• using R Under development (unstable) (2024-12-05 r87423)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (GCC) 14.2.0     GNU Fortran (GCC) 14.2.0
• running under: Fedora Linux 36 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• 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 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 ‘bcfrailph’ can be installed ... [23s/33s] OK See the install log for details.
• 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 ... 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 ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [45s/63s] OK
• checking Rd files ... 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 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 examples ... [37s/54s] OK
• checking PDF version of manual ... [7s/13s] OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 NOTE