* using log directory ‘/srv/hornik/tmp/CRAN/hhsmm.Rcheck’ * using R Under development (unstable) (2024-04-29 r86495) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.6 (5) Debian flang-new version 17.0.6 (5) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘hhsmm/DESCRIPTION’ ... OK * this is package ‘hhsmm’ version ‘0.3.7’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/5s] NOTE Maintainer: ‘Morteza Amini ’ The Description field contains its arxiv version: ). Please refer to arXiv e-prints via their arXiv DOI . * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘hhsmm’ can be installed ... [8s/8s] OK * used C compiler: ‘Debian clang version 17.0.6 (11)’ * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [14s/14s] OK * checking Rd files ... [0s/0s] NOTE checkRd: (-1) additive_reg_mstep.Rd:20: Lost braces 20 | \item \code{K}{ the degrees of freedom for the B-spline, default is \code{K=5}} | ^ checkRd: (-1) additive_reg_mstep.Rd:21: Lost braces 21 | \item \code{lambda0}{ the initial value of the smoothing parameter, default is \code{lambda0=0.01}} | ^ checkRd: (-1) additive_reg_mstep.Rd:22-24: Lost braces 22 | \item \code{resp.ind}{ a vector of the column numbers of \code{x} which contain response variables. | ^ checkRd: (-1) cov.miss.mix.wt.Rd:38: Lost braces 38 | \item \code{"unbiased"}{ the unbiased estimator is given} | ^ checkRd: (-1) cov.miss.mix.wt.Rd:39: Lost braces 39 | \item \code{"ML"}{ the maximum likelihood estimator is given} | ^ checkRd: (-1) cov.miss.mix.wt.Rd:45: Lost braces 45 | \item \code{center}{ the weighted mean of \code{x}} | ^ checkRd: (-1) cov.miss.mix.wt.Rd:46: Lost braces 46 | \item \code{cov}{ the weighted covariance of \code{x}} | ^ checkRd: (-1) cov.miss.mix.wt.Rd:47: Lost braces 47 | \item \code{n.obs}{ the number of observations in \code{x}} | ^ checkRd: (-1) cov.miss.mix.wt.Rd:48-49: Lost braces 48 | \item \code{cor}{ the weighted correlation of \code{x}, | ^ checkRd: (-1) cov.miss.mix.wt.Rd:50: Lost braces 50 | \item \code{wt1}{ the state weighs \code{wt1}} | ^ checkRd: (-1) cov.miss.mix.wt.Rd:51: Lost braces 51 | \item \code{wt2}{ the mixture component weights \code{wt2}} | ^ checkRd: (-1) cov.miss.mix.wt.Rd:52: Lost braces 52 | \item \code{pmix}{ the estimated mixture proportions} | ^ checkRd: (-1) cov.mix.wt.Rd:32: Lost braces 32 | \item \code{"unbiased"}{ the unbiased estimator is given} | ^ checkRd: (-1) cov.mix.wt.Rd:33: Lost braces 33 | \item \code{"ML"}{ the maximum likelihood estimator is given} | ^ checkRd: (-1) cov.mix.wt.Rd:39: Lost braces 39 | \item \code{center}{ the weighted mean of \code{x}} | ^ checkRd: (-1) cov.mix.wt.Rd:40: Lost braces 40 | \item \code{cov}{ the weighted covariance of \code{x}} | ^ checkRd: (-1) cov.mix.wt.Rd:41: Lost braces 41 | \item \code{n.obs}{ the number of observations in \code{x}} | ^ checkRd: (-1) cov.mix.wt.Rd:42-43: Lost braces 42 | \item \code{cor}{ the weighted correlation of \code{x}, | ^ checkRd: (-1) cov.mix.wt.Rd:44: Lost braces 44 | \item \code{wt1}{ the state weighs \code{wt1}} | ^ checkRd: (-1) cov.mix.wt.Rd:45: Lost braces 45 | \item \code{wt2}{ the mixture component weights \code{wt2}} | ^ checkRd: (-1) cov.mix.wt.Rd:46: Lost braces 46 | \item \code{pmix}{ the estimated mixture proportions} | ^ checkRd: (-1) dnorm_additive_reg.Rd:21: Lost braces 21 | \item \code{K}{ the degrees of freedom for the B-spline, default is \code{K=5}} | ^ checkRd: (-1) dnorm_additive_reg.Rd:22-24: Lost braces 22 | \item \code{resp.ind}{ a vector of the column numbers of \code{x} which contain response variables. | ^ checkRd: (-1) hhsmmfit.Rd:31: Lost braces 31 | \item \code{maxit}{ the maximum number of iterations for the EM algorithm} | ^ checkRd: (-1) hhsmmfit.Rd:32: Lost braces 32 | \item \code{lock.transition}{ logical. if TRUE the transition matrix will not be updated through the EM algorithm} | ^ checkRd: (-1) hhsmmfit.Rd:33: Lost braces 33 | \item \code{lock.d}{ logical. if TRUE the sojourn probability matrix d will not be updated through the EM algorithm} | ^ checkRd: (-1) hhsmmfit.Rd:34: Lost braces 34 | \item \code{lock.init}{ logical. if TRUE the initial probability vector will not be updated through the EM algorithm} | ^ checkRd: (-1) hhsmmfit.Rd:35: Lost braces 35 | \item \code{graphical}{ logical. if TRUE a plot of the sojourn probabilities will be plotted through the EM algorithm} | ^ checkRd: (-1) hhsmmfit.Rd:36: Lost braces 36 | \item \code{verbose}{ logical. if TRUE the outputs will be printed} | ^ checkRd: (-1) hhsmmfit.Rd:42: Lost braces 42 | \item \code{loglike}{ the log-likelihood of the fitted model} | ^ checkRd: (-1) hhsmmfit.Rd:43: Lost braces 43 | \item \code{AIC}{ the Akaike information criterion of the fitted model} | ^ checkRd: (-1) hhsmmfit.Rd:44: Lost braces 44 | \item \code{BIC}{ the Bayesian information criterion of the fitted model} | ^ checkRd: (-1) hhsmmfit.Rd:45: Lost braces 45 | \item \code{model}{ the fitted model} | ^ checkRd: (-1) hhsmmfit.Rd:46: Lost braces 46 | \item \code{estep_variables}{ the E step (forward-backward) probabilities of the final iteration of the EM algorithm} | ^ checkRd: (-1) hhsmmfit.Rd:47: Lost braces 47 | \item \code{M}{ the maximum duration in each state} | ^ checkRd: (-1) hhsmmfit.Rd:48: Lost braces 48 | \item \code{J}{ the number of states} | ^ checkRd: (-1) hhsmmfit.Rd:49: Lost braces 49 | \item \code{NN}{ the vector of sequence lengths} | ^ checkRd: (-1) hhsmmfit.Rd:50: Lost braces 50 | \item \code{f}{ the emission probability density function} | ^ checkRd: (-1) hhsmmfit.Rd:51: Lost braces 51 | \item \code{mstep}{ the M step function of the EM algorithm} | ^ checkRd: (-1) hhsmmfit.Rd:52: Lost braces 52 | \item \code{yhat}{ the estimated sequence of states} | ^ checkRd: (-1) initial_cluster.Rd:52: Lost braces 52 | \item \code{clust.X}{ a list of clustered observations for each sequence and state} | ^ checkRd: (-1) initial_cluster.Rd:53: Lost braces 53 | \item \code{mix.clus}{ a list of the clusters for the mixtures for each state} | ^ checkRd: (-1) initial_cluster.Rd:54: Lost braces 54 | \item \code{state.clus}{ the exact state clusters of each observation (available if \code{ltr}=FALSE)} | ^ checkRd: (-1) initial_cluster.Rd:55: Lost braces 55 | \item \code{nmix}{ the number of mixture components (a vector of positive (non-zero) integers of length \code{nstate})} | ^ checkRd: (-1) initial_cluster.Rd:56: Lost braces 56 | \item \code{ltr}{ logical. if TRUE a left to right hidden hybrid Markov/semi-Markov model is assumed} | ^ checkRd: (-1) initial_cluster.Rd:57: Lost braces 57 | \item \code{final.absorb}{ logical. if TRUE the final state of the sequence is assumed to be the absorbance state} | ^ checkRd: (-1) initial_cluster.Rd:58-59: Lost braces 58 | \item \code{miss}{ logical. if TRUE the \code{train$x} matrix contains missing | ^ checkRd: (-1) initial_estimate.Rd:21: Lost braces 21 | \item \code{emission}{ list the estimated parameterers of the emission distribution} | ^ checkRd: (-1) initial_estimate.Rd:22: Lost braces 22 | \item \code{leng}{ list of waiting times in each state for each sequence} | ^ checkRd: (-1) initial_estimate.Rd:23: Lost braces 23 | \item \code{clusters}{ the exact clusters of each observation (available if \code{ltr}=FALSE)} | ^ checkRd: (-1) initial_estimate.Rd:24: Lost braces 24 | \item \code{nmix}{ the number of mixture components (a vector of positive (non-zero) integers of length \code{nstate})} | ^ checkRd: (-1) initial_estimate.Rd:25: Lost braces 25 | \item \code{ltr}{ logical. if TRUE a left to right hidden hybrid Markovian/semi-Markovianmodel is assumed} | ^ checkRd: (-1) initialize_model.Rd:31: Lost braces 31 | \item \code{"nonparametric"}{ non-parametric sojourn distribution} | ^ checkRd: (-1) initialize_model.Rd:32: Lost braces 32 | \item \code{"nbinom"}{ negative binomial sojourn distribution} | ^ checkRd: (-1) initialize_model.Rd:33: Lost braces 33 | \item \code{"logarithmic"}{ logarithmic sojourn distribution} | ^ checkRd: (-1) initialize_model.Rd:34: Lost braces 34 | \item \code{"poisson"}{ poisson sojourn distribution} | ^ checkRd: (-1) initialize_model.Rd:35: Lost braces 35 | \item \code{"gamma"}{ gamma sojourn distribution} | ^ checkRd: (-1) initialize_model.Rd:36: Lost braces 36 | \item \code{"weibull"}{ weibull sojourn distribution} | ^ checkRd: (-1) initialize_model.Rd:37: Lost braces 37 | \item \code{"lnorm"}{ log-normal sojourn distribution} | ^ checkRd: (-1) initialize_model.Rd:38: Lost braces 38 | \item \code{"auto"}{automatic determination of the sojourn distribution using the chi-square test} | ^ checkRd: (-1) initialize_model.Rd:46-47: Lost braces 46 | \item \code{NULL}{ if \code{ltr}=TRUE then \code{semi = c(rep(TRUE,nstate-1),FALSE)}, else | ^ checkRd: (-1) initialize_model.Rd:60: Lost braces 60 | \item \code{init}{ initial probabilities of states} | ^ checkRd: (-1) initialize_model.Rd:61: Lost braces 61 | \item \code{transition}{ transition matrix} | ^ checkRd: (-1) initialize_model.Rd:62: Lost braces 62 | \item \code{parms.emission}{ parameters of the mixture normal emission (\code{mu}, \code{sigma}, \code{mix.p})} | ^ checkRd: (-1) initialize_model.Rd:63: Lost braces 63 | \item \code{sojourn}{ list of sojourn time distribution parameters and its \code{type}} | ^ checkRd: (-1) initialize_model.Rd:64: Lost braces 64 | \item \code{dens.emission}{ the emission probability density function} | ^ checkRd: (-1) initialize_model.Rd:65: Lost braces 65 | \item \code{mstep}{ the M step function of the EM algorithm} | ^ checkRd: (-1) initialize_model.Rd:66: Lost braces 66 | \item \code{semi}{ a logical vector of length nstate with the TRUE associated states are considered as semi-Markovian} | ^ checkRd: (-1) make_model.Rd:28-29: Lost braces 28 | \item \code{NULL}{ if \code{ltr}=TRUE then \code{semi = c(rep(TRUE,nstate-1),FALSE)}, else | ^ checkRd: (-1) make_model.Rd:36: Lost braces 36 | \item \code{"nonparametric"}{ non-parametric sojourn distribution} | ^ checkRd: (-1) make_model.Rd:37: Lost braces 37 | \item \code{"nbinom"}{ negative binomial sojourn distribution} | ^ checkRd: (-1) make_model.Rd:38: Lost braces 38 | \item \code{"logarithmic"}{ logarithmic sojourn distribution} | ^ checkRd: (-1) make_model.Rd:39: Lost braces 39 | \item \code{"poisson"}{ poisson sojourn distribution} | ^ checkRd: (-1) make_model.Rd:40: Lost braces 40 | \item \code{"gamma"}{ gamma sojourn distribution} | ^ checkRd: (-1) make_model.Rd:41: Lost braces 41 | \item \code{"weibull"}{ weibull sojourn distribution} | ^ checkRd: (-1) make_model.Rd:42: Lost braces 42 | \item \code{"lnorm"}{ log-normal sojourn distribution} | ^ checkRd: (-1) make_model.Rd:43: Lost braces 43 | \item \code{"auto"}{ automatic determination of the sojourn distribution using the chi-square test} | ^ checkRd: (-1) make_model.Rd:49: Lost braces 49 | \item \code{init}{ initial probabilities of states} | ^ checkRd: (-1) make_model.Rd:50: Lost braces 50 | \item \code{transition}{ transition matrix} | ^ checkRd: (-1) make_model.Rd:51: Lost braces 51 | \item \code{parms.emission}{ parameters of the mixture normal emission (\code{mu}, \code{sigma}, \code{mix.p})} | ^ checkRd: (-1) make_model.Rd:52: Lost braces 52 | \item \code{sojourn}{ list of sojourn distribution parameters and its \code{type}} | ^ checkRd: (-1) make_model.Rd:53: Lost braces 53 | \item \code{dens.emission}{ the emission probability density function} | ^ checkRd: (-1) make_model.Rd:54: Lost braces 54 | \item \code{mstep}{ the M step function of the EM algorithm} | ^ checkRd: (-1) make_model.Rd:55: Lost braces 55 | \item \code{semi}{ a logical vector of length nstate with the TRUE associated states are considered as semi-Markovian} | ^ checkRd: (-1) nonpar_mstep.Rd:20: Lost braces 20 | \item \code{K}{ the degrees of freedom for the B-spline, default is \code{K=5}} | ^ checkRd: (-1) nonpar_mstep.Rd:21: Lost braces 21 | \item \code{lambda0}{ the initial value of the smoothing parameter, default is \code{lambda0=0.5}} | ^ checkRd: (-1) predict.hhsmm.Rd:28: Lost braces 28 | \item \code{"viterbi"}{ (default) uses the Viterbi algorithm for prediction} | ^ checkRd: (-1) predict.hhsmm.Rd:29: Lost braces 29 | \item \code{"smoothing"}{ uses the smoothing algorithm for prediction} | ^ checkRd: (-1) predict.hhsmm.Rd:37-38: Lost braces 37 | \item \code{"max"}{ (default) the maximum probability as the point predict and the high probability critical | ^ checkRd: (-1) predict.hhsmm.Rd:39-40: Lost braces 39 | \item \code{"mean"}{ the mean value as the point predict and the normal confidence lower and upper bounds as the | ^ checkRd: (-1) predict.hhsmm.Rd:50: Lost braces 50 | \item \code{x}{ the observation sequence} | ^ checkRd: (-1) predict.hhsmm.Rd:51: Lost braces 51 | \item \code{s}{ the predicted state sequence} | ^ checkRd: (-1) predict.hhsmm.Rd:52: Lost braces 52 | \item \code{N}{ the vector of sequence lengths} | ^ checkRd: (-1) predict.hhsmm.Rd:53: Lost braces 53 | \item \code{p}{ the state probabilities } | ^ checkRd: (-1) predict.hhsmm.Rd:54: Lost braces 54 | \item \code{RUL}{ the point predicts of the RUL} | ^ checkRd: (-1) predict.hhsmm.Rd:55: Lost braces 55 | \item \code{RUL.low}{ the lower bounds for the prediction intervals of the RUL} | ^ checkRd: (-1) predict.hhsmm.Rd:56: Lost braces 56 | \item \code{RUL.up}{ the upper bounds for the prediction intervals of the RUL} | ^ checkRd: (-1) predict.hhsmmspec.Rd:16: Lost braces 16 | \item \code{"viterbi"}{ (default) uses the Viterbi algorithm for prediction} | ^ checkRd: (-1) predict.hhsmmspec.Rd:17: Lost braces 17 | \item \code{"smoothing"}{ uses the smoothing algorithm for prediction} | ^ checkRd: (-1) predict.hhsmmspec.Rd:27: Lost braces 27 | \item \code{x}{ the observation sequence} | ^ checkRd: (-1) predict.hhsmmspec.Rd:28: Lost braces 28 | \item \code{s}{ the predicted state sequence} | ^ checkRd: (-1) predict.hhsmmspec.Rd:29: Lost braces 29 | \item \code{N}{ the vector of sequence lengths} | ^ checkRd: (-1) predict.hhsmmspec.Rd:30: Lost braces 30 | \item \code{p}{ the state probabilities } | ^ checkRd: (-1) predict.hhsmmspec.Rd:31: Lost braces 31 | \item \code{RUL}{ the point predicts of the RUL} | ^ checkRd: (-1) predict.hhsmmspec.Rd:32: Lost braces 32 | \item \code{RUL.low}{ the lower bounds for the prediction intervals of the RUL} | ^ checkRd: (-1) predict.hhsmmspec.Rd:33: Lost braces 33 | \item \code{RUL.up}{ the upper bounds for the prediction intervals of the RUL} | ^ checkRd: (-1) raddreg.Rd:16: Lost braces 16 | \item \code{mean}{ the mean vector of covariates (to be generated from multivariate normal distribution)} | ^ checkRd: (-1) raddreg.Rd:17: Lost braces 17 | \item \code{cov}{ the variance-covariance matrix of covariates (to be generated from multivariate normal distribution)} | ^ checkRd: (-1) rmixlm.Rd:16: Lost braces 16 | \item \code{mean}{ the mean vector of covariates (to be generated from multivariate normal distribution)} | ^ checkRd: (-1) rmixlm.Rd:17: Lost braces 17 | \item \code{cov}{ the variance-covariance matrix of covariates (to be generated from multivariate normal distribution)} | ^ checkRd: (-1) simulate.hhsmmspec.Rd:31-32: Lost braces 31 | \item \code{autoregress}{ logical. if TRUE the auto-regressive data generation will be considered with | ^ checkRd: (-1) simulate.hhsmmspec.Rd:33-34: Lost braces 33 | \item \code{lags}{ a positive integer which is the number of lags to be considered for the | ^ checkRd: (-1) simulate.hhsmmspec.Rd:35-39: Lost braces 35 | \item \code{start}{ a list containing the items \code{mean} which is the mean vector | ^ checkRd: (-1) simulate.hhsmmspec.Rd:45: Lost braces 45 | \item \code{s}{ the vector of states} | ^ checkRd: (-1) simulate.hhsmmspec.Rd:46: Lost braces 46 | \item \code{x}{ observation matrix} | ^ checkRd: (-1) simulate.hhsmmspec.Rd:47: Lost braces 47 | \item\code{N}{ vector of sequence lengths} | ^ checkRd: (-1) train_test_split.Rd:25: Lost braces 25 | \item\code{train}{ the randomly selected subset of train data of class \code{"hhsmmdata"}} | ^ checkRd: (-1) train_test_split.Rd:26: Lost braces 26 | \item\code{test}{ the randomly selected subset of test data of class \code{"hhsmmdata"}} | ^ checkRd: (-1) train_test_split.Rd:27: Lost braces 27 | \item\code{trimmed}{ right trimmed test subset, if \code{trim}=TRUE, with trim ratios equal to \code{trim.ratio} } | ^ checkRd: (-1) train_test_split.Rd:28: Lost braces 28 | \item\code{trimmed.count}{ the number of right trimmed individuals in each sequence of the test subset, if \code{trim}=TRUE } | ^ * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'score.Rd': score Code: function(xnew, fit, ...) Docs: function(xnew, fit) Argument names in code not in docs: ... * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking examples ... [23s/23s] OK * checking PDF version of manual ... [4s/4s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 WARNING, 2 NOTEs