Last updated on 2026-06-14 07:54:01 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.1.1 | 69.33 | 306.48 | 375.81 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.1.1 | 44.39 | 175.31 | 219.70 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.1.1 | 94.00 | 516.75 | 610.75 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 2.1.1 | 122.00 | 525.09 | 647.09 | OK | |
| r-devel-windows-x86_64 | 2.1.1 | 78.00 | 357.00 | 435.00 | OK | |
| r-patched-linux-x86_64 | 2.1.1 | 63.60 | 293.40 | 357.00 | OK | |
| r-release-linux-x86_64 | 2.1.1 | 61.97 | 295.18 | 357.15 | OK | |
| r-release-macos-arm64 | 2.1.1 | 13.00 | 82.00 | 95.00 | OK | |
| r-release-macos-x86_64 | 2.1.1 | 7.00 | ERROR | |||
| r-release-windows-x86_64 | 2.1.1 | 78.00 | 383.00 | 461.00 | OK | |
| r-oldrel-macos-arm64 | 2.1.1 | 11.00 | 82.00 | 93.00 | OK | |
| r-oldrel-macos-x86_64 | 2.1.1 | 39.00 | 335.00 | 374.00 | OK | |
| r-oldrel-windows-x86_64 | 2.1.1 | 92.00 | 410.00 | 502.00 | OK |
Version: 2.1.1
Check: examples
Result: ERROR
Running examples in ‘LaMa-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MCreport
> ### Title: Sample parameters from approximate Gaussian posterior
> ### distribution
> ### Aliases: MCreport
>
> ### ** Examples
>
> step <- trex$step[1:1000] # subsetting trex data
> N <- 2 # 2 states
>
> # custom likelihood
> nll <- function(par) {
+ getAll(par)
+ Gamma <- tpm(eta)
+ delta <- stationary(Gamma)
+ mu <- exp(log_mu); REPORT(mu)
+ sigma <- exp(log_sigma); REPORT(sigma)
+ allprobs <- matrix(1, length(step), N)
+ for(j in 1:N) allprobs[,j] <- dgamma2(step, mu[j], sigma[j])
+ -forward(delta, Gamma, allprobs)
+ }
>
> # initial parameters in named list
> par0 <- list(eta = rep(-2,2),
+ log_mu = log(c(0.3, 1)),
+ log_sigma = log(c(0.2, 0.7)))
>
> # constructing AD object
> obj <- MakeADFun(nll, par0, silent = TRUE)
>
> # optimising
> opt <- nlminb(obj$par, obj$fn, obj$gr)
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
Warning in nlminb(obj$par, obj$fn, obj$gr) : NA/NaN function evaluation
>
> # sampling from distribution of the MLE
> samples <- MCreport(obj, nSamples = 10, report = TRUE)
Evaluating Hessian...
Warning in .local(A, ...) :
CHOLMOD warning 'matrix not positive definite' at file 'Supernodal/t_cholmod_super_numeric_worker.c', line 1114
Warning in .local(A, ...) :
CHOLMOD warning 'matrix not positive definite' at file 'Supernodal/t_cholmod_super_numeric_worker.c', line 1114
Warning in .local(A, ...) :
CHOLMOD warning 'matrix not positive definite' at file 'Supernodal/t_cholmod_super_numeric_worker.c', line 1114
Warning in .local(A, ...) :
CHOLMOD warning 'matrix not positive definite' at file 'Supernodal/t_cholmod_super_numeric_worker.c', line 1114
Warning in .local(A, ...) :
CHOLMOD warning 'matrix not positive definite' at file 'Supernodal/t_cholmod_super_numeric_worker.c', line 1114
Warning in .local(A, ...) :
CHOLMOD warning 'matrix not positive definite' at file 'Supernodal/t_cholmod_super_numeric_worker.c', line 1114
Warning in .local(A, ...) :
CHOLMOD warning 'matrix not positive definite' at file 'Supernodal/t_cholmod_super_numeric_worker.c', line 1114
Warning in .local(A, ...) :
CHOLMOD warning 'matrix not positive definite' at file 'Supernodal/t_cholmod_super_numeric_worker.c', line 1114
Warning in .local(A, ...) :
CHOLMOD warning 'matrix not positive definite' at file 'Supernodal/t_cholmod_super_numeric_worker.c', line 1114
Warning in .local(A, ...) :
CHOLMOD warning 'matrix not positive definite' at file 'Supernodal/t_cholmod_super_numeric_worker.c', line 1114
Warning in .local(A, ...) :
CHOLMOD warning 'matrix not positive definite' at file 'Supernodal/t_cholmod_super_numeric_worker.c', line 1114
Warning in .local(A, ...) :
CHOLMOD warning 'matrix not positive definite' at file 'Supernodal/t_cholmod_super_numeric_worker.c', line 1114
Warning in .local(A, ...) :
CHOLMOD warning 'matrix not positive definite' at file 'Supernodal/t_cholmod_super_numeric_worker.c', line 1114
Warning in .local(A, ...) :
CHOLMOD warning 'matrix not positive definite' at file 'Supernodal/t_cholmod_super_numeric_worker.c', line 1114
Warning in .local(A, ...) :
CHOLMOD warning 'matrix not positive definite' at file 'Supernodal/t_cholmod_super_numeric_worker.c', line 1114
Warning in .local(A, ...) :
CHOLMOD warning 'matrix not positive definite' at file 'Supernodal/t_cholmod_super_numeric_worker.c', line 1114
Warning in .local(A, ...) :
CHOLMOD warning 'matrix not positive definite' at file 'Supernodal/t_cholmod_super_numeric_worker.c', line 1114
Warning in .local(A, ...) :
CHOLMOD warning 'matrix not positive definite' at file 'Supernodal/t_cholmod_super_numeric_worker.c', line 1114
Warning in .local(A, ...) :
CHOLMOD warning 'matrix not positive definite' at file 'Supernodal/t_cholmod_super_numeric_worker.c', line 1114
Warning in .local(A, ...) :
CHOLMOD warning 'matrix not positive definite' at file 'Supernodal/t_cholmod_super_numeric_worker.c', line 1114
Warning in rgmrf(nSamples, p_hat, Q) :
Precision matrix is not PD, adding jitter...
Required 20 attempts
Error in rgmrf(nSamples, p_hat, Q) :
Matrix still not PD after 20 jitter attempts
Calls: MCreport -> <Anonymous> -> rgmrf
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Continuous_time_HMMs.Rmd’ using rmarkdown
--- finished re-building ‘Continuous_time_HMMs.Rmd’
--- re-building ‘Extensions.Rmd’ using rmarkdown
Quitting from Extensions.Rmd:262-290 [cov_visualization]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `rgmrf()`:
! Matrix still not PD after 20 jitter attempts
---
Backtrace:
▆
1. └─LaMa::MCreport(obj_cov)
2. └─RTMBdist::mcreport(...)
3. └─RTMBdist::rgmrf(nSamples, p_hat, Q)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Extensions.Rmd' failed with diagnostics:
Matrix still not PD after 20 jitter attempts
--- failed re-building ‘Extensions.Rmd’
--- re-building ‘HSMMs.Rmd’ using rmarkdown
--- finished re-building ‘HSMMs.Rmd’
--- re-building ‘Intro_to_LaMa.Rmd’ using rmarkdown
--- finished re-building ‘Intro_to_LaMa.Rmd’
--- re-building ‘LaMa_and_RTMB.Rmd’ using rmarkdown
--- finished re-building ‘LaMa_and_RTMB.Rmd’
--- re-building ‘Longitudinal_data.Rmd’ using rmarkdown
--- finished re-building ‘Longitudinal_data.Rmd’
--- re-building ‘MMMPPs.Rmd’ using rmarkdown
--- finished re-building ‘MMMPPs.Rmd’
--- re-building ‘Penalised_splines.Rmd’ using rmarkdown
--- finished re-building ‘Penalised_splines.Rmd’
--- re-building ‘State_space_models.Rmd’ using rmarkdown
--- finished re-building ‘State_space_models.Rmd’
SUMMARY: processing the following file failed:
‘Extensions.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.1.1
Check: package dependencies
Result: ERROR
Package required but not available: ‘RTMB’
Package required and available but unsuitable version: ‘RTMBdist’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-release-macos-x86_64