* using log directory 'd:/RCompile/CRANincoming/R-devel/HeckmanStan.Rcheck' * using R Under development (unstable) (2025-03-09 r87914 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'HeckmanStan/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'HeckmanStan' version '0.1.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Heeju Lim ' New submission Possibly misspelled words in DESCRIPTION: Heckman (3:8) The Title field should be in title case. Current version is: 'Heckman-selection models based on Bayesian analysis' In title case that is: 'Heckman-Selection Models Based on Bayesian Analysis' * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking serialization versions ... OK * checking whether package 'HeckmanStan' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... NOTE Author field differs from that derived from Authors@R Author: 'Heeju Lim [aut, cre, trl] (), Victor Eduardo Lachos Olivares [aut], Victor Hugo Lachos Davila [aut] ()' Authors@R: 'Heeju Lim [aut, cre, trl] (ORCID: ), Victor Eduardo Lachos Olivares [aut], Victor Hugo Lachos Davila [aut] (ORCID: )' * checking top-level files ... NOTE Non-standard file/directory found at top level: 'README.Rmd' * 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 ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... WARNING '::' or ':::' imports not declared from: 'loo' 'mvtnorm' 'rstan' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE HeckmanStan: no visible global function definition for 'sd' LaplaceDM.alg: no visible global function definition for 'HeckmanEM' LaplaceDM.alg: no visible global function definition for 'setDefaultCluster' LaplaceDM.alg: no visible global function definition for 'clusterExport' LaplaceDM.alg: no visible global function definition for 'optimParallel' LaplaceDM.alg: no visible global function definition for 'stopCluster' LaplaceDM.algN: no visible global function definition for 'HeckmanEM' LaplaceDM.algN: no visible global function definition for 'optim' geraHeckman: no visible global function definition for 'rbeta' geraHeckman: no visible global function definition for 'rgamma' geraHeckman: no visible global function definition for 'runif' likeL: no visible global function definition for 'dnorm' likeL: no visible global function definition for 'pnorm' likeLapmax: no visible global function definition for 'ghyp' likeLapmax: no visible global function definition for 'pghyp' likeLapmax: no visible global function definition for 'dghyp' likeLapmax2: no visible global function definition for 'ghyp' likeLapmax2: no visible global function definition for 'dghyp' likeLapmax2: no visible global function definition for 'pghyp' likeLmax: no visible global function definition for 'dnorm' likeLmax: no visible global function definition for 'pnorm' likeLt: no visible global function definition for 'dt' likeLt: no visible global function definition for 'pt' likeLt2: no visible global function definition for 'dt' likeLt2: no visible global function definition for 'pt' liketLmax: no visible global function definition for 'dt' liketLmax: no visible global function definition for 'pt' liketLmaxnu: no visible global function definition for 'dt' liketLmaxnu: no visible global function definition for 'pt' Undefined global functions or variables: HeckmanEM clusterExport dghyp dnorm dt ghyp optim optimParallel pghyp pnorm pt rbeta rgamma runif sd setDefaultCluster stopCluster Consider adding importFrom("stats", "dnorm", "dt", "optim", "pnorm", "pt", "rbeta", "rgamma", "runif", "sd") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'HeckmanStan.Rd': \examples lines wider than 100 characters: fit.n_stan <- HeckmanStan(y, x, w, cc, family="Normal", thin = 5, chains = 1, iter = 10000, warmup = 1000) # Plots for stanfit objects : https://mc-stan.org/rstan/reference/stanfit-method-plot.html#:~:text=plotfun.%20A%20character%20string%20 ... [TRUNCATED] plot(fit.n_stan[[1]], pars=c("beta[1]","beta[2]", "gamma[1]", "gamma[2]", "gamma[3]", "rho", "sigma_e")) plot(fit.n_stan[[1]], plotfun="hist", pars=c("beta[1]","beta[2]", "gamma[1]", "gamma[2]", "gamma[3]", "rho", "sigma_e")) plot(fit.n_stan[[1]], plotfun="trace", pars=c("beta[1]","beta[2]", "gamma[1]", "gamma[2]", "gamma[3]", "rho", "sigma_e")) fit.t_stan <- HeckmanStan(y, x, w, cc, family="T", thin = 5, chains = 1, iter = 10000, warmup = 1000) ResN<- HeckmanEM(y, x, w, cc, nu = NULL, family="Normal", error = 1e-05,iter.max = 200, im=TRUE, criteria = TRUE) fit.n_stan <- HeckmanStan( y, x, w, cc, family="Normal", init=initf1, thin = 5, chains = 1, iter = 10000, warmup = 1000) print(fit.cn_stan[[1]],par=c("beta","gamma","sigma_e","sigma2", "rho","nu1","nu2","likel","EAIC","EBIC")) initf2 <- function() {list(beta=ResN$beta, gamma=ResN$gamma,sigma_e=ResN$sigma,rho=ResN$rho, nu1=0.1,nu2=0.1)} fit.cn_stan <- HeckmanStan( y, x, w, cc, family="CN", init=initf2, thin = 5, chains = 1, iter = 10000, warmup = 1000) fit.t_stan <- HeckmanStan( y, x, w, cc, family="T", init=initf3, thin = 5, chains = 1, iter = 10000, warmup = 1000) These lines will be truncated in the PDF manual. * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: 'CPO' 'LaplaceDM.alg' 'LaplaceDM.algN' 'geraHeckman' 'hpd' 'likeL' 'likeLapmax' 'likeLapmax2' 'likeLmax' 'likeLt' 'likeLt2' 'liketLmax' 'liketLmaxnu' All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... WARNING 'library' or 'require' calls not declared from: 'AER' 'HeckmanEM' 'mvtnorm' 'rstan' * checking examples ... OK * checking PDF version of manual ... [16s] OK * checking HTML version of manual ... OK * DONE Status: 3 WARNINGs, 5 NOTEs