Error(s) in re-building vignettes:
--- re-building ‘GeneralModel.Rnw’ using Sweave
Loading required package: deSolve
Loading required package: parallel
Loading required package: RUnit
--- finished re-building ‘GeneralModel.Rnw’

--- re-building ‘ParameterEstimation.Rnw’ using Sweave
Loading required package: deSolve
Loading required package: parallel
Loading required package: RUnit
Loading required package: rootSolve
Loading required package: coda
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Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.
Warning in .local(t, A, ivList, initialValF, inputFluxes, inputFc, pass = pass,  :
  The argument Fc has been renamed to inputFc. The use of Fc is deprecated and will be removed in the next version. 
    Please change your code to use the new keyword argument inputFc.

Error: processing vignette 'ParameterEstimation.Rnw' failed with diagnostics:
 chunk 19 
Error in modMCMC(f = R14tCost, p = Fit$par, niter = 1000, jump = NULL,  : 
  values of 'p' should be inbetween 'lower' and 'upper'

--- failed re-building ‘ParameterEstimation.Rnw’

SUMMARY: processing the following file failed:
  ‘ParameterEstimation.Rnw’

Error: Vignette re-building failed.
Execution halted