Running ‘testthat.R’ [22s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(gcplyr)
  ## 
  ## gcplyr (Version 1.10.0, Build Date: 2024-07-09)
  ## See http://github.com/mikeblazanin/gcplyr for additional documentation
  ## Please cite software as:
  ##   Blazanin, Michael. gcplyr: an R package for microbial growth
  ##   curve data analysis. BMC Bioinformatics 25, 232 (2024).
  ##   https://doi.org/10.1186/s12859-024-05817-3
  ## 
  
  > 
  > test_check("gcplyr")
  
  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
  
  
  Attaching package: 'tidyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  Loading required package: nlme
  
  Attaching package: 'nlme'
  
  The following object is masked from 'package:dplyr':
  
      collapse
  
  This is mgcv 1.9-1. For overview type 'help("mgcv-package")'.
  Inferred 'into' column names as: name, name2
  Inferring nested_metadata to be TRUE
  
  Inferring nested_metadata to be TRUE
  
  Inferring nested_metadata to be TRUE
  
  Inferring nested_metadata to be TRUE
  
  block_name_location = 'filename' but there are multiple metadata entries.
  Putting block_names in filename and writing remaining metadata into file
  
  block_name_location = 'filename' but there are multiple metadata entries.
  Putting block_names in filename and writing remaining metadata into file
  
  block_name_location = 'filename' but there are multiple metadata entries.
  Putting block_names in filename and writing remaining metadata into file
  
  Inferred 'into' column names as: strain, rep
  Inferred 'into' column names as: strain, rep
  Inferred 'into' column names as: strain, rep
  Inferred 'into' column names as: strain_rep, bact_rep2
  Inferred 'into' column names as: strain, rep, bact, rep2
  Inferring nested_metadata to be FALSE
  
  Inferring nested_metadata to be FALSE
  
  Inferring nested_metadata to be FALSE
  
  Inferring nested_metadata to be FALSE
  
  Inferring nested_metadata to be TRUE
  
  Joining with `by = join_by(time, Pop1, run)`
  Joining with `by = join_by(time, Pop1, run)`
  Joining with `by = join_by(time, fake_treat, run)`
  Joining with `by = join_by(time, run)`
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 321 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_allfunctions_argumentsmatching.R:56:7'): all full arg matches have been checked ──
  <packageNotFoundError/error/condition>
  Error in `library(package = strsplit(calls$other_func[i], "::")[[1]][1], 
      character.only = TRUE)`: there is no package called 'caret'
  Backtrace:
      ▆
   1. └─base::library(...) at test_allfunctions_argumentsmatching.R:56:7
  ── Error ('test_allfunctions_argumentsmatching.R:119:7'): all partial arg matches have been checked ──
  <packageNotFoundError/error/condition>
  Error in `library(package = strsplit(calls$other_func[i], "::")[[1]][1], 
      character.only = TRUE)`: there is no package called 'caret'
  Backtrace:
      ▆
   1. └─base::library(...) at test_allfunctions_argumentsmatching.R:119:7
  ── Error ('test_analysisfunctions.R:420:3'): centroid works correctly ──────────
  Error: Package "sf" must be installed to calculate centroids
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test_analysisfunctions.R:420:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─gcplyr::centroid_both(x = 0:9, y = (0:9) * 2)
   5.   └─gcplyr::centroid(x = x, y = y, return = return, ...)
  ── Error ('test_smoothingfunctions.R:335:3'): train_smooth_data and train + makemethod_train_smooth_data match ──
  <packageNotFoundError/error/condition>
  Error in `library(caret)`: there is no package called 'caret'
  Backtrace:
      ▆
   1. └─base::library(caret) at test_smoothingfunctions.R:335:3
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 321 ]
  Error: Test failures
  Execution halted