Running ‘testthat.R’ [22s/31s]
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.
  Protein-level not available for Spectronaut.
  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 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:  Number of Protein Groups 
  For PD PeptideGroups.txt - the following column need to be present:  Number of Proteins 
  For PD PeptideGroups.txt - the following column need to be present:  Number of PSMs 
  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:  Number of Protein Groups 
  For PD PeptideGroups.txt - the following column need to be present:  Number of Proteins 
  For PD PeptideGroups.txt - the following column need to be present:  Number of PSMs 
  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 123 | SKIP 0 | PASS 633 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_utils_helpers.R:691:4'): prepare_Upset works ───────────────────
  Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector
  Backtrace:
      ▆
   1. ├─mpwR:::prepare_Upset(...) at test_utils_helpers.R:691:4
   2. │ └─flowTraceR::convert_proteingroups(input_df = input_df, software = software)
   3. │   └─flowTraceR:::sort_string_pg(...)
   4. │     └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ...
   5. └─base::unlist(., .data, use.names = FALSE)
  
  [ FAIL 1 | WARN 123 | SKIP 0 | PASS 633 ]
  Error: Test failures
  Execution halted