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INSTALL report for xcms on tokay2

This page was generated on 2020-10-17 11:58:00 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE xcms PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1892/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
xcms 3.10.2
Steffen Neumann
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/xcms
Branch: RELEASE_3_11
Last Commit: 4ff8895
Last Changed Date: 2020-09-18 09:32:16 -0400 (Fri, 18 Sep 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  TIMEOUT  skipped  skipped 

Summary

Package: xcms
Version: 3.10.2
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/xcms_3.10.2.tar.gz && rm -rf xcms.buildbin-libdir && mkdir xcms.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=xcms.buildbin-libdir xcms_3.10.2.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL xcms_3.10.2.zip && rm xcms_3.10.2.tar.gz xcms_3.10.2.zip
StartedAt: 2020-10-16 18:51:42 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 18:55:09 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 206.2 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/xcms_3.10.2.tar.gz && rm -rf xcms.buildbin-libdir && mkdir xcms.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=xcms.buildbin-libdir xcms_3.10.2.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL xcms_3.10.2.zip && rm xcms_3.10.2.tar.gz xcms_3.10.2.zip
###
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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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/xcms.buildbin-libdir/00LOCK-xcms/00new/xcms/libs/i386
** R
** 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  
    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  
    align-Chromatogram                      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  
    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  
    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  
    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-merge                  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  
    xcmsPapply                              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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/xcms.buildbin-libdir/xcms/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'xcms' as xcms_3.10.2.zip
* DONE (xcms)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'xcms' successfully unpacked and MD5 sums checked