• using R Under development (unstable) (2025-09-14 r88831)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-3) 15.2.0     GNU Fortran (Debian 15.2.0-3) 15.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘mpactr/DESCRIPTION’ ... OK
• this is package ‘mpactr’ version ‘0.3.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/2s] OK
• 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 whether package ‘mpactr’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘g++-15 (Debian 15.2.0-3) 15.2.0’
• 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/3s] 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/2s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/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 ... [8s/11s] 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 contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [1s/2s] 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 ... [22s/41s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [127s/198s] ERROR   Running ‘testthat.R’ [127s/198s] 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:32:1'      ══ 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 ... [88s/104s] OK
• checking PDF version of manual ... [5s/6s] OK
• checking HTML version of manual ... [0s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR