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BioC 3.1: CHECK report for xcms on petty

This page was generated on 2015-10-09 09:32:48 -0700 (Fri, 09 Oct 2015).

Package 1018/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
xcms 1.44.0
Steffen Neumann
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/xcms
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  TIMEOUT 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: xcms
Version: 1.44.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings xcms_1.44.0.tar.gz
StartedAt: 2015-10-09 02:35:25 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 02:44:34 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 548.4 seconds
RetCode: 0
Status:  OK 
CheckDir: xcms.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings xcms_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/xcms.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘xcms/DESCRIPTION’ ... OK
* this is package ‘xcms’ version ‘1.44.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘xcms’ can be installed ... [24s/24s] OK
* checking installed package size ... OK
* 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
* 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
Packages in Depends field not imported from:
  ‘Biobase’ ‘BiocGenerics’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘mzR:::rampCloseAll’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Calls with DUP:
   .C("ColMax", x, as.integer(n), as.integer(prod(dn)), double(prod(dn)), 
       DUP = FALSE, PACKAGE = "xcms")
   .C("continuousPtsAboveThreshold", y, as.integer(istart - 1), 
       length(y), threshold = as.double(threshold), num = as.integer(num), 
       n = integer(1), DUP = FALSE, PACKAGE = "xcms")
   .C("continuousPtsAboveThresholdIdx", y, as.integer(istart - 1), 
       length(y), threshold = as.double(threshold), num = as.integer(num), 
       n = integer(length(y)), DUP = FALSE, PACKAGE = "xcms")
   .C("DescendMin", y, length(y), as.integer(istart - 1), ilower = integer(1), 
       iupper = integer(1), DUP = FALSE, PACKAGE = "xcms")
   .C("DescendValue", y, length(y), as.integer(istart - 1), as.double(value), 
       ilower = integer(1), iupper = integer(1), DUP = FALSE, PACKAGE = "xcms")
   .C("DescendZero", y, length(y), as.integer(istart - 1), ilower = integer(1), 
       iupper = integer(1), DUP = FALSE, PACKAGE = "xcms")
   .C("FindEqualGreater", x, length(x), as.double(value), index = integer(1), 
       DUP = FALSE, PACKAGE = "xcms")
   .C("FindEqualGreaterM", x, length(x), values, length(values), 
       index = integer(length(values)), DUP = FALSE, PACKAGE = "xcms")
   .C("FindEqualGreaterUnsorted", x, length(x), as.double(value), 
       index = integer(1), DUP = FALSE, PACKAGE = "xcms")
   .C("FindEqualLess", x, length(x), as.double(value), index = integer(1), 
       DUP = FALSE, PACKAGE = "xcms")
   .C("FindEqualGreater", x, length(x), as.double(values[1]), integer(1), 
       NAOK = NAOK, DUP = FALSE, PACKAGE = "xcms")
   .C("FindEqualLess", x, length(x), as.double(values[2]), integer(1), 
       NAOK = NAOK, DUP = FALSE, PACKAGE = "xcms")
   .C("MedianFilter", x, as.integer(dimx[1]), as.integer(dimx[2]), 
       as.integer(mrad), as.integer(nrad), out = doubleMatrix(dimx[1], 
           dimx[2]), DUP = FALSE, PACKAGE = "xcms")
   .C("R_mzClust_hclust", x = as.double(x), num = N, d = as.double(d), 
       g = integer(length = N), eppm = as.double(eppm), eabs = as.double(eabs), 
       DUP = FALSE, NAOK = TRUE)
   .C("NetCDFMSPoints", as.integer(ncid), as.integer(length(scanIndex)), 
       scanIndex, as.integer(len), massValues = double(len), intensityValues = double(len), 
       status = integer(1), DUP = FALSE, PACKAGE = "xcms")
   .C("NetCDFVarDouble", as.integer(ncid), as.integer(var), data = double(len), 
       status = integer(1), DUP = FALSE, PACKAGE = "xcms")
   .C("NetCDFVarInt", as.integer(ncid), as.integer(var), data = integer(len), 
       status = integer(1), DUP = FALSE, PACKAGE = "xcms")
   .C("ProfBin", x, y, as.integer(length(x)), as.double(xstart), 
       as.double(xend), as.integer(num), out = double(num), DUP = FALSE, 
       PACKAGE = "xcms")
   .C("ProfBinLin", x, y, as.integer(length(x)), as.double(xstart), 
       as.double(xend), as.integer(num), out = double(num), DUP = FALSE, 
       PACKAGE = "xcms")
   .C("ProfBinLinBase", x, y, as.integer(length(x)), as.double(baselevel), 
       as.double(basespace), as.double(xstart), as.double(xend), 
       as.integer(num), out = double(num), DUP = FALSE, PACKAGE = "xcms")
   .C("ProfBinLinBaseM", x, y, as.integer(length(x)), as.integer(zidx), 
       as.integer(length(zidx)), as.double(baselevel), as.double(basespace), 
       as.double(xstart), as.double(xend), as.integer(num), out = doubleMatrix(num, 
           length(zidx)), NAOK = NAOK, DUP = FALSE, PACKAGE = "xcms")
   .C("ProfBinLinM", x, y, as.integer(length(x)), as.integer(zidx), 
       as.integer(length(zidx)), as.double(xstart), as.double(xend), 
       as.integer(num), out = doubleMatrix(num, length(zidx)), NAOK = NAOK, 
       DUP = FALSE, PACKAGE = "xcms")
   .C("ProfBinM", x, y, as.integer(length(x)), as.integer(zidx), 
       as.integer(length(zidx)), as.double(xstart), as.double(xend), 
       as.integer(num), out = doubleMatrix(num, length(zidx)), NAOK = NAOK, 
       DUP = FALSE, PACKAGE = "xcms")
   .C("ProfIntLin", x, y, as.integer(length(x)), as.double(xstart), 
       as.double(xend), as.integer(num), out = double(num), DUP = FALSE, 
       PACKAGE = "xcms")
   .C("ProfIntLinM", x, y, as.integer(length(x)), as.integer(zidx), 
       as.integer(length(zidx)), as.double(xstart), as.double(xend), 
       as.integer(num), out = doubleMatrix(num, length(zidx)), NAOK = NAOK, 
       DUP = FALSE, PACKAGE = "xcms")
   .C("ProfMaxIdx", x, y, as.integer(length(x)), as.double(xstart), 
       as.double(xend), as.integer(num), out = integer(num), DUP = FALSE, 
       PACKAGE = "xcms")
   .C("ProfMaxIdxM", x, y, as.integer(length(x)), as.integer(zidx), 
       as.integer(length(zidx)), as.double(xstart), as.double(xend), 
       as.integer(num), out = matrix(as.integer(0), num, length(zidx)), 
       NAOK = NAOK, DUP = FALSE, PACKAGE = "xcms")
   .C("RectUnique", m, as.integer(order - 1), nr, nc, as.double(xdiff), 
       as.double(ydiff), logical(nrow(m)), DUP = FALSE, PACKAGE = "xcms")
   .C("RowMax", x, as.integer(prod(dn)), as.integer(p), double(prod(dn)), 
       DUP = FALSE, PACKAGE = "xcms")
   .C("WhichColMax", x, as.integer(n), as.integer(prod(dn)), integer(prod(dn)), 
       DUP = FALSE, PACKAGE = "xcms")
   .C("WhichRowMax", x, as.integer(prod(dn)), as.integer(p), integer(prod(dn)), 
       DUP = FALSE, PACKAGE = "xcms")
DUP is no longer supported and will be ignored.
* checking R code for possible problems ... NOTE
fitGauss: warning in nls(d ˜ SSgauss(td, mu, sigma, h), algo = "port"):
  partial argument match of 'algo' to 'algorithm'
joinOverlappingPeaks: warning in which(upper.tri(matrix(0, Ngp, Ngp)),
  arr = TRUE): partial argument match of 'arr' to 'arr.ind'
joinOverlappingPeaks: warning in which(upper.tri(matrix(0, lcc, lcc)),
  arr = TRUE): partial argument match of 'arr' to 'arr.ind'
plot.xcmsEIC: warning in rgb(rgbvec[1], rgbvec[2], rgbvec[3], max =
  255): partial argument match of 'max' to 'maxColorValue'
plotQC: warning in apply(deviation_mzs[, sampOrder], MAR = 2, FUN =
  function(x) median(x, na.rm = TRUE)): partial argument match of 'MAR'
  to 'MARGIN'
plotQC: warning in apply(deviation_rts[, sampOrder], MAR = 2, FUN =
  function(x) median(x, na.rm = TRUE)): partial argument match of 'MAR'
  to 'MARGIN'
findPeaks.centWave,xcmsRaw : .local: warning in which(m == max(m), arr
  = T): partial argument match of 'arr' to 'arr.ind'
findPeaks.centWave,xcmsRaw : .local: warning in matrix(c(1, 2, 3), nr =
  3, nc = 1, byrow = T): partial argument match of 'nr' to 'nrow'
findPeaks.centWave,xcmsRaw : .local: warning in matrix(c(1, 2, 3), nr =
  3, nc = 1, byrow = T): partial argument match of 'nc' to 'ncol'
group.nearest,xcmsSet : .local: warning in assign("peakmat", peakmat,
  env = mplenv): partial argument match of 'env' to 'envir'
plotrt,xcmsSet : .local: warning in close.screen(all = TRUE): partial
  argument match of 'all' to 'all.screens'
retcor.peakgroups,xcmsSet : .local: warning in close.screen(all =
  TRUE): partial argument match of 'all' to 'all.screens'
.onLoad : <anonymous>: no visible global function definition for
  ‘mpi.comm.size’
.onLoad : <anonymous>: no visible global function definition for
  ‘mpi.close.Rslaves’
.onLoad : <anonymous>: no visible global function definition for
  ‘mpi.finalize’
.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’
fillPeaksChromPar: no visible binding for global variable ‘i’
fillPeaksChromPar: no visible binding for global variable ‘object’
patternVsRowScore: no visible global function definition for ‘nn2’
rampRawData: no visible global function definition for
  ‘rampScanHeaders’
rampRawData: no visible global function definition for ‘rampSIPeaks’
rampRawDataMSn: no visible global function definition for
  ‘rampScanHeaders’
rampRawDataMSn: no visible global function definition for ‘rampSIPeaks’
running: multiple local function definitions for ‘funct’ with different
  formal arguments
verify.mzQuantML: no visible global function definition for
  ‘xmlTreeParse’
verify.mzQuantML: no visible global function definition for
  ‘xmlInternalTreeParse’
verify.mzQuantML: no visible global function definition for
  ‘xmlSchemaValidate’
xcmsClusterApply: no visible global function definition for
  ‘checkCluster’
xcmsClusterApply : submit: no visible global function definition for
  ‘sendCall’
xcmsClusterApply: no visible global function definition for
  ‘recvOneResult’
xcmsClusterApply: no visible global function definition for
  ‘checkForRemoteErrors’
xcmsPapply: no visible global function definition for ‘mpi.comm.size’
xcmsPapply: no visible global function definition for
  ‘mpi.spawn.Rslaves’
xcmsPapply: no visible global function definition for ‘mpi.comm.rank’
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for ‘mpi.send.Robj’
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for ‘mpi.recv.Robj’
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for ‘mpi.any.source’
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for ‘mpi.any.tag’
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for ‘mpi.get.sourcetag’
xcmsPapply: no visible global function definition for
  ‘mpi.bcast.Robj2slave’
xcmsPapply: no visible global function definition for ‘mpi.bcast.cmd’
xcmsPapply: no visible global function definition for ‘mpi.recv.Robj’
xcmsPapply: no visible global function definition for ‘mpi.any.source’
xcmsPapply: no visible global function definition for ‘mpi.any.tag’
xcmsPapply: no visible global function definition for
  ‘mpi.get.sourcetag’
xcmsPapply: no visible global function definition for ‘mpi.send.Robj’
xcmsParallelSetup: no visible global function definition for
  ‘mpi.spawn.Rslaves’
xcmsParallelSetup: no visible global function definition for
  ‘mpi.comm.size’
xcmsParallelSetup: no visible global function definition for
  ‘mpi.comm.rank’
xcmsParallelSetup: no visible global function definition for
  ‘makeCluster’
xcmsSet: no visible global function definition for ‘mpi.close.Rslaves’
xcmsSet: no visible global function definition for ‘stopCluster’
diffreport,xcmsSet : .local: no visible global function definition for
  ‘mt.teststat’
fillPeaks.chrom,xcmsSet : .local: no visible global function definition
  for ‘mpi.close.Rslaves’
fillPeaks.chrom,xcmsSet : .local: no visible global function definition
  for ‘stopCluster’
findPeaks.MSW,xcmsRaw : .local: no visible global function definition
  for ‘peakDetectionCWT’
findPeaks.MSW,xcmsRaw : .local: no visible global function definition
  for ‘tuneInPeakInfo’
group.nearest,xcmsSet : .local : <anonymous>: no visible binding for
  global variable ‘s’
group.nearest,xcmsSet : .local : <anonymous>: no visible binding for
  global variable ‘coreList’
group.nearest,xcmsSet : .local : <anonymous>: no visible binding for
  global variable ‘peakIdxList’
plotSurf,xcmsRaw : .local: no visible global function definition for
  ‘rgl.clear’
plotSurf,xcmsRaw : .local: no visible global function definition for
  ‘rgl.surface’
plotSurf,xcmsRaw : .local: no visible global function definition for
  ‘rgl.points’
plotSurf,xcmsRaw : .local: no visible global function definition for
  ‘rgl.bbox’
plotTree,xcmsFragments : .local: no visible global function definition
  for ‘edgemode<-’
plotTree,xcmsFragments : .local: no visible global function definition
  for ‘addEdge’
write.cdf,xcmsRaw : .local: no visible global function definition for
  ‘dim.def.ncdf’
write.cdf,xcmsRaw : .local: no visible global function definition for
  ‘var.def.ncdf’
write.cdf,xcmsRaw : .local: no visible global function definition for
  ‘create.ncdf’
write.cdf,xcmsRaw : .local: no visible global function definition for
  ‘put.var.ncdf’
write.cdf,xcmsRaw : .local: no visible global function definition for
  ‘att.put.ncdf’
write.cdf,xcmsRaw : .local: no visible global function definition for
  ‘close.ncdf’
write.mzdata,xcmsRaw : .local: no visible global function definition
  for ‘base64encode’
write.mzQuantML,xcmsSet : .local: no visible global function definition
  for ‘saveXML’
* checking Rd files ... NOTE
prepare_Rd: split.xcmsRaw.Rd:18-20: Dropping empty section \usage
prepare_Rd: split.xcmsSet.Rd:19-21: Dropping empty section \usage
prepare_Rd: xcmsSet.Rd:51-53: Dropping empty section \note
* 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
File ‘xcms/libs/xcms.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘massifquant/TrMgr.o’

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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [74s/75s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
findPeaks.massifquant-methods 63.768  1.659  66.085
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’ [334s/343s]
 [334s/344s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/xcms.Rcheck/00check.log’
for details.


xcms.Rcheck/00install.out:

* installing *source* package ‘xcms’ ...
** libs
rm -f 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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
massifquant/xcms_massifquant.cpp: In function ‘SEXPREC* massifquant(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
massifquant/xcms_massifquant.cpp:122: warning: unused variable ‘scanLength’
massifquant/xcms_massifquant.cpp:33: warning: unused variable ‘vstcenter’
massifquant/xcms_massifquant.cpp:33: warning: unused variable ‘vintenmax’
massifquant/xcms_massifquant.cpp:76: warning: unused variable ‘maxScanNums’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c massifquant/Tracker.cpp -o massifquant/Tracker.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c massifquant/SegProc.cpp -o massifquant/SegProc.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c obiwarp/mat.cpp -o obiwarp/mat.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c obiwarp/vec.cpp -o obiwarp/vec.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c xcms_obiwarp.cpp -o xcms_obiwarp.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c fastMatch.c -o fastMatch.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c mzClust_hclust.c -o mzClust_hclust.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c mzROI.c -o mzROI.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c util.c -o util.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c xcms.c -o xcms.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o xcms.so 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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/xcms.Rcheck/xcms/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (xcms)

xcms.Rcheck/xcms-Ex.timings:

nameusersystemelapsed
AutoLockMass-methods0.0020.0000.002
descendZero0.0040.0010.004
findMZ0.0010.0000.001
findPeaks.massifquant-methods63.768 1.65966.085
findneutral0.0010.0010.001
group.mzClust0.0010.0000.001
group.nearest0.0020.0000.002
medianFilter0.0020.0000.002
msn2xcmsRaw1.7650.0922.046
netCdfSource-class0.0010.0000.002
peakTable-methods0.0020.0000.001
plotQC2.4860.0612.551
profGenerate0.0000.0000.001
profStep-methods0.0010.0000.001
rampSource-class0.0010.0010.001
rectUnique0.0060.0010.007
stitch-methods0.0020.0010.003
xcmsPapply0.0010.0000.002
xcmsRaw0.0030.0000.003