R Under development (unstable) (2024-01-20 r85814 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(GCalignR) > > test_check("GCalignR") Run GCalignR Start: 2024-01-22 21:56:07 Data for 3 samples loaded. Start correcting linear shifts with "M2" as a reference ... Start aligning peaks ... this might take a while! Merge redundant rows ... Remove contaminations and remove blanks ... done Alignment completed! Time: 2024-01-22 21:56:09 Run GCalignR Start: 2024-01-22 21:56:09 Data for 3 samples loaded. Apply retention time cut-offs ... done No reference was specified. Hence, a reference will be selected automatically ... 'C3' was selected on the basis of highest average similarity to all samples (score = 0.02). Start correcting linear shifts with "C3" as a reference ... Start aligning peaks ... this might take a while! Merge redundant rows ... remove single peaks ... 36 have been removed Alignment completed! Time: 2024-01-22 21:56:10 All checks passed! [1] "RT is not a valid variable name. Data contains: time & area" Computing chromatograms ... | | 0 % elapsed=00s |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s, remaining~00s Run GCalignR Start: 2024-01-22 21:56:21 Data for 5 samples loaded. Start correcting linear shifts with "M2" as a reference ... | | 0 % elapsed=00s |++++++++++ | 20% elapsed=00s, remaining~00s |++++++++++++++++++++ | 40% elapsed=00s, remaining~00s |++++++++++++++++++++++++++++++ | 60% elapsed=00s, remaining~00s |++++++++++++++++++++++++++++++++++++++++ | 80% elapsed=00s, remaining~00s |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s, remaining~00s Start aligning peaks ... this might take a while! Merge redundant rows ... Remove contaminations and remove blanks ... done Alignment completed! Time: 2024-01-22 21:56:21 Run GCalignR Start: 2024-01-22 21:56:21 Data for 5 samples loaded. Start correcting linear shifts with "M2" as a reference ... Start aligning peaks ... this might take a while! Merge redundant rows ... Remove contaminations and remove blanks ... done Alignment completed! Time: 2024-01-22 21:56:21 Run GCalignR Start: 2024-01-22 21:56:21 Data for 5 samples loaded. Start correcting linear shifts with "M2" as a reference ... Start aligning peaks ... this might take a while! Merge redundant rows ... Remove contaminations and remove blanks ... done Alignment completed! Time: 2024-01-22 21:56:21 Run GCalignR Start: 2024-01-22 21:56:21 Data for 5 samples loaded. No reference was specified. Hence, a reference will be selected automatically ... | | 0 % elapsed=00s |++++++++++ | 20% elapsed=00s, remaining~00s |++++++++++++++++++++ | 40% elapsed=00s, remaining~00s |++++++++++++++++++++++++++++++ | 60% elapsed=00s, remaining~00s |++++++++++++++++++++++++++++++++++++++++ | 80% elapsed=00s, remaining~00s |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s, remaining~00s 'C2' was selected on the basis of highest average similarity to all samples (score = 0.02). Start correcting linear shifts with "C2" as a reference ... Start aligning peaks ... this might take a while! Merge redundant rows ... Remove contaminations and remove blanks ... done Alignment completed! Time: 2024-01-22 21:56:21 | | 0 % elapsed=00s |+++++++++++++ | 25% elapsed=00s, remaining~00s |+++++++++++++++++++++++++ | 50% elapsed=00s, remaining~00s |++++++++++++++++++++++++++++++++++++++ | 75% elapsed=00s, remaining~00s |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s, remaining~00s Run GCalignR Start: 2024-01-22 21:56:22 Data for 4 samples loaded. No reference was specified. Hence, a reference will be selected automatically ... | | 0 % elapsed=00s |+++++++++++++ | 25% elapsed=00s, remaining~00s |+++++++++++++++++++++++++ | 50% elapsed=00s, remaining~00s |++++++++++++++++++++++++++++++++++++++ | 75% elapsed=00s, remaining~00s |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s, remaining~00s 'C2' was selected on the basis of highest average similarity to all samples (score = 0.15). Start correcting linear shifts with "C2" as a reference ... | | 0 % elapsed=00s |+++++++++++++ | 25% elapsed=00s, remaining~00s |+++++++++++++++++++++++++ | 50% elapsed=00s, remaining~00s |++++++++++++++++++++++++++++++++++++++ | 75% elapsed=00s, remaining~00s |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s, remaining~00s Start aligning peaks ... this might take a while! Merge redundant rows ... Alignment completed! Time: 2024-01-22 21:56:22 Summary of Peak Alignment running align_chromatograms Input: peak_data Start: 2017-07-19 16:31:47 Finished: 2017-07-19 17:30:47 Call: GCalignR::align_chromatograms(data=peak_data, rt_col_name=time, max_linear_shift=0.05, max_diff_peak2mean=0.02, min_diff_peak2peak=0.08, blanks=(C2, C3), delete_single_peak=T, sep=\t, rt_cutoff_low=NULL, rt_cutoff_high=NULL, reference=NULL) Summary of scored substances: total blanks singular retained 494 171 45 278 In total 494 substances were identified among all samples. 171 substances were present in blanks. The corresponding peaks as well as the blanks were removed from the data. 45 substances were present in just one single sample and were removed. 278 substances are retained after all filtering steps. Sample overview: The following 84 samples were aligned to the reference 'P20': M2, M3, M4, M5, M6, M7, M8, M9, M10, M12, M14, M15, M16, M17, M18, M19, M20, M21, M23, M24, M25, M26, M27, M28, M29, M30, M31, M33, M35, M36, M37, M38, M39, M40, M41, M43, M44, M45, M46, M47, M48, P2, P3, P4, P5, P6, P7, P8, P9, P10, P12, P14, P15, P16, P17, P18, P19, P20, P21, P23, P24, P25, P26, P27, P28, P29, P30, P31, P33, P35, P36, P37, P38, P39, P40, P41, P43, P44, P45, P46, P47, P48 For further details type: 'gc_heatmap(aligned_peak_data)' to retrieve heatmaps 'plot(aligned_peak_data)' to retrieve further diagnostic plotsRun GCalignR Start: 2024-01-22 21:56:22 Data for 5 samples loaded. No reference was specified. Hence, a reference will be selected automatically ... | | 0 % elapsed=00s |++++++++++ | 20% elapsed=00s, remaining~00s |++++++++++++++++++++ | 40% elapsed=00s, remaining~00s |++++++++++++++++++++++++++++++ | 60% elapsed=00s, remaining~00s |++++++++++++++++++++++++++++++++++++++++ | 80% elapsed=00s, remaining~00s |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s, remaining~00s 'M3' was selected on the basis of highest average similarity to all samples (score = 0.08). Start correcting linear shifts with "M3" as a reference ... | | 0 % elapsed=00s |++++++++++ | 20% elapsed=00s, remaining~00s |++++++++++++++++++++ | 40% elapsed=00s, remaining~00s |++++++++++++++++++++++++++++++ | 60% elapsed=00s, remaining~00s |++++++++++++++++++++++++++++++++++++++++ | 80% elapsed=00s, remaining~00s |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s, remaining~00s Start aligning peaks ... this might take a while! Merge redundant rows ... Alignment completed! Time: 2024-01-22 21:56:23 [ FAIL 0 | WARN 3 | SKIP 1 | PASS 33 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-align_peaks.R:26:1' [ FAIL 0 | WARN 3 | SKIP 1 | PASS 33 ] > > proc.time() user system elapsed 16.48 0.57 17.01