* using log directory 'd:/Rcompile/CRANpkg/local/4.4/RISCA.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 'RISCA/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'RISCA' version '1.0.6' * 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 'RISCA' 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 ... [5s] OK * checking whether the package can be loaded with stated dependencies ... [4s] OK * checking whether the package can be unloaded cleanly ... [4s] OK * checking whether the namespace can be loaded with stated dependencies ... [4s] OK * checking whether the namespace can be unloaded cleanly ... [5s] OK * checking loading without being on the library search path ... [5s] 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 ... [43s] OK * checking Rd files ... [2s] OK * 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... [2s] OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [19s] ERROR Running examples in 'RISCA-Ex.R' failed The error most likely occurred in: > ### Name: markov.3states.rsadd > ### Title: 3-state Relative Survival Markov Model with Additive Risks > ### Aliases: markov.3states.rsadd > ### Keywords: Markov > > ### ** Examples > > # import the observed data > # (X=1 corresponds to initial state with a functioning graft, X=2 to acute rejection episode, > # X=3 to return to dialysis, X=4 to death with a functioning graft) > > data(dataDIVAT1) > > # A subgroup analysis to reduce the time needed for this example > > dataDIVAT1$id<-c(1:nrow(dataDIVAT1)) > set.seed(2) > d3<-dataDIVAT1[dataDIVAT1$id %in% sample(dataDIVAT1$id, 200, replace = FALSE),] > > # Individuals with trajectory 13 and 123 are > # censored at the time of transition into state X=3 > > d3$trajectory[d3$trajectory==13]<-1 > d3$trajectory[d3$trajectory==123]<-12 > d3$trajectory[d3$trajectory==14]<-13 > d3$trajectory[d3$trajectory==124]<-123 > > # import the expected mortality rates > > data(fr.ratetable) > > # 3-state Markov model with additive risks including one explicative variable > # (z is the delayed graft function) on all transitions. We only reduced > # the precision and the number of iteration to save time in this example, > # prefer the default values. > > markov.3states.rsadd(times1=d3$time1, times2=d3$time2, sequences=d3$trajectory, + dist=c("E","E","E"), ini.dist.12=c(8.34), + ini.dist.13=c(10.70), ini.dist.23=c(11.10), + cov.12=d3$z, init.cov.12=c(0.04), names.12=c("beta12_z"), + cov.13=d3$z, init.cov.13=c(1.04), names.13=c("beta1E_z"), + cov.23=d3$z, init.cov.23=c(0.29), names.23=c("beta2E_z"), + p.age=d3$ageR*365.24, p.sex=d3$sexR, + p.year=as.date(paste("01","01",d3$year.tx), order = "mdy"), + p.rate.table=fr.ratetable, conf.int=TRUE, + silent=FALSE, precision=0.001) Error in as.date(paste("01", "01", d3$year.tx), order = "mdy") : could not find function "as.date" Calls: markov.3states.rsadd Execution halted * checking PDF version of manual ... [24s] OK * checking HTML version of manual ... [11s] OK * DONE Status: 1 ERROR