• using R version 4.6.1 (2026-06-24)
• using platform: x86_64-apple-darwin20
• R was compiled by     Apple clang version 14.0.0 (clang-1400.0.29.202)     GNU Fortran (GCC) 14.2.0
• running under: macOS Ventura 13.3.1
• using session charset: UTF-8 * current time: 2026-11-04 03:47:17 UTC
• checking for file ‘r2sbml/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘r2sbml’ version ‘0.1.0’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘r2sbml’ can be installed ... [327s/424s] OK See the install log for details.
• used C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
• used SDK: ‘MacOSX11.3.1.sdk’
• checking installed package size ... INFO   installed size is 10.5Mb   sub-directories of 1Mb or more:     libs 10.1Mb
• checking package directory ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [0s/1s] OK
• checking whether the package can be loaded with stated dependencies ... [0s/1s] OK
• checking whether the package can be unloaded cleanly ... [0s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [0s/1s] OK
• checking loading without being on the library search path ... [0s/1s] OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [2s/3s] OK
• checking Rd files ... [0s/1s] OK
• checking Rd metadata ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking line endings in shell scripts ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking compilation flags in Makevars ... OK
• checking for GNU extensions in Makefiles ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [1s/1s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [10s/27s] ERROR   Running ‘testthat.R’ [10s/27s] 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/RtmpHYPdsa/file12dcd2344a41f.xml     error(s): 0         File: /Volumes/Temp/tmp/RtmpHYPdsa/file12dcd2344a41f.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/RtmpHYPdsa/file12dcd5c08db09.xml     error(s): 0         File: /Volumes/Temp/tmp/RtmpHYPdsa/file12dcd5c08db09.xml (Level 3, version 2)        filename: /Volumes/Temp/tmp/RtmpHYPdsa/file12dcd2fa56bd9.xml     error(s): 0         File: /Volumes/Temp/tmp/RtmpHYPdsa/file12dcd2fa56bd9.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/RtmpHYPdsa/file12dcd787d895c.xml     error(s): 1      Encountered the following SBML errors:   line 1: (01035 [Error]) Main XML content is empty.           filename: /Volumes/Temp/tmp/RtmpHYPdsa/file12dcd787d895c.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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [23s/97s] OK
• checking PDF version of manual ... [7s/19s] OK
• DONE

Status: 1 ERROR