* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/serocalculator.Rcheck’
* using R Under development (unstable) (2025-12-11 r89152)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘serocalculator/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘serocalculator’ version ‘1.4.0’
* 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 ‘serocalculator’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
* 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 ... [11s/11s] 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... [13s/18s] OK
* checking examples with --run-donttest ... ERROR
Running examples in ‘serocalculator-Ex.R’ failed
The error most likely occurred in:

> ### Name: analyze_sims
> ### Title: Analyze simulation results
> ### Aliases: analyze_sims
> 
> ### ** Examples
> 
> ## No test: 
> dmcmc <- typhoid_curves_nostrat_100
> 
> n_cores <- 2
> 
> nclus <- 20
> # cross-sectional sample size
> nrep <- c(50, 200)
> 
> # incidence rate in e
> lambdas <- c(.05, .8)
> 
> antibodies <- c("HlyE_IgA", "HlyE_IgG")
> lifespan <- c(0, 10)
> dlims = rbind(
+ "HlyE_IgA" = c(min = 0, max = 0.5),
+ "HlyE_IgG" = c(min = 0, max = 0.5)
+ )
> sim_df <- sim_pop_data_multi(
+ n_cores = n_cores,
+ lambdas = lambdas,
+ nclus = nclus,
+ sample_sizes = nrep,
+ age_range = lifespan,
+ antigen_isos = antibodies,
+ renew_params = FALSE,
+ add_noise = TRUE,
+ curve_params = dmcmc,
+ noise_limits = dlims,
+ format = "long"
+ )
Error in .check_ncores(cores) : 31 simultaneous processes spawned
Calls: sim_pop_data_multi ... %dopar% -> <Anonymous> -> mclapply -> .check_ncores
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’ [50s/67s]
 [50s/67s] OK
* 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/serocalculator.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:35.73, 115.89 + 17.88