R Under development (unstable) (2024-09-18 r87177 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) > test_check("RaMS") Loading required package: RaMS ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ── ✔ dplyr 1.1.4 ✔ readr 2.1.5 ✔ forcats 1.0.0 ✔ stringr 1.5.1 ✔ ggplot2 3.5.1 ✔ tibble 3.2.1 ✔ lubridate 1.9.3 ✔ tidyr 1.3.1 ✔ purrr 1.0.2 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── ✖ dplyr::between() masks RaMS::between() ✖ readr::edition_get() masks testthat::edition_get() ✖ dplyr::filter() masks stats::filter() ✖ purrr::is_null() masks testthat::is_null() ✖ dplyr::lag() masks stats::lag() ✖ readr::local_edition() masks testthat::local_edition() ✖ dplyr::matches() masks tidyr::matches(), testthat::matches() ℹ Use the conflicted package () to force all conflicts to become errors Attaching package: 'data.table' The following objects are masked from 'package:lubridate': hour, isoweek, mday, minute, month, quarter, second, wday, week, yday, year The following objects are masked from 'package:dplyr': between, first, last The following object is masked from 'package:purrr': transpose | | | 0% Reading file Blank_129I_1L_pos_20240207-MS3.mzML.gz... 0.06 secs Reading MS1 data...0.02 secs Reading MS2 data...0.01 secs Reading BPC...0.01 secs Reading TIC...0.01 secs Reading file metadata...0.03 secs | |============== | 20% Reading file LB12HL_AB.mzML.gz... 0.13 secs Reading MS1 data...0.17 secs Reading MS2 data...0.01 secs Reading BPC...0.04 secs Reading TIC...0.04 secs Reading file metadata...0.06 secs | |============================ | 40% Reading file LB12HL_CD.mzML.gz... 0.13 secs Reading MS1 data...0.09 secs Reading MS2 data...0.01 secs Reading BPC...0.04 secs Reading TIC...0.04 secs Reading file metadata...0.06 secs | |========================================== | 60% Reading file LB12HL_EF.mzML.gz... 0.12 secs Reading MS1 data...0.06 secs Reading MS2 data...0.01 secs Reading BPC...0.03 secs Reading TIC...0.03 secs Reading file metadata...0.04 secs | |======================================================== | 80% Reading file S30657.mzML.gz... 0.15 secs Reading MS1 data...0.13 secs Reading MS2 data...0.03 secs Reading BPC...0.07 secs Reading TIC...0.07 secs Reading file metadata...0.11 secs | |======================================================================| 100% Binding files together into single data.table Total time: 1.81 secs | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% Total time: 1.85 secs | | | 0% Reading file Blank_129I_1L_pos_20240207-MS3.mzXML.gz... 0.01 secs Reading MS1 data...0 secs Reading MS2 data...0.01 secs Reading BPC...0 secs Reading TIC...0 secs Reading file metadata...0 secs | |======================= | 33% Reading file LB12HL_AB.mzXML.gz... 0.01 secs Reading MS1 data...0.05 secs Reading MS2 data...0 secs Reading BPC...0 secs Reading TIC...0 secs Reading file metadata...0 secs | |=============================================== | 67% Reading file S30657.mzXML.gz... 0.02 secs Reading MS1 data...0.07 secs Reading MS2 data...0.02 secs Reading BPC...0.01 secs Reading TIC...0.01 secs Reading file metadata...0.01 secs | |======================================================================| 100% Binding files together into single data.table Total time: 0.24 secs | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% Total time: 1.12 secs | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% Total time: 0.33 secs | | | 0% Reading file LB12HL_AB.mzML.gz... 0.13 secs Extracting EIC...0.08 secs Extracting EIC MS2...0.01 secs | |================== | 25% Reading file LB12HL_CD.mzML.gz... 0.13 secs Extracting EIC...0.11 secs Extracting EIC MS2...0.01 secs | |=================================== | 50% Reading file LB12HL_EF.mzML.gz... 0.12 secs Extracting EIC...0.08 secs Extracting EIC MS2...0.01 secs | |==================================================== | 75% Reading file S30657.mzML.gz... 0.23 secs Extracting EIC...0.11 secs Extracting EIC MS2...0.03 secs | |======================================================================| 100% Binding files together into single data.table Total time: 1.05 secs | | | 0% Reading file LB12HL_AB.mzXML.gz... 0.01 secs Extracting EIC...0.05 secs Extracting EIC MS2...0 secs | |=================================== | 50% Reading file S30657.mzXML.gz... 0.02 secs Extracting EIC...0.06 secs Extracting EIC MS2...0.01 secs | |======================================================================| 100% Binding files together into single data.table Total time: 0.17 secs | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% Total time: 1.13 secs | | | 0% | |=================================== | 50% | |======================================================================| 100% Total time: 0.08 secs | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% Some data seem to have incorrect names: MS1 Total time: 1.13 secs | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% Total time: 1.11 secs | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60% | |======================================================== | 80% | |======================================================================| 100% Total time: 1.23 secs Reading file uv_test_mini.mzML.gz... 0 secs Reading MS1 data...0 secs Reading MS2 data...0 secs Reading DAD data...0 secs Reading BPC...0 secs Reading TIC...0 secs Reading file metadata...0 secs Binding files together into single data.table Total time: 0.02 secs Reading file uv_test_mini.mzML.gz... 0 secs Reading DAD data...0 secs Binding files together into single data.table Total time: 0.01 secs Reading file LB12HL_AB.mzXML.gz... 0.01 secs Binding files together into single data.table Total time: 0.02 secs Reading file Blank_129I_1L_pos_20240207-MS3.mzML.gz... 0.07 secs Extracting EIC...0.01 secs Extracting EIC MS2...0.01 secs Extracting EIC MS3...0.05 secs Binding files together into single data.table Total time: 0.14 secs Reading file Blank_129I_1L_pos_20240207-MS3.mzXML.gz... 0.01 secs Extracting EIC...0 secs Extracting EIC MS2...0.01 secs Extracting EIC MS3...0.02 secs Binding files together into single data.table Total time: 0.05 secs Reading file Blank_129I_1L_pos_20240207-MS3.mzML.gz... 0.06 secs Reading MS3 data...0.03 secs Binding files together into single data.table Total time: 0.09 secs Reading file S30657.mzXML.gz... 0.02 secs Reading MS1 data...0.07 secs Reading MS2 data...0.01 secs Reading BPC...0.01 secs Reading TIC...0.01 secs Reading file metadata...0.01 secs Binding files together into single data.table Total time: 0.12 secs Reading file Blank_129I_1L_pos_20240207-MS3.mzXML.gz... 0.01 secs Reading MS1 data...0 secs Reading MS2 data...0.01 secs Reading MS3 data...0.03 secs Reading BPC...0 secs Reading TIC...0 secs Reading file metadata...0 secs Binding files together into single data.table Total time: 0.06 secs Reading file S30657.mzML.gz... 0.2 secs Reading MS1 data...0.14 secs Reading MS2 data...0.09 secs Reading BPC...0.09 secs Reading TIC...0.09 secs Reading file metadata...0.1 secs Binding files together into single data.table Total time: 0.73 secs Reading file Blank_129I_1L_pos_20240207-MS3.mzML.gz... 0.06 secs Reading MS1 data...0.01 secs Reading MS2 data...0.01 secs Reading MS3 data...0.03 secs Reading BPC...0.01 secs Reading TIC...0.01 secs Reading file metadata...0.02 secs Binding files together into single data.table Total time: 0.16 secs Reading file wk_chrom.mzML.gz... 0 secs Reading chromatograms...0 secs Binding files together into single data.table Total time: 0.01 secs Reading file wk_chrom.mzML.gz... 0 secs Reading MS1 data...0 secs Reading MS2 data...0 secs Reading BPC...0 secs Reading TIC...0 secs Reading chromatograms...0 secs Reading file metadata...0.01 secs Binding files together into single data.table Total time: 0.02 secs Reading file LB12HL_AB.mzXML.gz... 0.01 secs Binding files together into single data.table Total time: 0.01 secs | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% Total time: 1.11 secs | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% Total time: 1.17 secs | | | 0% Reading file file13ac8746058aa.mzML... Reading file LB12HL_AB.mzML.gz... 0.11 secs Reading MS1 data...0.09 secs Reading MS2 data...0.01 secs Reading BPC...0.04 secs Reading TIC...0.04 secs Reading file metadata...0.06 secs Binding files together into single data.table Total time: 0.36 secs Reading file LB12HL_AB.mzML.gz... 0.24 secs Reading MS1 data...0.09 secs Reading MS2 data...0.01 secs Reading BPC...0.04 secs Reading TIC...0.04 secs Reading file metadata...0.06 secs Binding files together into single data.table Total time: 0.49 secs | | | 0% Reading file mini_mzML.mzML... 0.11 secs Reading MS1 data...0.07 secs Reading MS2 data...0.01 secs Reading BPC...0.04 secs Reading TIC...0.04 secs Reading file metadata...0.06 secs Binding files together into single data.table Total time: 0.33 secs Reading file mini_mzML.mzML... 0.08 secs Reading MS1 data...0.06 secs Reading MS2 data...0.01 secs Reading BPC...0.04 secs Reading TIC...0.04 secs Reading file metadata...0.06 secs Binding files together into single data.table Total time: 0.3 secs Reading file mini_mzXML.mzXML... 0.01 secs Reading MS1 data...0.05 secs Reading MS2 data...0 secs Reading BPC...0 secs Reading TIC...0 secs Reading file metadata...0 secs Binding files together into single data.table Total time: 0.07 secs Reading file mini_mzXML.mzXML... 0.01 secs Reading MS1 data...0.04 secs Reading MS2 data...0 secs Reading BPC...0 secs Reading TIC...0 secs Reading file metadata...0 secs Binding files together into single data.table Total time: 0.07 secs Total time: 0.19 secs Reading file Blank_129I_1L_pos_20240207-MS3.mzML.gz... 0.06 secs Reading MS1 data...0.01 secs Reading MS2 data...0.01 secs Reading MS3 data...0.03 secs Reading BPC...0.01 secs Reading TIC...0.01 secs Reading file metadata...0.02 secs Binding files together into single data.table Total time: 0.16 secs Reading file mini_DDA.mzML... 0.06 secs Reading MS1 data...0.01 secs Reading MS2 data...0.01 secs Reading MS3 data...0.03 secs Reading BPC...0.01 secs Reading TIC...0.01 secs Reading file metadata...0.02 secs Binding files together into single data.table Total time: 0.14 secs [ FAIL 0 | WARN 0 | SKIP 0 | PASS 309 ] > > proc.time() user system elapsed 33.60 1.93 35.56