##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:xcms.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings xcms_3.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/xcms.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'xcms/DESCRIPTION' ... OK
* this is package 'xcms' version '3.14.1'
* 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 whether package 'xcms' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    help   2.3Mb
    html   1.4Mb
    libs   2.2Mb
* 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
* 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
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
.spectra_for_peaks: no visible global function definition for
  'featureData'
.spectra_for_peaks: no visible global function definition for
  'featureData<-'
.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<- featureData featureData<- 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 ... 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 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/xcms/libs/i386/xcms.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/xcms/libs/x64/xcms.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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
findPeaks.massifquant-methods 7.67   0.15    7.82
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                          user system elapsed
findPeaks.massifquant-methods             6.50   0.06    6.56
findChromPeaks-Chromatogram-CentWaveParam 5.05   0.11    5.15
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 6 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/xcms.Rcheck/00check.log'
for details.

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/xcms_3.14.1.tar.gz && rm -rf xcms.buildbin-libdir && mkdir xcms.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=xcms.buildbin-libdir xcms_3.14.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL xcms_3.14.1.zip && rm xcms_3.14.1.tar.gz xcms_3.14.1.zip
###
##############################################################################
##############################################################################


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100  760k  100  760k    0     0  1341k      0 --:--:-- --:--:-- --:--:-- 1343k

install for i386

* installing *source* package 'xcms' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c massifquant/Tracker.cpp -o massifquant/Tracker.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c massifquant/SegProc.cpp -o massifquant/SegProc.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c obiwarp/mat.cpp -o obiwarp/mat.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c obiwarp/vec.cpp -o obiwarp/vec.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
obiwarp/xcms_dynprog.cpp: In member function 'void DynProg::find_path(VEC::MatF&, VEC::VecF&, int, float, float, int, float)':
obiwarp/xcms_dynprog.cpp:1113:9: warning: variable 'bestscore' set but not used [-Wunused-but-set-variable]
   float bestscore;
         ^~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c xcms_obiwarp.cpp -o xcms_obiwarp.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -fno-inline -c fastMatch.c -o fastMatch.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -fno-inline -c mzClust_hclust.c -o mzClust_hclust.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -fno-inline -c mzROI.c -o mzROI.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -fno-inline -c util.c -o util.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -fno-inline -c xcms.c -o xcms.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -fno-inline -c binners.c -o binners.o
binners.c: In function '_breaks_on_binSize':
binners.c:357:7: warning: unused variable 'idx' [-Wunused-variable]
   int idx = 0;
       ^~~
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o xcms.dll tmp.def 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 -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/xcms.buildbin-libdir/00LOCK-xcms/00new/xcms/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'sigma' in package 'xcms'
Creating a generic function from function 'hasFilledChromPeaks' in package 'xcms'
** help
*** installing help indices
  converting help for package 'xcms'
    finding HTML links ... done
    AutoLockMass-methods                    html  
    GenericParam                            html  
    ProcessHistory-class                    html  
    SSgauss                                 html  
    XCMSnExp-class                          html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/xcms.buildbin-libdir/00LOCK-xcms/00new/xcms/help/processHistory.html
    finding level-2 HTML links ... done

    XCMSnExp-filter-methods                 html  
    XCMSnExp-inherited-methods              html  
    XCMSnExp-peak-grouping-results          html  
    XChromatogram                           html  
    absent-methods                          html  
    adjustRtime-obiwarp                     html  
    adjustRtime-peakGroups                  html  
    adjustRtime                             html  
    applyAdjustedRtime                      html  
    binYonX                                 html  
    breaks_on_binSize                       html  
    breaks_on_nBins                         html  
    c.xcmsSet                               html  
    calibrate-calibrant-mass                html  
    calibrate                               html  
    chromPeakSpectra                        html  
    chromatogram-method                     html  
    chromatographic-peak-detection          html  
    colMax                                  html  
    collect-methods                         html  
    correlate-Chromatogram                  html  
    descendZero                             html  
    diffreport-methods                      html  
    dirname                                 html  
    do_adjustRtime_peakGroups               html  
    do_findChromPeaks_centWave              html  
    do_findChromPeaks_centWaveWithPredIsoROIs
                                            html  
    do_findChromPeaks_massifquant           html  
    do_findChromPeaks_matchedFilter         html  
    do_findPeaks_MSW                        html  
    do_groupChromPeaks_density              html  
    do_groupChromPeaks_nearest              html  
    do_groupPeaks_mzClust                   html  
    doubleMatrix                            html  
    estimatePrecursorIntensity              html  
    etg                                     html  
    exportMetaboAnalyst                     html  
    extractMsData-method                    html  
    featureChromatograms                    html  
    featureSpectra                          html  
    featureSummary                          html  
    fillChromPeaks                          html  
    fillPeaks-methods                       html  
    fillPeaks.MSW-methods                   html  
    fillPeaks.chrom-methods                 html  
    filter-MChromatograms                   html  
    filtfft                                 html  
    findChromPeaks-Chromatogram-CentWaveParam
                                            html  
    findChromPeaks-Chromatogram-MatchedFilter
                                            html  
    findChromPeaks-centWave                 html  
    findChromPeaks-centWaveWithPredIsoROIs
                                            html  
    findChromPeaks-massifquant              html  
    findChromPeaks-matchedFilter            html  
    findChromPeaksIsolationWindow           html  
    findEqualGreater                        html  
    findMZ                                  html  
    findPeaks-MSW                           html  
    findPeaks-methods                       html  
    findPeaks.MS1-methods                   html  
    findPeaks.MSW-xcmsRaw-method            html  
    findPeaks.addPredictedIsotopeFeatures-methods
                                            html  
    findPeaks.centWave-methods              html  
    findPeaks.centWaveWithPredictedIsotopeROIs-methods
                                            html  
    findPeaks.massifquant-methods           html  
    findPeaks.matchedFilter-xcmsRaw-method
                                            html  
    findneutral                             html  
    getEIC-methods                          html  
    getPeaks-methods                        html  
    getScan-methods                         html  
    getSpec-methods                         html  
    getXcmsRaw-methods                      html  
    group-methods                           html  
    group.density                           html  
    group.mzClust                           html  
    group.nearest                           html  
    groupChromPeaks-density                 html  
    groupChromPeaks-mzClust                 html  
    groupChromPeaks-nearest                 html  
    groupChromPeaks                         html  
    groupOverlaps                           html  
    groupnames-XCMSnExp                     html  
    groupnames-methods                      html  
    groupval-methods                        html  
    highlightChromPeaks                     html  
    image.xcmsRaw                           html  
    imputeLinInterpol                       html  
    imputeRowMin                            html  
    imputeRowMinRand                        html  
    isolationWindowTargetMz-OnDiskMSnExp-method
                                            html  
    levelplot.xcmsRaw                       html  
    loadRaw-methods                         html  
    manualChromPeaks                        html  
    medianFilter                            html  
    msn2xcmsRaw                             html  
    na.flatfill                             html  
    overlappingFeatures                     html  
    panel.cor                               html  
    peakPlots-methods                       html  
    peakTable-methods                       html  
    peaksWithCentWave                       html  
    peaksWithMatchedFilter                  html  
    phenoDataFromPaths                      html  
    plot.xcmsEIC                            html  
    plotAdjustedRtime                       html  
    plotChrom-methods                       html  
    plotChromPeakDensity                    html  
    plotChromPeaks                          html  
    plotEIC-methods                         html  
    plotMsData                              html  
    plotPeaks-methods                       html  
    plotQC                                  html  
    plotRaw-methods                         html  
    plotScan-methods                        html  
    plotSpec-methods                        html  
    plotSurf-methods                        html  
    plotTIC-methods                         html  
    plotrt-methods                          html  
    profGenerate                            html  
    profMat-xcmsSet                         html  
    profMedFilt-methods                     html  
    profMethod-methods                      html  
    profRange-methods                       html  
    profStep-methods                        html  
    pval                                    html  
    rawEIC-methods                          html  
    rawMat-methods                          html  
    reconstructChromPeakSpectra             html  
    rectUnique                              html  
    refineChromPeaks-clean                  html  
    refineChromPeaks-filter-intensity       html  
    refineChromPeaks-merge                  html  
    removeIntensity-Chromatogram            html  
    retcor-methods                          html  
    retcor.obiwarp-methods                  html  
    retcor.peakgroups-methods               html  
    retexp                                  html  
    rla                                     html  
    sampnames-methods                       html  
    showError-xcmsSet-method                html  
    specDist-methods                        html  
    specDist.cosine-methods                 html  
    specDist.meanMZmatch-methods            html  
    specDist.peakCount-methods              html  
    specNoise                               html  
    specPeaks                               html  
    split.xcmsRaw                           html  
    split.xcmsSet                           html  
    stitch-methods                          html  
    sub-xcmsRaw-logicalOrNumeric-missing-missing-method
                                            html  
    updateObject-xcmsSet-method             html  
    useOriginalCode                         html  
    verify.mzQuantML                        html  
    write.cdf-methods                       html  
    write.mzQuantML                         html  
    write.mzdata-methods                    html  
    writeMSData-XCMSnExp-character-method   html  
    writeMzTab                              html  
    xcms-deprecated                         html  
    xcmsEIC-class                           html  
    xcmsFileSource-class                    html  
    xcmsFragments-class                     html  
    xcmsFragments                           html  
    xcmsPeaks-class                         html  
    xcmsRaw-class                           html  
    xcmsRaw                                 html  
    xcmsSet-class                           html  
    xcmsSet                                 html  
    xcmsSource-class                        html  
    xcmsSource-methods                      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 'xcms' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c massifquant/Tracker.cpp -o massifquant/Tracker.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c massifquant/SegProc.cpp -o massifquant/SegProc.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c obiwarp/mat.cpp -o obiwarp/mat.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c obiwarp/vec.cpp -o obiwarp/vec.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
obiwarp/xcms_dynprog.cpp: In member function 'void DynProg::find_path(VEC::MatF&, VEC::VecF&, int, float, float, int, float)':
obiwarp/xcms_dynprog.cpp:1113:9: warning: variable 'bestscore' set but not used [-Wunused-but-set-variable]
   float bestscore;
         ^~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c xcms_obiwarp.cpp -o xcms_obiwarp.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -fno-inline -c fastMatch.c -o fastMatch.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -fno-inline -c mzClust_hclust.c -o mzClust_hclust.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -fno-inline -c mzROI.c -o mzROI.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -fno-inline -c util.c -o util.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -fno-inline -c xcms.c -o xcms.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -fno-inline -c binners.c -o binners.o
binners.c: In function '_breaks_on_binSize':
binners.c:357:7: warning: unused variable 'idx' [-Wunused-variable]
   int idx = 0;
       ^~~
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o xcms.dll tmp.def 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 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/xcms.buildbin-libdir/xcms/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'xcms' as xcms_3.14.1.zip
* DONE (xcms)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'xcms' successfully unpacked and MD5 sums checked