* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/flowTraceR.Rcheck’ * using R Under development (unstable) (2025-02-26 r87830) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (1+b1) Debian flang-new version 19.1.7 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘flowTraceR/DESCRIPTION’ ... OK * this is package ‘flowTraceR’ version ‘0.1.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘flowTraceR’ can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/flowTraceR-00install.html' for details. * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [2s/2s] OK * checking whether the package can be loaded with stated dependencies ... [1s/2s] OK * checking whether the package can be unloaded cleanly ... [1s/2s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/2s] OK * checking loading without being on the library search path ... [1s/2s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [9s/12s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [3s/4s] 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 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [8s/9s] 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 ] â•â• Failed tests â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â• ── 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: â–† 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: â–† 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: â–† 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: â–† 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: â–† 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: â–† 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: â–† 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: â–† 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: â–† 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 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [6s/8s] 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 * checking PDF version of manual ... [6s/8s] OK * checking HTML version of manual ... [0s/1s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 3 ERRORs