Last updated on 2022-03-18 06:48:40 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.1 | 14.15 | 142.16 | 156.31 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.1 | 11.61 | 105.25 | 116.86 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.1 | 190.67 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.1 | 175.10 | ERROR | |||
| r-devel-windows-x86_64-new-UL | 1.0.1 | 47.00 | 152.00 | 199.00 | ERROR | |
| r-devel-windows-x86_64-new-TK | 1.0.1 | ERROR | ||||
| r-patched-linux-x86_64 | 1.0.1 | 10.65 | 170.49 | 181.14 | OK | |
| r-release-linux-x86_64 | 1.0.1 | 9.28 | 171.46 | 180.74 | OK | |
| r-release-macos-arm64 | 1.0.1 | OK | ||||
| r-release-macos-x86_64 | 1.0.1 | OK | ||||
| r-release-windows-ix86+x86_64 | 1.0.1 | 31.00 | 227.00 | 258.00 | OK | |
| r-oldrel-macos-x86_64 | 1.0.1 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 1.0.1 | 31.00 | 193.00 | 224.00 | OK |
Version: 1.0.1
Check: examples
Result: ERROR
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$noise
>
> LV_func = function(t, X, params) {
+ dxdt = cbind(
+ X[,1]*(params[1] - params[2]*X[,2]),
+ - X[,2]*(params[3] - params[4]*X[,1])
+ )
+ return(dxdt)
+ }
>
> # Example run only; to achieve convergence the number of iterations and
> # chains must be increased.
> param.result = agm(data=dataTest,time=timeTest,noise.sd=0.31,ode.system=LV_func,
+ numberOfParameters=4,temperMismatchParameter=TRUE,
+ chainNum=4, maxIterations=150,originalSignalOnlyPositive=TRUE,
+ logPrior="Gamma",defaultTemperingScheme="LB10")
Error in if (class(invCh) == "try-error") { :
the condition has length > 1
Calls: agm ... gpCreate -> gpExpandParam -> gpUpdateKernels -> .jitCholInv
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.0.1
Check: tests
Result: ERROR
Running 'testthat.R' [5s/8s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(deGradInfer)
>
> test_check("deGradInfer")
[ FAIL 1 | WARN 0 | SKIP 4 | PASS 2 ]
== Skipped tests ===============================================================
* On CRAN (4)
== Failed tests ================================================================
-- Error (test_likelihood_improvement.R:22:1): (code run outside of `test_that()`) --
Error in `if (class(invCh) == "try-error") {
return(NaN)
} else {
invM <- invCh %*% t(invCh)
if (jitter == 0) {
ans <- list(invM = invM, jitter = jitter, chol = Ch)
}
else ans <- list(invM = invM, jitM = M + jitter * eyeM, jitter = jitter,
chol = Ch)
return(ans)
}`: the condition has length > 1
Backtrace:
x
1. \-deGradInfer::agm(...) at test_likelihood_improvement.R:22:0
2. \-deGradInfer:::doMCMC(time, dataset, auxVars, options)
3. \-deGradInfer:::setupChains(timePoints, data, auxVars, options)
4. \-deGradInfer:::fitGP(...)
5. \-gptk::gpCreate(1, 1, time, y[, species, drop = F], options)
6. \-gptk::gpExpandParam(model, initParams)
7. \-gptk::gpUpdateKernels(model, model$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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.1
Check: re-building of vignette outputs
Result: ERROR
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
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.0.1
Check: tests
Result: ERROR
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$K_uu, silent = TRUE)
[ FAIL 1 | WARN 0 | SKIP 4 | PASS 2 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.1
Check: examples
Result: ERROR
Running examples in ‘deGradInfer-Ex.R’ failed
The error most likely occurred in:
> ### Name: agm
> ### Title: Main function for adaptive gradient matching
> ### Aliases: agm
>
> ### ** Examples
>
>
> dataTest <- LV_example_dataset$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
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-new-UL, r-devel-windows-x86_64-new-TK
Version: 1.0.1
Check: tests
Result: ERROR
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
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-new-TK
Version: 1.0.1
Check: re-building of vignette outputs
Result: ERROR
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
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-new-UL, r-devel-windows-x86_64-new-TK
Version: 1.0.1
Check: tests
Result: ERROR
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
Flavor: r-devel-windows-x86_64-new-UL