• using R Under development (unstable) (2025-12-18 r89199)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-11) 15.2.0     GNU Fortran (Debian 15.2.0-11) 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 ‘0.3.1’
• 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 15.2.0-11) 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 ... [1s/2s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the package can be unloaded cleanly ... [1s/1s] 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 ... [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 ... [7s/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 $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... NOTE File ‘mpactr/libs/mpactr.so’:   Found non-API call to R: ‘ATTRIB’ Compiled code should not call non-API entry points in R. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, and section ‘Moving into C API compliance’ for issues with the use of non-API entry points.
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [2s/3s] ERROR Running examples in ‘mpactr-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: filter_insource_ions > ### Title: Filter Insource ions > ### Aliases: filter_insource_ions > > ### ** Examples > > ## Don't show: > limit_cores() > ## End(Don't show) > data <- import_data( + example_path("coculture_peak_table.csv"), + example_path("metadata.csv"), + format = "Progenesis" + ) > > data_filter <- filter_insource_ions(data, + cluster_threshold = 0.95 + ) ℹ Parsing 1303 peaks for insource ions. Error in `[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, :   attempt access index 22/22 in VECTOR_ELT Calls: filter_insource_ions -> <Anonymous> -> <Anonymous> -> [ -> [.data.table Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [26s/33s] ERROR   Running ‘testthat.R’ [26s/33s] 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)   >   > limit_cores()   > 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.   Saving _problems/test-filter_pactr-methods-371.R   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.   Saving _problems/test-filters-176.R   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.   Saving _problems/test-filters-217.R   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.   Saving _problems/test-import_data-53.R   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.   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.   Saving _problems/test-qc_graph_pactr-class-25.R   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.   Saving _problems/test-quality_control-18.R   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.   Saving _problems/test-quality_control-44.R   [ FAIL 7 | WARN 0 | SKIP 0 | PASS 154 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-filter_pactr-methods.R:371:3'): filter_inscource_ions filters out data properly ──   Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT   Backtrace:       ▆    1. └─filter_class$filter_insource_ions(cluster_threshold = 0.95) at test-filter_pactr-methods.R:371:3    2. ├─self$mpactr_data$set_peak_table(...)    3. ├─...[]    4. └─data.table:::`[.data.table`(...)   ── Error ('test-filters.R:174:3'): filter insource ions wrapper works as expected ──   Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT   Backtrace:       ▆    1. └─mpactr::filter_insource_ions(...) at test-filters.R:174:3    2. └─mpactr_object$filter_insource_ions(cluster_threshold = cluster_threshold)    3. ├─self$mpactr_data$set_peak_table(...)    4. ├─...[]    5. └─data.table:::`[.data.table`(...)   ── Error ('test-filters.R:217:3'): filters abort if the filter has already been run ──   Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT   Backtrace:       ▆    1. └─mpactr::filter_insource_ions(data_mpactr, cluster_threshold = 0.95) at test-filters.R:217:3    2. └─mpactr_object$filter_insource_ions(cluster_threshold = cluster_threshold)    3. ├─self$mpactr_data$set_peak_table(...)    4. ├─...[]    5. └─data.table:::`[.data.table`(...)   ── Error ('test-import_data.R:45:3'): We can use a data.frame as input our peak table in import_data ──   Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT   Backtrace:       ▆    1. └─mpactr::filter_insource_ions(...) at test-import_data.R:45:3    2. └─mpactr_object$filter_insource_ions(cluster_threshold = cluster_threshold)    3. ├─self$mpactr_data$set_peak_table(...)    4. ├─...[]    5. └─data.table:::`[.data.table`(...)   ── Error ('test-qc_graph_pactr-class.R:25:3'): plot_QC_Tree generates the correct plot ──   Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT   Backtrace:       ▆    1. └─filter_class$filter_insource_ions(cluster_threshold = 0.95) at test-qc_graph_pactr-class.R:25:3    2. ├─self$mpactr_data$set_peak_table(...)    3. ├─...[]    4. └─data.table:::`[.data.table`(...)   ── Error ('test-quality_control.R:18:3'): qc_summary returns a summary data.table ──   Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT   Backtrace:       ▆    1. └─mpactr::filter_insource_ions(data, cluster_threshold = 0.95) at test-quality_control.R:18:3    2. └─mpactr_object$filter_insource_ions(cluster_threshold = cluster_threshold)    3. ├─self$mpactr_data$set_peak_table(...)    4. ├─...[]    5. └─data.table:::`[.data.table`(...)   ── Error ('test-quality_control.R:44:3'): qc plot returns a generates a plot ───   Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT   Backtrace:       ▆    1. └─mpactr::filter_insource_ions(data, cluster_threshold = 0.95) at test-quality_control.R:44:3    2. └─mpactr_object$filter_insource_ions(cluster_threshold = cluster_threshold)    3. ├─self$mpactr_data$set_peak_table(...)    4. ├─...[]    5. └─data.table:::`[.data.table`(...)      [ FAIL 7 | WARN 0 | SKIP 0 | PASS 154 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [32s/45s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘downstream_analyses.Rmd’ using rmarkdown Warning: Duplicated chunk option(s) 'warning' in both chunk header and pipe comments of the chunk 'unnamed-chunk-19'. [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘downstream_analyses.Rmd’ --- re-building ‘mpactr.Rmd’ using rmarkdown Quitting from mpactr.Rmd:296-301 [unnamed-chunk-23] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 34/34 in VECTOR_ELT --- Backtrace:     ▆  1. ├─mpactr::filter_insource_ions(...)  2. │ └─mpactr_object$filter_insource_ions(cluster_threshold = cluster_threshold)  3. │ ├─self$mpactr_data$set_peak_table(...)  4. │ ├─...[]  5. │ └─data.table:::`[.data.table`(...)  6. └─private$deconvolute_correlation(.SD, cluster_threshold)  7. ├─...[]  8. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'mpactr.Rmd' failed with diagnostics: attempt access index 34/34 in VECTOR_ELT --- failed re-building ‘mpactr.Rmd’ --- re-building ‘reference_semantics.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘reference_semantics.Rmd’ SUMMARY: processing the following file failed:   ‘mpactr.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [4s/5s] OK
• checking HTML version of manual ... [1s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 3 ERRORs, 1 NOTE