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### Running command:
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###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:xcms.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings xcms_4.5.2.tar.gz
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/xcms.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* 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 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘xcms/DESCRIPTION’ ... OK
* this is package ‘xcms’ version ‘4.5.2’
* package encoding: UTF-8
* 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
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    help   1.0Mb
    libs   2.4Mb
* 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 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
Unexported objects imported by ':::' calls:
  ‘MALDIquant:::.localMaxima’ ‘MSnbase:::.MSnExpReqFvarLabels’
  ‘MSnbase:::.plotXIC’ ‘MSnbase:::.vertical_sub_layout’
  ‘MSnbase:::formatFileSpectrumNames’ ‘Spectra:::.concatenate_spectra’
  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’ ‘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’
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’
xcmsSet: no visible global function definition for ‘bpstopOnError’
xcmsSet: no visible global function definition for ‘bptry’
xcmsSet: no visible global function definition for ‘bpok’
estimatePrecursorIntensity,MsExperiment: no visible global function
  definition for ‘spectraSampleIndex’
plotSurf,xcmsRaw: no visible global function definition for ‘clear3d’
plotSurf,xcmsRaw: no visible global function definition for ‘surface3d’
plotSurf,xcmsRaw: no visible global function definition for ‘points3d’
plotSurf,xcmsRaw: no visible global function definition for ‘bbox3d’
plotTree,xcmsFragments: no visible global function definition for
  ‘edgemode<-’
plotTree,xcmsFragments: no visible global function definition for
  ‘addEdge’
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:
  addChildren addEdge base64encode bbox3d bpok bpstopOnError bptry
  checkCluster checkForRemoteErrors clear3d 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 points3d recvOneResult
  sampleNames saveXML sendCall spectraSampleIndex surface3d
  xmlInternalTreeParse xmlSchemaValidate xmlTree xmlTreeParse
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  XCMSnExp-class.Rd: OnDiskMSnExp, Spectrum, MSnExp, bpparam,
    Chromatogram, quantify, SummarizedExperiment, pSet
  XCMSnExp-filter-methods.Rd: OnDiskMSnExp
  XCMSnExp-inherited-methods.Rd: OnDiskMSnExp, bin, clean,
    filterAcquisitionNum, normalize, pickPeaks, removePeaks
  XCMSnExp-peak-grouping-results.Rd: SummarizedExperiment
  XChromatogram.Rd: Chromatogram, MChromatograms, DataFrame,
    transformIntensity
  XcmsExperiment.Rd: bpparam, MChromatograms, Spectra,
    SummarizedExperiment
  adjustRtime.Rd: OnDiskMSnExp, MsExperiment, bpparam
  chromPeakSpectra.Rd: Spectra, bpparam, MSpectra, Spectrum-class,
    Spectrum2-class
  chromatogram-method.Rd: OnDiskMSnExp, MChromatograms, Chromatogram
  correlate-Chromatogram.Rd: compareChromatograms, MChromatograms,
    Chromatogram
  dirname.Rd: OnDiskMSnExp-class
  do_findPeaks_MSW.Rd: peakDetectionCWT, tuneInPeakInfo
  estimatePrecursorIntensity.Rd: bpparam
  feature-grouping.Rd: AbundanceSimilarityParam
  featureChromatograms.Rd: bpparam
  featureSpectra.Rd: Spectra
  fillPeaks.chrom-methods.Rd: bpparam
  filter-MChromatograms.Rd: MChromatograms, Chromatogram
  findChromPeaks-Chromatogram-CentWaveParam.Rd: Chromatogram,
    MChromatograms, bpparam
  findChromPeaks-Chromatogram-MatchedFilter.Rd: Chromatogram,
    MChromatograms
  findChromPeaks-centWave.Rd: OnDiskMSnExp, bpparam, register
  findChromPeaks-centWaveWithPredIsoROIs.Rd: OnDiskMSnExp, bpparam,
    register
  findChromPeaks-massifquant.Rd: OnDiskMSnExp, bpparam, register
  findChromPeaks-matchedFilter.Rd: OnDiskMSnExp, bpparam, register
  findChromPeaks.Rd: OnDiskMSnExp, MChromatograms, MsExperiment,
    Spectra, bpparam
  findChromPeaksIsolationWindow.Rd: bpparam
  findPeaks-MSW.Rd: OnDiskMSnExp, identifyMajorPeaks, peakDetectionCWT,
    bpparam, tuneInPeakInfo, register
  findPeaks.MSW-xcmsRaw-method.Rd: peakDetectionCWT,
    identifyMajorPeaks, tuneInPeakInfo
  groupFeatures-abundance-correlation.Rd: AbundanceSimilarityParam
  groupFeatures-eic-similarity.Rd: compareChromatograms, alignRt,
    groupSimilarityMatrix, SimilarRtimeParam
  highlightChromPeaks.Rd: Chromatogram, MChromatograms
  isolationWindowTargetMz-OnDiskMSnExp-method.Rd: OnDiskMSnExp-class
  manualChromPeaks.Rd: OnDiskMSnExp, bpparam
  plotChromatogramsOverlay.Rd: MChromatograms
  plotFeatureGroups.Rd: featureGroups, groupFeatures
  profMat-xcmsSet.Rd: bpparam
  reconstructChromPeakSpectra.Rd: bpparam, Spectra, CharacterList,
    NumericList
  refineChromPeaks.Rd: bpparam
  removeIntensity-Chromatogram.Rd: clean, filterIntensity,
    Chromatogram, MChromatograms
  useOriginalCode.Rd: SnowParam
  writeMSData-XCMSnExp-character-method.Rd: writeMSData
  xcmsSet.Rd: SerialParam, MulticoreParam, SnowParam
Please provide package anchors for all Rd \link{} targets not in the
package 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 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
XcmsExperiment                9.647  0.566  10.185
findPeaks.massifquant-methods 6.731  0.006   6.736
LamaParama                    4.992  1.042   5.369
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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
* DONE

Status: 6 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/xcms.Rcheck/00check.log’
for details.