* using log directory ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/bcfrailphdv.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 ‘bcfrailphdv/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bcfrailphdv’ 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 ‘bcfrailphdv’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-release-linux-x86_64/bcfrailphdv-00install.html' for details.
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
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* 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
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* 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 ... [54s/67s] OK
* checking Rd files ... [0s/0s] NOTE
checkRd: (-1) bcfraildv.Rd:35: Lost braces; missing escapes or markup?
    35 |   \item \code{coefficients} - {A vector of estimated Covariate coefficients.}
       |                               ^
checkRd: (-1) bcfraildv.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) bcfraildv.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) bcfraildv.Rd:42: Lost braces; missing escapes or markup?
    42 |   \item \code{X}-{Matrix of observed covariates.}
       |                  ^
checkRd: (-1) bcfraildv.Rd:43: Lost braces; missing escapes or markup?
    43 |   \item \code{time}-{the observed survival time.}
       |                     ^
checkRd: (-1) bcfraildv.Rd:44: Lost braces; missing escapes or markup?
    44 |   \item \code{censor}-{censoring indicator.}
       |                       ^
checkRd: (-1) bcfraildv.Rd:45: Lost braces; missing escapes or markup?
    45 |   \item \code{resid}-{the martingale residuals.}
       |                      ^
checkRd: (-1) bcfraildv.Rd:46: Lost braces; missing escapes or markup?
    46 |   \item \code{lin.prid}-{the vector of linear predictors.}
       |                         ^
checkRd: (-1) bcfraildv.Rd:47: Lost braces; missing escapes or markup?
    47 |   \item \code{frail}-{estimated Frailty values.}
       |                      ^
checkRd: (-1) bcfraildv.Rd:48: Lost braces; missing escapes or markup?
    48 |   \item \code{iteration}-{Number of outer iterations.}
       |                          ^
checkRd: (-1) bcfraildv.Rd:49: Lost braces; missing escapes or markup?
    49 |   \item \code{e.time}-{the vector of unique event times.}
       |                       ^
checkRd: (-1) bcfraildv.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) bcfraildv.Rd:51: Lost braces; missing escapes or markup?
    51 |   \item \code{convergence}-{an indicator, 0 if converge and 1 otherwise.}
       |                            ^
checkRd: (-1) bcfrailpar.Rd:41: Lost braces; missing escapes or markup?
    41 |   \item \code{coefficients} - {A vector of estimated Covariate coefficients.}
       |                               ^
checkRd: (-1) bcfrailpar.Rd:42: Lost braces; missing escapes or markup?
    42 |   \item \code{frailparest} - {A vector of estimated Frailty parameters i.e. frailty variance and correlation.}
       |                              ^
checkRd: (-1) bcfrailpar.Rd:43: Lost braces; missing escapes or markup?
    43 |   \item \code{basehazpar} - {A vector of estimated baseline hazard parameters i.e. scale and shape.}
       |                             ^
checkRd: (-1) bcfrailpar.Rd:44: Lost braces; missing escapes or markup?
    44 |   \item \code{stderr}-{A vector containing the Standard errors of the Estimated parameters with the order of frailty parameters,baseline hazard parameters and covariate coefficients.}
       |                       ^
checkRd: (-1) bcfrailpar.Rd:45: Lost braces; missing escapes or markup?
    45 |   \item \code{vcov}- {Variance Covariance matrix of the Estimated parameters.}
       |                      ^
checkRd: (-1) bcfrailpar.Rd:46: Lost braces; missing escapes or markup?
    46 |   \item \code{loglik}-{Log likelihood of the model.}
       |                       ^
checkRd: (-1) bcfrailpar.Rd:47: Lost braces; missing escapes or markup?
    47 |   \item \code{AIC}-{AIC of the model.}
       |                    ^
checkRd: (-1) bcfrailpar.Rd:48: Lost braces; missing escapes or markup?
    48 |   \item \code{BIC}-{BIC of the model.}
       |                    ^
checkRd: (-1) bcfrailpar.Rd:49: Lost braces
    49 |   \item \code{iterations}-{Number of outer iterations.See\link{constrOptim} for further.}
       |                           ^
checkRd: (-1) bcfrailpar.Rd:50: Lost braces
    50 |   \item \code{convergence}-{An indicator of convergence. See\link{constrOptim} for further.}
       |                            ^
checkRd: (-1) simbcfraildv.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simbcfraildv.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simbcfraildv.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simbcfraildv.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simbcfraildv.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
* checking Rd metadata ... OK
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* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
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* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... [16s/25s] OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
bcfraildv         4.524  0.106   6.841
summary.bcfraildv 4.304  0.016   6.856
print.bcfraildv   4.191  0.007   6.386
* checking PDF version of manual ... [5s/9s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 NOTE