R Under development (unstable) (2026-11-03 r90834) -- "Unsuffered Consequences"
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> pkgname <- "r2sbml"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> library('r2sbml')
> 
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
> cleanEx()
> nameEx("convertReactions")
> ### * convertReactions
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: convertReactions
> ### Title: Convert an SBML model to simulation code
> ### Aliases: convertReactions
> 
> ### ** Examples
> 
> sbml_file <- system.file("examples", "sbmlsimple.xml", package = "r2sbml")
> out_file <- tempfile(fileext = ".R")
> convertReactions(sbml_file, out_file, format = "R")
/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml/src/libsbml-src/src/sbml/validator/Validator.cpp:340:7: runtime error: downcast of address 0x7c32b4def920 which does not point to an object of type 'TConstraint'
0x7c32b4def920: note: object is of type 'VConstraintSpeciesReference20611'
 00 00 00 00  30 b7 05 aa d2 7b 00 00  83 50 00 00 02 00 00 00  70 41 eb b3 d2 7b 00 00  01 be be be
              ^~~~~~~~~~~~~~~~~~~~~~~
              vptr for 'VConstraintSpeciesReference20611'
    #0 0x7bd2a71634a6 in ValidatorConstraints::add(VConstraint*) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0xd634a6) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3)
    #1 0x7bd2a776c0c9 in ConsistencyValidator::init() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x136c0c9) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3)
    #2 0x7bd2a702413a in SBMLInternalValidator::checkConsistency(bool) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0xc2413a) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3)
    #3 0x7bd2a69fd1f0 in SBMLDocument::checkConsistency() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x5fd1f0) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3)
    #4 0x7bd2a7467e2c in SBMLReactionConverter::isDocumentValid() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x1067e2c) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3)
    #5 0x7bd2a7476ae9 in SBMLReactionConverter::convert() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x1076ae9) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3)
    #6 0x7bd2a6a054cd in SBMLDocument::convert(ConversionProperties const&) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x6054cd) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3)
    #7 0x7bd2a6590623 in convertReactions(SEXPREC*, SEXPREC*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x190623) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3)
    #8 0x7bd2a650d632 in _r2sbml_convertReactions (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x10d632) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3)
    #9 0x00000075fa3a in R_doDotCall /data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:760
    #10 0x000000904867 in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8708
    #11 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537
    #12 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167
    #13 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400
    #14 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316
    #15 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335
    #16 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278
    #17 0x000000a25478 in Rf_ReplIteration /data/localhost/ripley/R/svn/R-devel/src/main/main.c:264
    #18 0x000000a25478 in R_ReplConsole /data/localhost/ripley/R/svn/R-devel/src/main/main.c:319
    #19 0x000000a431da in run_Rmainloop /data/localhost/ripley/R/svn/R-devel/src/main/main.c:1239
    #20 0x000000a43272 in Rf_mainloop /data/localhost/ripley/R/svn/R-devel/src/main/main.c:1246
    #21 0x0000004122df in main /data/localhost/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #22 0x7fd2b840a680 in __libc_start_call_main (/lib64/libc.so.6+0x3680) (BuildId: 85075e2ae2e13352a1413d41c327dacf6461526c)
    #23 0x7fd2b840a797 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3797) (BuildId: 85075e2ae2e13352a1413d41c327dacf6461526c)
    #24 0x000000412ca4 in _start (/data/localhost/ripley/R/gcc-SAN3/bin/exec/R+0x412ca4) (BuildId: 71398c2e2422cbe6c955a1152125cb4edf0131ca)

/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml/src/libsbml-src/src/sbml/LocalParameter.cpp:655:17: runtime error: downcast of address 0x7d72b4f11a80 which does not point to an object of type 'LocalParameter'
0x7d72b4f11a80: note: object is of type 'Parameter'
 00 00 00 00  30 8d 06 aa d2 7b 00 00  98 1a f1 b4 72 7d 00 00  08 00 00 00 00 00 00 00  76 65 71 5f
              ^~~~~~~~~~~~~~~~~~~~~~~
              vptr for 'Parameter'
    #0 0x7bd2a6931ab7 in ListOfParameters::get(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x531ab7) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3)
    #1 0x7bd2a73dcf86 in getNewId(Model*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0xfdcf86) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3)
    #2 0x7bd2a73f565b in SBMLLocalParameterConverter::convert() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0xff565b) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3)
    #3 0x7bd2a6a054cd in SBMLDocument::convert(ConversionProperties const&) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x6054cd) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3)
    #4 0x7bd2a74772e1 in SBMLReactionConverter::convert() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x10772e1) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3)
    #5 0x7bd2a6a054cd in SBMLDocument::convert(ConversionProperties const&) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x6054cd) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3)
    #6 0x7bd2a6590623 in convertReactions(SEXPREC*, SEXPREC*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x190623) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3)
    #7 0x7bd2a650d632 in _r2sbml_convertReactions (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x10d632) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3)
    #8 0x00000075fa3a in R_doDotCall /data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:760
    #9 0x000000904867 in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8708
    #10 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537
    #11 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167
    #12 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400
    #13 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316
    #14 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335
    #15 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278
    #16 0x000000a25478 in Rf_ReplIteration /data/localhost/ripley/R/svn/R-devel/src/main/main.c:264
    #17 0x000000a25478 in R_ReplConsole /data/localhost/ripley/R/svn/R-devel/src/main/main.c:319
    #18 0x000000a431da in run_Rmainloop /data/localhost/ripley/R/svn/R-devel/src/main/main.c:1239
    #19 0x000000a43272 in Rf_mainloop /data/localhost/ripley/R/svn/R-devel/src/main/main.c:1246
    #20 0x0000004122df in main /data/localhost/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #21 0x7fd2b840a680 in __libc_start_call_main (/lib64/libc.so.6+0x3680) (BuildId: 85075e2ae2e13352a1413d41c327dacf6461526c)
    #22 0x7fd2b840a797 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3797) (BuildId: 85075e2ae2e13352a1413d41c327dacf6461526c)
    #23 0x000000412ca4 in _start (/data/localhost/ripley/R/gcc-SAN3/bin/exec/R+0x412ca4) (BuildId: 71398c2e2422cbe6c955a1152125cb4edf0131ca)

Conversion completed.
Number of ODEs - 4
> out_file_mrg <- tempfile(fileext = ".cpp")
> convertReactions(sbml_file, out_file_mrg, format = "mrgsolve")
Conversion completed.
Number of ODEs - 4
> out_file_rx <- tempfile(fileext = ".R")
> convertReactions(sbml_file, out_file_rx, format = "nlmixr2")
Conversion completed.
Number of ODEs - 4
> out_file_m <- tempfile(fileext = ".m")
> convertReactions(sbml_file, out_file_m, format = "MATLAB")
Conversion completed.
Number of ODEs - 4
> out_file_jl <- tempfile(fileext = ".jl")
> convertReactions(sbml_file, out_file_jl, format = "Julia")
Conversion completed.
Number of ODEs - 4
> out_file_ub <- tempfile(fileext = ".txt")
> convertReactions(sbml_file, out_file_ub, format = "ubiquity")
Conversion completed.
Number of ODEs - 4
> 
> 
> 
> cleanEx()
> nameEx("echoSBML")
> ### * echoSBML
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: echoSBML
> ### Title: Check an SBML file for errors
> ### Aliases: echoSBML
> 
> ### ** Examples
> 
> sbml_file <- system.file("examples", "sbmlsimple.xml", package = "r2sbml")
> echoSBML(sbml_file)

  filename: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
  error(s): 0

[1] 0
> 
> 
> 
> cleanEx()
> nameEx("getCmtNames")
> ### * getCmtNames
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: getCmtNames
> ### Title: Names of the compartments in a model
> ### Aliases: getCmtNames
> 
> ### ** Examples
> 
> sbml_file <- system.file("examples", "sbmlsimple.xml", package = "r2sbml")
> model <- getModel(sbml_file)

  filename: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
  error(s): 0


File: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
> getCmtNames(model)
[1] "comp"
> 
> 
> 
> cleanEx()
> nameEx("getCmtSizes")
> ### * getCmtSizes
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: getCmtSizes
> ### Title: Sizes of the compartments in a model
> ### Aliases: getCmtSizes
> 
> ### ** Examples
> 
> sbml_file <- system.file("examples", "sbmlsimple.xml", package = "r2sbml")
> model <- getModel(sbml_file)

  filename: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
  error(s): 0


File: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
> getCmtSizes(model)
[1] 1e-14
> 
> 
> 
> cleanEx()
> nameEx("getEventMath")
> ### * getEventMath
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: getEventMath
> ### Title: Print the events of a model
> ### Aliases: getEventMath
> 
> ### ** Examples
> 
> sbml_file <- system.file("examples", "sbmlevent.xml", package = "r2sbml")
> model <- getModel(sbml_file)

  filename: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlevent.xml
  error(s): 0


File: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlevent.xml (Level 3, version 2)
> getEventMath(model)
Event 0 trigger: 1 * (P1 > tau)
  EventAssignment 1, trigger: G2 = 1
Event 1 trigger: 1 * (P1 <= tau)
  EventAssignment 1, trigger: G2 = 0
[1] 0
> 
> 
> 
> cleanEx()
> nameEx("getFunctionDefinition")
> ### * getFunctionDefinition
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: getFunctionDefinition
> ### Title: Print the function definitions of a model
> ### Aliases: getFunctionDefinition
> 
> ### ** Examples
> 
> sbml_file <- system.file("examples", "sbmlfunctiondefinition.xml", package = "r2sbml")
> model <- getModel(sbml_file)

  filename: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlfunctiondefinition.xml
  error(s): 0


File: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlfunctiondefinition.xml (Level 3, version 2)
> getFunctionDefinition(model)
FunctionDefinition 0, f(x) := x * 2
[1] 0
> 
> 
> 
> cleanEx()
> nameEx("getModel")
> ### * getModel
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: getModel
> ### Title: Read an SBML model
> ### Aliases: getModel
> 
> ### ** Examples
> 
> sbml_file <- system.file("examples", "sbmlsimple.xml", package = "r2sbml")
> model <- getModel(sbml_file)

  filename: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
  error(s): 0


File: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
> 
> 
> 
> cleanEx()
> nameEx("getNumSpecies")
> ### * getNumSpecies
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: getNumSpecies
> ### Title: Number of species in a model
> ### Aliases: getNumSpecies
> 
> ### ** Examples
> 
> sbml_file <- system.file("examples", "sbmlsimple.xml", package = "r2sbml")
> model <- getModel(sbml_file)

  filename: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
  error(s): 0


File: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
> getNumSpecies(model)
[1] 4
> 
> 
> 
> cleanEx()
> nameEx("getParameterTable")
> ### * getParameterTable
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: getParameterTable
> ### Title: Table of the parameters in a model
> ### Aliases: getParameterTable
> 
> ### ** Examples
> 
> sbml_file <- system.file("examples", "sbmlassignmentrules.xml", package = "r2sbml")
> model <- getModel(sbml_file)

  filename: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlassignmentrules.xml
  error(s): 0


File: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlassignmentrules.xml (Level 3, version 2)
> getParameterTable(model)
  Number  ID Name Value         Units
1      1 Keq        2.5 dimensionless
> 
> 
> 
> cleanEx()
> nameEx("getReactionMath")
> ### * getReactionMath
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: getReactionMath
> ### Title: Print the rate laws of a model
> ### Aliases: getReactionMath
> 
> ### ** Examples
> 
> sbml_file <- system.file("examples", "sbmlsimple.xml", package = "r2sbml")
> model <- getModel(sbml_file)

  filename: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
  error(s): 0


File: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
> getReactionMath(model)
Reaction 0, formula: comp * (kon * E * S - koff * ES)
Reaction 1, formula: comp * kcat * ES
[1] 0
> 
> 
> 
> cleanEx()
> nameEx("getReactionTable")
> ### * getReactionTable
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: getReactionTable
> ### Title: Table of the reactions in a model
> ### Aliases: getReactionTable
> 
> ### ** Examples
> 
> sbml_file <- system.file("examples", "sbmlsimple.xml", package = "r2sbml")
> model <- getModel(sbml_file)

  filename: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
  error(s): 0


File: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
> getReactionTable(model)
  Number   ID Name Reversible                          RateLaw
1      1  veq            TRUE comp * (kon * E * S - koff * ES)
2      2 vcat           FALSE                 comp * kcat * ES
> 
> 
> 
> cleanEx()
> nameEx("getRuleMath")
> ### * getRuleMath
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: getRuleMath
> ### Title: Print the rules of a model
> ### Aliases: getRuleMath
> 
> ### ** Examples
> 
> sbml_file <- system.file("examples", "sbmlassignmentrules.xml", package = "r2sbml")
> model <- getModel(sbml_file)

  filename: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlassignmentrules.xml
  error(s): 0


File: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlassignmentrules.xml (Level 3, version 2)
> getRuleMath(model)
Rule 0, formula: S1 = T / (1 + Keq)
Rule 1, formula: S2 = Keq * S1
[1] 0
> 
> 
> 
> cleanEx()
> nameEx("getSpeciesIC")
> ### * getSpeciesIC
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: getSpeciesIC
> ### Title: Initial values of the species in a model
> ### Aliases: getSpeciesIC
> 
> ### ** Examples
> 
> sbml_file <- system.file("examples", "sbmlsimple.xml", package = "r2sbml")
> model <- getModel(sbml_file)

  filename: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
  error(s): 0


File: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
> getSpeciesIC(model)
    E     S     P    ES 
5e-21 1e-20 0e+00 0e+00 
> 
> 
> 
> cleanEx()
> nameEx("getSpeciesNames")
> ### * getSpeciesNames
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: getSpeciesNames
> ### Title: Names of the species in a model
> ### Aliases: getSpeciesNames
> 
> ### ** Examples
> 
> sbml_file <- system.file("examples", "sbmlsimple.xml", package = "r2sbml")
> model <- getModel(sbml_file)

  filename: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
  error(s): 0


File: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
> getSpeciesNames(model)
[1] "E"  "S"  "P"  "ES"
> 
> 
> 
> cleanEx()
> nameEx("getSpeciesTable")
> ### * getSpeciesTable
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: getSpeciesTable
> ### Title: Table of the species in a model
> ### Aliases: getSpeciesTable
> 
> ### ** Examples
> 
> sbml_file <- system.file("examples", "sbmlsimple.xml", package = "r2sbml")
> model <- getModel(sbml_file)

  filename: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
  error(s): 0


File: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
> getSpeciesTable(model)
  Number Name ID InitialConcentration InitialAmount Compartment CompartmentVol
1      1       E                  NaN         5e-21        comp          1e-14
2      2       S                  NaN         1e-20        comp          1e-14
3      3       P                  NaN         0e+00        comp          1e-14
4      4      ES                  NaN         0e+00        comp          1e-14
  BoundaryCondition Constant
1                 0    FALSE
2                 0    FALSE
3                 0    FALSE
4                 0    FALSE
> 
> 
> 
> cleanEx()
> nameEx("printSBML")
> ### * printSBML
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: printSBML
> ### Title: Summarise an SBML file
> ### Aliases: printSBML
> 
> ### ** Examples
> 
> sbml_file <- system.file("examples", "sbmlsimple.xml", package = "r2sbml")
> printSBML(sbml_file)

  filename: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml
  error(s): 0


File: /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/examples/sbmlsimple.xml (Level 3, version 2)
                 id: (empty)
functionDefinitions: 0
    unitDefinitions: 2
   compartmentTypes: 0
        specieTypes: 0
       compartments: 1
            species: 4
         parameters: 0
 initialAssignments: 0
              rules: 0
        constraints: 0
          reactions: 2
             events: 0

[1] 0
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  1.24 0.134 1.382 0 0 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')