R Under development (unstable) (2025-05-11 r88197 ucrt) -- "Unsuffered Consequences"
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> 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 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 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 0 | WARN 123 | SKIP 0 | PASS 660 ]

[ FAIL 0 | WARN 123 | SKIP 0 | PASS 660 ]
> 
> proc.time()
   user  system elapsed 
  24.31    1.10   25.43