* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/expertsurv.Rcheck’
* using R Under development (unstable) (2024-05-02 r86508)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    clang version 18.1.5
    flang-new version 18.1.5
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘expertsurv/DESCRIPTION’ ... OK
* this is package ‘expertsurv’ version ‘1.3.0’
* 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 ... OK
* checking whether package ‘expertsurv’ can be installed ... [18m/24m] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/expertsurv-00install.html' for details.
* used C++ compiler: ‘clang version 18.1.5’
* checking C++ specification ... OK
  Not all R platforms support C++17
* checking installed package size ... NOTE
  installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   7.0Mb
* checking package directory ... 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 ... [10s/10s] 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 ... [11s/11s] OK
* checking loading without being on the library search path ... [17s/17s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [81s/82s] OK
* checking Rd files ... [18s/18s] 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [18s/19s] ERROR
Running examples in ‘expertsurv-Ex.R’ failed
The error most likely occurred in:

> ### Name: expertsurv-package
> ### Title: Incorporating Expert Opinion with Parametric Survival Models
> ### Aliases: expertsurv-package expertsurv
> ### Keywords: Economic Evaluation Expert Health Modelling Opinion Survival
> 
> ### ** Examples
> 
> #Define expert opinion
> require("dplyr")
Loading required package: dplyr

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> param_expert_example1 <- list()
> #1 timepoint and 2 experts with equal weight,
> #first a normal distribution, second a non-standard t-distribution with
> #3 degrees of freedom
> 
> param_expert_example1[[1]] <- data.frame(dist = c("norm","t"),
+                                wi = c(0.5,0.5), # Ensure Weights sum to 1
+                                param1 = c(0.1,0.12),
+                                param2 = c(0.05,0.05),
+                                 param3 = c(NA,3))
> 
> 
> timepoint_expert <- 14
> 
> data2 <- data %>% rename(status = censored) %>% mutate(time2 = ifelse(time > 10, 10, time),
+                   status2 = ifelse(time> 10, 0, status))
> 
> example1  <- fit.models.expert(formula=Surv(time2,status2)~1,data=data2,
+                               distr=c("wph", "gomp"),
+                               method="mle",
+                               pool_type = "log pool", 
+                               opinion_type = "survival",
+                               times_expert = timepoint_expert, 
+                               param_expert = param_expert_example1)
Error in get(x, envir = ns, inherits = FALSE) : 
  object 'deriv.test' not found
Calls: fit.models.expert ... format_output_fit.models -> lapply -> lapply -> FUN -> runMLE
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [23s/25s] OK
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 3 NOTEs