Last updated on 2025-02-26 14:54:23 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.5 | 10.92 | 126.90 | 137.82 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.1.5 | 5.85 | 88.96 | 94.81 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.5 | 217.73 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.5 | 217.87 | OK | |||
| r-devel-macos-arm64 | 0.1.5 | 69.00 | OK | |||
| r-devel-macos-x86_64 | 0.1.5 | 145.00 | OK | |||
| r-devel-windows-x86_64 | 0.1.5 | 11.00 | 134.00 | 145.00 | OK | |
| r-patched-linux-x86_64 | 0.1.5 | 7.10 | 117.38 | 124.48 | OK | |
| r-release-linux-x86_64 | 0.1.5 | 10.01 | 118.14 | 128.15 | OK | |
| r-release-macos-arm64 | 0.1.5 | 74.00 | OK | |||
| r-release-macos-x86_64 | 0.1.5 | 147.00 | OK | |||
| r-release-windows-x86_64 | 0.1.5 | 10.00 | 133.00 | 143.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.5 | OK | ||||
| r-oldrel-macos-x86_64 | 0.1.5 | 152.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.1.5 | 15.00 | 170.00 | 185.00 | OK |
Version: 0.1.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [32s/45s]
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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [21s/29s]
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
Flavor: r-devel-linux-x86_64-debian-gcc