Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:05:37 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the IPO package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IPO.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 993/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
IPO 1.24.0 (landing page) Thomas Lieb
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: IPO |
Version: 1.24.0 |
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:IPO.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings IPO_1.24.0.tar.gz |
StartedAt: 2023-04-11 02:35:45 -0400 (Tue, 11 Apr 2023) |
EndedAt: 2023-04-11 02:54:59 -0400 (Tue, 11 Apr 2023) |
EllapsedTime: 1153.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: IPO.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:IPO.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings IPO_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/IPO.Rcheck' * using R version 4.2.3 (2023-03-15 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'IPO/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'IPO' version '1.24.0' * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'IPO' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE License components with restrictions not permitted: GPL (>= 2) + file LICENSE * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... 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 ... OK * checking Rd files ... OK * checking Rd metadata ... 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 files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed findIsotopes.IPO 1.52 0.05 14.42 calcPPS 1.53 0.03 14.33 findIsotopes.CAMERA 0.83 0.02 13.97 calculateXcmsSet 0.73 0.00 16.14 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'runTests.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See 'F:/biocbuild/bbs-3.16-bioc/meat/IPO.Rcheck/00check.log' for details.
IPO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL IPO ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library' * installing *source* package 'IPO' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (IPO)
IPO.Rcheck/tests/runTests.Rout
R version 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) 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("msdata") > > BiocGenerics:::testPackage("IPO") Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Attaching package: 'IPO' The following object is masked from 'package:S4Vectors': decode starting new DoE with: min_peakwidth: c(3, 9.5) max_peakwidth: c(10, 20) ppm: 56 mzdiff: -0.001 snthresh: 10 noise: 0 prefilter: 3 value_of_prefilter: 100 mzCenterFun: wMean integrate: 1 fitgauss: FALSE verbose.columns: FALSE 1 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 805 regions of interest ... OK: 235 found. 2 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found! 3 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 805 regions of interest ... OK: 88 found. 4 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found! 5 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 536 regions of interest ... OK: 194 found. 6 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 805 regions of interest ... OK: 215 found. 7 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found! 8 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 536 regions of interest ... OK: 149 found. 9 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 536 regions of interest ... OK: 101 found. 10 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 536 regions of interest ... OK: 194 found. Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 628 regions of interest ... OK: 225 found. starting new DoE with: min_peakwidth: c(3, 8.2) max_peakwidth: c(9.2, 19.2) ppm: 56 mzdiff: -0.001 snthresh: 10 noise: 0 prefilter: 3 value_of_prefilter: 100 mzCenterFun: wMean integrate: 1 fitgauss: FALSE verbose.columns: FALSE 1 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 805 regions of interest ... OK: 235 found. 2 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 372 regions of interest ... FAIL: none found! 3 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 805 regions of interest ... OK: 143 found. 4 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 372 regions of interest ... FAIL: none found! 5 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 628 regions of interest ... OK: 222 found. 6 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 805 regions of interest ... OK: 225 found. 7 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 372 regions of interest ... FAIL: none found! 8 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 628 regions of interest ... OK: 144 found. 9 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 628 regions of interest ... OK: 139 found. 10 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 628 regions of interest ... OK: 222 found. Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 718 regions of interest ... OK: 220 found. no increase, stopping best parameter settings: min_peakwidth: 5.6 max_peakwidth: 13 ppm: 56 mzdiff: -0.001 snthresh: 10 noise: 0 prefilter: 3 value_of_prefilter: 100 mzCenterFun: wMean integrate: 1 fitgauss: FALSE verbose.columns: FALSE starting new DoE with: min_peakwidth: c(3, 9.5) max_peakwidth: c(10, 20) ppm: 56 mzdiff: -0.001 snthresh: 10 noise: 0 prefilter: 3 value_of_prefilter: 100 mzCenterFun: wMean integrate: 1 fitgauss: FALSE verbose.columns: FALSE 1 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 805 regions of interest ... OK: 235 found. xsAnnotate contains no pseudospectra. Regroup all peaks into one! Generating peak matrix! Run isotope peak annotation % finished: 100 Found isotopes: 59 2 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found! 3 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 805 regions of interest ... OK: 88 found. xsAnnotate contains no pseudospectra. Regroup all peaks into one! Generating peak matrix! Run isotope peak annotation % finished: 100 Found isotopes: 18 4 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found! 5 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 536 regions of interest ... OK: 194 found. xsAnnotate contains no pseudospectra. Regroup all peaks into one! Generating peak matrix! Run isotope peak annotation % finished: 100 Found isotopes: 52 6 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 805 regions of interest ... OK: 215 found. xsAnnotate contains no pseudospectra. Regroup all peaks into one! Generating peak matrix! Run isotope peak annotation % finished: 100 Found isotopes: 55 7 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found! 8 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 536 regions of interest ... OK: 149 found. xsAnnotate contains no pseudospectra. Regroup all peaks into one! Generating peak matrix! Run isotope peak annotation % finished: 100 Found isotopes: 35 9 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 536 regions of interest ... OK: 101 found. xsAnnotate contains no pseudospectra. Regroup all peaks into one! Generating peak matrix! Run isotope peak annotation % finished: 100 Found isotopes: 26 10 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 536 regions of interest ... OK: 194 found. xsAnnotate contains no pseudospectra. Regroup all peaks into one! Generating peak matrix! Run isotope peak annotation % finished: 100 Found isotopes: 52 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 718 regions of interest ... OK: 221 found. xsAnnotate contains no pseudospectra. Regroup all peaks into one! Generating peak matrix! Run isotope peak annotation % finished: 100 Found isotopes: 62 starting new DoE with: min_peakwidth: c(3, 9.5) max_peakwidth: c(10.5, 20.5) ppm: 56 mzdiff: -0.001 snthresh: 10 noise: 0 prefilter: 3 value_of_prefilter: 100 mzCenterFun: wMean integrate: 1 fitgauss: FALSE verbose.columns: FALSE 1 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 805 regions of interest ... OK: 244 found. xsAnnotate contains no pseudospectra. Regroup all peaks into one! Generating peak matrix! Run isotope peak annotation % finished: 100 Found isotopes: 57 2 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found! 3 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 805 regions of interest ... OK: 88 found. xsAnnotate contains no pseudospectra. Regroup all peaks into one! Generating peak matrix! Run isotope peak annotation % finished: 100 Found isotopes: 18 4 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found! 5 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 536 regions of interest ... OK: 192 found. xsAnnotate contains no pseudospectra. Regroup all peaks into one! Generating peak matrix! Run isotope peak annotation % finished: 100 Found isotopes: 50 6 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 805 regions of interest ... OK: 215 found. xsAnnotate contains no pseudospectra. Regroup all peaks into one! Generating peak matrix! Run isotope peak annotation % finished: 100 Found isotopes: 55 7 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 283 regions of interest ... FAIL: none found! 8 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 536 regions of interest ... OK: 149 found. xsAnnotate contains no pseudospectra. Regroup all peaks into one! Generating peak matrix! Run isotope peak annotation % finished: 100 Found isotopes: 35 9 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 536 regions of interest ... OK: 101 found. xsAnnotate contains no pseudospectra. Regroup all peaks into one! Generating peak matrix! Run isotope peak annotation % finished: 100 Found isotopes: 26 10 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 536 regions of interest ... OK: 192 found. xsAnnotate contains no pseudospectra. Regroup all peaks into one! Generating peak matrix! Run isotope peak annotation % finished: 100 Found isotopes: 50 Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 56 ppm ... OK Detecting chromatographic peaks in 718 regions of interest ... OK: 218 found. xsAnnotate contains no pseudospectra. Regroup all peaks into one! Generating peak matrix! Run isotope peak annotation % finished: 100 Found isotopes: 60 no increase, stopping best parameter settings: min_peakwidth: 4.95 max_peakwidth: 13.5 ppm: 56 mzdiff: -0.001 snthresh: 10 noise: 0 prefilter: 3 value_of_prefilter: 100 mzCenterFun: wMean integrate: 1 fitgauss: FALSE verbose.columns: FALSE Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 30 ppm ... OK Detecting chromatographic peaks in 211 regions of interest ... OK: 196 found. Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.24.2 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws This is xcms version 3.20.0 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 30 ppm ... OK Detecting chromatographic peaks in 217 regions of interest ... OK: 194 found. starting new DoE with: distFunc: cor_opt gapInit: 0.34 gapExtend: c(2.1, 2.7) profStep: 1 plottype: none response: 1 factorDiag: 2 factorGap: 1 localAlignment: 0 retcorMethod: obiwarp bw: c(22, 38) minfrac: 1 mzwid: 0.026 minsamp: 1 max: 50 center: 2 center sample: MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818 Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Processing 54877 mz slices ... OK center sample: MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818 Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Processing 54877 mz slices ... OK center sample: MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818 Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Processing 54877 mz slices ... OK center sample: MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818 Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Processing 54877 mz slices ... OK center sample: MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818 Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Processing 54877 mz slices ... OK center sample: MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818 Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Processing 54877 mz slices ... OK center sample: MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818 Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Processing 54877 mz slices ... OK center sample: MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818 Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Processing 54877 mz slices ... OK center sample: MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818 Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Processing 54877 mz slices ... OK center sample: MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818 Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Processing 54877 mz slices ... OK center sample: MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818 Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Processing 54877 mz slices ... OK starting new DoE with: gapExtend: c(1.74, 2.46) bw: c(12.4, 31.6) distFunc: cor_opt gapInit: 0.34 profStep: 1 plottype: none response: 1 factorDiag: 2 factorGap: 1 localAlignment: 0 retcorMethod: obiwarp minfrac: 1 mzwid: 0.026 minsamp: 1 max: 50 center: 2 center sample: MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818 Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Processing 54877 mz slices ... OK center sample: MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818 Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Processing 54877 mz slices ... OK center sample: MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818 Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Processing 54877 mz slices ... OK center sample: MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818 Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Processing 54877 mz slices ... OK center sample: MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818 Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Processing 54877 mz slices ... OK center sample: MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818 Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Processing 54877 mz slices ... OK center sample: MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818 Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Processing 54877 mz slices ... OK center sample: MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818 Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Processing 54877 mz slices ... OK center sample: MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818 Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Processing 54877 mz slices ... OK center sample: MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818 Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Processing 54877 mz slices ... OK center sample: MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820 Processing: MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818 Create profile matrix with method 'bin' and step 1 ... OK Create profile matrix with method 'bin' and step 1 ... OK Processing 54877 mz slices ... OK no increase stopping starting new DoE with: missing: 0 extra: 0 span: c(0.1, 0.3) smooth: loess family: gaussian plottype: none retcorMethod: loess bw: c(22, 38) minfrac: c(0.3, 0.7) mzwid: c(0.015, 0.035) minsamp: 1 max: 50 center: 2 Processing 95119 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 95119 mz slices ... OK Processing 95119 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 95119 mz slices ... OK Processing 95119 mz slices ... OK Performing retention time correction using 181 peak groups. Processing 95119 mz slices ... OK Processing 95119 mz slices ... OK Performing retention time correction using 181 peak groups. Processing 95119 mz slices ... OK Processing 95119 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 95119 mz slices ... OK Processing 95119 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 95119 mz slices ... OK Processing 95119 mz slices ... OK Performing retention time correction using 181 peak groups. Processing 95119 mz slices ... OK Processing 95119 mz slices ... OK Performing retention time correction using 181 peak groups. Processing 95119 mz slices ... OK Processing 40766 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 40766 mz slices ... OK Processing 40766 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 40766 mz slices ... OK Processing 40766 mz slices ... OK Performing retention time correction using 179 peak groups. Processing 40766 mz slices ... OK Processing 40766 mz slices ... OK Performing retention time correction using 179 peak groups. Processing 40766 mz slices ... OK Processing 40766 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 40766 mz slices ... OK Processing 40766 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 40766 mz slices ... OK Processing 40766 mz slices ... OK Performing retention time correction using 179 peak groups. Processing 40766 mz slices ... OK Processing 40766 mz slices ... OK Performing retention time correction using 179 peak groups. Processing 40766 mz slices ... OK Processing 57072 mz slices ... OK Performing retention time correction using 183 peak groups. Processing 57072 mz slices ... OK Processing 57072 mz slices ... OK Performing retention time correction using 183 peak groups. Processing 57072 mz slices ... OK Processing 57072 mz slices ... OK Performing retention time correction using 183 peak groups. Processing 57072 mz slices ... OK Processing 57072 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 57072 mz slices ... OK Processing 57072 mz slices ... OK Performing retention time correction using 181 peak groups. Processing 57072 mz slices ... OK Processing 57072 mz slices ... OK Performing retention time correction using 183 peak groups. Processing 57072 mz slices ... OK Processing 57072 mz slices ... OK Performing retention time correction using 183 peak groups. Processing 57072 mz slices ... OK Processing 95119 mz slices ... OK Performing retention time correction using 183 peak groups. Processing 95119 mz slices ... OK Processing 40766 mz slices ... OK Performing retention time correction using 183 peak groups. Processing 40766 mz slices ... OK Processing 57072 mz slices ... OK Performing retention time correction using 183 peak groups. Processing 57072 mz slices ... OK Processing 75094 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 75094 mz slices ... OK starting new DoE with: span: c(0.001, 0.22) bw: c(12.4, 31.6) minfrac: c(0.46, 0.94) mzwid: c(0.009, 0.029) missing: 0 extra: 0 smooth: loess family: gaussian plottype: none retcorMethod: loess minsamp: 1 max: 50 center: 2 Processing 158530 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 158530 mz slices ... OK Processing 158530 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 158530 mz slices ... OK Processing 158530 mz slices ... OK Performing retention time correction using 181 peak groups. Processing 158530 mz slices ... OK Processing 158530 mz slices ... OK Performing retention time correction using 181 peak groups. Processing 158530 mz slices ... OK Processing 158530 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 158530 mz slices ... OK Processing 158530 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 158530 mz slices ... OK Processing 158530 mz slices ... OK Performing retention time correction using 181 peak groups. Processing 158530 mz slices ... OK Processing 158530 mz slices ... OK Performing retention time correction using 181 peak groups. Processing 158530 mz slices ... OK Processing 49200 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 49200 mz slices ... OK Processing 49200 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 49200 mz slices ... OK Processing 49200 mz slices ... OK Performing retention time correction using 181 peak groups. Processing 49200 mz slices ... OK Processing 49200 mz slices ... OK Performing retention time correction using 181 peak groups. Processing 49200 mz slices ... OK Processing 49200 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 49200 mz slices ... OK Processing 49200 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 49200 mz slices ... OK Processing 49200 mz slices ... OK Performing retention time correction using 181 peak groups. Processing 49200 mz slices ... OK Processing 49200 mz slices ... OK Performing retention time correction using 181 peak groups. Processing 49200 mz slices ... OK Processing 75094 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 75094 mz slices ... OK Processing 75094 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 75094 mz slices ... OK Processing 75094 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 75094 mz slices ... OK Processing 75094 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 75094 mz slices ... OK Processing 75094 mz slices ... OK Performing retention time correction using 181 peak groups. Processing 75094 mz slices ... OK Processing 75094 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 75094 mz slices ... OK Processing 75094 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 75094 mz slices ... OK Processing 158530 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 158530 mz slices ... OK Processing 49200 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 49200 mz slices ... OK Processing 75094 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 75094 mz slices ... OK Processing 75094 mz slices ... OK Performing retention time correction using 185 peak groups. Processing 75094 mz slices ... OK no increase stopping RUNIT TEST PROTOCOL -- Tue Apr 11 02:54:48 2023 *********************************************** Number of test functions: 1 Number of errors: 0 Number of failures: 0 1 Test Suite : IPO RUnit Tests - 1 test function, 0 errors, 0 failures Number of test functions: 1 Number of errors: 0 Number of failures: 0 There were 30 warnings (use warnings() to see them) > > proc.time() user system elapsed 264.67 6.70 872.84
IPO.Rcheck/IPO-Ex.timings
name | user | system | elapsed | |
IPO-package | 0 | 0 | 0 | |
attachList | 0 | 0 | 0 | |
calcPPS | 1.53 | 0.03 | 14.33 | |
calculateXcmsSet | 0.73 | 0.00 | 16.14 | |
combineParams | 0.02 | 0.00 | 0.02 | |
createModel | 0.17 | 0.00 | 0.34 | |
decode | 0 | 0 | 0 | |
findIsotopes.CAMERA | 0.83 | 0.02 | 13.97 | |
findIsotopes.IPO | 1.52 | 0.05 | 14.42 | |
getBbdParameter | 0 | 0 | 0 | |
getCcdParameter | 0.01 | 0.00 | 0.01 | |
getDefaultRetCorCenterSample | 0 | 0 | 0 | |
getDefaultRetGroupStartingParams | 0 | 0 | 0 | |
getDefaultXcmsSetStartingParams | 0 | 0 | 0 | |
getNormalizedResponse | 0 | 0 | 0 | |
getRGTVValues | 0 | 0 | 0 | |
optimizeRetGroup | 0 | 0 | 0 | |
optimizeXcmsSet | 0 | 0 | 0 | |
toMatrix | 0 | 0 | 0 | |
typeCastParams | 0 | 0 | 0 | |
writeParamsTable | 0 | 0 | 0 | |
writeRScript | 0 | 0 | 0 | |