* using log directory 'd:/RCompile/CRANincoming/R-devel/mpactr.Rcheck'
* using R Under development (unstable) (2025-09-10 r88809 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'mpactr/DESCRIPTION' ... OK
* this is package 'mpactr' version '0.3.1'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [16s] NOTE
Maintainer: 'Patrick Schloss <pschloss@umich.edu>'

Days since last update: 4
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'mpactr' can be installed ... OK
* used C++ compiler: 'g++.exe (GCC) 14.2.0'
* checking installed package size ... OK
* 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [12s] OK
* checking Rd files ... 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [14s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [68s] ERROR
  Running 'testthat.R' [68s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(mpactr)
  > 
  > test_check("mpactr")
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Parsing 484 peaks for replicability across technical replicates.
  v 33 ions failed the cv_filter filter, 451 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1303 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 796 ions failed the Blanks filter, 507 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Parsing 484 peaks for replicability across technical replicates.
  v 33 ions failed the cv_filter filter, 451 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Parsing 484 peaks for replicability across technical replicates.
  v 33 ions failed the cv_filter filter, 451 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method .
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  ! Argument remove_ions is FALSE. Peaks from Blanks will not be removed.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Parsing 484 peaks for replicability across technical replicates.
  v 33 ions failed the cv_filter filter, 451 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Checking 1289 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 65 ions failed the mispicked filter, 1224 ions remain.
  i Parsing 1224 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 698 ions failed the Blanks filter, 526 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Parsing 484 peaks for insource ions.
  v 27 ions failed the insource filter, 457 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1233 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 0 ions failed the mispicked filter, 1233 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  ! Argument merge_peaks is: FALSE. Mispicked peaks will not be merged.
  v 70 ions failed the mispicked filter, 1303 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  ! Argument merge_peaks is: FALSE. Mispicked peaks will not be merged.
  v 70 ions failed the mispicked filter, 1303 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  ! Argument remove_ions is FALSE. Peaks from Blanks will not be removed.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Parsing 484 peaks for replicability across technical replicates.
  v 33 ions failed the cv_filter filter, 451 ions remain.
  i Parsing 484 peaks for replicability across technical replicates.
  v 33 ions failed the cv_filter filter, 451 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Parsing 484 peaks for insource ions.
  v 27 ions failed the insource filter, 457 ions remain.
  i Parsing 484 peaks for insource ions.
  v 27 ions failed the insource filter, 457 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Parsing 484 peaks for replicability across technical replicates.
  v 33 ions failed the cv_filter filter, 451 ions remain.
  i Parsing 451 peaks for insource ions.
  v 25 ions failed the insource filter, 426 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks for replicability across technical replicates.
  v 279 ions failed the cv_filter filter, 954 ions remain.
  i Parsing 954 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 384 ions failed the Blanks filter, 570 ions remain.
  i Parsing 570 peaks for insource ions.
  v 26 ions failed the insource filter, 544 ions remain.
  Found duplicate compound values, will add a suffix to unique the value.
  Found duplicate compound values, will add a suffix to unique the value.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Coculture.
  i Argument remove_ions is: TRUE.Removing peaks from Coculture.
  v 354 ions failed the Coculture filter, 879 ions remain.
  Rows: 1306 Columns: 21
  -- Column specification --------------------------------------------------------
  Delimiter: ","
  dbl (21): Compound, mz, rt, 102623_UM1848B_JC1_69_1_5004, 102623_UM1846B_Med...
  
  i Use `spec()` to retrieve the full column specification for this data.
  i Specify the column types or set `show_col_types = FALSE` to quiet this message.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Parsing 484 peaks for insource ions.
  v 27 ions failed the insource filter, 457 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Parsing 484 peaks based on the sample group: Coculture.
  i Argument remove_ions is: TRUE.Removing peaks from Coculture.
  v 293 ions failed the Coculture filter, 191 ions remain.
  i Parsing 191 peaks for insource ions.
  v 15 ions failed the insource filter, 176 ions remain.
  i Checking 1303 peaks for mispicked peaks.
  i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
  v 70 ions failed the mispicked filter, 1233 ions remain.
  i Parsing 1233 peaks based on the sample group: Blanks.
  i Argument remove_ions is: TRUE.Removing peaks from Blanks.
  v 749 ions failed the Blanks filter, 484 ions remain.
  i Parsing 484 peaks for insource ions.
  v 27 ions failed the insource filter, 457 ions remain.
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 171 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • empty test (1): 'test-peak_table_formatter.R:34:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-qc_graph_pactr-class.R:32:3'): plot_QC_Tree generates the correct plot ──
  class(plot) (`actual`) not equal to c("gg", "ggplot") (`expected`).
  
  `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
  `expected[2:2]`:                                                      "ggplot"
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 171 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [58s] OK
* checking PDF version of manual ... [23s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE