CRAN Package Check Results for Package mpwR

Last updated on 2025-03-09 05:52:37 CET.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	0.1.5	9.86	128.10	137.96	ERROR
r-devel-linux-x86_64-debian-gcc	0.1.5	6.83	87.72	94.55	ERROR
r-devel-linux-x86_64-fedora-clang	0.1.5			243.15	ERROR
r-devel-linux-x86_64-fedora-gcc	0.1.5			242.08	ERROR
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	130.00	141.00	ERROR
r-patched-linux-x86_64	0.1.5	9.68	117.50	127.18	OK
r-release-linux-x86_64	0.1.5	8.80	117.23	126.03	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	136.00	146.00	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	14.00	163.00	177.00	OK

Check Details

Version: 0.1.5
Check: tests
Result: ERROR Running ‘testthat.R’ [33s/43s] 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/27s] 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

Version: 0.1.5
Check: tests
Result: ERROR Running ‘testthat.R’ [57s/154s] 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-fedora-clang

Version: 0.1.5
Check: tests
Result: ERROR Running ‘testthat.R’ [53s/168s] 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-fedora-gcc

Version: 0.1.5
Check: tests
Result: ERROR Running 'testthat.R' [26s] 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-windows-x86_64