Back to Multiple platform build/check report for BioC 3.14 

This page was generated on 20220413 12:06:17 0400 (Wed, 13 Apr 2022).
Hostname  OS  Arch (*)  R version  Installed pkgs 

nebbiolo2  Linux (Ubuntu 20.04.4 LTS)  x86_64  4.1.3 (20220310)  "One PushUp"  4324 
tokay2  Windows Server 2012 R2 Standard  x64  4.1.3 (20220310)  "One PushUp"  4077 
machv2  macOS 10.14.6 Mojave  x86_64  4.1.3 (20220310)  "One PushUp"  4137 
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To the developers/maintainers of the CAMERA package:  Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CAMERA.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 239/2083  Hostname  OS / Arch  INSTALL  BUILD  CHECK  BUILD BIN  
CAMERA 1.50.0 (landing page) Steffen Neumann
 nebbiolo2  Linux (Ubuntu 20.04.4 LTS) / x86_64  OK  OK  OK  
tokay2  Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK  
machv2  macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK  
Package: CAMERA 
Version: 1.50.0 
Command: C:\Users\biocbuild\bbs3.14bioc\R\bin\R.exe CMD check forcemultiarch install=check:CAMERA.installout.txt library=C:\Users\biocbuild\bbs3.14bioc\R\library novignettes timings CAMERA_1.50.0.tar.gz 
StartedAt: 20220412 16:46:33 0400 (Tue, 12 Apr 2022) 
EndedAt: 20220412 17:15:17 0400 (Tue, 12 Apr 2022) 
EllapsedTime: 1724.2 seconds 
RetCode: 0 
Status: OK 
CheckDir: CAMERA.Rcheck 
Warnings: 0 
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs3.14bioc\R\bin\R.exe CMD check forcemultiarch install=check:CAMERA.installout.txt library=C:\Users\biocbuild\bbs3.14bioc\R\library novignettes timings CAMERA_1.50.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs3.14bioc/meat/CAMERA.Rcheck' * using R version 4.1.3 (20220310) * using platform: x86_64w64mingw32 (64bit) * using session charset: ISO88591 * using option 'novignettes' * checking for file 'CAMERA/DESCRIPTION' ... OK * this is package 'CAMERA' version '1.50.0' * 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 ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. * checking for portable file names ... OK * checking whether package 'CAMERA' can be installed ... OK * checking installed package size ... NOTE installed size is 8.2Mb subdirectories of 1Mb or more: mzdata 1.7Mb quantiles 5.0Mb * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION metainformation ... NOTE Malformed Description field: should contain one or more complete sentences. Packages listed in more than one of Depends, Imports, Suggests, Enhances: 'methods' 'xcms' A package should be listed in only one of these fields. * checking toplevel files ... OK * checking for leftover files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for nonASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... NOTE 'library' or 'require' call to 'methods' which was already attached by Depends. Please remove these calls from your code. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: 'annotateGrp' 'combineHypothese' 'fastMatch' 'naOmit' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... NOTE Foreign function call to a different package: .Call("getEIC", ..., PACKAGE = "xcms") See chapter 'System and foreign language interfaces' in the 'Writing R Extensions' manual. * checking R code for possible problems ... NOTE File 'CAMERA/R/zzz.R': .onLoad calls: require(methods) Package startup functions should not change the search path. See section 'Good practice' in '?.onAttach'. annotateGrp: no visible global function definition for 'na.omit' annotateGrpMPI2: no visible binding for global variable 'papply_commondata' cleanParallel: no visible global function definition for 'mpi.close.Rslaves' cleanParallel: no visible global function definition for 'stopCluster' compoundQuantiles: no visible global function definition for 'tail' createHypothese: no visible global function definition for 'cutree' createHypothese: no visible global function definition for 'hclust' createHypothese: no visible global function definition for 'dist' extractfragments: no visible global function definition for 'median' fast_corr: no visible global function definition for 'pt' findIsotopesForPS: no visible binding for global variable 'tableMM48' findKendrickMasses: no visible global function definition for 'rainbow' findKendrickMasses : <anonymous>: no visible global function definition for 'lines' findNeutralLoss: no visible global function definition for 'dist' findNeutralLossSpecs : <anonymous>: no visible global function definition for 'dist' fragments2metfrag : <anonymous>: no visible global function definition for 'write.table' fragments2metfusion : <anonymous>: no visible binding for global variable 'object' fragments2metfusion : <anonymous>: no visible global function definition for 'write.table' getIsotopeCluster : <anonymous>: no visible global function definition for 'na.omit' xsAnnotate: no visible global function definition for 'mpi.comm.size' xsAnnotate: no visible global function definition for 'mpi.spawn.Rslaves' xsAnnotate: no visible global function definition for 'makeCluster' xsAnnotate: no visible binding for global variable 'graphMethod' findAdducts,xsAnnotate: no visible global function definition for 'mpi.comm.size' findAdducts,xsAnnotate: no visible global function definition for 'xcmsPapply' findIsotopesWithValidation,xsAnnotate : <anonymous>: no visible global function definition for 'median' getReducedPeaklist,xsAnnotate : <anonymous> : <anonymous>: no visible global function definition for 'median' getReducedPeaklist,xsAnnotate : <anonymous>: no visible global function definition for 'prcomp' getReducedPeaklist,xsAnnotate : <anonymous>: no visible global function definition for 'na.omit' groupComplete,xsAnnotate: no visible global function definition for 'dist' groupComplete,xsAnnotate: no visible global function definition for 'cutree' groupComplete,xsAnnotate: no visible global function definition for 'hclust' groupDen,xsAnnotate: no visible global function definition for 'density' groupFWHM,xsAnnotate : <anonymous>: no visible global function definition for 'na.omit' plotEICs,xsAnnotate: no visible global function definition for 'rainbow' plotEICs,xsAnnotate: no visible global function definition for 'na.omit' plotPeakEICs,xsAnnotate : <anonymous>: no visible binding for global variable 'pc' plotPeakEICs,xsAnnotate: no visible binding for global variable 'pspec' plotPeakEICs,xsAnnotate: no visible global function definition for 'rainbow' plotPeakEICs,xsAnnotate: no visible global function definition for 'na.omit' plotPsSpectrum,xsAnnotate: no visible global function definition for 'median' plotPsSpectrum,xsAnnotate: no visible global function definition for 'na.omit' Undefined global functions or variables: cutree density dist graphMethod hclust lines makeCluster median mpi.close.Rslaves mpi.comm.size mpi.spawn.Rslaves na.omit object papply_commondata pc prcomp pspec pt rainbow stopCluster tableMM48 tail write.table xcmsPapply Consider adding importFrom("grDevices", "rainbow") importFrom("graphics", "lines") importFrom("stats", "cutree", "density", "dist", "hclust", "median", "na.omit", "prcomp", "pt") importFrom("utils", "tail", "write.table") to your NAMESPACE file. * checking Rd files ... NOTE prepare_Rd: findKendrickMasses.Rd:2122: Dropping empty section \details * checking Rd metadata ... OK * checking Rd crossreferences ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for nonASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs3.14bioc/R/library/CAMERA/libs/i386/CAMERA.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs3.14bioc/R/library/CAMERA/libs/x64/CAMERA.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed groupCorrmethods 15.81 0.28 29.39 getIsotopeCluster 4.00 0.43 37.90 annotatemethods 3.69 0.47 19.84 findAdductsmethods 2.90 0.16 16.20 pspec2metfrag 2.69 0.11 16.45 getPeaklistmethods 2.67 0.10 17.88 getReducedPeaklistmethods 2.56 0.15 17.94 groupFWHMmethods 2.63 0.02 16.09 groupDenmethods 2.53 0.01 16.94 annotateDiffreport 2.40 0.01 26.63 findIsotopesWithValidationmethods 1.32 0.09 16.92 findNeutralLossSpecs 0.72 0.00 13.89 findIsotopesmethods 0.71 0.00 13.89 findNeutralLoss 0.67 0.03 15.35 getpspectra 0.66 0.02 14.29 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed groupCorrmethods 15.90 0.31 28.26 annotatemethods 4.14 0.19 18.87 getIsotopeCluster 4.08 0.02 39.33 findAdductsmethods 3.03 0.00 17.68 getReducedPeaklistmethods 2.93 0.00 17.97 pspec2metfrag 2.87 0.02 15.92 getPeaklistmethods 2.80 0.03 17.52 groupFWHMmethods 2.75 0.01 15.07 groupDenmethods 2.63 0.02 32.22 annotateDiffreport 2.48 0.00 20.61 findIsotopesWithValidationmethods 1.59 0.00 16.45 findIsotopesmethods 0.91 0.03 16.28 getpspectra 0.79 0.02 15.14 findNeutralLossSpecs 0.79 0.00 15.25 findNeutralLoss 0.76 0.01 15.57 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... 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 rebuilding of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 8 NOTEs See 'C:/Users/biocbuild/bbs3.14bioc/meat/CAMERA.Rcheck/00check.log' for details.
CAMERA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe O http://155.52.207.166/BBS/3.14/bioc/src/contrib/CAMERA_1.50.0.tar.gz && rm rf CAMERA.buildbinlibdir && mkdir CAMERA.buildbinlibdir && C:\Users\biocbuild\bbs3.14bioc\R\bin\R.exe CMD INSTALL mergemultiarch build library=CAMERA.buildbinlibdir CAMERA_1.50.0.tar.gz && C:\Users\biocbuild\bbs3.14bioc\R\bin\R.exe CMD INSTALL CAMERA_1.50.0.zip && rm CAMERA_1.50.0.tar.gz CAMERA_1.50.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 :: :: :: 0 86 1801k 86 1551k 0 0 1735k 0 0:00:01 :: 0:00:01 1735k 100 1801k 100 1801k 0 0 1857k 0 :: :: :: 1857k install for i386 * installing *source* package 'CAMERA' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc I"C:/Users/BIOCBU~1/BBS3~1.14/R/include" DNDEBUG I"C:/extsoft/include" O2 Wall std=gnu99 mfpmath=sse msse2 mstackrealign c fastMatch.c o fastMatch.o C:/rtools40/mingw32/bin/gcc shared s staticlibgcc o CAMERA.dll tmp.def fastMatch.o LC:/extsoft/lib/i386 LC:/extsoft/lib LC:/Users/BIOCBU~1/BBS3~1.14/R/bin/i386 lR installing to C:/Users/biocbuild/bbs3.14bioc/meat/CAMERA.buildbinlibdir/00LOCKCAMERA/00new/CAMERA/libs/i386 ** R ** data ** inst ** bytecompile and prepare package for lazy loading ** help *** installing help indices converting help for package 'CAMERA' finding HTML links ... done annotatemethods html annotateDiffreport html finding level2 HTML links ... done calcCaSmethods html calcCiSmethods html calcIsotopesmethods html calcPCmethods html calcPC.hcsmethods html calcPC.lpcmethods html cleanParallel html combinexsAnnos html compoundLibraries html compoundQuantilesclass html compoundQuantiles html findAdductsmethods html findIsotopesmethods html findIsotopesWithValidationmethods html findKendrickMasses html findNeutralLoss html findNeutralLossSpecs html getAllPeakEICsmethods html getAtomCountcompoundQuantilesmethod html getIsotopeCluster html getIsotopeProportioncompoundQuantilesmethod html getPeaklistmethods html getReducedPeaklistmethods html getpspectra html groupCorrmethods html groupDenmethods html groupFWHMmethods html massWindowSizes html mm14 html plotEIC.xsAnnotate html plotPsSpectrum.xsAnnotate html psDistmethods html pspec2metfrag html ruleSetclass html xsAnnotateclass html xsAnnotate html ** 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 install for x64 * installing *source* package 'CAMERA' ... ** libs "C:/rtools40/mingw64/bin/"gcc I"C:/Users/BIOCBU~1/BBS3~1.14/R/include" DNDEBUG I"C:/extsoft/include" O2 Wall std=gnu99 mfpmath=sse msse2 mstackrealign c fastMatch.c o fastMatch.o C:/rtools40/mingw64/bin/gcc shared s staticlibgcc o CAMERA.dll tmp.def fastMatch.o LC:/extsoft/lib/x64 LC:/extsoft/lib LC:/Users/BIOCBU~1/BBS3~1.14/R/bin/x64 lR installing to C:/Users/biocbuild/bbs3.14bioc/meat/CAMERA.buildbinlibdir/CAMERA/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'CAMERA' as CAMERA_1.50.0.zip * DONE (CAMERA) * installing to library 'C:/Users/biocbuild/bbs3.14bioc/R/library' package 'CAMERA' successfully unpacked and MD5 sums checked
CAMERA.Rcheck/tests_i386/runTests.Rout R version 4.1.3 (20220310)  "One PushUp" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: i386w64mingw32/i386 (32bit) 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 online help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > require("CAMERA")  stop("unable to load CAMERA") Loading required package: CAMERA Loading required package: Biobase 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, 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")'. Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase 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 2.20.4 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 3.16.1 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma [1] TRUE > BiocGenerics:::testPackage("CAMERA") Processing 3195 mz slices ... OK 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, 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 2.20.4 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 3.16.1 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma C:/Users/biocbuild/bbs3.14bioc/R/library/faahKO/cdf/KO/ko19.CDF method: bin step: 0.1 C:/Users/biocbuild/bbs3.14bioc/R/library/faahKO/cdf/KO/ko21.CDF method: bin step: 0.1 C:/Users/biocbuild/bbs3.14bioc/R/library/faahKO/cdf/KO/ko22.CDF method: bin step: 0.1 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, 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 2.20.4 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 3.16.1 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma C:/Users/biocbuild/bbs3.14bioc/R/library/faahKO/cdf/KO/ko15.CDF method: bin step: 0.1 C:/Users/biocbuild/bbs3.14bioc/R/library/faahKO/cdf/KO/ko16.CDF method: bin step: 0.1 C:/Users/biocbuild/bbs3.14bioc/R/library/faahKO/cdf/KO/ko18.CDF method: bin step: 0.1 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, 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 2.20.4 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 3.16.1 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma C:/Users/biocbuild/bbs3.14bioc/R/library/faahKO/cdf/WT/wt19.CDF method: bin step: 0.1 C:/Users/biocbuild/bbs3.14bioc/R/library/faahKO/cdf/WT/wt21.CDF method: bin step: 0.1 C:/Users/biocbuild/bbs3.14bioc/R/library/faahKO/cdf/WT/wt22.CDF method: bin step: 0.1 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, 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 2.20.4 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 3.16.1 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma C:/Users/biocbuild/bbs3.14bioc/R/library/faahKO/cdf/WT/wt15.CDF method: bin step: 0.1 C:/Users/biocbuild/bbs3.14bioc/R/library/faahKO/cdf/WT/wt16.CDF method: bin step: 0.1 C:/Users/biocbuild/bbs3.14bioc/R/library/faahKO/cdf/WT/wt18.CDF method: bin step: 0.1 Warning message: In .getPeaks_new(object, peakrange, step = step) : getPeaks: Peak m/z:246.05246.1, RT:2501.3782531.8945is out of retention time range for this sample (C:/Users/biocbuild/bbs3.14bioc/R/library/faahKO/cdf/KO/ko18.CDF), using zero intensity value. Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 321 xsAnnotate has now 321 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 321 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating peak correlations across samples. % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 229 xsAnnotate has now 229 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 229 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Calculating peak correlations across samples. % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 244 xsAnnotate has now 244 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 244 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 321 xsAnnotate has now 321 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 321 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 321 xsAnnotate has now 321 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 321 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating isotope assignments in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 289 xsAnnotate has now 289 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 289 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 321 xsAnnotate has now 321 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 321 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 313 xsAnnotate has now 313 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 313 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating peak correlations across samples. % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 229 xsAnnotate has now 229 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 229 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating peak correlations across samples. % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 218 xsAnnotate has now 218 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 218 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 375 xsAnnotate has now 375 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 375 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 314 xsAnnotate has now 314 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 314 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 375 xsAnnotate has now 375 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 375 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 317 xsAnnotate has now 317 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 317 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 314 xsAnnotate has now 314 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 314 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Processing 3195 mz slices ... OK Start grouping after retention time. Created 148 pseudospectra. Start grouping after correlation. Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 148 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 148 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 333 xsAnnotate has now 333 groups, instead of 148 Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 22 Generating peak matrix for peak annotation! Found and use userdefined ruleset! Calculating possible adducts in 333 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Start grouping after correlation. Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 254 xsAnnotate has now 254 groups, instead of 133 Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 32 Generating peak matrix for peak annotation! Found and use userdefined ruleset! Calculating possible adducts in 254 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Start grouping after correlation. Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 329 xsAnnotate has now 329 groups, instead of 133 Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 20 Generating peak matrix for peak annotation! Found and use userdefined ruleset! Calculating possible adducts in 329 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 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, 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 2.20.4 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 3.16.1 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 30 ppm ... OK Detecting chromatographic peaks in 456 regions of interest ... OK: 126 found. Start grouping after retention time. Created 14 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 20 50 60 70 80 90 100 Found isotopes: 32 Found and use userdefined ruleset! Calculating possible adducts in 14 Groups... % finished: 20 50 60 70 80 90 100 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, 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 2.20.4 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 3.16.1 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 30 ppm ... OK Detecting chromatographic peaks in 456 regions of interest ... OK: 126 found. Start grouping after retention time. Created 14 pseudospectra. Start grouping after correlation. Calculating peak correlations in 14 Groups... % finished: 20 50 60 70 80 90 100 Calculating graph cross linking in 14 Groups... % finished: 20 50 60 70 80 90 100 New number of psgroups: 35 xsAnnotate has now 35 groups, instead of 14 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, 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 2.20.4 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 3.16.1 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 30 ppm ... OK Detecting chromatographic peaks in 456 regions of interest ... OK: 126 found. Created 11 pseudospectra. Processing 3195 mz slices ... OK Start grouping after retention time. Created 148 pseudospectra. Start grouping after correlation. Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 148 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 148 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 333 xsAnnotate has now 333 groups, instead of 148 Start grouping after retention time. Created 133 pseudospectra. Start grouping after correlation. Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 329 xsAnnotate has now 329 groups, instead of 133 Start grouping after correlation. Data was not preprocessed with groupFWHM, creating one pseudospectrum with all peaks. Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 1 Groups... % finished: 100 Calculating graph cross linking in 1 Groups... % finished: 100 New number of psgroups: 316 xsAnnotate has now 316 groups, instead of 1 Start grouping after correlation. Data was not preprocessed with groupFWHM, creating one pseudospectrum with all peaks. Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 1 Groups... % finished: 100 Calculating graph cross linking in 1 Groups... % finished: 100 New number of psgroups: 316 xsAnnotate has now 316 groups, instead of 1 Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 22 Generating peak matrix for peak annotation! Found and use userdefined ruleset! Calculating possible adducts in 316 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 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, 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 2.20.4 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 3.16.1 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 30 ppm ... OK Detecting chromatographic peaks in 456 regions of interest ... OK: 126 found. Start grouping after retention time. Created 14 pseudospectra. Start grouping after correlation. Data was not preprocessed with groupFWHM, creating one pseudospectrum with all peaks. Calculating peak correlations in 1 Groups... % finished: 100 Calculating graph cross linking in 1 Groups... % finished: 100 New number of psgroups: 48 xsAnnotate has now 48 groups, instead of 1 Start grouping after correlation. Calculating peak correlations in 14 Groups... % finished: 20 50 60 70 80 90 100 Calculating graph cross linking in 14 Groups... % finished: 20 50 60 70 80 90 100 New number of psgroups: 48 xsAnnotate has now 48 groups, instead of 14 Start grouping after correlation. Calculating peak correlations in 8 Groups... % finished: 30 60 70 80 90 100 Calculating graph cross linking in 8 Groups... % finished: 30 60 70 80 90 100 New number of psgroups: 29 xsAnnotate has now 29 groups, instead of 14 Generating peak matrix! Run isotope peak annotation % finished: 20 50 60 70 80 90 100 Found isotopes: 32 Start grouping after correlation. Calculating peak correlations in 14 Groups... % finished: 20 50 60 70 80 90 100 Calculating graph cross linking in 14 Groups... % finished: 20 50 60 70 80 90 100 New number of psgroups: 48 xsAnnotate has now 48 groups, instead of 14 xsAnnotate contains no pseudospectra. Regroup all peaks into one! Generating peak matrix! Run isotope peak annotation % finished: 100 Found isotopes: 32 Found and use userdefined ruleset! Calculating possible adducts in 1 Groups... % finished: 100 Generating peak matrix! Run isotope peak annotation % finished: 20 40 50 60 70 80 90 100 Found isotopes: 23 Calculating possible adducts in 48 Groups... % finished: 20 40 50 60 70 80 90 100 Calculating possible adducts in 8 Groups... % finished: 10 Processing 3195 mz slices ... OK 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, 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 2.20.4 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 3.16.1 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 30 ppm ... OK Detecting chromatographic peaks in 456 regions of interest ... OK: 126 found. Start grouping after retention time. Created 14 pseudospectra. 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, 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 2.20.4 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 3.16.1 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 30 ppm ... OK Detecting chromatographic peaks in 456 regions of interest ... OK: 126 found. Start grouping after retention time. Created 14 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 20 50 60 70 80 90 100 Found isotopes: 32 Calculating possible adducts in 14 Groups... % finished: 20 50 60 70 80 90 100 RUNIT TEST PROTOCOL  Tue Apr 12 17:08:17 2022 *********************************************** Number of test functions: 20 Number of errors: 0 Number of failures: 0 1 Test Suite : CAMERA RUnit Tests  20 test functions, 0 errors, 0 failures Number of test functions: 20 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 245.45 4.15 353.90 
CAMERA.Rcheck/tests_x64/runTests.Rout R version 4.1.3 (20220310)  "One PushUp" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64w64mingw32/x64 (64bit) 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 online help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > require("CAMERA")  stop("unable to load CAMERA") Loading required package: CAMERA Loading required package: Biobase 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, 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")'. Loading required package: xcms Loading required package: BiocParallel Loading required package: MSnbase 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 2.20.4 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 3.16.1 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma [1] TRUE > BiocGenerics:::testPackage("CAMERA") Processing 3195 mz slices ... OK 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, 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 2.20.4 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 3.16.1 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma C:/Users/biocbuild/bbs3.14bioc/R/library/faahKO/cdf/KO/ko15.CDF method: bin step: 0.1 C:/Users/biocbuild/bbs3.14bioc/R/library/faahKO/cdf/KO/ko16.CDF method: bin step: 0.1 C:/Users/biocbuild/bbs3.14bioc/R/library/faahKO/cdf/KO/ko18.CDF method: bin step: 0.1 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, 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 2.20.4 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 3.16.1 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma C:/Users/biocbuild/bbs3.14bioc/R/library/faahKO/cdf/WT/wt15.CDF method: bin step: 0.1 C:/Users/biocbuild/bbs3.14bioc/R/library/faahKO/cdf/WT/wt16.CDF method: bin step: 0.1 C:/Users/biocbuild/bbs3.14bioc/R/library/faahKO/cdf/WT/wt18.CDF method: bin step: 0.1 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, 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 2.20.4 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 3.16.1 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma C:/Users/biocbuild/bbs3.14bioc/R/library/faahKO/cdf/WT/wt19.CDF method: bin step: 0.1 C:/Users/biocbuild/bbs3.14bioc/R/library/faahKO/cdf/WT/wt21.CDF method: bin step: 0.1 C:/Users/biocbuild/bbs3.14bioc/R/library/faahKO/cdf/WT/wt22.CDF method: bin step: 0.1 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, 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 2.20.4 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 3.16.1 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma C:/Users/biocbuild/bbs3.14bioc/R/library/faahKO/cdf/KO/ko19.CDF method: bin step: 0.1 C:/Users/biocbuild/bbs3.14bioc/R/library/faahKO/cdf/KO/ko21.CDF method: bin step: 0.1 C:/Users/biocbuild/bbs3.14bioc/R/library/faahKO/cdf/KO/ko22.CDF method: bin step: 0.1 Warning message: In .getPeaks_new(object, peakrange, step = step) : getPeaks: Peak m/z:246.05246.1, RT:2501.3782531.8945is out of retention time range for this sample (C:/Users/biocbuild/bbs3.14bioc/R/library/faahKO/cdf/KO/ko18.CDF), using zero intensity value. Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 321 xsAnnotate has now 321 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 321 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating peak correlations across samples. % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 229 xsAnnotate has now 229 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 229 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Calculating peak correlations across samples. % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 244 xsAnnotate has now 244 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 244 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 321 xsAnnotate has now 321 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 321 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 321 xsAnnotate has now 321 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 321 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating isotope assignments in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 289 xsAnnotate has now 289 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 289 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 321 xsAnnotate has now 321 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 321 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 312 xsAnnotate has now 312 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 312 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating peak correlations across samples. % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 229 xsAnnotate has now 229 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 229 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating peak correlations across samples. % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 218 xsAnnotate has now 218 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 218 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 375 xsAnnotate has now 375 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 375 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 314 xsAnnotate has now 314 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 314 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 375 xsAnnotate has now 375 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 375 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 317 xsAnnotate has now 317 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 317 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 61 Start grouping after correlation. Generating EIC's .. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 314 xsAnnotate has now 314 groups, instead of 133 Generating peak matrix for peak annotation! Calculating possible adducts in 314 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Processing 3195 mz slices ... OK Start grouping after retention time. Created 148 pseudospectra. Start grouping after correlation. Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 148 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 148 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 333 xsAnnotate has now 333 groups, instead of 148 Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 22 Generating peak matrix for peak annotation! Found and use userdefined ruleset! Calculating possible adducts in 333 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Start grouping after correlation. Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 254 xsAnnotate has now 254 groups, instead of 133 Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 32 Generating peak matrix for peak annotation! Found and use userdefined ruleset! Calculating possible adducts in 254 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Start grouping after retention time. Created 133 pseudospectra. Start grouping after correlation. Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 329 xsAnnotate has now 329 groups, instead of 133 Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 20 Generating peak matrix for peak annotation! Found and use userdefined ruleset! Calculating possible adducts in 329 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 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, 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 2.20.4 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 3.16.1 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 30 ppm ... OK Detecting chromatographic peaks in 456 regions of interest ... OK: 126 found. Start grouping after retention time. Created 14 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 20 50 60 70 80 90 100 Found isotopes: 32 Found and use userdefined ruleset! Calculating possible adducts in 14 Groups... % finished: 20 50 60 70 80 90 100 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, 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 2.20.4 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 3.16.1 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 30 ppm ... OK Detecting chromatographic peaks in 456 regions of interest ... OK: 126 found. Start grouping after retention time. Created 14 pseudospectra. Start grouping after correlation. Calculating peak correlations in 14 Groups... % finished: 20 50 60 70 80 90 100 Calculating graph cross linking in 14 Groups... % finished: 20 50 60 70 80 90 100 New number of psgroups: 35 xsAnnotate has now 35 groups, instead of 14 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, 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 2.20.4 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 3.16.1 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 30 ppm ... OK Detecting chromatographic peaks in 456 regions of interest ... OK: 126 found. Created 11 pseudospectra. Processing 3195 mz slices ... OK Start grouping after retention time. Created 148 pseudospectra. Start grouping after correlation. Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 148 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 148 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 333 xsAnnotate has now 333 groups, instead of 148 Start grouping after retention time. Created 133 pseudospectra. Start grouping after correlation. Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 Calculating graph cross linking in 133 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 New number of psgroups: 329 xsAnnotate has now 329 groups, instead of 133 Start grouping after correlation. Data was not preprocessed with groupFWHM, creating one pseudospectrum with all peaks. Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 1 Groups... % finished: 100 Calculating graph cross linking in 1 Groups... % finished: 100 New number of psgroups: 316 xsAnnotate has now 316 groups, instead of 1 Start grouping after correlation. Data was not preprocessed with groupFWHM, creating one pseudospectrum with all peaks. Generating EIC's .. Warning: Found NA peaks in selected sample. Calculating peak correlations in 1 Groups... % finished: 100 Calculating graph cross linking in 1 Groups... % finished: 100 New number of psgroups: 316 xsAnnotate has now 316 groups, instead of 1 Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100 Found isotopes: 22 Generating peak matrix for peak annotation! Found and use userdefined ruleset! Calculating possible adducts in 316 Groups... % finished: 10 20 30 40 50 60 70 80 90 100 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, 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 2.20.4 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 3.16.1 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 30 ppm ... OK Detecting chromatographic peaks in 456 regions of interest ... OK: 126 found. Start grouping after retention time. Created 14 pseudospectra. Start grouping after correlation. Data was not preprocessed with groupFWHM, creating one pseudospectrum with all peaks. Calculating peak correlations in 1 Groups... % finished: 100 Calculating graph cross linking in 1 Groups... % finished: 100 New number of psgroups: 48 xsAnnotate has now 48 groups, instead of 1 Start grouping after correlation. Calculating peak correlations in 14 Groups... % finished: 20 50 60 70 80 90 100 Calculating graph cross linking in 14 Groups... % finished: 20 50 60 70 80 90 100 New number of psgroups: 48 xsAnnotate has now 48 groups, instead of 14 Start grouping after correlation. Calculating peak correlations in 8 Groups... % finished: 30 60 70 80 90 100 Calculating graph cross linking in 8 Groups... % finished: 30 60 70 80 90 100 New number of psgroups: 29 xsAnnotate has now 29 groups, instead of 14 Generating peak matrix! Run isotope peak annotation % finished: 20 50 60 70 80 90 100 Found isotopes: 32 Start grouping after correlation. Calculating peak correlations in 14 Groups... % finished: 20 50 60 70 80 90 100 Calculating graph cross linking in 14 Groups... % finished: 20 50 60 70 80 90 100 New number of psgroups: 48 xsAnnotate has now 48 groups, instead of 14 xsAnnotate contains no pseudospectra. Regroup all peaks into one! Generating peak matrix! Run isotope peak annotation % finished: 100 Found isotopes: 32 Found and use userdefined ruleset! Calculating possible adducts in 1 Groups... % finished: 100 Generating peak matrix! Run isotope peak annotation % finished: 20 40 50 60 70 80 90 100 Found isotopes: 23 Calculating possible adducts in 48 Groups... % finished: 20 40 50 60 70 80 90 100 Calculating possible adducts in 8 Groups... % finished: 10 Processing 3195 mz slices ... OK 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, 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 2.20.4 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 3.16.1 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 30 ppm ... OK Detecting chromatographic peaks in 456 regions of interest ... OK: 126 found. Start grouping after retention time. Created 14 pseudospectra. 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, 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 2.20.4 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 3.16.1 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma Detecting mass traces at 30 ppm ... OK Detecting chromatographic peaks in 456 regions of interest ... OK: 126 found. Start grouping after retention time. Created 14 pseudospectra. Generating peak matrix! Run isotope peak annotation % finished: 20 50 60 70 80 90 100 Found isotopes: 32 Calculating possible adducts in 14 Groups... % finished: 20 50 60 70 80 90 100 RUNIT TEST PROTOCOL  Tue Apr 12 17:15:08 2022 *********************************************** Number of test functions: 20 Number of errors: 0 Number of failures: 0 1 Test Suite : CAMERA RUnit Tests  20 test functions, 0 errors, 0 failures Number of test functions: 20 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 302.81 4.07 409.79 
CAMERA.Rcheck/examples_i386/CAMERAEx.timings

CAMERA.Rcheck/examples_x64/CAMERAEx.timings
