##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:xcms.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings xcms_3.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/xcms.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘xcms/DESCRIPTION’ ... OK
* this is package ‘xcms’ version ‘3.20.0’
* 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:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘xcms’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  GPL (>= 2) + file LICENSE
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘MALDIquant:::.localMaxima’ ‘MSnbase:::.MSnExpReqFvarLabels’
  ‘MSnbase:::.plotXIC’ ‘MSnbase:::.vertical_sub_layout’
  ‘MSnbase:::formatFileSpectrumNames’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.copy_env’ ‘.getChromPeakData’ ‘.get_closest_index’
  ‘.spectra_for_peaks’ ‘.split_by_file2’ ‘.validChromPeaksMatrix’
  ‘MSW.cwt’ ‘MSW.getLocalMaximumCWT’ ‘MSW.getRidge’ ‘descendMin’
  ‘descendMinTol’ ‘estimateChromNoise’ ‘getLocalNoiseEstimate’
  ‘na.flatfill’ ‘patternVsRowScore’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.xcmsFragments.plotTree: no visible global function definition for
  ‘edgemode<-’
.xcmsFragments.plotTree: no visible global function definition for
  ‘addEdge’
buildAnalysisSummary: no visible global function definition for
  ‘newXMLNode’
buildAssayList : <anonymous>: no visible global function definition for
  ‘newXMLNode’
buildAssayList: no visible global function definition for ‘newXMLNode’
buildAuditCollection: no visible global function definition for
  ‘newXMLNode’
buildCVlist: no visible global function definition for ‘newXMLNode’
buildCVlist: no visible global function definition for ‘addChildren’
buildCvParams : <anonymous>: no visible global function definition for
  ‘newXMLNode’
buildDataProcessingList: no visible global function definition for
  ‘newXMLNode’
buildFeatureList : <anonymous>: no visible global function definition
  for ‘newXMLNode’
buildInputFiles : <anonymous>: no visible global function definition
  for ‘newXMLNode’
buildInputFiles: no visible global function definition for ‘newXMLNode’
buildMzq: no visible global function definition for ‘xmlTree’
buildSmallMoleculeList : <anonymous>: no visible global function
  definition for ‘newXMLNode’
buildSmallMoleculeList: no visible global function definition for
  ‘newXMLNode’
buildSoftwareList: no visible global function definition for
  ‘newXMLNode’
buildStudyVariableList : <anonymous>: no visible global function
  definition for ‘newXMLNode’
buildStudyVariableList : <anonymous> : <anonymous>: no visible global
  function definition for ‘newXMLNode’
buildStudyVariableList: no visible global function definition for
  ‘newXMLNode’
chromPeakSpectra: no visible global function definition for ‘List’
featureSpectra: no visible global function definition for ‘List’
plotQC: no visible global function definition for ‘sampleNames’
running: multiple local function definitions for ‘funct’ with different
  formal arguments
verify.mzQuantML: no visible global function definition for
  ‘xmlTreeParse’
verify.mzQuantML: no visible global function definition for
  ‘xmlInternalTreeParse’
verify.mzQuantML: no visible global function definition for
  ‘xmlSchemaValidate’
xcmsClusterApply: no visible global function definition for
  ‘checkCluster’
xcmsClusterApply : submit: no visible global function definition for
  ‘sendCall’
xcmsClusterApply: no visible global function definition for
  ‘recvOneResult’
xcmsClusterApply: no visible global function definition for
  ‘checkForRemoteErrors’
xcmsPapply: no visible global function definition for ‘mpi.comm.size’
xcmsPapply: no visible global function definition for
  ‘mpi.spawn.Rslaves’
xcmsPapply: no visible global function definition for ‘mpi.comm.rank’
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for ‘mpi.send.Robj’
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for ‘mpi.recv.Robj’
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for ‘mpi.any.source’
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for ‘mpi.any.tag’
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for ‘mpi.get.sourcetag’
xcmsPapply: no visible global function definition for
  ‘mpi.bcast.Robj2slave’
xcmsPapply: no visible global function definition for ‘mpi.bcast.cmd’
xcmsPapply: no visible global function definition for ‘mpi.recv.Robj’
xcmsPapply: no visible global function definition for ‘mpi.any.source’
xcmsPapply: no visible global function definition for ‘mpi.any.tag’
xcmsPapply: no visible global function definition for
  ‘mpi.get.sourcetag’
xcmsPapply: no visible global function definition for ‘mpi.send.Robj’
xcmsParallelSetup: no visible global function definition for
  ‘mpi.spawn.Rslaves’
xcmsParallelSetup: no visible global function definition for
  ‘mpi.comm.size’
xcmsParallelSetup: no visible global function definition for
  ‘mpi.comm.rank’
xcmsParallelSetup: no visible global function definition for
  ‘makeCluster’
[,XChromatograms-ANY-ANY-ANY: no visible global function definition for
  ‘pData<-’
plotSurf,xcmsRaw: no visible global function definition for ‘rgl.clear’
plotSurf,xcmsRaw: no visible global function definition for
  ‘rgl.surface’
plotSurf,xcmsRaw: no visible global function definition for
  ‘rgl.points’
plotSurf,xcmsRaw: no visible global function definition for ‘rgl.bbox’
plotTree,xcmsFragments: no visible global function definition for
  ‘edgemode<-’
plotTree,xcmsFragments: no visible global function definition for
  ‘addEdge’
refineChromPeaks,XCMSnExp-FilterIntensityParam: no visible binding for
  global variable ‘value’
write.cdf,xcmsRaw: no visible global function definition for
  ‘ncdim_def’
write.cdf,xcmsRaw: no visible global function definition for
  ‘ncvar_def’
write.cdf,xcmsRaw: no visible global function definition for
  ‘nc_create’
write.cdf,xcmsRaw: no visible global function definition for
  ‘ncvar_put’
write.cdf,xcmsRaw: no visible global function definition for
  ‘ncatt_put’
write.cdf,xcmsRaw: no visible global function definition for ‘nc_close’
write.mzQuantML,xcmsSet: no visible global function definition for
  ‘saveXML’
write.mzdata,xcmsRaw: no visible global function definition for
  ‘base64encode’
Undefined global functions or variables:
  List addChildren addEdge base64encode checkCluster
  checkForRemoteErrors edgemode<- makeCluster mpi.any.source
  mpi.any.tag mpi.bcast.Robj2slave mpi.bcast.cmd mpi.comm.rank
  mpi.comm.size mpi.get.sourcetag mpi.recv.Robj mpi.send.Robj
  mpi.spawn.Rslaves nc_close nc_create ncatt_put ncdim_def ncvar_def
  ncvar_put newXMLNode pData<- recvOneResult rgl.bbox rgl.clear
  rgl.points rgl.surface sampleNames saveXML sendCall value
  xmlInternalTreeParse xmlSchemaValidate xmlTree xmlTreeParse
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'findPeaks-MSW.Rd':
  ‘sav.gol’

Missing link or links in documentation object 'findPeaks.MSW-xcmsRaw-method.Rd':
  ‘sav.gol’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
groupFeatures-eic-similarity  5.707  0.101   5.809
findPeaks.massifquant-methods 5.369  0.288   5.657
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/xcms.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL xcms
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘xcms’ ...
** using staged installation
** libs
rm -f massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o binners.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c massifquant/Tracker.cpp -o massifquant/Tracker.o
In file included from massifquant/Tracker.cpp:8:
massifquant/Tracker.h:49:16: warning: private field 'r_val_i' is not used [-Wunused-private-field]
        double r_val_i;
               ^
massifquant/Tracker.h:50:16: warning: private field 'p_val_i' is not used [-Wunused-private-field]
        double p_val_i;
               ^
massifquant/Tracker.h:53:16: warning: private field 'r_val_m' is not used [-Wunused-private-field]
        double r_val_m;
               ^
massifquant/Tracker.h:54:16: warning: private field 'p_val_m' is not used [-Wunused-private-field]
        double p_val_m;
               ^
4 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c massifquant/SegProc.cpp -o massifquant/SegProc.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
In file included from massifquant/DataKeeper.cpp:4:
massifquant/DataKeeper.h:36:26: warning: private field 'scbuf' is not used [-Wunused-private-field]
        struct scanBuf * scbuf;
                         ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c obiwarp/mat.cpp -o obiwarp/mat.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c obiwarp/vec.cpp -o obiwarp/vec.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
obiwarp/xcms_dynprog.cpp:1113:9: warning: variable 'bestscore' set but not used [-Wunused-but-set-variable]
  float bestscore;
        ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c xcms_obiwarp.cpp -o xcms_obiwarp.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fastMatch.c -o fastMatch.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c mzClust_hclust.c -o mzClust_hclust.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c mzROI.c -o mzROI.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c util.c -o util.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c xcms.c -o xcms.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c binners.c -o binners.o
binners.c:357:7: warning: unused variable 'idx' [-Wunused-variable]
  int idx = 0;
      ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o xcms.so massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o binners.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-xcms/00new/xcms/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘group’ in package ‘xcms’
Creating a new generic function for ‘sigma’ in package ‘xcms’
Creating a generic function from function ‘hasFilledChromPeaks’ in package ‘xcms’
** 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 (xcms)

R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(xcms)
Loading required package: BiocParallel
Loading required package: MSnbase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

The following object is masked from 'package:stats':

    smooth


This is MSnbase version 2.24.2 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

The following object is masked from 'package:base':

    trimws


This is xcms version 3.20.0 


Attaching package: 'xcms'

The following object is masked from 'package:stats':

    sigma

> library(faahKO)
> library(msdata)
> 
> if (.Platform$OS.type == "unix") {
+     prm <- MulticoreParam(3)
+ } else {
+     # prm <- SnowParam(3)
+     prm <- SerialParam()
+ }
> register(bpstart(prm))
> 
> ## Create some objects we can re-use in different tests:
> faahko_3_files <- c(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
+                     system.file('cdf/KO/ko16.CDF', package = "faahKO"),
+                     system.file('cdf/KO/ko18.CDF', package = "faahKO"))
> 
> faahko_od <- readMSData(faahko_3_files, mode = "onDisk")
Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.
> faahko_xod <- findChromPeaks(
+     faahko_od, param = CentWaveParam(noise = 10000, snthresh = 40,
+                                      prefilter = c(3, 10000)))
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... OK: 61 found.

Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 87 found.

Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 1025 regions of interest ... OK: 100 found.

> od_x <- faahko_od
> mzr <- matrix(c(335, 335, 344, 344), ncol = 2, byrow = TRUE)
> od_chrs <- chromatogram(od_x, mz = mzr)
> xod_x <- faahko_xod
> pdp <- PeakDensityParam(sampleGroups = rep(1, 3))
> xod_xg <- groupChromPeaks(xod_x, param = pdp)
Processing 2572 mz slices ... OK
> xod_xgr <- adjustRtime(xod_xg, param = PeakGroupsParam(span = 0.4))
Performing retention time correction using 19 peak groups.
Applying retention time adjustment to the identified chromatographic peaks ... OK
> xod_xgrg <- groupChromPeaks(xod_xgr, param = pdp)
Processing 2572 mz slices ... OK
> xod_r <- adjustRtime(as(od_x, "XCMSnExp"), param = ObiwarpParam())
Sample number 2 used as center sample.
Aligning ko15.CDF against ko16.CDF ... OK

Aligning ko18.CDF against ko16.CDF ... OK

> 
> xod_chr <- findChromPeaks(filterMz(filterRt(od_x, rt = c(2500, 3500)),
+                                    mz = c(334.9, 344.1)),
+                           param = CentWaveParam())
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 515 regions of interest ... OK: 20 found.

Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 514 regions of interest ... OK: 23 found.

Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 551 regions of interest ... OK: 29 found.

Warning message:
In .local(object, param, ...) :
  Your data appears to be not centroided! CentWave works best on data in centroid mode.
> 
> microtofq_fs <- c(system.file("microtofq/MM14.mzML", package = "msdata"),
+                   system.file("microtofq/MM8.mzML", package = "msdata"))
> microtofq_od <- readMSData(microtofq_fs, mode = "onDisk")
> 
> ## Direct injection data:
> fticrf <- list.files(system.file("fticr-mzML", package = "msdata"),
+                      recursive = TRUE, full.names = TRUE)
> fticr <- readMSData(fticrf[1:2], msLevel. = 1, mode = "onDisk")
> fticr_xod <- findChromPeaks(fticr, MSWParam(scales = c(1, 7),
+                                             peakThr = 80000, ampTh = 0.005,
+                                             SNR.method = "data.mean",
+                                             winSize.noise = 500))
> ## Pesticide data
> fl <- system.file("TripleTOF-SWATH", "PestMix1_SWATH.mzML", package = "msdata")
> pest_swth <- readMSData(fl, mode = "onDisk")
> cwp <- CentWaveParam(snthresh = 5, noise = 100, ppm = 10,
+                      peakwidth = c(3, 20), prefilter = c(3, 1000))
> pest_swth <- findChromPeaks(pest_swth, param = cwp)
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 11 regions of interest ... OK: 11 found.

> pest_swth <- findChromPeaksIsolationWindow(pest_swth, param = cwp)
Detecting mass traces at 10 ppm ... OK

Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 2 regions of interest ... OK: 2 found.

Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 7 regions of interest ... OK: 7 found.

Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 3 regions of interest ... OK: 3 found.

Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 17 regions of interest ... OK: 17 found.

Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 3 regions of interest ... OK: 2 found.

Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 10 regions of interest ... OK: 10 found.

Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 3 regions of interest ... OK: 3 found.

Warning message:
In .processResultList(resList, getProcHist = return.type == "xcmsSet",  :
  No peaks found in sample number 1.
> 
> fl <- system.file("TripleTOF-SWATH", "PestMix1_DDA.mzML", package = "msdata")
> pest_dda <- readMSData(fl, mode = "onDisk")
> pest_dda <- findChromPeaks(pest_dda, param = cwp)
Detecting mass traces at 10 ppm ... OK
Detecting chromatographic peaks in 29 regions of interest ... OK: 28 found.

> 
> ## Sciex test data.
> ## fl <- dir(system.file("sciex", package = "msdata"), full.names = TRUE)
> ## sciex_data <- readMSData(fl, mode = "onDisk")
> ## sciex_data <- pickPeaks(sciex_data)
> 
> test_check("xcms")
Object of class:  CleanPeaksParam 
 Parameters:
 - maxPeakwidth: [1] 13.2
Object of class:  MergeNeighboringPeaksParam 
 Parameters:
 - expandRt: [1] 5
 - expandMz: [1] 0.1
 - ppm: [1] 20
 - minProp: [1] 0.9
8.00  16.00  24.00  28.00  32.00  40.00  48.00  52.00  56.00  60.00  64.00  72.00  80.00  84.00  88.00  96.00  100.00  
8.00  16.00  28.00  32.00  40.00  64.00  80.00  96.00  100.00  
8.00  16.00  24.00  28.00  32.00  40.00  48.00  52.00  56.00  60.00  64.00  72.00  80.00  84.00  88.00  96.00  100.00  
8.00  16.00  28.00  32.00  40.00  56.00  64.00  80.00  88.00  96.00  100.00  
8.00  16.00  24.00  28.00  32.00  40.00  48.00  52.00  56.00  60.00  64.00  72.00  80.00  84.00  88.00  96.00  100.00  
Object of class: XChromatogram
length of object: 0
from file: 
mz range: [NA, NA]
MS level: 1
Identified chromatographic peaks (0):
 rt	rtmin	rtmax	into	maxo	sn 
[ FAIL 0 | WARN 673 | SKIP 11 | PASS 2876 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (11)

[ FAIL 0 | WARN 673 | SKIP 11 | PASS 2876 ]
> 
> bpstop(prm)
> 
> 
> proc.time()
   user  system elapsed 
151.731   6.651 333.277