* using log directory ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/bcfrailph.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.2.0-16) 14.2.0
    GNU Fortran (Debian 14.2.0-16) 14.2.0
* running under: Debian GNU/Linux trixie/sid
* 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 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 ... OK
See 'https://www.r-project.org/nosvn/R.check/r-release-linux-x86_64/bcfrailph-00install.html' for details.
* 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/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 ... [30s/41s] OK
* checking Rd files ... [0s/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 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 ... [22s/32s] OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
shrgamsp 4.983  0.007   7.739
* checking PDF version of manual ... [5s/7s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 NOTE