* using log directory ‘/srv/hornik/tmp/CRAN/icenReg.Rcheck’ * using R Under development (unstable) (2024-01-12 r85803) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.6 (3) Debian flang-new version 17.0.6 (3) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘icenReg/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘icenReg’ version ‘2.0.16’ * checking CRAN incoming feasibility ... [3s/3s] Note_to_CRAN_maintainers Maintainer: ‘Clifford Anderson-Bergman ’ * 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 serialization versions ... OK * checking whether package ‘icenReg’ can be installed ... [28s/28s] OK * used C compiler: ‘Debian clang version 17.0.6 (3)’ * used C++ compiler: ‘Debian clang version 17.0.6 (3)’ * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: Fixed bug when fitting Bayesian model without covariates (regression parameter names) Cannot process chunk/lines: Condensed handling of predictor/response from formula/data Cannot process chunk/lines: Set default argument of newdata = NULL in getFitEsts for compatiability with ICcforest Cannot process chunk/lines: Removed warnings involved with "contrasts" issue in model.matrix Cannot process chunk/lines: Added warning to getFitEsts if newdata is a data.frame Cannot process chunk/lines: Fixed issue when bootstrap sample drops observations with only one covariate Cannot process chunk/lines: Fixed issue with lnorm distribution Cannot process chunk/lines: Fixed contrast warning Cannot process chunk/lines: Fixed bug when fitting Bayesian model without covariates Cannot process chunk/lines: Changed C++ PI to M_PI at Dirk's request Cannot process chunk/lines: Added ir_clustBoot to account for repeated measures Cannot process chunk/lines: Reduced run time for survCIs example (switched from ic_bayes to ic_par) Cannot process chunk/lines: Allows for weights in ic_np Cannot process chunk/lines: Allows `plot_legend = F` for ic_npList Cannot process chunk/lines: Fixed bug with linear predictor being offset pointed out by Ferenci Tamas Cannot process chunk/lines: Added JSS citation Cannot process chunk/lines: Fixed bug in NAs being mishandled Cannot process chunk/lines: Fixed bug with expanding splines Cannot process chunk/lines: Offset covariates to have mean 0 for faster computation Cannot process chunk/lines: Fixed bug regarding releveling with a single covariate with only two levels inside formula Cannot process chunk/lines: Internal changes to plotting Cannot process chunk/lines: Allowed p OR q to be supplied to survCIs Cannot process chunk/lines: Allowed MCMC chains to be run in parallel Cannot process chunk/lines: Fixed rownames bug for imputeCens when imputeType = ‘median’ Cannot process chunk/lines: Fixed open/closed interval bug pointed out by Dr Bogaerts Cannot process chunk/lines: Added sampling from posterior survival curves Cannot process chunk/lines: Added confidence intervals Cannot process chunk/lines: Added names(fit) method Cannot process chunk/lines: Added coef active binding for regression models (i.e. fit$coef is allowed) Cannot process chunk/lines: Fixed issue with fitting model with no regression parameters Cannot process chunk/lines: Reorganized code files Cannot process chunk/lines: Added Bayes models Cannot process chunk/lines: Allow for declaration of whether intervals are open or closed for Cannot process chunk/lines: ic_sp and ic_np Cannot process chunk/lines: Added simulationFunctions.R Cannot process chunk/lines: Uses Roxygen for man files Cannot process chunk/lines: Added parametric AFT models Cannot process chunk/lines: fixed bug in plot.icenRegFit regarding xlim and ylim for semiparametric model Cannot process chunk/lines: sped up ic_sp Cannot process chunk/lines: added vignette Cannot process chunk/lines: fixed show() for summary class with no covariates Cannot process chunk/lines: added ic_np for fitting NPMLE specifically (*much* faster) Cannot process chunk/lines: switched syntax from “final_llk” to “llk” for all models Cannot process chunk/lines: made plot() and lines() more user-friendly Cannot process chunk/lines: Switched to RcppEigen, rather than including static C++ library Cannot process chunk/lines: Fixed memory access issue reported by CRAN Cannot process chunk/lines: Preparing for JSS submission Cannot process chunk/lines: Removed unpublished algorithms and methods Cannot process chunk/lines: Imported method as reported by CRAN Cannot process chunk/lines: getFitEsts is much faster Cannot process chunk/lines: added predict function Cannot process chunk/lines: added imputeCens function Cannot process chunk/lines: added generalized gamma distribution to choice of parametric families Cannot process chunk/lines: added imputed cross validation Cannot process chunk/lines: added plot method for sp_curves Cannot process chunk/lines: numerically stabilized ic_sp(model = 'ph') Cannot process chunk/lines: Resolved issue of licenses and gave proper credit to the Eigen team for Cannot process chunk/lines: using their code for matrix algebra Cannot process chunk/lines: Switched to reference classes for fits, rather than lists with reassigned classes Cannot process chunk/lines: Fixed bug with getFitEsts Cannot process chunk/lines: Added methods for calculating the NPMLE (univariate or bivariate) Cannot process chunk/lines: ic_par sped up, especially for models with lots of covariates Cannot process chunk/lines: included use of cbind for response (i.e. cbind(l, u) ~…), rather than Surv(l, u, type = ‘interval’) ~ …, which is still supported Cannot process chunk/lines: Added constrained gradient ascent step to ic_sp Cannot process chunk/lines: Switched to partially numeric derivatives for ic_par, greatly speeding up calculations for models with many covariates Cannot process chunk/lines: Added dependencies to “methods” package into NAMESPACE and DESCRIPTION Cannot process chunk/lines: models allow for no covariates Cannot process chunk/lines: summary(fit) now returns a summary object rather than just printing Cannot process chunk/lines: At C++ level, switched isnan to ISNAN Cannot process chunk/lines: removed browser() call Cannot process chunk/lines: Adding “weights” options to model fits Cannot process chunk/lines: Cleaned up manual Cannot process chunk/lines: Added warning to diag_covar if incorrect yType selected Cannot process chunk/lines: Added essIncData and essIncData_small datasets Cannot process chunk/lines: Switched to analytic derivatives for ic_sp Cannot process chunk/lines: Stabilized ic_par algorithm Cannot process chunk/lines: Preprocessed covariates with PCA Cannot process chunk/lines: Fixing bugs reported by CRAN check Cannot process chunk/lines: Added fully parametric models Cannot process chunk/lines: Added diagnostic tools diag_baseline and diag_covar Cannot process chunk/lines: Switched to Active Set Algorithm for semi-parametric models Cannot process chunk/lines: Added proportional odds model Cannot process chunk/lines: At C++ level, switched to abstract class IC_OptimInfo instead of ICPH_OptimInfo Cannot process chunk/lines: Added simulation of proportional odds Cannot process chunk/lines: Stricter convergence criteria (10^-10 instead of 10^-7) Cannot process chunk/lines: Allows for bs_samples = 0 in ic_ph Cannot process chunk/lines: Allows for fitting of models with only 1 covariate Cannot process chunk/lines: Fixed bug in parameterization of imputation model Cannot process chunk/lines: Fixed bug that imputation model sometimes simulates Inf, breaking coxph Cannot process chunk/lines: Added dataset (mdata) Cannot process chunk/lines: slight modification in plot of survival curve * checking R 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 ... [11s/11s] OK * checking Rd files ... [0s/0s] NOTE checkRd: (-1) getFitEsts.Rd:27: Lost braces; missing escapes or markup? 27 | If \code{p} is provided, will return the estimated F^{-1}(p | x). If \code{q} is provided, | ^ * 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 ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [0s/0s] OK * checking data for ASCII and uncompressed saves ... 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 sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [6s/6s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [24s/24s] OK * checking PDF version of manual ... [3s/3s] 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: 2 NOTEs