BioC 3.5: CHECK report for xcms on tokay2

Package: xcms

Version: 1.52.0

Command: rm -rf xcms.buildbin-libdir xcms.Rcheck && mkdir xcms.buildbin-libdir xcms.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=xcms.buildbin-libdir xcms_1.52.0.tar.gz >xcms.Rcheck\00install.out 2>&1 && cp xcms.Rcheck\00install.out xcms-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=xcms.buildbin-libdir --install="check:xcms-install.out" --force-multiarch --no-vignettes --timings xcms_1.52.0.tar.gz

StartedAt: 2017-10-18 03:38:32 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 04:16:47 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 2295.5 seconds

RetCode: 0

Status:  OK

CheckDir: xcms.Rcheck

Warnings: 0

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###
### Running command:
###
###   rm -rf xcms.buildbin-libdir xcms.Rcheck && mkdir xcms.buildbin-libdir xcms.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=xcms.buildbin-libdir xcms_1.52.0.tar.gz >xcms.Rcheck\00install.out 2>&1 && cp xcms.Rcheck\00install.out xcms-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=xcms.buildbin-libdir --install="check:xcms-install.out" --force-multiarch --no-vignettes --timings xcms_1.52.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/xcms.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '1.52.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'xcms' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    2.2Mb
    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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'descendMin' '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-3.5-bioc/meat/xcms.buildbin-libdir/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 the system RNG.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
findChromPeaks-matchedFilter  8.30   0.07    8.38
findPeaks.massifquant-methods 6.14   0.04    6.17
adjustRtime-obiwarp           5.28   0.18   14.39
fillChromPeaks                4.11   0.06   36.92
XCMSnExp-class                3.17   0.59   28.03
adjustRtime-peakGroups        1.89   0.02   10.78
XCMSnExp-filter-methods       1.47   0.04   14.49
findChromPeaks-centWave       1.05   0.00   10.36
findChromPeaks-massifquant    0.78   0.00   12.59
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
findChromPeaks-matchedFilter  9.98   0.01   10.00
adjustRtime-obiwarp           6.05   0.18   16.72
findPeaks.massifquant-methods 5.98   0.02    6.00
fillChromPeaks                4.97   0.05   41.70
XCMSnExp-class                3.21   0.45   29.03
adjustRtime-peakGroups        2.12   0.02   12.28
XCMSnExp-filter-methods       1.81   0.03   15.39
findChromPeaks-centWave       1.49   0.06   11.99
findChromPeaks-massifquant    1.05   0.04   12.56
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'doRUnit.R'
 OK
** running tests for arch 'x64' ...
  Running 'doRUnit.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-3.5-bioc/meat/xcms.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'xcms' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c massifquant/Tracker.cpp -o massifquant/Tracker.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c massifquant/SegProc.cpp -o massifquant/SegProc.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c obiwarp/mat.cpp -o obiwarp/mat.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c obiwarp/vec.cpp -o obiwarp/vec.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -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˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c xcms_obiwarp.cpp -o xcms_obiwarp.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c fastMatch.c -o fastMatch.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c mzClust_hclust.c -o mzClust_hclust.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c mzROI.c -o mzROI.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c util.c -o util.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c xcms.c -o xcms.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c binners.c -o binners.o
binners.c: In function '_breaks_on_binSize':
binners.c:334:7: 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:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/xcms.buildbin-libdir/xcms/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a new generic function for 'sigma' in package 'xcms'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'xcms' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c massifquant/Tracker.cpp -o massifquant/Tracker.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c massifquant/SegProc.cpp -o massifquant/SegProc.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c obiwarp/mat.cpp -o obiwarp/mat.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c obiwarp/vec.cpp -o obiwarp/vec.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -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˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c xcms_obiwarp.cpp -o xcms_obiwarp.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c fastMatch.c -o fastMatch.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c mzClust_hclust.c -o mzClust_hclust.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c mzROI.c -o mzROI.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c util.c -o util.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c xcms.c -o xcms.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c binners.c -o binners.o
binners.c: In function '_breaks_on_binSize':
binners.c:334:7: 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:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/xcms.buildbin-libdir/xcms/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'xcms' as xcms_1.52.0.zip
* DONE (xcms)

name	user	system	elapsed
AutoLockMass-methods	0	0	0
Chromatogram-class	0.04	0.00	0.05
GenericParam	0	0	0
XCMSnExp-class	3.17	0.59	28.03
XCMSnExp-filter-methods	1.47	0.04	14.49
adjustRtime-obiwarp	5.28	0.18	14.39
adjustRtime-peakGroups	1.89	0.02	10.78
binYonX	0	0	0
breaks_on_binSize	0	0	0
breaks_on_nBins	0	0	0
descendZero	0	0	0
do_findChromPeaks_centWave	1.78	0.01	1.80
do_findChromPeaks_massifquant	4.12	0.04	4.15
do_findChromPeaks_matchedFilter	3.66	0.23	3.89
do_groupChromPeaks_density	1.43	0.02	1.45
extractChromatograms-method	1.69	0.03	1.72
fillChromPeaks	4.11	0.06	36.92
findChromPeaks-centWave	1.05	0.00	10.36
findChromPeaks-centWaveWithPredIsoROIs	0.08	0.00	0.08
findChromPeaks-massifquant	0.78	0.00	12.59
findChromPeaks-matchedFilter	8.30	0.07	8.38
findMZ	0	0	0
findPeaks-MSW	2.69	0.03	3.22
findPeaks.massifquant-methods	6.14	0.04	6.17
findneutral	0	0	0
group.mzClust	0	0	0
group.nearest	0	0	0
groupChromPeaks-density	3.03	0.01	3.05
groupChromPeaks-mzClust	1.78	0.03	1.81
groupChromPeaks-nearest	2.8	0.0	2.8
imputeLinInterpol	0	0	0
medianFilter	0	0	0
msn2xcmsRaw	2.21	0.07	3.47
peakTable-methods	0.01	0.00	0.02
plotAdjustedRtime	3.28	0.03	3.31
plotQC	1.52	0.00	1.51
profGenerate	0	0	0
profMat-xcmsSet	1.72	0.03	1.75
profStep-methods	0	0	0
rectUnique	0	0	0
stitch-methods	0	0	0
sub-xcmsRaw-logicalOrNumeric-missing-missing-method	0.71	0.01	0.72
writeMzTab	1.21	0.00	1.22
xcmsPapply	0	0	0
xcmsRaw	0	0	0

name	user	system	elapsed
AutoLockMass-methods	0	0	0
Chromatogram-class	0.06	0.00	0.06
GenericParam	0.01	0.00	0.01
XCMSnExp-class	3.21	0.45	29.03
XCMSnExp-filter-methods	1.81	0.03	15.39
adjustRtime-obiwarp	6.05	0.18	16.72
adjustRtime-peakGroups	2.12	0.02	12.28
binYonX	0	0	0
breaks_on_binSize	0	0	0
breaks_on_nBins	0	0	0
descendZero	0	0	0
do_findChromPeaks_centWave	2.19	0.00	2.19
do_findChromPeaks_massifquant	3.53	0.09	3.62
do_findChromPeaks_matchedFilter	4.20	0.06	4.27
do_groupChromPeaks_density	1.49	0.02	1.50
extractChromatograms-method	2.48	0.01	2.50
fillChromPeaks	4.97	0.05	41.70
findChromPeaks-centWave	1.49	0.06	11.99
findChromPeaks-centWaveWithPredIsoROIs	0.09	0.00	0.09
findChromPeaks-massifquant	1.05	0.04	12.56
findChromPeaks-matchedFilter	9.98	0.01	10.00
findMZ	0	0	0
findPeaks-MSW	2.58	0.00	2.58
findPeaks.massifquant-methods	5.98	0.02	6.00
findneutral	0	0	0
group.mzClust	0	0	0
group.nearest	0	0	0
groupChromPeaks-density	3.39	0.00	3.39
groupChromPeaks-mzClust	2.27	0.01	2.28
groupChromPeaks-nearest	3.5	0.0	3.5
imputeLinInterpol	0.00	0.02	0.02
medianFilter	0	0	0
msn2xcmsRaw	1.59	0.03	1.62
peakTable-methods	0	0	0
plotAdjustedRtime	3.61	0.00	3.61
plotQC	1.52	0.00	1.52
profGenerate	0	0	0
profMat-xcmsSet	2.25	0.00	2.25
profStep-methods	0	0	0
rectUnique	0.01	0.00	0.02
stitch-methods	0	0	0
sub-xcmsRaw-logicalOrNumeric-missing-missing-method	0.88	0.01	0.89
writeMzTab	1.26	0.00	1.26
xcmsPapply	0	0	0
xcmsRaw	0	0	0