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CHECK report for xcms on tokay1

This page was generated on 2019-04-13 11:19:37 -0400 (Sat, 13 Apr 2019).

Package 1637/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
xcms 3.4.4
Steffen Neumann
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/xcms
Branch: RELEASE_3_8
Last Commit: 6a9e67f
Last Changed Date: 2019-02-20 07:54:58 -0400 (Wed, 20 Feb 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: xcms
Version: 3.4.4
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:xcms.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings xcms_3.4.4.tar.gz
StartedAt: 2019-04-13 06:13:44 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 06:47:04 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 2000.3 seconds
RetCode: 0
Status:  OK  
CheckDir: xcms.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:xcms.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings xcms_3.4.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/xcms.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '3.4.4'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'xcms' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    html   1.2Mb
    libs   1.7Mb
* 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:::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:
  'MSW.cwt' 'MSW.getLocalMaximumCWT' 'MSW.getRidge' 'XProcessHistory'
  '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'
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'
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'
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 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
  recvOneResult rgl.bbox rgl.clear rgl.points rgl.surface saveXML
  sendCall 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 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 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-3.8-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)

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 or elapsed time > 5s
                              user system elapsed
findPeaks.massifquant-methods 6.95   0.01    6.97
plotChromPeakDensity          6.60   0.08    6.68
adjustRtime-obiwarp           4.68   0.11   13.69
featureChromatograms          3.42   0.36   44.78
fillChromPeaks                3.64   0.01   32.54
XCMSnExp-filter-methods       2.04   0.19   11.31
applyAdjustedRtime            2.00   0.01   14.70
adjustRtime-peakGroups        1.82   0.09   10.42
chromatogram-method           1.72   0.05   31.00
extractMsData-method          1.61   0.16   10.05
XCMSnExp-class                1.39   0.20   17.78
findChromPeaks-centWave       1.03   0.02    9.44
findChromPeaks-massifquant    1.01   0.00   12.49
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
findPeaks.massifquant-methods 7.41   0.00    7.41
plotChromPeakDensity          7.19   0.09    7.29
adjustRtime-obiwarp           4.28   0.05   13.25
fillChromPeaks                3.88   0.02   34.52
featureChromatograms          3.55   0.11   45.93
applyAdjustedRtime            2.08   0.02   15.17
XCMSnExp-filter-methods       2.06   0.01   11.41
chromatogram-method           1.90   0.03   31.15
adjustRtime-peakGroups        1.86   0.00   10.77
extractMsData-method          1.69   0.07    9.42
XCMSnExp-class                1.47   0.03   18.42
findChromPeaks-centWave       1.12   0.05   10.34
findChromPeaks-massifquant    1.13   0.00   12.41
* 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: 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/xcms.Rcheck/00check.log'
for details.

Installation output

xcms.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/xcms_3.4.4.tar.gz && rm -rf xcms.buildbin-libdir && mkdir xcms.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=xcms.buildbin-libdir xcms_3.4.4.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL xcms_3.4.4.zip && rm xcms_3.4.4.tar.gz xcms_3.4.4.zip
###
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100  595k  100  595k    0     0  13.5M      0 --:--:-- --:--:-- --:--:-- 14.9M

install for i386

* installing *source* package 'xcms' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c massifquant/Tracker.cpp -o massifquant/Tracker.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c massifquant/SegProc.cpp -o massifquant/SegProc.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c obiwarp/mat.cpp -o obiwarp/mat.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c obiwarp/vec.cpp -o obiwarp/vec.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c xcms_obiwarp.cpp -o xcms_obiwarp.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -fno-inline -c fastMatch.c -o fastMatch.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -fno-inline -c mzClust_hclust.c -o mzClust_hclust.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -fno-inline -c mzROI.c -o mzROI.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -fno-inline -c util.c -o util.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -fno-inline -c xcms.c -o xcms.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -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:/Rtools/mingw_32/bin/g++ -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˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/xcms.buildbin-libdir/xcms/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'sigma' 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  
    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  
    descendZero                             html  
    diffreport-methods                      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  
    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  
    groupnames-XCMSnExp                     html  
    groupnames-methods                      html  
    groupval-methods                        html  
    highlightChromPeaks                     html  
    image.xcmsRaw                           html  
    imputeLinInterpol                       html  
    imputeRowMin                            html  
    imputeRowMinRand                        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  
    rectUnique                              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
In R CMD INSTALL

install for x64

* installing *source* package 'xcms' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c massifquant/Tracker.cpp -o massifquant/Tracker.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c massifquant/SegProc.cpp -o massifquant/SegProc.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c obiwarp/mat.cpp -o obiwarp/mat.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c obiwarp/vec.cpp -o obiwarp/vec.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c xcms_obiwarp.cpp -o xcms_obiwarp.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -fno-inline -c fastMatch.c -o fastMatch.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -fno-inline -c mzClust_hclust.c -o mzClust_hclust.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -fno-inline -c mzROI.c -o mzROI.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -fno-inline -c util.c -o util.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -fno-inline -c xcms.c -o xcms.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -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:/Rtools/mingw_64/bin/g++ -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˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/xcms.buildbin-libdir/xcms/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'xcms' as xcms_3.4.4.zip
* DONE (xcms)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'xcms' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

xcms.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

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

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

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: ProtGenerics

This is MSnbase version 2.8.3 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

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

    smooth

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

    trimws


This is xcms version 3.4.4 


Attaching package: 'xcms'

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

    sigma

> library(faahKO)
> library(msdata)
> 
> attr(faahko, "filepaths") <- sapply(
+     as.list(basename(attr(faahko, "filepaths"))),
+     function(x) system.file("cdf", if (length(grep("ko",x)) > 0) "KO" else "WT",
+                             x, package = "faahKO"))
> if (.Platform$OS.type == "unix") {
+     prm <- MulticoreParam(2)
+ } else {
+     prm <- SnowParam(2)
+ }
> 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"))
> 
> ## An xcmsRaw for the first file:
> faahko_xr_1 <- xcmsRaw(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
+                        profstep = 0)
Error in R_nc4_close: NetCDF: Not a valid ID
> 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))
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.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... OK: 61 found.
> faahko_xs <- xcmsSet(faahko_3_files, profparam = list(step = 0),
+                      method = "centWave", noise = 10000, snthresh = 40)
Loading required package: xcms
Loading required package: BiocParallel

This is xcms version 3.4.4 


Attaching package: 'xcms'

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

    sigma

Error in R_nc4_close: NetCDF: Not a valid ID
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 87 found.
Loading required package: xcms
Loading required package: BiocParallel

This is xcms version 3.4.4 


Attaching package: 'xcms'

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

    sigma

Error in R_nc4_close: NetCDF: Not a valid ID
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 1025 regions of interest ... OK: 100 found.
Error in R_nc4_close: NetCDF: Not a valid ID
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... OK: 61 found.
> faahko_xsg <- group(faahko_xs)
Processing 2572 mz slices ... OK
> ## Doing also the retention time correction etc
> od_x <- faahko_od
> 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
> 
> faahko_grouped_filled <- fillPeaks(group(faahko))
Processing 3195 mz slices ... OK
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/KO/ko15.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/KO/ko16.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/KO/ko18.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/KO/ko19.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/KO/ko21.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/KO/ko22.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/WT/wt15.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/WT/wt16.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/WT/wt18.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/WT/wt19.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/WT/wt21.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/WT/wt22.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
> faahko_grouped_retcor_filled <-
+     fillPeaks(group(retcor(group(updateObject(faahko)))))
Processing 3195 mz slices ... OK
Performing retention time correction using 132 peak groups.
Processing 3195 mz slices ... OK
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/KO/ko15.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/KO/ko16.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/KO/ko18.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/KO/ko19.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/KO/ko21.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/KO/ko22.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/WT/wt15.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/WT/wt16.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/WT/wt18.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/WT/wt19.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/WT/wt21.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/WT/wt22.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
>     
> microtofq_fs <- c(system.file("microtofq/MM14.mzML", package = "msdata"),
+                   system.file("microtofq/MM8.mzML", package = "msdata"))
> microtofq_xr <- xcmsRaw(microtofq_fs[1], profstep = 0)
> microtofq_od <- readMSData(microtofq_fs, mode = "onDisk")
> 
> ## Direct injection data:
> fticrf <- list.files(system.file("fticr", 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))
> fticr_xs <- xcmsSet(method="MSW", files=fticrf[1:2], scales=c(1,7),
+                     SNR.method='data.mean' , winSize.noise=500,
+                     peakThr=80000,  amp.Th=0.005)
> 
> fs <- 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"),
+         system.file('cdf/KO/ko19.CDF', package = "faahKO"))
> xs_1 <- xcmsSet(fs, profparam = list(step = 0), method = "centWave",
+                 noise = 10000, snthresh = 50)
Error in R_nc4_close: NetCDF: Not a valid ID
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... OK: 41 found.
Error in R_nc4_close: NetCDF: Not a valid ID
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 781 regions of interest ... OK: 46 found.
Error in R_nc4_close: NetCDF: Not a valid ID
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 75 found.
Error in R_nc4_close: NetCDF: Not a valid ID
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 1025 regions of interest ... OK: 79 found.
> 
> test_check("xcms")
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  
center sample:  ko16 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID
ko18  Error in R_nc4_close: NetCDF: Not a valid ID

center sample:  ko18 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID
ko16  Error in R_nc4_close: NetCDF: Not a valid ID

center sample:  ko18 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID
ko16  Error in R_nc4_close: NetCDF: Not a valid ID

Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
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  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  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  
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  
HAM004_641fE_14-11-07--Exp1.extracted HAM004_641fE_14-11-07--Exp2.extracted 
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
method:  bin 
step:  0.3 
method:  binlin 
step:  0.2 
method:  binlinbase 
step:  0.2 
method:  intlin 
step:  0.2 
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
center sample:  ko15 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko16  Error in R_nc4_close: NetCDF: Not a valid ID

Error in R_nc4_close: NetCDF: Not a valid ID
center sample:  ko16 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID

center sample:  ko16 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID

center sample:  ko16 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID

center sample:  ko16 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID

center sample:  ko16 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID

center sample:  ko16 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID

center sample:  ko16 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID

Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Comparing peaks...OK
Comparing peaks...OK
Comparing peaks...OK
Comparing peak groups...OK
Comparing peaks...OK
Comparing peak groups...OK
Comparing peaks...OK
Comparing peak groups...OK
Error in R_nc4_close: NetCDF: Not a valid ID
== testthat results  ===========================================================
OK: 2615 SKIPPED: 4 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 419.23    9.34  531.70

xcms.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

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

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

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: ProtGenerics

This is MSnbase version 2.8.3 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

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

    smooth

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

    trimws


This is xcms version 3.4.4 


Attaching package: 'xcms'

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

    sigma

> library(faahKO)
> library(msdata)
> 
> attr(faahko, "filepaths") <- sapply(
+     as.list(basename(attr(faahko, "filepaths"))),
+     function(x) system.file("cdf", if (length(grep("ko",x)) > 0) "KO" else "WT",
+                             x, package = "faahKO"))
> if (.Platform$OS.type == "unix") {
+     prm <- MulticoreParam(2)
+ } else {
+     prm <- SnowParam(2)
+ }
> 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"))
> 
> ## An xcmsRaw for the first file:
> faahko_xr_1 <- xcmsRaw(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
+                        profstep = 0)
Error in R_nc4_close: NetCDF: Not a valid ID
> 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))
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.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... OK: 61 found.
> faahko_xs <- xcmsSet(faahko_3_files, profparam = list(step = 0),
+                      method = "centWave", noise = 10000, snthresh = 40)
Loading required package: xcms
Loading required package: BiocParallel

This is xcms version 3.4.4 


Attaching package: 'xcms'

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

    sigma

Error in R_nc4_close: NetCDF: Not a valid ID
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 87 found.
Loading required package: xcms
Loading required package: BiocParallel

This is xcms version 3.4.4 


Attaching package: 'xcms'

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

    sigma

Error in R_nc4_close: NetCDF: Not a valid ID
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 1025 regions of interest ... OK: 100 found.
Error in R_nc4_close: NetCDF: Not a valid ID
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... OK: 61 found.
> faahko_xsg <- group(faahko_xs)
Processing 2572 mz slices ... OK
> ## Doing also the retention time correction etc
> od_x <- faahko_od
> 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
> 
> faahko_grouped_filled <- fillPeaks(group(faahko))
Processing 3195 mz slices ... OK
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/KO/ko15.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/KO/ko16.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/KO/ko18.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/KO/ko19.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/KO/ko21.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/KO/ko22.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/WT/wt15.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/WT/wt16.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/WT/wt18.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/WT/wt19.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/WT/wt21.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/WT/wt22.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
> faahko_grouped_retcor_filled <-
+     fillPeaks(group(retcor(group(updateObject(faahko)))))
Processing 3195 mz slices ... OK
Performing retention time correction using 132 peak groups.
Processing 3195 mz slices ... OK
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/KO/ko15.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/KO/ko16.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/KO/ko18.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/KO/ko19.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/KO/ko21.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/KO/ko22.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/WT/wt15.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/WT/wt16.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/WT/wt18.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/WT/wt19.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/WT/wt21.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
C:/Users/biocbuild/bbs-3.8-bioc/R/library/faahKO/cdf/WT/wt22.CDF 
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
>     
> microtofq_fs <- c(system.file("microtofq/MM14.mzML", package = "msdata"),
+                   system.file("microtofq/MM8.mzML", package = "msdata"))
> microtofq_xr <- xcmsRaw(microtofq_fs[1], profstep = 0)
> microtofq_od <- readMSData(microtofq_fs, mode = "onDisk")
> 
> ## Direct injection data:
> fticrf <- list.files(system.file("fticr", 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))
> fticr_xs <- xcmsSet(method="MSW", files=fticrf[1:2], scales=c(1,7),
+                     SNR.method='data.mean' , winSize.noise=500,
+                     peakThr=80000,  amp.Th=0.005)
> 
> fs <- 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"),
+         system.file('cdf/KO/ko19.CDF', package = "faahKO"))
> xs_1 <- xcmsSet(fs, profparam = list(step = 0), method = "centWave",
+                 noise = 10000, snthresh = 50)
Error in R_nc4_close: NetCDF: Not a valid ID
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 919 regions of interest ... OK: 41 found.
Error in R_nc4_close: NetCDF: Not a valid ID
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 781 regions of interest ... OK: 46 found.
Error in R_nc4_close: NetCDF: Not a valid ID
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 937 regions of interest ... OK: 75 found.
Error in R_nc4_close: NetCDF: Not a valid ID
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 1025 regions of interest ... OK: 79 found.
> 
> test_check("xcms")
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  
center sample:  ko16 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID
ko18  Error in R_nc4_close: NetCDF: Not a valid ID

center sample:  ko18 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID
ko16  Error in R_nc4_close: NetCDF: Not a valid ID

center sample:  ko18 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID
ko16  Error in R_nc4_close: NetCDF: Not a valid ID

Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
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  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  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  
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  
HAM004_641fE_14-11-07--Exp1.extracted HAM004_641fE_14-11-07--Exp2.extracted 
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
method:  bin 
step:  0.1 
method:  bin 
step:  0.3 
method:  binlin 
step:  0.2 
method:  binlinbase 
step:  0.2 
method:  intlin 
step:  0.2 
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
center sample:  ko15 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko16  Error in R_nc4_close: NetCDF: Not a valid ID

Error in R_nc4_close: NetCDF: Not a valid ID
center sample:  ko16 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID

center sample:  ko16 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID

center sample:  ko16 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID

center sample:  ko16 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID

center sample:  ko16 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID

center sample:  ko16 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID

center sample:  ko16 
Processing: Error in R_nc4_close: NetCDF: Not a valid ID
ko15  Error in R_nc4_close: NetCDF: Not a valid ID

Error in R_nc4_close: NetCDF: Not a valid ID
Error in R_nc4_close: NetCDF: Not a valid ID
Comparing peaks...OK
Comparing peaks...OK
Comparing peaks...OK
Comparing peak groups...OK
Comparing peaks...OK
Comparing peak groups...OK
Comparing peaks...OK
Comparing peak groups...OK
Error in R_nc4_close: NetCDF: Not a valid ID
== testthat results  ===========================================================
OK: 2615 SKIPPED: 4 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 456.23    6.65  578.76

Example timings

xcms.Rcheck/examples_i386/xcms-Ex.timings

nameusersystemelapsed
AutoLockMass-methods000
GenericParam0.030.000.03
XCMSnExp-class 1.39 0.2017.78
XCMSnExp-filter-methods 2.04 0.1911.31
adjustRtime-obiwarp 4.68 0.1113.69
adjustRtime-peakGroups 1.82 0.0910.42
applyAdjustedRtime 2.00 0.0114.70
binYonX000
breaks_on_binSize000
breaks_on_nBins000
chromatogram-method 1.72 0.0531.00
descendZero000
do_findChromPeaks_centWave1.970.052.01
do_findChromPeaks_massifquant4.160.014.17
do_findChromPeaks_matchedFilter3.360.223.58
do_groupChromPeaks_density1.470.001.47
extractMsData-method 1.61 0.1610.05
featureChromatograms 3.42 0.3644.78
fillChromPeaks 3.64 0.0132.54
findChromPeaks-Chromatogram-CentWaveParam1.450.001.46
findChromPeaks-Chromatogram-MatchedFilter1.280.001.28
findChromPeaks-centWave1.030.029.44
findChromPeaks-centWaveWithPredIsoROIs0.040.000.03
findChromPeaks-massifquant 1.01 0.0012.49
findChromPeaks-matchedFilter2.390.032.42
findMZ000
findPeaks-MSW1.710.142.09
findPeaks.massifquant-methods6.950.016.97
findneutral000
group.mzClust000
group.nearest000
groupChromPeaks-density3.330.023.34
groupChromPeaks-mzClust1.900.061.97
groupChromPeaks-nearest3.260.023.28
highlightChromPeaks404
imputeLinInterpol0.000.010.02
imputeRowMin1.410.081.48
imputeRowMinRand1.530.001.53
medianFilter000
msn2xcmsRaw1.530.092.05
overlappingFeatures3.80.03.8
peakTable-methods000
peaksWithCentWave1.860.001.85
peaksWithMatchedFilter1.250.001.25
phenoDataFromPaths000
plotAdjustedRtime3.450.023.47
plotChromPeakDensity6.600.086.68
plotChromPeaks4.120.044.17
plotMsData1.280.041.31
plotQC1.830.001.83
profGenerate000
profMat-xcmsSet1.160.031.19
profStep-methods000
rectUnique000
rla0.010.000.01
stitch-methods000
sub-xcmsRaw-logicalOrNumeric-missing-missing-method0.940.040.99
writeMzTab1.50.01.5
xcmsPapply000
xcmsRaw000

xcms.Rcheck/examples_x64/xcms-Ex.timings

nameusersystemelapsed
AutoLockMass-methods000
GenericParam0.010.000.01
XCMSnExp-class 1.47 0.0318.42
XCMSnExp-filter-methods 2.06 0.0111.41
adjustRtime-obiwarp 4.28 0.0513.25
adjustRtime-peakGroups 1.86 0.0010.77
applyAdjustedRtime 2.08 0.0215.17
binYonX000
breaks_on_binSize000
breaks_on_nBins000
chromatogram-method 1.90 0.0331.15
descendZero000
do_findChromPeaks_centWave2.020.002.02
do_findChromPeaks_massifquant4.050.014.08
do_findChromPeaks_matchedFilter3.590.053.64
do_groupChromPeaks_density1.420.051.47
extractMsData-method1.690.079.42
featureChromatograms 3.55 0.1145.93
fillChromPeaks 3.88 0.0234.52
findChromPeaks-Chromatogram-CentWaveParam1.530.001.53
findChromPeaks-Chromatogram-MatchedFilter1.440.001.44
findChromPeaks-centWave 1.12 0.0510.34
findChromPeaks-centWaveWithPredIsoROIs0.030.000.03
findChromPeaks-massifquant 1.13 0.0012.41
findChromPeaks-matchedFilter2.720.012.73
findMZ000
findPeaks-MSW1.840.051.89
findPeaks.massifquant-methods7.410.007.41
findneutral000
group.mzClust000
group.nearest000
groupChromPeaks-density3.590.013.61
groupChromPeaks-mzClust1.940.102.03
groupChromPeaks-nearest3.70.03.7
highlightChromPeaks4.230.034.27
imputeLinInterpol000
imputeRowMin1.530.001.54
imputeRowMinRand1.610.011.62
medianFilter000
msn2xcmsRaw1.590.051.64
overlappingFeatures4.180.004.17
peakTable-methods000
peaksWithCentWave1.640.001.64
peaksWithMatchedFilter1.400.001.41
phenoDataFromPaths000
plotAdjustedRtime3.720.023.73
plotChromPeakDensity7.190.097.29
plotChromPeaks4.220.054.26
plotMsData1.470.031.50
plotQC1.830.011.84
profGenerate000
profMat-xcmsSet1.280.021.30
profStep-methods000
rectUnique000
rla0.020.000.01
stitch-methods000
sub-xcmsRaw-logicalOrNumeric-missing-missing-method1.120.021.14
writeMzTab1.550.001.55
xcmsPapply000
xcmsRaw000