* using log directory 'd:/Rcompile/CRANpkg/local/4.4/serocalculator.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'serocalculator/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'serocalculator' 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'serocalculator' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* checking installed package size ... 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [6s] OK
* checking whether the package can be loaded with stated dependencies ... [5s] OK
* checking whether the package can be unloaded cleanly ... [5s] OK
* checking whether the namespace can be loaded with stated dependencies ... [5s] OK
* checking whether the namespace can be unloaded cleanly ... [6s] OK
* checking loading without being on the library search path ... [6s] 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 ... [18s] OK
* checking Rd files ... [2s] OK
* checking Rd metadata ... 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] 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 compiled code ... OK
* checking examples ... [36s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [54s] ERROR
  Running 'spelling.R' [0s]
  Running 'testthat.R' [53s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(serocalculator)
  > 
  > test_check("serocalculator", stop_on_warning = TRUE)
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  
  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
  
  Saving _problems/test-as_curve_params-33.R
  Proceeding to use "`Age`"
  
  Attaching package: 'tidyr'
  
  The following object is masked from 'package:magrittr':
  
      extract
  
  i Data has been stratified.
  i Here are the strata that will be analyzed:
  
  # A tibble: 2 x 3
    Stratum   catchment     n
    <chr>     <chr>     <int>
  1 Stratum 1 aku          53
  2 Stratum 2 kgh          47
  starting new stratum: Stratum 1
  # A tibble: 1 x 3
    Stratum   catchment     n
    <chr>     <chr>     <int>
  1 Stratum 1 aku          53
  nrow(curve_params) = 200
  Initial negative log-likelihood: 271.620368416703
  about to call `nlm()`
  iteration = 0
  Step:
  [1] 0
  Parameter:
  [1] -2.302585
  Function Value
  [1] 271.6204
  Gradient:
  [1] -12.19684
  
  iteration = 1
  Step:
  [1] 0.3
  Parameter:
  [1] -2.002585
  Function Value
  [1] 269.4844
  Gradient:
  [1] -1.521341
  
  iteration = 2
  Step:
  [1] 0.0427523
  Parameter:
  [1] -1.959833
  Function Value
  [1] 269.4571
  Gradient:
  [1] 0.2566987
  
  iteration = 3
  Step:
  [1] -0.006172225
  Parameter:
  [1] -1.966005
  Function Value
  [1] 269.4563
  Gradient:
  [1] -0.003952892
  
  iteration = 4
  Parameter:
  [1] -1.965911
  Function Value
  [1] 269.4563
  Gradient:
  [1] -9.975515e-06
  
  Relative gradient close to zero.
  Current iterate is probably solution.
  
  
  Elapsed time: 
     user  system elapsed 
     0.33    0.00    0.33 
  starting new stratum: Stratum 2
  # A tibble: 1 x 3
    Stratum   catchment     n
    <chr>     <chr>     <int>
  1 Stratum 2 kgh          47
  nrow(curve_params) = 200
  Initial negative log-likelihood: 261.759517614626
  about to call `nlm()`
  iteration = 0
  Step:
  [1] 0
  Parameter:
  [1] -2.302585
  Function Value
  [1] 261.7595
  Gradient:
  [1] -23.7431
  
  iteration = 1
  Step:
  [1] 0.498822
  Parameter:
  [1] -1.803763
  Function Value
  [1] 253.5433
  Gradient:
  [1] -7.990928
  
  iteration = 2
  Step:
  [1] 0.2530477
  Parameter:
  [1] -1.550715
  Function Value
  [1] 252.8398
  Gradient:
  [1] 2.718074
  
  iteration = 3
  Step:
  [1] -0.06422655
  Parameter:
  [1] -1.614942
  Function Value
  [1] 252.7582
  Gradient:
  [1] -0.161689
  
  iteration = 4
  Step:
  [1] 0.003606105
  Parameter:
  [1] -1.611336
  Function Value
  [1] 252.7579
  Gradient:
  [1] -0.002816973
  
  iteration = 5
  Parameter:
  [1] -1.611272
  Function Value
  [1] 252.7579
  Gradient:
  [1] 3.069238e-06
  
  Relative gradient close to zero.
  Current iterate is probably solution.
  
  
  Elapsed time: 
     user  system elapsed 
      0.3     0.0     0.3 
  i Elapsed time for loop over strata:
     user  system elapsed 
     1.62    0.05    1.67 
  i Data has been stratified.
  i Here are the strata that will be analyzed:
  
  # A tibble: 2 x 3
    Stratum   catchment     n
    <chr>     <chr>     <int>
  1 Stratum 1 aku          53
  2 Stratum 2 kgh          47
  Setting up parallel processing with `num_cores` = 2.
  i Elapsed time for parallelized code:
     user  system elapsed 
     0.00    0.00    0.89 
  
  Attaching package: 'readr'
  
  The following objects are masked from 'package:testthat':
  
      edition_get, local_edition
  
  [ FAIL 1 | WARN 0 | SKIP 15 | PASS 33 ]
  
  ══ Skipped tests (15) ══════════════════════════════════════════════════════════
  • On CRAN (15): 'test-ab0.R:1:1', 'test-as_noise_params.R:13:1',
    'test-autoplot.pop_data.R:19:1', 'test-autoplot.pop_data.R:28:1',
    'test-autoplot.pop_data.R:37:1', 'test-class_attributes.R:9:1',
    'test-df_to_array.R:1:1', 'test-est.incidence.R:1:1',
    'test-est.incidence.by.R:35:1', 'test-f_dev.R:1:1',
    'test-log_likelihood.R:1:1', 'test-plot_curve_params_one_ab.R:1:1',
    'test-stratify_data.R:1:1', 'test-summary.pop_data.R:12:1',
    'test-summary.pop_data.R:16:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-as_curve_params.R:33:3'): `as_curve_params()` produces expected results ──
  Error in `test_data %>% ssdtools:::expect_snapshot_data(name = "curve-data")`: object 'expect_snapshot_data' not found
  Backtrace:
      ▆
   1. └─test_data %>% ssdtools:::expect_snapshot_data(name = "curve-data") at test-as_curve_params.R:33:3
  
  [ FAIL 1 | WARN 0 | SKIP 15 | PASS 33 ]
  Deleting unused snapshots: 'as_curve_params/curve-data.csv'
  Error:
  ! Test failures.
  Execution halted
* checking PDF version of manual ... [19s] OK
* checking HTML version of manual ... [10s] OK
* DONE
Status: 1 ERROR