* 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 ]
  
  ══ 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:
      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