Running examples in 'deGradInfer-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: agm
> ### Title: Main function for adaptive gradient matching
> ### Aliases: agm
> 
> ### ** Examples
> 
> 
> dataTest <- LV_example_dataset$data
> timeTest <- LV_example_dataset$time
> noiseTest <- LV_example_dataset$noise
> 
> LV_func = function(t, X, params) {
+ 	dxdt = cbind(
+ 	  X[,1]*(params[1] - params[2]*X[,2]),
+  	- X[,2]*(params[3] - params[4]*X[,1])
+ 	)
+ 	return(dxdt)
+ }
> 
> # Example run only; to achieve convergence the number of iterations and
> # chains must be increased.
> param.result = agm(data=dataTest,time=timeTest,noise.sd=0.31,ode.system=LV_func,
+     numberOfParameters=4,temperMismatchParameter=TRUE,
+     chainNum=4, maxIterations=150,originalSignalOnlyPositive=TRUE,
+     logPrior="Gamma",defaultTemperingScheme="LB10")
Error in if (class(invCh) == "try-error") { : 
  the condition has length > 1
Calls: agm ... gpCreate -> gpExpandParam -> gpUpdateKernels -> .jitCholInv
Execution halted
Running 'testthat.R' [5s/8s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(deGradInfer)
  > 
  > test_check("deGradInfer")
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 2 ]
  
  == Skipped tests ===============================================================
  * On CRAN (4)
  
  == Failed tests ================================================================
  -- Error (test_likelihood_improvement.R:22:1): (code run outside of `test_that()`) --
  Error in `if (class(invCh) == "try-error") {
      return(NaN)
  } else {
      invM <- invCh %*% t(invCh)
      if (jitter == 0) {
          ans <- list(invM = invM, jitter = jitter, chol = Ch)
      }
      else ans <- list(invM = invM, jitM = M + jitter * eyeM, jitter = jitter, 
          chol = Ch)
      return(ans)
  }`: the condition has length > 1
  Backtrace:
      x
   1. \-deGradInfer::agm(...) at test_likelihood_improvement.R:22:0
   2.   \-deGradInfer:::doMCMC(time, dataset, auxVars, options)
   3.     \-deGradInfer:::setupChains(timePoints, data, auxVars, options)
   4.       \-deGradInfer:::fitGP(...)
   5.         \-gptk::gpCreate(1, 1, time, y[, species, drop = F], options)
   6.           \-gptk::gpExpandParam(model, initParams)
   7.             \-gptk::gpUpdateKernels(model, model$X, model$X_u)
   8.               \-gptk:::.jitCholInv(model$K_uu, silent = TRUE)
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 2 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'ODE_parameter_inference.Rmd' using rmarkdown
Quitting from lines 104-110 (ODE_parameter_inference.Rmd) 
Error: processing vignette 'ODE_parameter_inference.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building 'ODE_parameter_inference.Rmd'

SUMMARY: processing the following file failed:
  'ODE_parameter_inference.Rmd'

Error: Vignette re-building failed.
Execution halted
Running examples in ‘deGradInfer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: agm
> ### Title: Main function for adaptive gradient matching
> ### Aliases: agm
> 
> ### ** Examples
> 
> 
> dataTest <- LV_example_dataset$data
> timeTest <- LV_example_dataset$time
> noiseTest <- LV_example_dataset$noise
> 
> LV_func = function(t, X, params) {
+ 	dxdt = cbind(
+ 	  X[,1]*(params[1] - params[2]*X[,2]),
+  	- X[,2]*(params[3] - params[4]*X[,1])
+ 	)
+ 	return(dxdt)
+ }
> 
> # Example run only; to achieve convergence the number of iterations and
> # chains must be increased.
> param.result = agm(data=dataTest,time=timeTest,noise.sd=0.31,ode.system=LV_func,
+     numberOfParameters=4,temperMismatchParameter=TRUE,
+     chainNum=4, maxIterations=150,originalSignalOnlyPositive=TRUE,
+     logPrior="Gamma",defaultTemperingScheme="LB10")
Error in if (class(invCh) == "try-error") { : 
  the condition has length > 1
Calls: agm ... gpCreate -> gpExpandParam -> gpUpdateKernels -> .jitCholInv
Execution halted
Running ‘testthat.R’ [4s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(deGradInfer)
  > 
  > test_check("deGradInfer")
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 2 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (4)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_likelihood_improvement.R:22:1): (code run outside of `test_that()`) ──
  Error in `if (class(invCh) == "try-error") {
      return(NaN)
  } else {
      invM <- invCh %*% t(invCh)
      if (jitter == 0) {
          ans <- list(invM = invM, jitter = jitter, chol = Ch)
      }
      else ans <- list(invM = invM, jitM = M + jitter * eyeM, jitter = jitter, 
          chol = Ch)
      return(ans)
  }`: the condition has length > 1
  Backtrace:
      ▆
   1. └─deGradInfer::agm(...) at test_likelihood_improvement.R:22:0
   2.   └─deGradInfer:::doMCMC(time, dataset, auxVars, options)
   3.     └─deGradInfer:::setupChains(timePoints, data, auxVars, options)
   4.       └─deGradInfer:::fitGP(...)
   5.         └─gptk::gpCreate(1, 1, time, y[, species, drop = F], options)
   6.           └─gptk::gpExpandParam(model, initParams)
   7.             └─gptk::gpUpdateKernels(model, model$X, model$X_u)
   8.               └─gptk:::.jitCholInv(model$K_uu, silent = TRUE)
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 2 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ODE_parameter_inference.Rmd’ using rmarkdown
Quitting from lines 104-110 (ODE_parameter_inference.Rmd) 
Error: processing vignette ‘ODE_parameter_inference.Rmd’ failed with diagnostics:
the condition has length > 1
--- failed re-building ‘ODE_parameter_inference.Rmd’

SUMMARY: processing the following file failed:
  ‘ODE_parameter_inference.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘deGradInfer-Ex.R’ failed
The error most likely occurred in:

> ### Name: agm
> ### Title: Main function for adaptive gradient matching
> ### Aliases: agm
> 
> ### ** Examples
> 
> 
> dataTest <- LV_example_dataset$data
> timeTest <- LV_example_dataset$time
> noiseTest <- LV_example_dataset$noise
> 
> LV_func = function(t, X, params) {
+ 	dxdt = cbind(
+ 	  X[,1]*(params[1] - params[2]*X[,2]),
+  	- X[,2]*(params[3] - params[4]*X[,1])
+ 	)
+ 	return(dxdt)
+ }
> 
> # Example run only; to achieve convergence the number of iterations and
> # chains must be increased.
> param.result = agm(data=dataTest,time=timeTest,noise.sd=0.31,ode.system=LV_func,
+     numberOfParameters=4,temperMismatchParameter=TRUE,
+     chainNum=4, maxIterations=150,originalSignalOnlyPositive=TRUE,
+     logPrior="Gamma",defaultTemperingScheme="LB10")
Error in if (class(invCh) == "try-error") { : 
  the condition has length > 1
Calls: agm ... gpCreate -> gpExpandParam -> gpUpdateKernels -> .jitCholInv
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(deGradInfer)
  > 
  > test_check("deGradInfer")
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 2 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (4)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_likelihood_improvement.R:22:1): (code run outside of `test_that()`) ──
  Error in `if (class(invCh) == "try-error") {
      return(NaN)
  } else {
      invM <- invCh %*% t(invCh)
      if (jitter == 0) {
          ans <- list(invM = invM, jitter = jitter, chol = Ch)
      }
      else ans <- list(invM = invM, jitM = M + jitter * eyeM, jitter = jitter, 
          chol = Ch)
      return(ans)
  }`: the condition has length > 1
  Backtrace:
      ▆
   1. └─deGradInfer::agm(...) at test_likelihood_improvement.R:22:0
   2.   └─deGradInfer:::doMCMC(time, dataset, auxVars, options)
   3.     └─deGradInfer:::setupChains(timePoints, data, auxVars, options)
   4.       └─deGradInfer:::fitGP(...)
   5.         └─gptk::gpCreate(1, 1, time, y[, species, drop = F], options)
   6.           └─gptk::gpExpandParam(model, initParams)
   7.             └─gptk::gpUpdateKernels(model, model$X, model$X_u)
   8.               └─gptk:::.jitCholInv(model$K_uu, silent = TRUE)
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 2 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘ODE_parameter_inference.Rmd’ using rmarkdown
Quitting from lines 104-110 (ODE_parameter_inference.Rmd) 
Error: processing vignette 'ODE_parameter_inference.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building ‘ODE_parameter_inference.Rmd’

SUMMARY: processing the following file failed:
  ‘ODE_parameter_inference.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘deGradInfer-Ex.R’ failed
The error most likely occurred in:

> ### Name: agm
> ### Title: Main function for adaptive gradient matching
> ### Aliases: agm
> 
> ### ** Examples
> 
> 
> dataTest <- LV_example_dataset$data
> timeTest <- LV_example_dataset$time
> noiseTest <- LV_example_dataset$noise
> 
> LV_func = function(t, X, params) {
+ 	dxdt = cbind(
+ 	  X[,1]*(params[1] - params[2]*X[,2]),
+  	- X[,2]*(params[3] - params[4]*X[,1])
+ 	)
+ 	return(dxdt)
+ }
> 
> # Example run only; to achieve convergence the number of iterations and
> # chains must be increased.
> param.result = agm(data=dataTest,time=timeTest,noise.sd=0.31,ode.system=LV_func,
+     numberOfParameters=4,temperMismatchParameter=TRUE,
+     chainNum=4, maxIterations=150,originalSignalOnlyPositive=TRUE,
+     logPrior="Gamma",defaultTemperingScheme="LB10")
Error in if (class(invCh) == "try-error") { : 
  the condition has length > 1
Calls: agm ... gpCreate -> gpExpandParam -> gpUpdateKernels -> .jitCholInv
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(deGradInfer)
  > 
  > test_check("deGradInfer")
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 2 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (4)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_likelihood_improvement.R:22:1): (code run outside of `test_that()`) ──
  Error in `if (class(invCh) == "try-error") {
      return(NaN)
  } else {
      invM <- invCh %*% t(invCh)
      if (jitter == 0) {
          ans <- list(invM = invM, jitter = jitter, chol = Ch)
      }
      else ans <- list(invM = invM, jitM = M + jitter * eyeM, jitter = jitter, 
          chol = Ch)
      return(ans)
  }`: the condition has length > 1
  Backtrace:
      ▆
   1. └─deGradInfer::agm(...) at test_likelihood_improvement.R:22:0
   2.   └─deGradInfer:::doMCMC(time, dataset, auxVars, options)
   3.     └─deGradInfer:::setupChains(timePoints, data, auxVars, options)
   4.       └─deGradInfer:::fitGP(...)
   5.         └─gptk::gpCreate(1, 1, time, y[, species, drop = F], options)
   6.           └─gptk::gpExpandParam(model, initParams)
   7.             └─gptk::gpUpdateKernels(model, model$X, model$X_u)
   8.               └─gptk:::.jitCholInv(model$K_uu, silent = TRUE)
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 2 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘ODE_parameter_inference.Rmd’ using rmarkdown
Quitting from lines 104-110 (ODE_parameter_inference.Rmd) 
Error: processing vignette 'ODE_parameter_inference.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building ‘ODE_parameter_inference.Rmd’

SUMMARY: processing the following file failed:
  ‘ODE_parameter_inference.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in 'deGradInfer-Ex.R' failed
The error most likely occurred in:

> ### Name: agm
> ### Title: Main function for adaptive gradient matching
> ### Aliases: agm
> 
> ### ** Examples
> 
> 
> dataTest <- LV_example_dataset$data
> timeTest <- LV_example_dataset$time
> noiseTest <- LV_example_dataset$noise
> 
> LV_func = function(t, X, params) {
+ 	dxdt = cbind(
+ 	  X[,1]*(params[1] - params[2]*X[,2]),
+  	- X[,2]*(params[3] - params[4]*X[,1])
+ 	)
+ 	return(dxdt)
+ }
> 
> # Example run only; to achieve convergence the number of iterations and
> # chains must be increased.
> param.result = agm(data=dataTest,time=timeTest,noise.sd=0.31,ode.system=LV_func,
+     numberOfParameters=4,temperMismatchParameter=TRUE,
+     chainNum=4, maxIterations=150,originalSignalOnlyPositive=TRUE,
+     logPrior="Gamma",defaultTemperingScheme="LB10")
Error in if (class(invCh) == "try-error") { : 
  the condition has length > 1
Calls: agm ... gpCreate -> gpExpandParam -> gpUpdateKernels -> .jitCholInv
Execution halted
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(deGradInfer)
  > 
  > test_check("deGradInfer")
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 2 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (4)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_likelihood_improvement.R:22:1): (code run outside of `test_that()`) ──
  Error in `if (class(invCh) == "try-error") {
      return(NaN)
  } else {
      invM <- invCh %*% t(invCh)
      if (jitter == 0) {
          ans <- list(invM = invM, jitter = jitter, chol = Ch)
      }
      else ans <- list(invM = invM, jitM = M + jitter * eyeM, jitter = jitter, 
          chol = Ch)
      return(ans)
  }`: the condition has length > 1
  Backtrace:
      ▆
   1. └─deGradInfer::agm(...) at test_likelihood_improvement.R:22:0
   2.   └─deGradInfer:::doMCMC(time, dataset, auxVars, options)
   3.     └─deGradInfer:::setupChains(timePoints, data, auxVars, options)
   4.       └─deGradInfer:::fitGP(...)
   5.         └─gptk::gpCreate(1, 1, time, y[, species, drop = F], options)
   6.           └─gptk::gpExpandParam(model, initParams)
   7.             └─gptk::gpUpdateKernels(model, model$X, model$X_u)
   8.               └─gptk:::.jitCholInv(model$K_uu, silent = TRUE)
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 2 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'ODE_parameter_inference.Rmd' using rmarkdown
Quitting from lines 104-110 (ODE_parameter_inference.Rmd) 
Error: processing vignette 'ODE_parameter_inference.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building 'ODE_parameter_inference.Rmd'

SUMMARY: processing the following file failed:
  'ODE_parameter_inference.Rmd'

Error: Vignette re-building failed.
Execution halted
Running examples in 'deGradInfer-Ex.R' failed
The error most likely occurred in:

> ### Name: agm
> ### Title: Main function for adaptive gradient matching
> ### Aliases: agm
> 
> ### ** Examples
> 
> 
> dataTest <- LV_example_dataset$data
> timeTest <- LV_example_dataset$time
> noiseTest <- LV_example_dataset$noise
> 
> LV_func = function(t, X, params) {
+ 	dxdt = cbind(
+ 	  X[,1]*(params[1] - params[2]*X[,2]),
+  	- X[,2]*(params[3] - params[4]*X[,1])
+ 	)
+ 	return(dxdt)
+ }
> 
> # Example run only; to achieve convergence the number of iterations and
> # chains must be increased.
> param.result = agm(data=dataTest,time=timeTest,noise.sd=0.31,ode.system=LV_func,
+     numberOfParameters=4,temperMismatchParameter=TRUE,
+     chainNum=4, maxIterations=150,originalSignalOnlyPositive=TRUE,
+     logPrior="Gamma",defaultTemperingScheme="LB10")
Error in if (class(invCh) == "try-error") { : 
  the condition has length > 1
Calls: agm ... gpCreate -> gpExpandParam -> gpUpdateKernels -> .jitCholInv
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(deGradInfer)
  > 
  > test_check("deGradInfer")
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 2 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (4)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_likelihood_improvement.R:22:1): (code run outside of `test_that()`) ──
  Error in `if (class(invCh) == "try-error") {
      return(NaN)
  } else {
      invM <- invCh %*% t(invCh)
      if (jitter == 0) {
          ans <- list(invM = invM, jitter = jitter, chol = Ch)
      }
      else ans <- list(invM = invM, jitM = M + jitter * eyeM, jitter = jitter, 
          chol = Ch)
      return(ans)
  }`: the condition has length > 1
  Backtrace:
      ▆
   1. └─deGradInfer::agm(...) at test_likelihood_improvement.R:22:0
   2.   └─deGradInfer:::doMCMC(time, dataset, auxVars, options)
   3.     └─deGradInfer:::setupChains(timePoints, data, auxVars, options)
   4.       └─deGradInfer:::fitGP(...)
   5.         └─gptk::gpCreate(1, 1, time, y[, species, drop = F], options)
   6.           └─gptk::gpExpandParam(model, initParams)
   7.             └─gptk::gpUpdateKernels(model, model$X, model$X_u)
   8.               └─gptk:::.jitCholInv(model$K_uu, silent = TRUE)
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 2 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'ODE_parameter_inference.Rmd' using rmarkdown
Quitting from lines 104-110 (ODE_parameter_inference.Rmd) 
Error: processing vignette 'ODE_parameter_inference.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building 'ODE_parameter_inference.Rmd'

SUMMARY: processing the following file failed:
  'ODE_parameter_inference.Rmd'

Error: Vignette re-building failed.
Execution halted