Running 'testthat.R' [68s]
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(mpactr)
  > 
  > test_check("mpactr")
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Parsing 484 peaks for replicability across technical replicates.
  v 33 ions failed the cv_filter filter, 451 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1303 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 796 ions failed the Blanks filter, 507 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Parsing 484 peaks for replicability across technical replicates.
  v 33 ions failed the cv_filter filter, 451 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Parsing 484 peaks for replicability across technical replicates.
  v 33 ions failed the cv_filter filter, 451 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method .
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  ! Argument remove_ions is FALSE. Peaks from Blanks will not be removed.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Parsing 484 peaks for replicability across technical replicates.
  v 33 ions failed the cv_filter filter, 451 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Checking 1289 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 65 ions failed the mispicked filter, 1224 ions remain.
  i Parsing 1224 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 698 ions failed the Blanks filter, 526 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Parsing 484 peaks for insource ions.
  v 27 ions failed the insource filter, 457 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1233 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 0 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  ! Argument merge_peaks is: FALSE. Mispicked peaks will not be merged.
  v 70 ions failed the mispicked filter, 1303 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  ! Argument merge_peaks is: FALSE. Mispicked peaks will not be merged.
  v 70 ions failed the mispicked filter, 1303 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  ! Argument remove_ions is FALSE. Peaks from Blanks will not be removed.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Parsing 484 peaks for replicability across technical replicates.
  v 33 ions failed the cv_filter filter, 451 ions remain.
  i Parsing 484 peaks for replicability across technical replicates.
  v 33 ions failed the cv_filter filter, 451 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Parsing 484 peaks for insource ions.
  v 27 ions failed the insource filter, 457 ions remain.
  i Parsing 484 peaks for insource ions.
  v 27 ions failed the insource filter, 457 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Parsing 484 peaks for replicability across technical replicates.
  v 33 ions failed the cv_filter filter, 451 ions remain.
  i Parsing 451 peaks for insource ions.
  v 25 ions failed the insource filter, 426 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks for replicability across technical replicates.
  v 279 ions failed the cv_filter filter, 954 ions remain.
  i Parsing 954 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 384 ions failed the Blanks filter, 570 ions remain.
  i Parsing 570 peaks for insource ions.
  v 26 ions failed the insource filter, 544 ions remain.
  Found duplicate compound values, will add a suffix to unique the value.
  Found duplicate compound values, will add a suffix to unique the value.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Coculture.
  i Argument remove_ions is: TRUE.Removing peaks from Coculture.
  v 354 ions failed the Coculture filter, 879 ions remain.
  Rows: 1306 Columns: 21
  -- Column specification --------------------------------------------------------
  Delimiter: ","
  dbl (21): Compound, mz, rt, 102623_UM1848B_JC1_69_1_5004, 102623_UM1846B_Med...
  
  i Use `spec()` to retrieve the full column specification for this data.
  i Specify the column types or set `show_col_types = FALSE` to quiet this message.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Parsing 484 peaks for insource ions.
  v 27 ions failed the insource filter, 457 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Parsing 484 peaks based on the sample group: Coculture.
  i Argument remove_ions is: TRUE.Removing peaks from Coculture.
  v 293 ions failed the Coculture filter, 191 ions remain.
  i Parsing 191 peaks for insource ions.
  v 15 ions failed the insource filter, 176 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Parsing 484 peaks for insource ions.
  v 27 ions failed the insource filter, 457 ions remain.
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 171 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • empty test (1): 'test-peak_table_formatter.R:32:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-qc_graph_pactr-class.R:32:3'): plot_QC_Tree generates the correct plot ──
  class(plot) (`actual`) not equal to c("gg", "ggplot") (`expected`).
  
  `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
  `expected[2:2]`:                                                      "ggplot"
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 171 ]
  Error: Test failures
  Execution halted