• using R Under development (unstable) (2025-11-13 r89017)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 21.1.5     flang version 21.1.5
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• 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 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 ... [32s/107s] OK See the install log for details.
• used C compiler: ‘clang version 21.1.5’
• 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 ... [8s/25s] OK
• checking whether the package can be loaded with stated dependencies ... [7s/26s] OK
• checking whether the package can be unloaded cleanly ... [7s/23s] OK
• checking whether the namespace can be loaded with stated dependencies ... [7s/15s] OK
• checking whether the namespace can be unloaded cleanly ... [8s/26s] OK
• checking loading without being on the library search path ... [8s/21s] 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 ... [47s/142s] 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 pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking examples ... [35s/114s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [41s/259s] ERROR   Running ‘spelling.R’   Running ‘testthat.R’ [40s/257s] 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     0.198 0.000 0.674   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     0.220 0.001 0.836   i Elapsed time for loop over strata:      user system elapsed     1.499 0.001 5.720   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     0.003 0.003 2.425      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 ... [11s/35s] OK
• checking HTML version of manual ... [8s/15s] OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR