* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/WEE.Rcheck’
* using R Under development (unstable) (2023-03-24 r84037)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 11.3.1 20220421 (Red Hat 11.3.1-2)
    GNU Fortran (GCC) 11.3.1 20220421 (Red Hat 11.3.1-2)
* running under: Fedora 34 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘WEE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘WEE’ version ‘1.0’
* 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 ‘WEE’ 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 R 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 ... [10s/10s] 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 examples ... OK
* checking examples with --run-donttest ... ERROR
Running examples in ‘WEE-Ex.R’ failed
The error most likely occurred in:

> ### Name: WEE-package
> ### Title: Weighted Estimated Equation (WEE) Approaches in Genetic
> ###   Case-Control Studies
> ### Aliases: WEE-package WEE
> ### Keywords: package
> 
> ### ** Examples
> 
> #---------------------- WEE logistic regression ----------------------#
> ## Generate simulated data
> # set population size as 500000
> n = 500000 
> 
> # set parameters
> beta = c(0.2, 0.1) # P(Y|X,Z)
> gamma = c(0.3, log(2), log(2)) #P(D|X,Y,Z)
> 
> # generate the genetic variant X
> x = rbinom(n,size=2,prob=0.3)
> 
> # generate the standardized continuous covariate Z correlated with X
> z = rnorm(n, mean=0.5*x-0.3, sd=1)
> 
> # generate the binary secondary trait Y
> py = exp(-1+beta[1]*x+beta[2]*z)/
+         (1+exp(-1+beta[1]*x+beta[2]*z))
> y = rbinom(n,1, py)
> 
> # generate the primary disease D 
> # (alpha changes to make sure the disease prevalence = 0.1 )
> alpha = -2.88
> pd = exp(alpha+x*gamma[1]+y*log(2)+z*log(2))/
+ (1+exp(alpha+x*gamma[1]+y*log(2)+z*log(2)))
> d = rbinom(n,size=1,prob=pd)
> 
> # form the population dataset
> dat = as.data.frame(cbind(d, y, z, x))
> 
> # generate sample dataset with 200 cases and 200 controls
> dat_cases = dat[which(dat$d==1),]
> dat_controls= dat[which(dat$d==0),]
> dat_cases_sample = dat_cases[sample(sum(dat$d==1),
+                              200,replace=FALSE),]
> dat_controls_sample = dat_controls[sample(sum(dat$d==0), 
+                                    200,replace=FALSE),]
> 
> dat_logistic = rbind(dat_cases_sample,dat_controls_sample)	
> colnames(dat_logistic) = c("D", "y", "z","x")
> D = dat_logistic$D # Disease status
> pD = sum(dat$d==1)/500000 # Population disease prevalence
> 
> ## WEE logsitic regression
> WEE.logistic(y ~ x + z, D, 
+              data = dat_logistic, pD)	  
Call:
WEE.logistic(formula = y ~ x + z, D = D, data = dat_logistic, 
    pd_pop = pD)

Coefficients:
(Intercept)           x           z 
 -1.1603134   0.3852332  -0.1878349 
> ## No test: 
> WEE.logistic(y ~ x + z, D, 
+              data = dat_logistic, pD, boot = 500)	 
Error in .check_ncores(cores) : 31 simultaneous processes spawned
Calls: WEE.logistic ... %dopar% -> <Anonymous> -> mclapply -> .check_ncores
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/WEE.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 1:01.39, 53.82 + 7.12