* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/simexaft.Rcheck’ * using R Under development (unstable) (2024-10-11 r87226) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 13.2.1 20240316 (Red Hat 13.2.1-7) GNU Fortran (GCC) 13.2.1 20240316 (Red Hat 13.2.1-7) * running under: Fedora Linux 38 (Workstation Edition) * using session charset: UTF-8 * checking for file ‘simexaft/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘simexaft’ version ‘1.0.7.1’ * 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 ‘simexaft’ can be installed ... 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 ... 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 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 ... OK * checking Rd files ... OK * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [14s/14s] OK * checking examples with --run-donttest ... [14s/14s] ERROR Running examples in ‘simexaft-Ex.R’ failed The error most likely occurred in: > ### Name: simexaft > ### Title: SIMEX Algorithm for Accelerated Failure Time Model with > ### Covariates Subject to Measurement Error > ### Aliases: simexaft > > ### ** Examples > > library("simexaft") > library("survival") > data("BHS") > > dataset <- BHS > > dataset$SBP <- log(dataset$SBP - 50) > > ###Naive AFT approach > formula <- Surv(SURVTIME,DTHCENS) ~ SBP + CHOL + AGE + BMI + SMOKE1 + SMOKE2 > > out1 <- survreg(formula = formula, data = dataset, dist = "weibull") > > summary(out1) Call: survreg(formula = formula, data = dataset, dist = "weibull") Value Std. Error z p (Intercept) 12.5302 3.3587 3.73 0.00019 SBP -1.2524 0.7766 -1.61 0.10681 CHOL -0.0512 0.1096 -0.47 0.64036 AGE -0.0603 0.0223 -2.71 0.00669 BMI 0.0337 0.0400 0.84 0.39992 SMOKE1 -0.7392 0.3993 -1.85 0.06416 SMOKE2 -0.8232 0.4178 -1.97 0.04881 Log(scale) -0.5142 0.2079 -2.47 0.01338 Scale= 0.598 Weibull distribution Loglik(model)= -83.5 Loglik(intercept only)= -98.5 Chisq= 30.02 on 6 degrees of freedom, p= 3.9e-05 Number of Newton-Raphson Iterations: 9 n= 100 > > > ###fit a AFT model with quadratic extrapolation > set.seed(120) > > ind <- c("SBP", "CHOL") > > err.mat <- diag(rep(0.5625, 2)) > > out2 <- simexaft(formula = formula, data = dataset, SIMEXvariable = ind, + repeated = FALSE, repind = list(), err.mat = err.mat, B = 50, + lambda = seq(0, 2, 0.1),extrapolation = "quadratic", dist = "weibull") > > summary(out2) $coefficients Estimate Std. Error P value Intercept 16.58799926 4.04749227 4.161238e-05 SBP -2.53767745 0.96448269 8.510197e-03 CHOL -0.03846337 0.13392975 7.739664e-01 AGE -0.04726355 0.02071209 2.249345e-02 BMI 0.06639892 0.04406360 1.318393e-01 SMOKE1 -0.55254932 0.36197784 1.268922e-01 SMOKE2 -0.87297952 0.40043208 2.925051e-02 $scalereg (Intercept) 0.5823691 $extrapolation [1] "quad" $SIMEXvariable [1] "SBP" "CHOL" attr(,"class") [1] "summary.simaxaft" > > > > > > > ## No test: > #################### repeated measurements ################################# > data("rhDNase") > > ###true model > rhDNase$fev.ave <- (rhDNase$fev + rhDNase$fev2)/2 Error in `$<-.data.frame`(`*tmp*`, fev.ave, value = numeric(0)) : replacement has 0 rows, data has 767 Calls: $<- -> $<-.data.frame 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/simexaft.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 1:08.31, 61.60 + 6.37