* using log directory 'd:/Rcompile/CRANpkg/local/4.4/bcfrailph.Rcheck' * using R version 4.4.2 (2024-10-31 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 'bcfrailph/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'bcfrailph' version '0.1.1' * package encoding: UTF-8 * 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 whether package 'bcfrailph' can be installed ... OK * checking installed package size ... OK * checking package 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 ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [2s] OK * checking whether the package can be loaded with stated dependencies ... [2s] OK * checking whether the package can be unloaded cleanly ... [2s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s] OK * checking whether the namespace can be unloaded cleanly ... [1s] OK * checking loading without being on the library search path ... [2s] 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 ... [17s] OK * checking Rd files ... [1s] NOTE checkRd: (-1) bcfrailph.Rd:35: Lost braces; missing escapes or markup? 35 | \item \code{coefficients} - {A vector of estimated Covariate coefficients.} | ^ checkRd: (-1) bcfrailph.Rd:36: Lost braces; missing escapes or markup? 36 | \item \code{frailparest} - {A vector of estimated Frailty parameters i.e. frailty variance and correlation.} | ^ checkRd: (-1) bcfrailph.Rd:37: Lost braces; missing escapes or markup? 37 | \item \code{stderr}-{A vector containing the Standard error of the Estimated parameters both covariate coefficients and frailty parameters.} | ^ checkRd: (-1) bcfrailph.Rd:42: Lost braces; missing escapes or markup? 42 | \item \code{X}-{Matrix of observed covariates.} | ^ checkRd: (-1) bcfrailph.Rd:43: Lost braces; missing escapes or markup? 43 | \item \code{time}-{the observed survival time.} | ^ checkRd: (-1) bcfrailph.Rd:44: Lost braces; missing escapes or markup? 44 | \item \code{censor}-{censoring indicator.} | ^ checkRd: (-1) bcfrailph.Rd:45: Lost braces; missing escapes or markup? 45 | \item \code{resid}-{the martingale residuals.} | ^ checkRd: (-1) bcfrailph.Rd:46: Lost braces; missing escapes or markup? 46 | \item \code{lin.prid}-{the vector of linear predictors.} | ^ checkRd: (-1) bcfrailph.Rd:47: Lost braces; missing escapes or markup? 47 | \item \code{frail}-{estimated Frailty values.} | ^ checkRd: (-1) bcfrailph.Rd:48: Lost braces; missing escapes or markup? 48 | \item \code{iteration}-{Number of outer iterations.} | ^ checkRd: (-1) bcfrailph.Rd:49: Lost braces; missing escapes or markup? 49 | \item \code{e.time}-{the vector of unique event times.} | ^ checkRd: (-1) bcfrailph.Rd:50: Lost braces; missing escapes or markup? 50 | \item \code{n.event}- {the number of events at each of the unique event times.} | ^ checkRd: (-1) bcfrailph.Rd:51: Lost braces; missing escapes or markup? 51 | \item \code{convergence}-{an indicator, 1 if converge and 0 otherwise.} | ^ checkRd: (-1) bcfrailph.Rd:52: Lost braces; missing escapes or markup? 52 | \item \code{history}-{an array containing records of estimates and other information on each iterations.} | ^ checkRd: (-1) fitbccv.gammasp.Rd:32: Lost braces; missing escapes or markup? 32 | \item \code{coefficients} - {A vector of estimated Covariate coefficients.} | ^ checkRd: (-1) fitbccv.gammasp.Rd:33: Lost braces; missing escapes or markup? 33 | \item \code{frailparest} - {A vector of estimated Frailty parameters i.e. frailty variance and correlation.} | ^ checkRd: (-1) fitbccv.gammasp.Rd:34: Lost braces; missing escapes or markup? 34 | \item \code{stderr}-{A vector containing the Standard error of the Estimated parameters both covariate coefficients and frailty parameters.} | ^ checkRd: (-1) fitbccv.gammasp.Rd:39: Lost braces; missing escapes or markup? 39 | \item \code{X}-{Matrix of observed covariates.} | ^ checkRd: (-1) fitbccv.gammasp.Rd:40: Lost braces; missing escapes or markup? 40 | \item \code{time}-{the observed survival time.} | ^ checkRd: (-1) fitbccv.gammasp.Rd:41: Lost braces; missing escapes or markup? 41 | \item \code{censor}-{censoring indicator.} | ^ checkRd: (-1) fitbccv.gammasp.Rd:42: Lost braces; missing escapes or markup? 42 | \item \code{resid}-{the martingale residuals.} | ^ checkRd: (-1) fitbccv.gammasp.Rd:43: Lost braces; missing escapes or markup? 43 | \item \code{lin.prid}-{the vector of linear predictors.} | ^ checkRd: (-1) fitbccv.gammasp.Rd:44: Lost braces; missing escapes or markup? 44 | \item \code{frail}-{estimated Frailty values.} | ^ checkRd: (-1) fitbccv.gammasp.Rd:45: Lost braces; missing escapes or markup? 45 | \item \code{iteration}-{Number of outer iterations.} | ^ checkRd: (-1) fitbccv.gammasp.Rd:46: Lost braces; missing escapes or markup? 46 | \item \code{e.time}-{the vector of unique event times.} | ^ checkRd: (-1) fitbccv.gammasp.Rd:47: Lost braces; missing escapes or markup? 47 | \item \code{n.event}- {the number of events at each of the unique event times.} | ^ checkRd: (-1) fitbccv.gammasp.Rd:48: Lost braces; missing escapes or markup? 48 | \item \code{convergence}-{an indicator, 1 if converge and 0 otherwise.} | ^ checkRd: (-1) fitbccv.gammasp.Rd:49: Lost braces; missing escapes or markup? 49 | \item \code{history}-{an array containing records of estimates and other information on each iterations.} | ^ checkRd: (-1) fitbccv.lognsp.Rd:21: Lost braces; missing escapes or markup? 21 | \item \code{coefficients} - {A vector of estimated Covariate coefficients.} | ^ checkRd: (-1) fitbccv.lognsp.Rd:22: Lost braces; missing escapes or markup? 22 | \item \code{frailparest} - {A vector of estimated Frailty parameters i.e. frailty variance and correlation.} | ^ checkRd: (-1) fitbccv.lognsp.Rd:23: Lost braces; missing escapes or markup? 23 | \item \code{stderr}-{A vector containing the Standard error of the Estimated parameters both covariate coefficients and frailty parameters.} | ^ checkRd: (-1) fitbccv.lognsp.Rd:28: Lost braces; missing escapes or markup? 28 | \item \code{X}-{Matrix of observed covariates.} | ^ checkRd: (-1) fitbccv.lognsp.Rd:29: Lost braces; missing escapes or markup? 29 | \item \code{time}-{the observed survival time.} | ^ checkRd: (-1) fitbccv.lognsp.Rd:30: Lost braces; missing escapes or markup? 30 | \item \code{censor}-{censoring indicator.} | ^ checkRd: (-1) fitbccv.lognsp.Rd:31: Lost braces; missing escapes or markup? 31 | \item \code{resid}-{the martingale residuals.} | ^ checkRd: (-1) fitbccv.lognsp.Rd:32: Lost braces; missing escapes or markup? 32 | \item \code{lin.prid}-{the vector of linear predictors.} | ^ checkRd: (-1) fitbccv.lognsp.Rd:33: Lost braces; missing escapes or markup? 33 | \item \code{frail}-{estimated Frailty values.} | ^ checkRd: (-1) fitbccv.lognsp.Rd:34: Lost braces; missing escapes or markup? 34 | \item \code{iteration}-{Number of outer iterations.} | ^ checkRd: (-1) fitbccv.lognsp.Rd:35: Lost braces; missing escapes or markup? 35 | \item \code{e.time}-{the vector of unique event times.} | ^ checkRd: (-1) fitbccv.lognsp.Rd:36: Lost braces; missing escapes or markup? 36 | \item \code{n.event}- {the number of events at each of the unique event times.} | ^ checkRd: (-1) fitbccv.lognsp.Rd:37: Lost braces; missing escapes or markup? 37 | \item \code{convergence}-{an indicator, 1 if converge and 0 otherwise.} | ^ checkRd: (-1) fitbccv.lognsp.Rd:38: Lost braces; missing escapes or markup? 38 | \item \code{history}-{an array containing records of estimates and other information on each iterations.} | ^ checkRd: (-1) shrgamsp.Rd:32: Lost braces; missing escapes or markup? 32 | \item \code{coefficients} - {A vector of estimated Covariate coefficients.} | ^ checkRd: (-1) shrgamsp.Rd:33: Lost braces; missing escapes or markup? 33 | \item \code{frailparest} - {A vector of estimated Frailty parameters i.e. frailty variance and correlation.} | ^ checkRd: (-1) shrgamsp.Rd:34: Lost braces; missing escapes or markup? 34 | \item \code{vcov}- {Variance Covariance matrix of the Estimated Covariate coefficients obtained from the observed information matrix.} | ^ checkRd: (-1) shrgamsp.Rd:35: Lost braces; missing escapes or markup? 35 | \item \code{stderr}-{A vector containing the Standard error of the Estimated parameters both covariate coefficients and frailty parameter.} | ^ checkRd: (-1) shrgamsp.Rd:40: Lost braces; missing escapes or markup? 40 | \item \code{X}-{Matrix of observed covariates.} | ^ checkRd: (-1) shrgamsp.Rd:41: Lost braces; missing escapes or markup? 41 | \item \code{time}-{the observed survival time.} | ^ checkRd: (-1) shrgamsp.Rd:42: Lost braces; missing escapes or markup? 42 | \item \code{censor}-{censoring indicator.} | ^ checkRd: (-1) shrgamsp.Rd:43: Lost braces; missing escapes or markup? 43 | \item \code{resid}-{the martingale residuals.} | ^ checkRd: (-1) shrgamsp.Rd:44: Lost braces; missing escapes or markup? 44 | \item \code{lin.prid}-{the vector of linear predictors.} | ^ checkRd: (-1) shrgamsp.Rd:45: Lost braces; missing escapes or markup? 45 | \item \code{frail}-{estimated Frailty values.} | ^ checkRd: (-1) shrgamsp.Rd:46: Lost braces; missing escapes or markup? 46 | \item \code{iteration}-{Number of outer iterations.} | ^ checkRd: (-1) shrgamsp.Rd:47: Lost braces; missing escapes or markup? 47 | \item \code{e.time}-{the vector of unique event times.} | ^ checkRd: (-1) shrgamsp.Rd:48: Lost braces; missing escapes or markup? 48 | \item \code{n.event}- {the number of events at each of the unique event times.} | ^ checkRd: (-1) shrgamsp.Rd:49: Lost braces 49 | \item \code{convergence}-{an indicator of convergence . see \code{\link{nlminb}}.} | ^ checkRd: (-1) simbcfrailph.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) simbcfrailph.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) simbcfrailph.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) simbcfrailph.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) simbcfrailph.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) simbcfrailph.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) simbcfrailph.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) simstdybcf.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) simstdybcf.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) simstdybcf.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) simstdybcf.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) simstdybcf.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) simstdybcf.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) simstdybcf.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly * checking Rd metadata ... 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 examples ... [20s] OK * checking PDF version of manual ... [20s] OK * checking HTML version of manual ... [3s] OK * DONE Status: 1 NOTE