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BioC 2.13: CHECK report for xcms on moscato1

This page was generated on 2014-04-05 09:49:11 -0700 (Sat, 05 Apr 2014).

Package 744/750HostnameOS / ArchBUILDCHECKBUILD BIN
xcms 1.38.0
Ralf Tautenhahn
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/xcms
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ WARNINGS ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  WARNINGS  OK 

Summary

Package: xcms
Version: 1.38.0
Command: rm -rf xcms.buildbin-libdir && mkdir xcms.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=xcms.buildbin-libdir xcms_1.38.0.tar.gz >xcms-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=xcms.buildbin-libdir --install="check:xcms-install.out" --force-multiarch --no-vignettes --timings xcms_1.38.0.tar.gz && mv xcms.buildbin-libdir/* xcms.Rcheck/ && rmdir xcms.buildbin-libdir
StartedAt: 2014-04-05 07:25:04 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 07:41:22 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 977.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: xcms.Rcheck
Warnings: 2

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/xcms.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'xcms/DESCRIPTION' ... OK
* this is package 'xcms' version '1.38.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'KEGGSOAP'
* 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 ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... WARNING
---- unloading
Warning message:
.onUnload failed in unloadNamespace() for 'xcms', details:
  call: .C("RampRCloseAll", PACKAGE = "xcms")
  error: "RampRCloseAll" not available for .C() for package "xcms" 
* 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 ... WARNING
---- unloading
Warning message:
.onUnload failed in unloadNamespace() for 'xcms', details:
  call: .C("RampRCloseAll", PACKAGE = "xcms")
  error: "RampRCloseAll" not available for .C() for package "xcms" 
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'methods' which was already attached by Depends.
  Please remove these calls from your code.
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.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'mzClust_hclust'
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File 'xcms/R/unix/zzz.R':
  .onLoad calls:
    require(methods)

File 'xcms/R/windows/zzz.R':
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.

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'
.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'
KeggSearch: no visible global function definition for
  'search.compounds.by.mass'
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'
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'
xcmsSet: no visible global function definition for 'mpi.close.Rslaves'
* 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 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 'D:/biocbld/bbs-2.13-bioc/meat/xcms.buildbin-libdir/xcms/libs/i386/xcms.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-2.13-bioc/meat/xcms.buildbin-libdir/xcms/libs/x64/xcms.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.  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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'xcmsDirect.Rnw', 'xcmsInstall.Rnw', 'xcmsMSn.Rnw',
  'xcmsPreprocess.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [60s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
findPeaks.massifquant-methods 13.12   0.18   14.29
msn2xcmsRaw                   11.07   0.78   41.44
** running examples for arch 'x64' ... [37s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
findPeaks.massifquant-methods 11.45   0.23   16.42
msn2xcmsRaw                   10.89   0.61   16.44
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'doRUnit.R' [336s]
 [337s] OK
** running tests for arch 'x64'
  Running 'doRUnit.R' [340s]
 [340s] 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

WARNING: There were 2 warnings.
NOTE: There were 7 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/xcms.Rcheck/00check.log'
for details.

xcms.Rcheck/00install.out:


install for i386

* installing *source* package 'xcms' ...
** libs
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
massifquant/xcms_massifquant.cpp: In function 'SEXPREC* massifquant(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
massifquant/xcms_massifquant.cpp:122:6: warning: unused variable 'scanLength' [-Wunused-variable]
massifquant/xcms_massifquant.cpp:33:58: warning: unused variable 'vstcenter' [-Wunused-variable]
massifquant/xcms_massifquant.cpp:33:93: warning: unused variable 'vintenmax' [-Wunused-variable]
massifquant/xcms_massifquant.cpp:76:12: warning: unused variable 'maxScanNums' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c massifquant/Tracker.cpp -o massifquant/Tracker.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c massifquant/SegProc.cpp -o massifquant/SegProc.o
massifquant/SegProc.cpp: In member function 'void SegProc::collapseSubsets()':
massifquant/SegProc.cpp:119:13: warning: variable 'combinedUnions' set but not used [-Wunused-but-set-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c obiwarp/mat.cpp -o obiwarp/mat.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c obiwarp/vec.cpp -o obiwarp/vec.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/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]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c xcms_obiwarp.cpp -o xcms_obiwarp.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c fastMatch.c -o fastMatch.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c mzClust_hclust.c -o mzClust_hclust.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c mzROI.c -o mzROI.o
mzROI.c: In function 'getMZ':
mzROI.c:486:17: warning: variable 'pintensity' set but not used [-Wunused-but-set-variable]
mzROI.c: In function 'findmzROI':
mzROI.c:538:41: warning: variable 'mzrangeTo' set but not used [-Wunused-but-set-variable]
mzROI.c:538:29: warning: variable 'mzrangeFrom' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c util.c -o util.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c xcms.c -o xcms.o
g++ -m32 -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 -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.13-/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.13-bioc/meat/xcms.buildbin-libdir/xcms/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'xcms' ...
** libs
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
massifquant/xcms_massifquant.cpp: In function 'SEXPREC* massifquant(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
massifquant/xcms_massifquant.cpp:122:6: warning: unused variable 'scanLength' [-Wunused-variable]
massifquant/xcms_massifquant.cpp:33:58: warning: unused variable 'vstcenter' [-Wunused-variable]
massifquant/xcms_massifquant.cpp:33:93: warning: unused variable 'vintenmax' [-Wunused-variable]
massifquant/xcms_massifquant.cpp:76:12: warning: unused variable 'maxScanNums' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c massifquant/Tracker.cpp -o massifquant/Tracker.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c massifquant/SegProc.cpp -o massifquant/SegProc.o
massifquant/SegProc.cpp: In member function 'void SegProc::collapseSubsets()':
massifquant/SegProc.cpp:119:13: warning: variable 'combinedUnions' set but not used [-Wunused-but-set-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c obiwarp/mat.cpp -o obiwarp/mat.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c obiwarp/vec.cpp -o obiwarp/vec.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/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]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c xcms_obiwarp.cpp -o xcms_obiwarp.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c fastMatch.c -o fastMatch.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c mzClust_hclust.c -o mzClust_hclust.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c mzROI.c -o mzROI.o
mzROI.c: In function 'getMZ':
mzROI.c:486:17: warning: variable 'pintensity' set but not used [-Wunused-but-set-variable]
mzROI.c: In function 'findmzROI':
mzROI.c:538:41: warning: variable 'mzrangeTo' set but not used [-Wunused-but-set-variable]
mzROI.c:538:29: warning: variable 'mzrangeFrom' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c util.c -o util.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -fno-inline -c xcms.c -o xcms.o
g++ -m64 -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 -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.13-/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.13-bioc/meat/xcms.buildbin-libdir/xcms/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'xcms' as xcms_1.38.0.zip
* DONE (xcms)

xcms.Rcheck/examples_i386/xcms-Ex.timings:

nameusersystemelapsed
AutoLockMass-methods0.060.000.06
descendZero0.020.000.02
findMZ000
findPeaks.massifquant-methods13.12 0.1814.29
findneutral0.020.000.01
group.mzClust000
group.nearest0.010.000.02
medianFilter000
msn2xcmsRaw11.07 0.7841.44
netCdfSource-class000
peakTable-methods000
profGenerate000
profStep-methods0.070.000.06
ramp000
rampSource-class0.000.020.01
rectUnique000
stitch-methods000
xcmsPapply0.010.000.01
xcmsRaw000

xcms.Rcheck/examples_x64/xcms-Ex.timings:

nameusersystemelapsed
AutoLockMass-methods000
descendZero0.010.000.01
findMZ0.020.000.02
findPeaks.massifquant-methods11.45 0.2316.42
findneutral000
group.mzClust0.090.000.09
group.nearest0.020.000.02
medianFilter000
msn2xcmsRaw10.89 0.6116.44
netCdfSource-class000
peakTable-methods000
profGenerate0.020.000.02
profStep-methods0.020.000.02
ramp000
rampSource-class000
rectUnique0.010.000.01
stitch-methods0.020.000.02
xcmsPapply0.010.000.01
xcmsRaw0.020.000.02