* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/simexaft.Rcheck’
* using R Under development (unstable) (2024-03-16 r86144)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 13.2.1 20231011 (Red Hat 13.2.1-4)
    GNU Fortran (GCC) 13.2.1 20231011 (Red Hat 13.2.1-4)
* 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 ... [24s/24s] OK
* checking examples with --run-donttest ... [24s/24s] 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 1:51.86, 101.92 + 9.16