CRAN Package Check Results for Package flowTraceR

Last updated on 2025-03-01 09:51:51 CET.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	0.1.0	5.85	60.76	66.61	ERROR
r-devel-linux-x86_64-debian-gcc	0.1.0	4.15	44.68	48.83	ERROR
r-devel-linux-x86_64-fedora-clang	0.1.0			105.88	ERROR
r-devel-linux-x86_64-fedora-gcc	0.1.0			118.33	ERROR
r-devel-macos-arm64	0.1.0			65.00	OK
r-devel-macos-x86_64	0.1.0			80.00	OK
r-devel-windows-x86_64	0.1.0	8.00	83.00	91.00	ERROR
r-patched-linux-x86_64	0.1.0	5.49	62.78	68.27	OK
r-release-linux-x86_64	0.1.0	5.54	63.04	68.58	OK
r-release-macos-arm64	0.1.0			44.00	OK
r-release-macos-x86_64	0.1.0			110.00	OK
r-release-windows-x86_64	0.1.0	7.00	91.00	98.00	OK
r-oldrel-macos-arm64	0.1.0				OK
r-oldrel-macos-x86_64	0.1.0			68.00	OK
r-oldrel-windows-x86_64	0.1.0	9.00	98.00	107.00	OK

Check Details

Version: 0.1.0
Check: examples
Result: ERROR Running examples in ‘flowTraceR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: convert_all_levels > ### Title: Conversion of software specific levels > ### Aliases: convert_all_levels > > ### ** Examples > > # Load libraries > library(dplyr) Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union > library(stringr) > library(tidyr) > library(comprehenr) > library(tibble) > > # MaxQuant example data > evidence <- tibble::tibble( + "Modified sequence" = c("_AACLLPK_", + "_ALTDM(Oxidation (M))PQM(Oxidation (M))R_", + "ALTDM(Dummy_Modification)PQMK"), + Charge = c(2,2,3), + "Protein group IDs" = c("26", "86;17", "86;17") + ) > > proteingroups <- tibble::tibble( + "Protein IDs" = c("A0A075B6P5;P01615;A0A087WW87;P01614;A0A075B6S6", "P02671", "P02672"), + id = c(26, 86, 17) + ) > > # Conversion > convert_all_levels( + input_df = evidence, + input_MQ_pg = proteingroups, + software = "MaxQuant" + ) Error in unlist(., .data, use.names = FALSE) : 'recursive' must be a length-1 vector Calls: convert_all_levels -> sort_string_pg -> %>% -> unlist Execution halted Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 0.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [7s/9s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(flowTraceR) > > test_check("flowTraceR") [ FAIL 9 | WARN 26 | SKIP 0 | PASS 143 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_conversion.R:160:3'): convert_proteingroups with MaxQuant output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_proteingroups(input_df = data, software = "MaxQuant") at test_conversion.R:160:3 2. │ └─flowTraceR:::sort_string_pg(...) 3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 4. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:178:3'): convert_proteingroups with PD output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_proteingroups(input_df = data, software = "PD") at test_conversion.R:178:3 2. │ └─flowTraceR:::sort_string_pg(...) 3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 4. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:196:3'): convert_proteingroups with DIA-NN output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_proteingroups(input_df = data, software = "DIA-NN") at test_conversion.R:196:3 2. │ └─flowTraceR:::sort_string_pg(...) 3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 4. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:214:3'): convert_proteingroups with Spectronaut output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_proteingroups(input_df = data, software = "Spectronaut") at test_conversion.R:214:3 2. │ └─flowTraceR:::sort_string_pg(...) 3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 4. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:239:3'): convert_all_levels with MaxQuant output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_all_levels(...) at test_conversion.R:239:3 2. │ └─flowTraceR:::sort_string_pg(...) 3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 4. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:260:3'): convert_all_levels with PD output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_all_levels(input_df = data, software = "PD") at test_conversion.R:260:3 2. │ └─... %>% convert_precursor(software = "PD") 3. ├─flowTraceR::convert_precursor(., software = "PD") 4. │ ├─"Annotated Sequence" %in% colnames(input_df) 5. │ └─base::colnames(input_df) 6. │ └─base::is.data.frame(x) 7. ├─flowTraceR::convert_modified_peptides(., software = "PD") 8. │ ├─"Annotated Sequence" %in% colnames(input_df) 9. │ └─base::colnames(input_df) 10. │ └─base::is.data.frame(x) 11. ├─flowTraceR::convert_proteingroups(., software = "PD") 12. │ └─flowTraceR:::sort_string_pg(...) 13. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 14. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:278:3'): convert_all_levels with DIA-NN output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_all_levels(input_df = data, software = "DIA-NN") at test_conversion.R:278:3 2. │ └─... %>% convert_precursor(software = "DIA-NN") 3. ├─flowTraceR::convert_precursor(., software = "DIA-NN") 4. │ ├─"Precursor.Id" %in% colnames(input_df) 5. │ └─base::colnames(input_df) 6. │ └─base::is.data.frame(x) 7. ├─flowTraceR::convert_modified_peptides(., software = "DIA-NN") 8. │ ├─"Precursor.Id" %in% colnames(input_df) 9. │ └─base::colnames(input_df) 10. │ └─base::is.data.frame(x) 11. ├─flowTraceR::convert_proteingroups(., software = "DIA-NN") 12. │ └─flowTraceR:::sort_string_pg(...) 13. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 14. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:296:3'): convert_all_levels with Spectronaut output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_all_levels(input_df = data, software = "Spectronaut") at test_conversion.R:296:3 2. │ └─... %>% convert_precursor(software = "Spectronaut") 3. ├─flowTraceR::convert_precursor(., software = "Spectronaut") 4. │ ├─"EG.PrecursorId" %in% colnames(input_df) 5. │ └─base::colnames(input_df) 6. │ └─base::is.data.frame(x) 7. ├─flowTraceR::convert_modified_peptides(., software = "Spectronaut") 8. │ ├─"EG.PrecursorId" %in% colnames(input_df) 9. │ └─base::colnames(input_df) 10. │ └─base::is.data.frame(x) 11. ├─flowTraceR::convert_proteingroups(., software = "Spectronaut") 12. │ └─flowTraceR:::sort_string_pg(...) 13. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 14. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_utils.R:44:3'): sort_string_pg is succesful ──────────────────── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR:::sort_string_pg(...) at test_utils.R:44:3 2. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 3. └─base::unlist(., .data, use.names = FALSE) [ FAIL 9 | WARN 26 | SKIP 0 | PASS 143 ] 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 ‘Example_RT_distribution.Rmd’ using rmarkdown Quitting from lines 51-55 [all levels] (Example_RT_distribution.Rmd) Error: processing vignette 'Example_RT_distribution.Rmd' failed with diagnostics: 'recursive' must be a length-1 vector --- failed re-building ‘Example_RT_distribution.Rmd’ --- re-building ‘Requirements.Rmd’ using rmarkdown --- finished re-building ‘Requirements.Rmd’ --- re-building ‘Workflow.Rmd’ using rmarkdown Quitting from lines 97-101 [proteinGroup] (Workflow.Rmd) Error: processing vignette 'Workflow.Rmd' failed with diagnostics: 'recursive' must be a length-1 vector --- failed re-building ‘Workflow.Rmd’ SUMMARY: processing the following files failed: ‘Example_RT_distribution.Rmd’ ‘Workflow.Rmd’ Error: Vignette re-building failed. Execution halted Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 0.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [5s/6s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(flowTraceR) > > test_check("flowTraceR") [ FAIL 9 | WARN 26 | SKIP 0 | PASS 143 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_conversion.R:160:3'): convert_proteingroups with MaxQuant output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_proteingroups(input_df = data, software = "MaxQuant") at test_conversion.R:160:3 2. │ └─flowTraceR:::sort_string_pg(...) 3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 4. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:178:3'): convert_proteingroups with PD output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_proteingroups(input_df = data, software = "PD") at test_conversion.R:178:3 2. │ └─flowTraceR:::sort_string_pg(...) 3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 4. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:196:3'): convert_proteingroups with DIA-NN output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_proteingroups(input_df = data, software = "DIA-NN") at test_conversion.R:196:3 2. │ └─flowTraceR:::sort_string_pg(...) 3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 4. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:214:3'): convert_proteingroups with Spectronaut output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_proteingroups(input_df = data, software = "Spectronaut") at test_conversion.R:214:3 2. │ └─flowTraceR:::sort_string_pg(...) 3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 4. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:239:3'): convert_all_levels with MaxQuant output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_all_levels(...) at test_conversion.R:239:3 2. │ └─flowTraceR:::sort_string_pg(...) 3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 4. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:260:3'): convert_all_levels with PD output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_all_levels(input_df = data, software = "PD") at test_conversion.R:260:3 2. │ └─... %>% convert_precursor(software = "PD") 3. ├─flowTraceR::convert_precursor(., software = "PD") 4. │ ├─"Annotated Sequence" %in% colnames(input_df) 5. │ └─base::colnames(input_df) 6. │ └─base::is.data.frame(x) 7. ├─flowTraceR::convert_modified_peptides(., software = "PD") 8. │ ├─"Annotated Sequence" %in% colnames(input_df) 9. │ └─base::colnames(input_df) 10. │ └─base::is.data.frame(x) 11. ├─flowTraceR::convert_proteingroups(., software = "PD") 12. │ └─flowTraceR:::sort_string_pg(...) 13. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 14. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:278:3'): convert_all_levels with DIA-NN output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_all_levels(input_df = data, software = "DIA-NN") at test_conversion.R:278:3 2. │ └─... %>% convert_precursor(software = "DIA-NN") 3. ├─flowTraceR::convert_precursor(., software = "DIA-NN") 4. │ ├─"Precursor.Id" %in% colnames(input_df) 5. │ └─base::colnames(input_df) 6. │ └─base::is.data.frame(x) 7. ├─flowTraceR::convert_modified_peptides(., software = "DIA-NN") 8. │ ├─"Precursor.Id" %in% colnames(input_df) 9. │ └─base::colnames(input_df) 10. │ └─base::is.data.frame(x) 11. ├─flowTraceR::convert_proteingroups(., software = "DIA-NN") 12. │ └─flowTraceR:::sort_string_pg(...) 13. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 14. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:296:3'): convert_all_levels with Spectronaut output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_all_levels(input_df = data, software = "Spectronaut") at test_conversion.R:296:3 2. │ └─... %>% convert_precursor(software = "Spectronaut") 3. ├─flowTraceR::convert_precursor(., software = "Spectronaut") 4. │ ├─"EG.PrecursorId" %in% colnames(input_df) 5. │ └─base::colnames(input_df) 6. │ └─base::is.data.frame(x) 7. ├─flowTraceR::convert_modified_peptides(., software = "Spectronaut") 8. │ ├─"EG.PrecursorId" %in% colnames(input_df) 9. │ └─base::colnames(input_df) 10. │ └─base::is.data.frame(x) 11. ├─flowTraceR::convert_proteingroups(., software = "Spectronaut") 12. │ └─flowTraceR:::sort_string_pg(...) 13. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 14. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_utils.R:44:3'): sort_string_pg is succesful ──────────────────── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR:::sort_string_pg(...) at test_utils.R:44:3 2. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 3. └─base::unlist(., .data, use.names = FALSE) [ FAIL 9 | WARN 26 | SKIP 0 | PASS 143 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.1.0
Check: examples
Result: ERROR Running examples in ‘flowTraceR-Ex.R’ failed The error most likely occurred in: > ### Name: convert_all_levels > ### Title: Conversion of software specific levels > ### Aliases: convert_all_levels > > ### ** Examples > > # Load libraries > library(dplyr) Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union > library(stringr) > library(tidyr) > library(comprehenr) > library(tibble) > > # MaxQuant example data > evidence <- tibble::tibble( + "Modified sequence" = c("_AACLLPK_", + "_ALTDM(Oxidation (M))PQM(Oxidation (M))R_", + "ALTDM(Dummy_Modification)PQMK"), + Charge = c(2,2,3), + "Protein group IDs" = c("26", "86;17", "86;17") + ) > > proteingroups <- tibble::tibble( + "Protein IDs" = c("A0A075B6P5;P01615;A0A087WW87;P01614;A0A075B6S6", "P02671", "P02672"), + id = c(26, 86, 17) + ) > > # Conversion > convert_all_levels( + input_df = evidence, + input_MQ_pg = proteingroups, + software = "MaxQuant" + ) Error in unlist(., .data, use.names = FALSE) : 'recursive' must be a length-1 vector Calls: convert_all_levels -> sort_string_pg -> %>% -> unlist Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64

Version: 0.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [11s/15s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(flowTraceR) > > test_check("flowTraceR") [ FAIL 9 | WARN 26 | SKIP 0 | PASS 143 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_conversion.R:160:3'): convert_proteingroups with MaxQuant output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_proteingroups(input_df = data, software = "MaxQuant") at test_conversion.R:160:3 2. │ └─flowTraceR:::sort_string_pg(...) 3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 4. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:178:3'): convert_proteingroups with PD output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_proteingroups(input_df = data, software = "PD") at test_conversion.R:178:3 2. │ └─flowTraceR:::sort_string_pg(...) 3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 4. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:196:3'): convert_proteingroups with DIA-NN output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_proteingroups(input_df = data, software = "DIA-NN") at test_conversion.R:196:3 2. │ └─flowTraceR:::sort_string_pg(...) 3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 4. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:214:3'): convert_proteingroups with Spectronaut output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_proteingroups(input_df = data, software = "Spectronaut") at test_conversion.R:214:3 2. │ └─flowTraceR:::sort_string_pg(...) 3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 4. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:239:3'): convert_all_levels with MaxQuant output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_all_levels(...) at test_conversion.R:239:3 2. │ └─flowTraceR:::sort_string_pg(...) 3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 4. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:260:3'): convert_all_levels with PD output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_all_levels(input_df = data, software = "PD") at test_conversion.R:260:3 2. │ └─... %>% convert_precursor(software = "PD") 3. ├─flowTraceR::convert_precursor(., software = "PD") 4. │ ├─"Annotated Sequence" %in% colnames(input_df) 5. │ └─base::colnames(input_df) 6. │ └─base::is.data.frame(x) 7. ├─flowTraceR::convert_modified_peptides(., software = "PD") 8. │ ├─"Annotated Sequence" %in% colnames(input_df) 9. │ └─base::colnames(input_df) 10. │ └─base::is.data.frame(x) 11. ├─flowTraceR::convert_proteingroups(., software = "PD") 12. │ └─flowTraceR:::sort_string_pg(...) 13. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 14. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:278:3'): convert_all_levels with DIA-NN output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_all_levels(input_df = data, software = "DIA-NN") at test_conversion.R:278:3 2. │ └─... %>% convert_precursor(software = "DIA-NN") 3. ├─flowTraceR::convert_precursor(., software = "DIA-NN") 4. │ ├─"Precursor.Id" %in% colnames(input_df) 5. │ └─base::colnames(input_df) 6. │ └─base::is.data.frame(x) 7. ├─flowTraceR::convert_modified_peptides(., software = "DIA-NN") 8. │ ├─"Precursor.Id" %in% colnames(input_df) 9. │ └─base::colnames(input_df) 10. │ └─base::is.data.frame(x) 11. ├─flowTraceR::convert_proteingroups(., software = "DIA-NN") 12. │ └─flowTraceR:::sort_string_pg(...) 13. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 14. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:296:3'): convert_all_levels with Spectronaut output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_all_levels(input_df = data, software = "Spectronaut") at test_conversion.R:296:3 2. │ └─... %>% convert_precursor(software = "Spectronaut") 3. ├─flowTraceR::convert_precursor(., software = "Spectronaut") 4. │ ├─"EG.PrecursorId" %in% colnames(input_df) 5. │ └─base::colnames(input_df) 6. │ └─base::is.data.frame(x) 7. ├─flowTraceR::convert_modified_peptides(., software = "Spectronaut") 8. │ ├─"EG.PrecursorId" %in% colnames(input_df) 9. │ └─base::colnames(input_df) 10. │ └─base::is.data.frame(x) 11. ├─flowTraceR::convert_proteingroups(., software = "Spectronaut") 12. │ └─flowTraceR:::sort_string_pg(...) 13. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 14. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_utils.R:44:3'): sort_string_pg is succesful ──────────────────── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR:::sort_string_pg(...) at test_utils.R:44:3 2. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 3. └─base::unlist(., .data, use.names = FALSE) [ FAIL 9 | WARN 26 | SKIP 0 | PASS 143 ] 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 ‘Example_RT_distribution.Rmd’ using rmarkdown Quitting from lines 51-55 [all levels] (Example_RT_distribution.Rmd) Error: processing vignette 'Example_RT_distribution.Rmd' failed with diagnostics: 'recursive' must be a length-1 vector --- failed re-building ‘Example_RT_distribution.Rmd’ --- re-building ‘Requirements.Rmd’ using rmarkdown --- finished re-building ‘Requirements.Rmd’ --- re-building ‘Workflow.Rmd’ using rmarkdown Quitting from lines 97-101 [proteinGroup] (Workflow.Rmd) Error: processing vignette 'Workflow.Rmd' failed with diagnostics: 'recursive' must be a length-1 vector --- failed re-building ‘Workflow.Rmd’ SUMMARY: processing the following files failed: ‘Example_RT_distribution.Rmd’ ‘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

Version: 0.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [11s/16s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(flowTraceR) > > test_check("flowTraceR") [ FAIL 9 | WARN 26 | SKIP 0 | PASS 143 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_conversion.R:160:3'): convert_proteingroups with MaxQuant output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_proteingroups(input_df = data, software = "MaxQuant") at test_conversion.R:160:3 2. │ └─flowTraceR:::sort_string_pg(...) 3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 4. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:178:3'): convert_proteingroups with PD output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_proteingroups(input_df = data, software = "PD") at test_conversion.R:178:3 2. │ └─flowTraceR:::sort_string_pg(...) 3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 4. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:196:3'): convert_proteingroups with DIA-NN output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_proteingroups(input_df = data, software = "DIA-NN") at test_conversion.R:196:3 2. │ └─flowTraceR:::sort_string_pg(...) 3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 4. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:214:3'): convert_proteingroups with Spectronaut output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_proteingroups(input_df = data, software = "Spectronaut") at test_conversion.R:214:3 2. │ └─flowTraceR:::sort_string_pg(...) 3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 4. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:239:3'): convert_all_levels with MaxQuant output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_all_levels(...) at test_conversion.R:239:3 2. │ └─flowTraceR:::sort_string_pg(...) 3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 4. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:260:3'): convert_all_levels with PD output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_all_levels(input_df = data, software = "PD") at test_conversion.R:260:3 2. │ └─... %>% convert_precursor(software = "PD") 3. ├─flowTraceR::convert_precursor(., software = "PD") 4. │ ├─"Annotated Sequence" %in% colnames(input_df) 5. │ └─base::colnames(input_df) 6. │ └─base::is.data.frame(x) 7. ├─flowTraceR::convert_modified_peptides(., software = "PD") 8. │ ├─"Annotated Sequence" %in% colnames(input_df) 9. │ └─base::colnames(input_df) 10. │ └─base::is.data.frame(x) 11. ├─flowTraceR::convert_proteingroups(., software = "PD") 12. │ └─flowTraceR:::sort_string_pg(...) 13. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 14. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:278:3'): convert_all_levels with DIA-NN output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_all_levels(input_df = data, software = "DIA-NN") at test_conversion.R:278:3 2. │ └─... %>% convert_precursor(software = "DIA-NN") 3. ├─flowTraceR::convert_precursor(., software = "DIA-NN") 4. │ ├─"Precursor.Id" %in% colnames(input_df) 5. │ └─base::colnames(input_df) 6. │ └─base::is.data.frame(x) 7. ├─flowTraceR::convert_modified_peptides(., software = "DIA-NN") 8. │ ├─"Precursor.Id" %in% colnames(input_df) 9. │ └─base::colnames(input_df) 10. │ └─base::is.data.frame(x) 11. ├─flowTraceR::convert_proteingroups(., software = "DIA-NN") 12. │ └─flowTraceR:::sort_string_pg(...) 13. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 14. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:296:3'): convert_all_levels with Spectronaut output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_all_levels(input_df = data, software = "Spectronaut") at test_conversion.R:296:3 2. │ └─... %>% convert_precursor(software = "Spectronaut") 3. ├─flowTraceR::convert_precursor(., software = "Spectronaut") 4. │ ├─"EG.PrecursorId" %in% colnames(input_df) 5. │ └─base::colnames(input_df) 6. │ └─base::is.data.frame(x) 7. ├─flowTraceR::convert_modified_peptides(., software = "Spectronaut") 8. │ ├─"EG.PrecursorId" %in% colnames(input_df) 9. │ └─base::colnames(input_df) 10. │ └─base::is.data.frame(x) 11. ├─flowTraceR::convert_proteingroups(., software = "Spectronaut") 12. │ └─flowTraceR:::sort_string_pg(...) 13. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 14. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_utils.R:44:3'): sort_string_pg is succesful ──────────────────── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR:::sort_string_pg(...) at test_utils.R:44:3 2. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 3. └─base::unlist(., .data, use.names = FALSE) [ FAIL 9 | WARN 26 | SKIP 0 | PASS 143 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.1.0
Check: tests
Result: ERROR Running 'testthat.R' [6s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(flowTraceR) > > test_check("flowTraceR") [ FAIL 9 | WARN 26 | SKIP 0 | PASS 143 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_conversion.R:160:3'): convert_proteingroups with MaxQuant output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_proteingroups(input_df = data, software = "MaxQuant") at test_conversion.R:160:3 2. │ └─flowTraceR:::sort_string_pg(...) 3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 4. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:178:3'): convert_proteingroups with PD output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_proteingroups(input_df = data, software = "PD") at test_conversion.R:178:3 2. │ └─flowTraceR:::sort_string_pg(...) 3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 4. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:196:3'): convert_proteingroups with DIA-NN output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_proteingroups(input_df = data, software = "DIA-NN") at test_conversion.R:196:3 2. │ └─flowTraceR:::sort_string_pg(...) 3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 4. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:214:3'): convert_proteingroups with Spectronaut output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_proteingroups(input_df = data, software = "Spectronaut") at test_conversion.R:214:3 2. │ └─flowTraceR:::sort_string_pg(...) 3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 4. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:239:3'): convert_all_levels with MaxQuant output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_all_levels(...) at test_conversion.R:239:3 2. │ └─flowTraceR:::sort_string_pg(...) 3. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 4. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:260:3'): convert_all_levels with PD output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_all_levels(input_df = data, software = "PD") at test_conversion.R:260:3 2. │ └─... %>% convert_precursor(software = "PD") 3. ├─flowTraceR::convert_precursor(., software = "PD") 4. │ ├─"Annotated Sequence" %in% colnames(input_df) 5. │ └─base::colnames(input_df) 6. │ └─base::is.data.frame(x) 7. ├─flowTraceR::convert_modified_peptides(., software = "PD") 8. │ ├─"Annotated Sequence" %in% colnames(input_df) 9. │ └─base::colnames(input_df) 10. │ └─base::is.data.frame(x) 11. ├─flowTraceR::convert_proteingroups(., software = "PD") 12. │ └─flowTraceR:::sort_string_pg(...) 13. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 14. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:278:3'): convert_all_levels with DIA-NN output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_all_levels(input_df = data, software = "DIA-NN") at test_conversion.R:278:3 2. │ └─... %>% convert_precursor(software = "DIA-NN") 3. ├─flowTraceR::convert_precursor(., software = "DIA-NN") 4. │ ├─"Precursor.Id" %in% colnames(input_df) 5. │ └─base::colnames(input_df) 6. │ └─base::is.data.frame(x) 7. ├─flowTraceR::convert_modified_peptides(., software = "DIA-NN") 8. │ ├─"Precursor.Id" %in% colnames(input_df) 9. │ └─base::colnames(input_df) 10. │ └─base::is.data.frame(x) 11. ├─flowTraceR::convert_proteingroups(., software = "DIA-NN") 12. │ └─flowTraceR:::sort_string_pg(...) 13. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 14. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_conversion.R:296:3'): convert_all_levels with Spectronaut output is succesful ── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR::convert_all_levels(input_df = data, software = "Spectronaut") at test_conversion.R:296:3 2. │ └─... %>% convert_precursor(software = "Spectronaut") 3. ├─flowTraceR::convert_precursor(., software = "Spectronaut") 4. │ ├─"EG.PrecursorId" %in% colnames(input_df) 5. │ └─base::colnames(input_df) 6. │ └─base::is.data.frame(x) 7. ├─flowTraceR::convert_modified_peptides(., software = "Spectronaut") 8. │ ├─"EG.PrecursorId" %in% colnames(input_df) 9. │ └─base::colnames(input_df) 10. │ └─base::is.data.frame(x) 11. ├─flowTraceR::convert_proteingroups(., software = "Spectronaut") 12. │ └─flowTraceR:::sort_string_pg(...) 13. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 14. └─base::unlist(., .data, use.names = FALSE) ── Error ('test_utils.R:44:3'): sort_string_pg is succesful ──────────────────── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: ▆ 1. ├─flowTraceR:::sort_string_pg(...) at test_utils.R:44:3 2. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 3. └─base::unlist(., .data, use.names = FALSE) [ FAIL 9 | WARN 26 | SKIP 0 | PASS 143 ] Error: Test failures Execution halted Flavor: r-devel-windows-x86_64