CRAN Package Check Results for Package LaMa

Last updated on 2026-06-14 07:54:01 CEST.

Check Details

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