* using log directory ‘/home/hornik/tmp/CRAN_special_donttest/serocalculator.Rcheck’
* using R Under development (unstable) (2026-03-23 r89685)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-15 (Debian 15.2.0-14) 15.2.0
    GNU Fortran (Debian 15.2.0-14) 15.2.0
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* current time: 2026-03-24 08:12:12 UTC
* using option ‘--run-donttest’
* checking for file ‘serocalculator/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘serocalculator’ version ‘1.4.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/9s] NOTE
Maintainer: ‘Kristina Lai <kwlai@ucdavis.edu>’

New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
  Serological (3:40)
  seroconversions (16:5)
  seroincidence (17:28)

Unknown, possibly misspelled, fields in DESCRIPTION:
  ‘Remotes’

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2026-01-16 as issues were not addressed
    in time.

Suggests or Enhances not in mainstream repositories:
  snapr
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: ‘snapr’
* 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 ... [6s/6s] OK
* used C compiler: ‘gcc-15 (Debian 15.2.0-15) 15.2.0’
* checking package directory ... OK
* checking for future file timestamps ... 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 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 ... [9s/9s] OK
* checking Rd files ... [0s/0s] 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 ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... [219s/146s] ERROR
Running examples in ‘serocalculator-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sim_pop_data_multi
> ### Title: Simulate multiple data sets
> ### Aliases: sim_pop_data_multi
> 
> ### ** Examples
> 
> ## No test: 
> # Load curve parameters
> dmcmc <- typhoid_curves_nostrat_100
> 
> # Specify the antibody-isotype responses to include in analyses
> antibodies <- c("HlyE_IgA", "HlyE_IgG")
> 
> # Set seed to reproduce results
> set.seed(54321)
> 
> # Simulated incidence rate per person-year
> lambdas = c(.05, .1, .15, .2, .3)
> 
> # Range covered in simulations
> lifespan <- c(0, 10);
> 
> # Cross-sectional sample size
> nrep <- 100
> 
> # Biologic noise distribution
> dlims <- rbind(
+   "HlyE_IgA" = c(min = 0, max = 0.5),
+   "HlyE_IgG" = c(min = 0, max = 0.5)
+ )
> 
> sim_data <- sim_pop_data_multi(
+   curve_params = dmcmc,
+   lambdas = lambdas,
+   sample_sizes = nrep,
+   age_range = lifespan,
+   antigen_isos = antibodies,
+   n_mcmc_samples = 0,
+   renew_params = TRUE,
+   add_noise = TRUE,
+   noise_limits = dlims,
+   format = "long",
+   nclus = 10)
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 ... [58s/74s] OK
  Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [58s/74s]
* checking PDF version of manual ... [4s/4s] OK
* checking HTML version of manual ... [4s/4s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 NOTE