds/packages/big-sur-arm64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
Conversion completed.
Number of ODEs - 4
filename: /Volumes/Builds/packages/big-sur-arm64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
error(s): 0
File: /Volumes/Builds/packages/big-sur-arm64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
filename: /Volumes/Temp/tmp/Rtmpdt0I0T/file70a35ac9e40.xml
error(s): 0
File: /Volumes/Temp/tmp/Rtmpdt0I0T/file70a35ac9e40.xml (Level 3, version 2)
filename: /Volumes/Temp/tmp/Rtmpdt0I0T/file70a36daebf63.xml
error(s): 0
File: /Volumes/Temp/tmp/Rtmpdt0I0T/file70a36daebf63.xml (Level 3, version 2)
filename: /Volumes/Builds/packages/big-sur-arm64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
error(s): 0
File: /Volumes/Builds/packages/big-sur-arm64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
filename: /Volumes/Builds/packages/big-sur-arm64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
error(s): 0
File: /Volumes/Builds/packages/big-sur-arm64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
filename: /Volumes/Builds/packages/big-sur-arm64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlfunctiondefinition.xml
error(s): 0
File: /Volumes/Builds/packages/big-sur-arm64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlfunctiondefinition.xml (Level 3, version 2)
filename: /Volumes/Temp/tmp/Rtmpdt0I0T/file70a31f8d643d.xml
error(s): 1
Encountered the following SBML errors:
line 1: (01035 [Error]) Main XML content is empty.
filename: /Volumes/Temp/tmp/Rtmpdt0I0T/file70a31f8d643d.xml
error(s): 1
Encountered the following SBML errors:
line 1: (01035 [Error]) Main XML content is empty.
Encountered the following SBML errors:
line 1: (01035 [Error]) Main XML content is empty.
Encountered the following SBML errors:
line 1: (01035 [Error]) Main XML content is empty.
filename: /Volumes/Builds/packages/big-sur-arm64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
error(s): 0
File: /Volumes/Builds/packages/big-sur-arm64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 1
Unable to perform conversion due to the following:
line 1: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'r2sbml_J0_A_reactants' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-reaction-terms-78.R
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 0
Renamed p to p_: the name is reserved in Julia.
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Renamed t to t_: the name is reserved in nlmixr2.
Conversion completed.
Number of ODEs - 2
Renamed t to t_: the name is reserved in MATLAB.
Conversion completed.
Number of ODEs - 2
Renamed t to t_: the name is reserved in Julia.
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Unable to perform conversion due to the following:
line 14: (20801 [Error]) The value of 'symbol' in an <initialAssignment> definition must be the identifier of an existing <compartment>, <species>, or <parameter> defined in the model or <speciesReference> in Level 3, or in Level 3 Version 2, any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.8
The <initialAssignment> with symbol 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 14: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 14: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 14: (20801 [Error]) The value of 'symbol' in an <initialAssignment> definition must be the identifier of an existing <compartment>, <species>, or <parameter> defined in the model or <speciesReference> in Level 3, or in Level 3 Version 2, any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.8
The <initialAssignment> with symbol 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 15: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 15: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 15: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 1: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'r2sbml_J0_A_reactants' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 6
Conversion completed.
Number of ODEs - 18
[ FAIL 12 | WARN 0 | SKIP 9 | PASS 928 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On CRAN (9): 'test-algebraic-solved.R:80:5', 'test-convert.R:536:5',
'test-convert.R:614:5', 'test-names.R:104:5', 'test-outputs.R:88:5',
'test-sbml-test-suite.R:40:5', 'test-spelling.R:233:5',
'test-spelling.R:394:5', 'test-spelling.R:461:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-initial-values.R:132:9'): a rule-set stoichiometry reaches the generated derivative ──
<Rcpp::exception/C++Error/error/condition>
Error: Conversion failed.
Backtrace:
▆
1. ├─testthat::expect_no_warning(convertReactions(sbml, out, format = "R")) at test-initial-values.R:132:9
2. │ └─testthat:::expect_no_(...)
3. │ └─testthat:::quasi_capture(enquo(object), NULL, capture)
4. │ ├─testthat (local) .capture(...)
5. │ │ ├─base::withRestarts(...)
6. │ │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
7. │ │ │ └─base (local) doWithOneRestart(return(expr), restart)
8. │ │ └─base::withCallingHandlers(...)
9. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
10. └─r2sbml::convertReactions(sbml, out, format = "R")
── Error ('test-initial-values.R:146:9'): a rule-set stoichiometry reproduces its analytic solution ──
<Rcpp::exception/C++Error/error/condition>
Error: Conversion failed.
Backtrace:
▆
1. └─r2sbml (local) solve_r(stoich_cases[[nm]]$model(), times) at test-initial-values.R:146:9
2. └─r2sbml::convertReactions(sbml, out, format = "R") at test-initial-values.R:30:5
── Error ('test-initial-values.R:154:5'): a rate-rule stoichiometry is integrated from its declared value ──
<Rcpp::exception/C++Error/error/condition>
Error: Conversion failed.
Backtrace:
▆
1. └─r2sbml::convertReactions(sbml, out, format = "R") at test-initial-values.R:154:5
── Error ('test-reaction-terms.R:78:5'): repeated references whose stoichiometry is assigned add too ──
<Rcpp::exception/C++Error/error/condition>
Error: Conversion failed.
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-reaction-terms.R:78:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─r2sbml (local) solve_r(m, times)
5. └─r2sbml (local) source_r(sbml) at test-reaction-terms.R:35:5
6. └─r2sbml::convertReactions(sbml, out, format = "R") at test-reaction-terms.R:29:5
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 00969 ─────────
case 00969: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 00970 ─────────
case 00970: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 00971 ─────────
case 00971: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 01102 ─────────
case 01102: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 01104 ─────────
case 01104: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 01105 ─────────
case 01105: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 01107 ─────────
case 01107: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 01434 ─────────
case 01434: error: convertReactions: Conversion failed.
[ FAIL 12 | WARN 0 | SKIP 9 | PASS 928 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-macos-arm64
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [11s/43s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(r2sbml)
>
> test_check("r2sbml")
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Renamed p to p_: the name is reserved in Julia.
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Renamed p to p_: the name is reserved in Julia.
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Unable to perform conversion due to the following:
line 9: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-initial-values-132.R
Unable to perform conversion due to the following:
line 9: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-initial-values-146.R
Unable to perform conversion due to the following:
line 9: (20902 [Error]) The value of a <rateRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.4
The <rateRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-initial-values-154.R
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
filename: /Volumes/Builds/packages/big-sur-x86_64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
error(s): 0
File: /Volumes/Builds/packages/big-sur-x86_64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
filename: /Volumes/Builds/packages/big-sur-x86_64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlassignmentrules.xml
error(s): 0
File: /Volumes/Builds/packages/big-sur-x86_64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlassignmentrules.xml (Level 3, version 2)
filename: /Volumes/Temp/tmp/RtmpqKT1C8/file124d86a3a772d.xml
error(s): 0
File: /Volumes/Temp/tmp/RtmpqKT1C8/file124d86a3a772d.xml (Level 3, version 2)
filename: /Volumes/Builds/packages/big-sur-x86_64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
error(s): 0
File: /Volumes/Builds/packages/big-sur-x86_64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
Conversion completed.
Number of ODEs - 4
filename: /Volumes/Builds/packages/big-sur-x86_64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
error(s): 0
File: /Volumes/Builds/packages/big-sur-x86_64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
filename: /Volumes/Temp/tmp/RtmpqKT1C8/file124d849105d0.xml
error(s): 0
File: /Volumes/Temp/tmp/RtmpqKT1C8/file124d849105d0.xml (Level 3, version 2)
filename: /Volumes/Temp/tmp/RtmpqKT1C8/file124d879f8ff2c.xml
error(s): 0
File: /Volumes/Temp/tmp/RtmpqKT1C8/file124d879f8ff2c.xml (Level 3, version 2)
filename: /Volumes/Builds/packages/big-sur-x86_64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
error(s): 0
File: /Volumes/Builds/packages/big-sur-x86_64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
filename: /Volumes/Builds/packages/big-sur-x86_64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
error(s): 0
File: /Volumes/Builds/packages/big-sur-x86_64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
filename: /Volumes/Builds/packages/big-sur-x86_64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlfunctiondefinition.xml
error(s): 0
File: /Volumes/Builds/packages/big-sur-x86_64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlfunctiondefinition.xml (Level 3, version 2)
filename: /Volumes/Temp/tmp/RtmpqKT1C8/file124d8ae36c70.xml
error(s): 1
Encountered the following SBML errors:
line 1: (01035 [Error]) Main XML content is empty.
filename: /Volumes/Temp/tmp/RtmpqKT1C8/file124d8ae36c70.xml
error(s): 1
Encountered the following SBML errors:
line 1: (01035 [Error]) Main XML content is empty.
Encountered the following SBML errors:
line 1: (01035 [Error]) Main XML content is empty.
Encountered the following SBML errors:
line 1: (01035 [Error]) Main XML content is empty.
filename: /Volumes/Builds/packages/big-sur-x86_64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
error(s): 0
File: /Volumes/Builds/packages/big-sur-x86_64/results/4.5/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 1
Unable to perform conversion due to the following:
line 1: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'r2sbml_J0_A_reactants' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-reaction-terms-78.R
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 0
Renamed p to p_: the name is reserved in Julia.
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 0
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 1
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Renamed t to t_: the name is reserved in nlmixr2.
Conversion completed.
Number of ODEs - 2
Renamed t to t_: the name is reserved in MATLAB.
Conversion completed.
Number of ODEs - 2
Renamed t to t_: the name is reserved in Julia.
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 3
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Unable to perform conversion due to the following:
line 14: (20801 [Error]) The value of 'symbol' in an <initialAssignment> definition must be the identifier of an existing <compartment>, <species>, or <parameter> defined in the model or <speciesReference> in Level 3, or in Level 3 Version 2, any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.8
The <initialAssignment> with symbol 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 14: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 14: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 14: (20801 [Error]) The value of 'symbol' in an <initialAssignment> definition must be the identifier of an existing <compartment>, <species>, or <parameter> defined in the model or <speciesReference> in Level 3, or in Level 3 Version 2, any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.8
The <initialAssignment> with symbol 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 15: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 15: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 15: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'Xref' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Unable to perform conversion due to the following:
line 1: (20901 [Error]) The value of an <assignmentRule>'s 'variable' must be the identifier of an existing <compartment>, <species>, globally-defined <parameter>, or (in Level 3) <speciesReference>, or (in Level 3 Version 2), any identifier in the SId namespace of the model belonging to an element defined by an SBML Level 3 package as having with mathematical meaning.
Reference: L3V2 Section 4.9.3
The <assignmentRule> with variable 'r2sbml_J0_A_reactants' does not refer to an existing <compartment>, <species>, <parameter> or <speciesReference>.
Saving _problems/test-sbml-test-suite-18.R
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 2
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 4
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 15
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 5
Conversion completed.
Number of ODEs - 6
Conversion completed.
Number of ODEs - 18
[ FAIL 12 | WARN 0 | SKIP 9 | PASS 928 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On CRAN (9): 'test-algebraic-solved.R:80:5', 'test-convert.R:536:5',
'test-convert.R:614:5', 'test-names.R:104:5', 'test-outputs.R:88:5',
'test-sbml-test-suite.R:40:5', 'test-spelling.R:233:5',
'test-spelling.R:394:5', 'test-spelling.R:461:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-initial-values.R:132:9'): a rule-set stoichiometry reaches the generated derivative ──
<Rcpp::exception/C++Error/error/condition>
Error: Conversion failed.
Backtrace:
▆
1. ├─testthat::expect_no_warning(convertReactions(sbml, out, format = "R")) at test-initial-values.R:132:9
2. │ └─testthat:::expect_no_(...)
3. │ └─testthat:::quasi_capture(enquo(object), NULL, capture)
4. │ ├─testthat (local) .capture(...)
5. │ │ ├─base::withRestarts(...)
6. │ │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
7. │ │ │ └─base (local) doWithOneRestart(return(expr), restart)
8. │ │ └─base::withCallingHandlers(...)
9. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
10. └─r2sbml::convertReactions(sbml, out, format = "R")
── Error ('test-initial-values.R:146:9'): a rule-set stoichiometry reproduces its analytic solution ──
<Rcpp::exception/C++Error/error/condition>
Error: Conversion failed.
Backtrace:
▆
1. └─r2sbml (local) solve_r(stoich_cases[[nm]]$model(), times) at test-initial-values.R:146:9
2. └─r2sbml::convertReactions(sbml, out, format = "R") at test-initial-values.R:30:5
── Error ('test-initial-values.R:154:5'): a rate-rule stoichiometry is integrated from its declared value ──
<Rcpp::exception/C++Error/error/condition>
Error: Conversion failed.
Backtrace:
▆
1. └─r2sbml::convertReactions(sbml, out, format = "R") at test-initial-values.R:154:5
── Error ('test-reaction-terms.R:78:5'): repeated references whose stoichiometry is assigned add too ──
<Rcpp::exception/C++Error/error/condition>
Error: Conversion failed.
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-reaction-terms.R:78:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─r2sbml (local) solve_r(m, times)
5. └─r2sbml (local) source_r(sbml) at test-reaction-terms.R:35:5
6. └─r2sbml::convertReactions(sbml, out, format = "R") at test-reaction-terms.R:29:5
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 00969 ─────────
case 00969: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 00970 ─────────
case 00970: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 00971 ─────────
case 00971: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 01102 ─────────
case 01102: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 01104 ─────────
case 01104: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 01105 ─────────
case 01105: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 01107 ─────────
case 01107: error: convertReactions: Conversion failed.
── Failure ('test-sbml-test-suite.R:17:9'): SBML Test Suite case 01434 ─────────
case 01434: error: convertReactions: Conversion failed.
[ FAIL 12 | WARN 0 | SKIP 9 | PASS 928 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-macos-x86_64