* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/mpwR.Rcheck’
* using R Under development (unstable) (2025-02-23 r87804)
* 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 ‘mpwR/DESCRIPTION’ ... OK
* this is package ‘mpwR’ version ‘0.1.5’
* 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 ‘mpwR’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/mpwR-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/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/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 ... [19s/27s] OK
* checking Rd files ... [0s/1s] 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 ... [8s/10s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [33s/46s] ERROR
  Running ‘testthat.R’ [32s/45s]
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:
      â–†
   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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [25s/36s] OK
* checking PDF version of manual ... [5s/8s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 ERROR