* using log directory ‘/srv/hornik/tmp/CRAN_pretest/crmPack.Rcheck’
* using R Under development (unstable) (2026-01-07 r89288)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 21.1.8 (1)
    Debian flang version 21.1.8 (1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘crmPack/DESCRIPTION’ ... OK
* this is package ‘crmPack’ version ‘2.0.2’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [6s/10s] OK
* 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 ‘crmPack’ can be installed ... [16s/16s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking whether startup messages can be suppressed ... [1s/1s] 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 ... [19s/19s] OK
* checking Rd files ... [3s/3s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [52s/52s] ERROR
Running examples in ‘crmPack-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summary,PseudoDualFlexiSimulations-method
> ### Title: Summarize 'PseudoDualFlexiSimulations'
> ### Aliases: summary,PseudoDualFlexiSimulations-method
> ###   summary-PseudoDualFlexiSimulations
> 
> ### ** Examples
> 
> # nolint start
> 
> ## If DLE and efficacy responses are considered in the simulations and the 'EffFlexi' class is used
> ## we need a data object with doses >= 1:
> data <- DataDual(doseGrid = seq(25, 300, 25))
> ## First for the DLE model
> ## The DLE model must be of 'ModelTox' (e.g 'LogisticIndepBeta') class
> DLEmodel <- LogisticIndepBeta(
+   binDLE = c(1.05, 1.8),
+   DLEweights = c(3, 3),
+   DLEdose = c(25, 300),
+   data = data
+ )
> 
> ## for the efficacy model
> Effmodel <- EffFlexi(
+   eff = c(1.223, 2.513),
+   eff_dose = c(25, 300),
+   sigma2W = c(a = 0.1, b = 0.1),
+   sigma2betaW = c(a = 20, b = 50),
+   rw1 = FALSE,
+   data = data
+ )
> 
> 
> ## specified the next best
> mynextbest <- NextBestMaxGainSamples(
+   prob_target_drt = 0.35,
+   prob_target_eot = 0.3,
+   derive = function(samples) {
+     as.numeric(quantile(samples, prob = 0.3))
+   },
+   mg_derive = function(mg_samples) {
+     as.numeric(quantile(mg_samples, prob = 0.5))
+   }
+ )
> 
> ## The increments (see Increments class examples)
> ## 200% allowable increase for dose below 300 and 200% increase for dose above 300
> myIncrements <- IncrementsRelative(
+   intervals = c(25, 300),
+   increments = c(2, 2)
+ )
> ## cohort size of 3
> mySize <- CohortSizeConst(size = 3)
> ## Stop only when 10 subjects are treated:
> ## very low sample size is just for illustration here
> myStopping <- StoppingMinPatients(nPatients = 10)
> 
> ## Specified the design
> design <- DualResponsesSamplesDesign(
+   nextBest = mynextbest,
+   cohort_size = mySize,
+   startingDose = 25,
+   model = DLEmodel,
+   eff_model = Effmodel,
+   data = data,
+   stopping = myStopping,
+   increments = myIncrements
+ )
> ## specified the true DLE curve and the true expected efficacy values at all dose levels
> myTruthDLE <- probFunction(DLEmodel, phi1 = -53.66584, phi2 = 10.50499)
> 
> myTruthEff <- c(
+   -0.5478867,
+   0.1645417,
+   0.5248031,
+   0.7604467,
+   0.9333009,
+   1.0687031,
+   1.1793942,
+   1.2726408,
+   1.3529598,
+   1.4233411,
+   1.4858613,
+   1.5420182
+ )
> 
> 
> ## specify the options for MCMC
> # for illustration purposes, in reality larger number of burnin and samples shoud be used
> options <- McmcOptions(burnin = 5, step = 1, samples = 10)
> ## The simulation
> ## For illustration purpose only 1 simulation is produced (nsim=1).
> mySim <- simulate(
+   object = design,
+   args = NULL,
+   trueDLE = myTruthDLE,
+   trueEff = myTruthEff,
+   trueSigma2 = 0.025,
+   trueSigma2betaW = 1,
+   nsim = 1,
+   seed = 819,
+   parallel = FALSE,
+   mcmcOptions = options
+ )
Error in prob(dose = dose, model = model, samples = samples) : 
  Assertion on 'dose' failed: Contains missing values (element 1).
Calls: simulate ... prob -> prob -> assert_numeric -> makeAssertion -> mstop
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [39s/39s] OK
  Running ‘test-package-load.R’ [1s/1s]
  Running ‘testthat.R’ [38s/38s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [11s/11s] OK
* checking HTML version of manual ... [17s/17s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR