Last updated on 2022-12-19 07:53:34 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.0 | 11.61 | 192.76 | 204.37 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.1.0 | 7.97 | 140.42 | 148.39 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.0 | 262.04 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.0 | 245.39 | ERROR | |||
| r-devel-windows-x86_64 | 0.1.0 | 28.00 | 233.00 | 261.00 | ERROR | |
| r-patched-linux-x86_64 | 0.1.0 | 8.26 | 185.77 | 194.03 | ERROR | |
| r-release-linux-x86_64 | 0.1.0 | 11.65 | 180.50 | 192.15 | ERROR | |
| r-release-macos-arm64 | 0.1.0 | 60.00 | OK | |||
| r-release-macos-x86_64 | 0.1.0 | 79.00 | OK | |||
| r-release-windows-x86_64 | 0.1.0 | 16.00 | 233.00 | 249.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.1.0 | 50.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.1.0 | 81.00 | OK | |||
| r-oldrel-windows-ix86+x86_64 | 0.1.0 | 29.00 | 224.00 | 253.00 | ERROR |
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in 'mpwR-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_Upset_list
> ### Title: Generate Upset list
> ### Aliases: get_Upset_list
>
> ### ** Examples
>
> # Load libraries
> library(tibble)
> library(magrittr)
> library(stringr)
>
> # Example data
> data <- list(
+ DIANN = list(
+ filename = "B",
+ software = "DIA-NN",
+ data = list(
+ "DIA-NN" = tibble::tibble(
+ Run_mpwR = rep(c("A","B"), times = 10),
+ Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
+ Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
+ Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 4),
+ ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
+ )
+ )
+ ),
+ Spectronaut = list(
+ filename = "C",
+ software = "Spectronaut",
+ data = list(
+ "Spectronaut" = tibble::tibble(
+ Run_mpwR = rep(c("A","B"), times = 15),
+ Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6),
+ Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 6),
+ ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6)
+ )
+ )
+ )
+ )
>
> # Result
> output <- get_Upset_list(
+ input_list = data,
+ level = "Precursor.IDs"
+ )
Error in `stringr::str_detect()`:
! `pattern` can't be the empty string (`""`).
Backtrace:
x
1. \-mpwR::get_Upset_list(input_list = data, level = "Precursor.IDs")
2. +-base::which(...)
3. \-stringr::str_detect(string = names(output_list), pattern = "")
4. \-stringr:::no_empty()
5. \-cli::cli_abort(...)
6. \-rlang::abort(...)
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.0
Check: tests
Result: ERROR
Running 'testthat.R' [88s/117s]
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:
x
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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building 'Import.Rmd' using rmarkdown
--- finished re-building 'Import.Rmd'
--- re-building 'Requirements.Rmd' using rmarkdown
--- finished re-building 'Requirements.Rmd'
--- re-building 'Workflow.Rmd' using rmarkdown
Quitting from lines 225-226 (Workflow.Rmd)
Error: processing vignette 'Workflow.Rmd' failed with diagnostics:
`pattern` can't be the empty string (`""`).
--- failed re-building 'Workflow.Rmd'
SUMMARY: processing the following file failed:
'Workflow.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘mpwR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_Upset_list
> ### Title: Generate Upset list
> ### Aliases: get_Upset_list
>
> ### ** Examples
>
> # Load libraries
> library(tibble)
> library(magrittr)
> library(stringr)
>
> # Example data
> data <- list(
+ DIANN = list(
+ filename = "B",
+ software = "DIA-NN",
+ data = list(
+ "DIA-NN" = tibble::tibble(
+ Run_mpwR = rep(c("A","B"), times = 10),
+ Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
+ Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
+ Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 4),
+ ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
+ )
+ )
+ ),
+ Spectronaut = list(
+ filename = "C",
+ software = "Spectronaut",
+ data = list(
+ "Spectronaut" = tibble::tibble(
+ Run_mpwR = rep(c("A","B"), times = 15),
+ Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6),
+ Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 6),
+ ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6)
+ )
+ )
+ )
+ )
>
> # Result
> output <- get_Upset_list(
+ input_list = data,
+ level = "Precursor.IDs"
+ )
Error in `stringr::str_detect()`:
! `pattern` can't be the empty string (`""`).
Backtrace:
▆
1. └─mpwR::get_Upset_list(input_list = data, level = "Precursor.IDs")
2. ├─base::which(...)
3. └─stringr::str_detect(string = names(output_list), pattern = "")
4. └─stringr:::no_empty()
5. └─cli::cli_abort(...)
6. └─rlang::abort(...)
Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [63s/105s]
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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘mpwR-Ex.R’ failed
The error most likely occurred in:
> ### Name: get_Upset_list
> ### Title: Generate Upset list
> ### Aliases: get_Upset_list
>
> ### ** Examples
>
> # Load libraries
> library(tibble)
> library(magrittr)
> library(stringr)
>
> # Example data
> data <- list(
+ DIANN = list(
+ filename = "B",
+ software = "DIA-NN",
+ data = list(
+ "DIA-NN" = tibble::tibble(
+ Run_mpwR = rep(c("A","B"), times = 10),
+ Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
+ Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
+ Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 4),
+ ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
+ )
+ )
+ ),
+ Spectronaut = list(
+ filename = "C",
+ software = "Spectronaut",
+ data = list(
+ "Spectronaut" = tibble::tibble(
+ Run_mpwR = rep(c("A","B"), times = 15),
+ Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6),
+ Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 6),
+ ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6)
+ )
+ )
+ )
+ )
>
> # Result
> output <- get_Upset_list(
+ input_list = data,
+ level = "Precursor.IDs"
+ )
Error in `stringr::str_detect()`:
! `pattern` can't be the empty string (`""`).
Backtrace:
▆
1. └─mpwR::get_Upset_list(input_list = data, level = "Precursor.IDs")
2. ├─base::which(...)
3. └─stringr::str_detect(string = names(output_list), pattern = "")
4. └─stringr:::no_empty()
5. └─cli::cli_abort(...)
6. └─rlang::abort(...)
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [109s/277s]
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
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘Import.Rmd’ using rmarkdown
--- finished re-building ‘Import.Rmd’
--- re-building ‘Requirements.Rmd’ using rmarkdown
--- finished re-building ‘Requirements.Rmd’
--- re-building ‘Workflow.Rmd’ using rmarkdown
Quitting from lines 225-226 (Workflow.Rmd)
Error: processing vignette 'Workflow.Rmd' failed with diagnostics:
`pattern` can't be the empty string (`""`).
--- failed re-building ‘Workflow.Rmd’
SUMMARY: processing the following file failed:
‘Workflow.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [99s/113s]
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
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.1.0
Check: tests
Result: ERROR
Running 'testthat.R' [86s]
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
Flavor: r-devel-windows-x86_64
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [84s/99s]
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
Flavor: r-patched-linux-x86_64
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [83s/93s]
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
Flavor: r-release-linux-x86_64
Version: 0.1.0
Check: tests
Result: ERROR
Running 'testthat.R' [90s]
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
Flavor: r-release-windows-x86_64
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in 'mpwR-Ex.R' failed
The error most likely occurred in:
> ### Name: get_Upset_list
> ### Title: Generate Upset list
> ### Aliases: get_Upset_list
>
> ### ** Examples
>
> # Load libraries
> library(tibble)
> library(magrittr)
> library(stringr)
>
> # Example data
> data <- list(
+ DIANN = list(
+ filename = "B",
+ software = "DIA-NN",
+ data = list(
+ "DIA-NN" = tibble::tibble(
+ Run_mpwR = rep(c("A","B"), times = 10),
+ Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
+ Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
+ Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 4),
+ ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
+ )
+ )
+ ),
+ Spectronaut = list(
+ filename = "C",
+ software = "Spectronaut",
+ data = list(
+ "Spectronaut" = tibble::tibble(
+ Run_mpwR = rep(c("A","B"), times = 15),
+ Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6),
+ Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 6),
+ ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6)
+ )
+ )
+ )
+ )
>
> # Result
> output <- get_Upset_list(
+ input_list = data,
+ level = "Precursor.IDs"
+ )
Error in `stringr::str_detect()`:
! `pattern` can't be the empty string (`""`).
Backtrace:
x
1. \-mpwR::get_Upset_list(input_list = data, level = "Precursor.IDs")
2. +-base::which(...)
3. \-stringr::str_detect(string = names(output_list), pattern = "")
4. \-stringr:::no_empty()
5. \-cli::cli_abort(...)
6. \-rlang::abort(...)
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64
Version: 0.1.0
Check: tests
Result: ERROR
Running 'testthat.R' [96s]
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:
x
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
Flavor: r-oldrel-windows-ix86+x86_64
Version: 0.1.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building 'Import.Rmd' using rmarkdown
--- finished re-building 'Import.Rmd'
--- re-building 'Requirements.Rmd' using rmarkdown
--- finished re-building 'Requirements.Rmd'
--- re-building 'Workflow.Rmd' using rmarkdown
Quitting from lines 225-226 (Workflow.Rmd)
Error: processing vignette 'Workflow.Rmd' failed with diagnostics:
`pattern` can't be the empty string (`""`).
--- failed re-building 'Workflow.Rmd'
SUMMARY: processing the following file failed:
'Workflow.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64