* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/bcfrailph.Rcheck’ * using R Under development (unstable) (2026-02-08 r89381) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) * running under: Fedora Linux 40 (Workstation Edition) * using session charset: UTF-8 * current time: 2026-02-08 10:19:52 UTC * checking for file ‘bcfrailph/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘bcfrailph’ version ‘0.1.2’ * 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 ... 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ERROR Running examples in ‘bcfrailph-Ex.R’ failed The error most likely occurred in: > ### Name: bcfrailph > ### Title: Semi-parametric bivariate correlated frailty model. > ### Aliases: bcfrailph > > ### ** Examples > > set.seed(4) > simdata<-simbcfrail(psize=300, cenr= c(0.3),beta=c(2),frailty=c("gamma"), + frailpar=c(0.5,0.5),bhaz=c("weibull"), + bhazpar=list(shape =c(5), scale = c(0.1)), + covartype= c("B"),covarpar=list(fargs=c(1),sargs=c(0.5))) > dataa<-simdata$data > > fitbcfrgam=bcfrailph(Surv(time,censor)~ X1+frailty(PID) ,data=dataa,frailty="gamma") > fitbcfrgam Call: bcfrailph(formula = Surv(time, censor) ~ X1 + frailty(PID), data = dataa, frailty = "gamma") n= 600 and number of events= 420 Regression Coefficients: Estimate StdErr z.value p.value X1 1.85604 0.22769 8.1515 4.441e-16 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Frailty Distribution:Bivariate correlated gamma Frailty variance = 0.4538638 ( 0.2299491 ) Correlation Estimate = 0.5266489 ( 0.3030276 ) Log likelihood with frailty = -2379.245 Log likelihood without frailty= -2383.632 > > ## No test: > # now for lognormal > > set.seed(18) > simdata<-simbcfrail(psize=100, cenr= c(0.2),beta=c(1,-0.7,0.5),frailty=c("lognormal"), + frailpar=c(0.5,-0.25),bhaz=c("exponential"), + bhazpar=list(scale = c(0.1)),covartype= c("N","N","B"), + covarpar=list(fargs=c(0,0,1),sargs=c(1,1,0.5)),comncovar=2) > dataa<-simdata$data > > #fit > fitbcfrlogn=bcfrailph(Surv(time,censor)~ X1+X2+X3+frailty(PID) ,data=dataa,frailty="lognormal") > fitbcfrlogn Call: bcfrailph(formula = Surv(time, censor) ~ X1 + X2 + X3 + frailty(PID), data = dataa, frailty = "lognormal") n= 200 and number of events= 160 Regression Coefficients: Estimate StdErr z.value p.value X1 1.09987 0.12144 9.0568 < 2.2e-16 *** X2 -0.64995 0.10467 -6.2093 5.322e-10 *** X3 0.34151 0.19510 1.7504 0.08005 . --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Frailty Distribution:Bivariate correlated log-normal Variance of random effect = 0.4593624 ( 0.172842 ) Correlation Estimate of random effects = -0.4974594 ( 0.3284772 ) Approximated Log likelihood with frailty = -696.001 Log likelihood without frailty= -697.4393 > # the output looks like > # Call: > # bcfrailph(formula = Surv(time, censor) ~ X1 + X2 + X3 + frailty(PID), > # data = dataa, frailty = "lognormal") > # > # n= 200 and number of events= 160 > # > # Regression Coefficients: > # Estimate StdErr z.value p.value > # X1 1.09987 0.12144 9.0568 < 2.2e-16 *** > # X2 -0.64995 0.10467 -6.2093 5.322e-10 *** > # X3 0.34151 0.19510 1.7504 0.08005 . > # --- > # Frailty Distribution:Bivariate Correlated log-normal > # Variance of random effect = 0.459363 ( 0.1728421 ) > # Correlation Estimate of random effects = -0.4974605 ( 0.3284767 ) > # Approximated Log likelihood with frailty = -696.001 > # Log likelihood without frailty= -697.4393 > > ## one can set the initial parameter for the frailty parameters > fitbcfrailph=bcfrailph(Surv(time,censor)~ X1+frailty(PID),data=dataa,initfrailp = c(0.1,0.5), + frailty="lognormal") > fitbcfrailph Call: bcfrailph(formula = Surv(time, censor) ~ X1 + frailty(PID), data = dataa, initfrailp = c(0.1, 0.5), frailty = "lognormal") n= 200 and number of events= 160 Regression Coefficients: Estimate StdErr z.value p.value X1 0.89037 0.10896 8.1716 2.22e-16 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Frailty Distribution:Bivariate correlated log-normal Variance of random effect = 0.2506744 ( 0.1351861 ) Correlation Estimate of random effects = 0.492468 ( 0.4595191 ) Approximated Log likelihood with frailty = -715.2778 Log likelihood without frailty= -715.7564 > > # Not run > > #if covariates are not included > fitmoe=bcfrailph(Surv(time,censor)~0,data=dataa,frailty="lognormal") Warning in bcfrailph(Surv(time, censor) ~ 0, data = dataa, frailty = "lognormal") : Since frailty variable is not specified bcfrailph fits assumed consecutive two observations as a pair Error in bcfrailph(Surv(time, censor) ~ 0, data = dataa, frailty = "lognormal") : covariates must be included Execution halted * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... OK * DONE Status: 1 ERROR See ‘/data/blackswan/ripley/R/packages/tests-devel/bcfrailph.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 2:10.36, 100.15 + 29.46