CRAN Package Check Results for Package r2sbml

Last updated on 2026-11-03 21:00:28 CET.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-fedora-clang	0.1.0	346.00	2.01	348.01	ERROR
r-devel-linux-x86_64-fedora-gcc	0.1.0	343.00	42.37	385.37	OK
r-release-macos-arm64	0.1.0	110.00	-18.00	92.00	ERROR
r-release-macos-x86_64	0.1.0	323.00	186.00	509.00	ERROR
r-oldrel-macos-arm64	0.1.0	124.00	-16.00	108.00	ERROR
r-oldrel-macos-x86_64	0.1.0	323.00	205.00	528.00	ERROR

Additional issues

clang-ASAN gcc-UBSAN M1-SAN

Check Details

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/4s] 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/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/RtmpzcUAfB/file1797c56f0a3ab.xml error(s): 0 File: /Volumes/Temp/tmp/RtmpzcUAfB/file1797c56f0a3ab.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/RtmpzcUAfB/file1797c10bf05d6.xml error(s): 0 File: /Volumes/Temp/tmp/RtmpzcUAfB/file1797c10bf05d6.xml (Level 3, version 2) filename: /Volumes/Temp/tmp/RtmpzcUAfB/file1797c279067e.xml error(s): 0 File: /Volumes/Temp/tmp/RtmpzcUAfB/file1797c279067e.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/RtmpzcUAfB/file1797c6ca367cc.xml error(s): 1 Encountered the following SBML errors: line 1: (01035 [Error]) Main XML content is empty. filename: /Volumes/Temp/tmp/RtmpzcUAfB/file1797c6ca367cc.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/24s] 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/RtmpDGxOUJ/file209c3c1858f9.xml error(s): 0 File: /Volumes/Temp/tmp/RtmpDGxOUJ/file209c3c1858f9.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/RtmpDGxOUJ/file209c6b664ad3.xml error(s): 0 File: /Volumes/Temp/tmp/RtmpDGxOUJ/file209c6b664ad3.xml (Level 3, version 2) filename: /Volumes/Temp/tmp/RtmpDGxOUJ/file209c31f70640.xml error(s): 0 File: /Volumes/Temp/tmp/RtmpDGxOUJ/file209c31f70640.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/RtmpDGxOUJ/file209c13267af4.xml error(s): 1 Encountered the following SBML errors: line 1: (01035 [Error]) Main XML content is empty. filename: /Volumes/Temp/tmp/RtmpDGxOUJ/file209c13267af4.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’ [4s/4s] 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/RtmpFGFBdA/file404048efaf12.xml error(s): 0 File: /Volumes/Temp/tmp/RtmpFGFBdA/file404048efaf12.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/RtmpFGFBdA/file404078883ab8.xml error(s): 0 File: /Volumes/Temp/tmp/RtmpFGFBdA/file404078883ab8.xml (Level 3, version 2) filename: /Volumes/Temp/tmp/RtmpFGFBdA/file4040788878a.xml error(s): 0 File: /Volumes/Temp/tmp/RtmpFGFBdA/file4040788878a.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/RtmpFGFBdA/file404048f56233.xml error(s): 1 Encountered the following SBML errors: line 1: (01035 [Error]) Main XML content is empty. filename: /Volumes/Temp/tmp/RtmpFGFBdA/file404048f56233.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’ [10s/26s] 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/RtmptSO6RK/file9d744c2be687.xml error(s): 0 File: /Volumes/Temp/tmp/RtmptSO6RK/file9d744c2be687.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/RtmptSO6RK/file9d744f7cddbb.xml error(s): 0 File: /Volumes/Temp/tmp/RtmptSO6RK/file9d744f7cddbb.xml (Level 3, version 2) filename: /Volumes/Temp/tmp/RtmptSO6RK/file9d74228e4dab.xml error(s): 0 File: /Volumes/Temp/tmp/RtmptSO6RK/file9d74228e4dab.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/RtmptSO6RK/file9d742f67afd1.xml error(s): 1 Encountered the following SBML errors: line 1: (01035 [Error]) Main XML content is empty. filename: /Volumes/Temp/tmp/RtmptSO6RK/file9d742f67afd1.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. 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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