Running ‘testthat.R’ [64s/98s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mpwR)
  > 
  > test_check("mpwR")
  For DIA-NN no quantitative LFQ data on peptide-level.
  For PD no quantitative LFQ data on peptide-level.
  For DIA-NN no quantitative LFQ data on peptide-level.
  For PD no quantitative LFQ data on proteingroup-level.
  For ProteinGroup.IDs - No flowTraceR filtering applied
  For ProteinGroup.IDs - No flowTraceR filtering applied
  For ProteinGroup.IDs - No flowTraceR filtering applied
  For ProteinGroup.IDs - No flowTraceR filtering applied
  For MaxQuant evidence.txt - the following column need to be present:  Raw file 
  For MaxQuant evidence.txt - the following column need to be present:  Proteins 
  For MaxQuant evidence.txt - the following column need to be present:  Modified sequence 
  For MaxQuant evidence.txt - the following column need to be present:  Sequence 
  For MaxQuant evidence.txt - the following column need to be present:  Missed cleavages 
  For MaxQuant evidence.txt - the following column need to be present:  Charge 
  For MaxQuant evidence.txt - the following column need to be present:  Retention time 
  For MaxQuant evidence.txt - the following column need to be present:  Potential contaminant 
  For MaxQuant evidence.txt - the following column need to be present:  Reverse 
  
  For MaxQuant proteinGroups.txt input - the following column need to be present:  Protein IDs 
  For MaxQuant proteinGroups.txt input - the following column need to be present:  Majority protein IDs 
  For MaxQuant proteinGroups.txt input - the following column need to be present:  Peptide counts (all) 
  For MaxQuant proteinGroups.txt input - the following column need to be present:  Potential contaminant 
  For MaxQuant proteinGroups.txt input - the following column need to be present:  Reverse 
  
  For DIA-NN input - the following column need to be present:  Run 
  For DIA-NN input - the following column need to be present:  Protein.Group 
  For DIA-NN input - the following column need to be present:  Protein.Ids 
  For DIA-NN input - the following column need to be present:  Modified.Sequence 
  For DIA-NN input - the following column need to be present:  Stripped.Sequence 
  For DIA-NN input - the following column need to be present:  Precursor.Id 
  For DIA-NN input - the following column need to be present:  Precursor.Charge 
  For DIA-NN input - the following column need to be present:  RT 
  For DIA-NN input - the following column need to be present:  PG.MaxLFQ 
  
  For DIA-NN input - the following column need to be present:  Run 
  For DIA-NN input - the following column need to be present:  Protein.Group 
  For DIA-NN input - the following column need to be present:  Protein.Ids 
  For DIA-NN input - the following column need to be present:  Modified.Sequence 
  For DIA-NN input - the following column need to be present:  Stripped.Sequence 
  For DIA-NN input - the following column need to be present:  Precursor.Id 
  For DIA-NN input - the following column need to be present:  Precursor.Charge 
  For DIA-NN input - the following column need to be present:  RT 
  For DIA-NN input - the following column need to be present:  PG.MaxLFQ 
  
  For PD PSMs.txt - the following column need to be present:  Confidence 
  For PD PSMs.txt - the following column need to be present:  Spectrum File 
  For PD PSMs.txt - the following column need to be present:  Protein Accessions 
  For PD PSMs.txt - the following column need to be present:  Annotated Sequence 
  For PD PSMs.txt - the following column need to be present:  Modifications 
  For PD PSMs.txt - the following column need to be present:  Number of Missed Cleavages 
  For PD PSMs.txt - the following column need to be present:  Charge 
  For PD PSMs.txt - the following column need to be present:  RT in min 
  
  For PD PeptideGroups.txt - the following column(s) need to be present: Found in Sample
  For PD PeptideGroups.txt - the following column need to be present:  Peptide Groups Peptide Group ID 
  For PD PeptideGroups.txt - the following column need to be present:  Confidence 
  For PD PeptideGroups.txt - the following column need to be present:  Sequence 
  For PD PeptideGroups.txt - the following column need to be present:  Modifications 
  For PD PeptideGroups.txt - the following column need to be present:  Number of Missed Cleavages 
  
  For PD PeptideGroups.txt - the following column(s) need to be present: Found in Sample
  For PD PeptideGroups.txt - the following column need to be present:  Peptide Groups Peptide Group ID 
  For PD PeptideGroups.txt - the following column need to be present:  Confidence 
  For PD PeptideGroups.txt - the following column need to be present:  Sequence 
  For PD PeptideGroups.txt - the following column need to be present:  Modifications 
  For PD PeptideGroups.txt - the following column need to be present:  Number of Missed Cleavages 
  
  For PD Proteins.txt - the following column(s) need to be present: Found in Sample
  For PD Proteins.txt - the following column need to be present:  Proteins Unique Sequence ID 
  For PD Proteins.txt - the following column need to be present:  Accession 
  For PD Proteins.txt - the following column need to be present:  Description 
  
  For PD Proteins.txt - the following column(s) need to be present: Found in Sample
  For PD Proteins.txt - the following column need to be present:  Proteins Unique Sequence ID 
  For PD Proteins.txt - the following column need to be present:  Accession 
  For PD Proteins.txt - the following column need to be present:  Description 
  
  For PD ProteinGroups.txt - the following column(s) need to be present: Found in Sample
  For PD ProteinGroups.txt - the following column need to be present:  Protein Groups Protein Group ID 
  For PD ProteinGroups.txt - the following column need to be present:  Group Description 
  For PD ProteinGroups.txt - the following column need to be present:  Number of Proteins 
  For PD ProteinGroups.txt - the following column need to be present:  Number of Unique Peptides 
  
  For PD ProteinGroups.txt - the following column(s) need to be present: Found in Sample
  For PD ProteinGroups.txt - the following column need to be present:  Protein Groups Protein Group ID 
  For PD ProteinGroups.txt - the following column need to be present:  Group Description 
  For PD ProteinGroups.txt - the following column need to be present:  Number of Proteins 
  For PD ProteinGroups.txt - the following column need to be present:  Number of Unique Peptides 
  
  For plotting density: CV_Retention.time_mpwR is not detected in submitted data.
  For plotting density: CV_Peptide_LFQ_mpwR is not detected in submitted data.
  For plotting density: CV_ProteinGroup_LFQ_mpwR is not detected in submitted data.
  For plotting barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
  For plotting stacked barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
  For plotting barplot: Only NA detected for Protein.IDs! Not included in vizualisation.
  For plotting boxplot: Only NA detected for Protein.IDs! Not included in vizualisation.
  [ FAIL 1 | WARN 553 | SKIP 0 | PASS 598 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_Upset.R:72'): get_Upset_list works ─────────────────────────────
  Error in `stringr::str_detect(string = names(output_list), pattern = "")`: `pattern` can't be the empty string (`""`).
  Backtrace:
      ▆
   1. └─mpwR::get_Upset_list(input_list = data, level = "Precursor.IDs") at test_Upset.R:72:3
   2.   ├─base::which(...)
   3.   └─stringr::str_detect(string = names(output_list), pattern = "")
   4.     └─stringr:::no_empty()
   5.       └─cli::cli_abort(...)
   6.         └─rlang::abort(...)
  
  [ FAIL 1 | WARN 553 | SKIP 0 | PASS 598 ]
  Error: Test failures
  Execution halted