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Type 'q()' to quit R. > # 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) Loading required package: data.table Attaching package: 'mpactr' The following object is masked from 'package:utils': example > > 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 61 ions failed the cv_filter filter, 423 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 86 ions failed the cv_filter filter, 398 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 86 ions failed the cv_filter filter, 398 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 86 ions failed the cv_filter filter, 398 ions remain. i Parsing 484 peaks for replicability across technical replicates. v 61 ions failed the cv_filter filter, 423 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 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 86 ions failed the cv_filter filter, 398 ions remain. i Parsing 484 peaks for replicability across technical replicates. v 86 ions failed the cv_filter filter, 398 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 61 ions failed the cv_filter filter, 423 ions remain. i Parsing 484 peaks for replicability across technical replicates. v 61 ions failed the cv_filter filter, 423 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 61 ions failed the cv_filter filter, 423 ions remain. i Parsing 423 peaks for insource ions. v 23 ions failed the insource filter, 400 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: 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. 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 0 | WARN 0 | SKIP 1 | PASS 148 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-peak_table_formatter.R:32:1' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 148 ] > > proc.time() user system elapsed 76.68 9.53 77.98