Movatterモバイル変換

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:CAMERA.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings CAMERA_1.66.0.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/CAMERA.Rcheck’* using R version 4.5.2 (2025-10-31)* using platform: x86_64-pc-linux-gnu* R was compiled by    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0* running under: Ubuntu 24.04.3 LTS* using session charset: UTF-8* checking for file ‘CAMERA/DESCRIPTION’ ... OK* this is package ‘CAMERA’ version ‘1.66.0’* 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 ... NOTEFound the following hidden files and directories:  .travis.ymlThese were most likely included in error. See section ‘Packagestructure’ in the ‘Writing R Extensions’ manual.* checking for portable file names ... OK* checking for sufficient/correct file permissions ... OK* checking whether package ‘CAMERA’ can be installed ... WARNINGFound the following significant warnings:  fastMatch.c:65:68: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]See ‘/home/biocbuild/bbs-3.22-bioc/meat/CAMERA.Rcheck/00install.out’ for details.* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’* checking installed package size ... INFO  installed size is  8.9Mb  sub-directories of 1Mb or more:    mzML        2.7Mb    quantiles   5.0Mb* checking package directory ... OK* checking ‘build’ directory ... OK* checking DESCRIPTION meta-information ... NOTEMalformed 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 top-level files ... OK* checking for left-over files ... OK* checking index information ... OK* checking package subdirectories ... OK* checking code files for non-ASCII characters ... OK* checking R files for syntax errors ... OK* checking whether the package can be loaded ... OK* checking whether the package can be loaded with stated dependencies ... OK* checking whether the package can be unloaded cleanly ... OK* checking whether the namespace can be loaded with stated dependencies ... OK* checking whether the namespace can be unloaded cleanly ... OK* checking loading without being on the library search path ... OK* checking whether startup messages can be suppressed ... 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 ... NOTEForeign function call to a different package:  .Call("getEIC", ..., PACKAGE = "xcms")See chapter ‘System and foreign language interfaces’ in the ‘Writing RExtensions’ manual.* checking R code for possible problems ... NOTEFile ‘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 xcmsPapplyConsider 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 ... NOTEprepare_Rd: findKendrickMasses.Rd:21-22: Dropping empty section \details* checking Rd metadata ... OK* checking Rd cross-references ... NOTEFound the following Rd file(s) with Rd \link{} targets missing packageanchors:  annotateDiffreport.Rd: diffreport  calcPC.hcs-methods.Rd: highlyConnSG  calcPC.lpc-methods.Rd: label.propagation.community  ruleSet-class.Rd: Versioned-class  xsAnnotate-class.Rd: xcmsSetPlease provide package anchors for all Rd \link{} targets not in thepackage itself and the base packages.* 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 non-ASCII 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 ... NOTENote: information on .o files is not available* checking files in ‘vignettes’ ... OK* checking examples ... OKExamples with CPU (user + system) or elapsed time > 5s                                     user system elapsedgroupCorr-methods                  23.518  4.173  23.911getIsotopeCluster                  20.849  6.255  10.953calcCaS-methods                    19.814  5.607   1.837annotate-methods                    8.459  1.128   9.498findIsotopesWithValidation-methods  5.368  2.974   3.819getAllPeakEICs-methods              6.195  1.749   4.477groupFWHM-methods                   4.337  1.830   6.010pspec2metfrag                       4.213  1.893   5.983findAdducts-methods                 4.114  1.764   5.758getReducedPeaklist-methods          3.977  1.554   5.403getPeaklist-methods                 4.012  1.457   5.342groupDen-methods                    3.954  1.193   5.009annotateDiffreport                  1.449  0.176   7.370* checking for unstated dependencies in ‘tests’ ... OK* checking tests ...  Running ‘runTests.R’ OK* checking for unstated dependencies in vignettes ... OK* checking package vignettes ... OK* checking re-building of vignette outputs ... OK* checking PDF version of manual ... OK* DONEStatus: 1 WARNING, 8 NOTEsSee  ‘/home/biocbuild/bbs-3.22-bioc/meat/CAMERA.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL CAMERA###############################################################################################################################################################* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’* installing *source* package ‘CAMERA’ ...** this is package ‘CAMERA’ version ‘1.66.0’** using staged installation** libsusing C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c fastMatch.c -o fastMatch.ofastMatch.c: In function ‘fastMatch’:fastMatch.c:65:68: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]   65 |         error("fastMatch/calloc: memory could not be allocated ! (%d bytes)\n", nx  * sizeof(struct idxStruct) );      |                                                                   ~^            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~      |                                                                    |                |      |                                                                    int              long unsigned int      |                                                                   %ldgcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o CAMERA.so fastMatch.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lRinstalling to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-CAMERA/00new/CAMERA/libs** R** data** inst** byte-compile and prepare package for lazy loading** help*** installing help indices** building package indices** installing vignettes** testing if installed package can be loaded from temporary location** checking absolute paths in shared objects and dynamic libraries** testing if installed package can be loaded from final location** testing if installed package keeps a record of temporary installation path* DONE (CAMERA)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: x86_64-pc-linux-gnuR is free software and comes with ABSOLUTELY NO WARRANTY.You are welcome to redistribute it under certain conditions.Type 'license()' or 'licence()' for distribution details.R is a collaborative project with many contributors.Type 'contributors()' for more information and'citation()' on how to cite R or R packages in publications.Type 'demo()' for some demos, 'help()' for on-line help, or'help.start()' for an HTML browser interface to help.Type 'q()' to quit R.> require("CAMERA") || stop("unable to load CAMERA")Loading required package: CAMERALoading required package: BiobaseLoading required package: BiocGenericsLoading required package: genericsAttaching package: 'generics'The following objects are masked from 'package:base':    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,    setequal, unionAttaching package: 'BiocGenerics'The following objects are masked from 'package:stats':    IQR, mad, sd, var, xtabsThe following objects are masked from 'package:base':    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,    as.data.frame, basename, cbind, colnames, dirname, do.call,    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,    unsplit, which.max, which.minWelcome to Bioconductor    Vignettes contain introductory material; view with    'browseVignettes()'. To cite Bioconductor, see    'citation("Biobase")', and for packages 'citation("pkgname")'.Loading required package: xcmsLoading required package: BiocParallelThis is xcms version 4.8.0 [1] TRUE> BiocGenerics:::testPackage("CAMERA")/home/biocbuild/bbs-3.22-bioc/R/site-library/faahKO/cdf/KO/ko15.CDF method:  bin step:  0.1 /home/biocbuild/bbs-3.22-bioc/R/site-library/faahKO/cdf/KO/ko16.CDF method:  bin step:  0.1 /home/biocbuild/bbs-3.22-bioc/R/site-library/faahKO/cdf/KO/ko18.CDF method:  bin step:  0.1 /home/biocbuild/bbs-3.22-bioc/R/site-library/faahKO/cdf/WT/wt15.CDF method:  bin step:  0.1 /home/biocbuild/bbs-3.22-bioc/R/site-library/faahKO/cdf/WT/wt16.CDF method:  bin step:  0.1 /home/biocbuild/bbs-3.22-bioc/R/site-library/faahKO/cdf/WT/wt18.CDF method:  bin step:  0.1 /home/biocbuild/bbs-3.22-bioc/R/site-library/faahKO/cdf/KO/ko19.CDF method:  bin step:  0.1 /home/biocbuild/bbs-3.22-bioc/R/site-library/faahKO/cdf/KO/ko21.CDF method:  bin step:  0.1 /home/biocbuild/bbs-3.22-bioc/R/site-library/faahKO/cdf/KO/ko22.CDF method:  bin step:  0.1 /home/biocbuild/bbs-3.22-bioc/R/site-library/faahKO/cdf/WT/wt19.CDF method:  bin step:  0.1 /home/biocbuild/bbs-3.22-bioc/R/site-library/faahKO/cdf/WT/wt21.CDF method:  bin step:  0.1 /home/biocbuild/bbs-3.22-bioc/R/site-library/faahKO/cdf/WT/wt22.CDF method:  bin step:  0.1 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 ps-groups:  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 ps-groups:  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 ps-groups:  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 ps-groups:  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 ps-groups:  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 ps-groups:  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 ps-groups:  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 ps-groups:  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 ps-groups:  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 ps-groups:  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 ps-groups:  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 ps-groups:  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 ps-groups:  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 ps-groups:  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 ps-groups:  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 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 ps-groups:  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 user-defined 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 ps-groups:  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 user-defined 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 ps-groups:  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 user-defined ruleset!Calculating possible adducts in 329 Groups...  % finished: 10  20  30  40  50  60  70  80  90  100  Detecting mass traces at 30 ppm ... OKDetecting 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 user-defined ruleset!Calculating possible adducts in 14 Groups...  % finished: 20  50  60  70  80  90  100  Detecting mass traces at 30 ppm ... OKDetecting 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 ps-groups:  35 xsAnnotate has now 35 groups, instead of 14 Detecting mass traces at 30 ppm ... OKDetecting chromatographic peaks in 456 regions of interest ... OK: 126 found.Created 11 pseudospectra.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 ps-groups:  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 ps-groups:  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 ps-groups:  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 ps-groups:  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 user-defined ruleset!Calculating possible adducts in 316 Groups...  % finished: 10  20  30  40  50  60  70  80  90  100  Detecting mass traces at 30 ppm ... OKDetecting 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 ps-groups:  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 ps-groups:  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 ps-groups:  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 ps-groups:  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 user-defined 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  Detecting mass traces at 30 ppm ... OKDetecting chromatographic peaks in 456 regions of interest ... OK: 126 found.Start grouping after retention time.Created 14 pseudospectra.Detecting mass traces at 30 ppm ... OKDetecting 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 -- Thu Dec 11 22:51:31 2025 *********************************************** 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 failuresNumber of test functions: 20 Number of errors: 0 Number of failures: 0 > > proc.time()   user  system elapsed 336.858  21.432 338.163