R Under development (unstable) (2025-01-24 r87627 ucrt) -- "Unsuffered Consequences"
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> # 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 object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Proceeding to use "`Age`"

Attaching package: 'tidyr'

The following object is masked from 'package:magrittr':

    extract

The following object is masked from 'package:testthat':

    matches

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 
   0.29    0.00    0.29 
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 
   1.05    0.01    1.06 
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    0.72 

Attaching package: 'readr'

The following objects are masked from 'package:testthat':

    edition_get, local_edition

[ FAIL 0 | WARN 0 | SKIP 16 | PASS 33 ]

══ Skipped tests (16) ══════════════════════════════════════════════════════════
• On CRAN (16): 'test-ab0.R:16:3', 'test-as_curve_params.R:29:3',
  'test-as_noise_params.R:19:3', 'test-autoplot.pop_data.R:23:13',
  'test-autoplot.pop_data.R:32:13', 'test-autoplot.pop_data.R:40:13',
  'test-class_attributes.R:12:3', 'test-df_to_array.R:17:3',
  'test-est.incidence.R:9:3', 'test-est.incidence.by.R:49:13',
  'test-f_dev.R:45:3', 'test-log_likelihood.R:12:3',
  'test-plot_curve_params_one_ab.R:20:3', 'test-stratify_data.R:26:3',
  'test-summary.pop_data.R:13:3', 'test-summary.pop_data.R:17:3'

[ FAIL 0 | WARN 0 | SKIP 16 | PASS 33 ]
Deleting unused snapshots:
• as_curve_params/curve-data.csv
> 
> proc.time()
   user  system elapsed 
  20.48    0.84   32.32