Package: xps

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch xps_1.16.0.tar.gz

StartedAt: 2012-09-24 02:02:36 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 02:07:33 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 296.4 seconds

RetCode: 0

Status:  OK

CheckDir: xps.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/xps.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'xps/DESCRIPTION' ... OK
* this is package 'xps' version '1.16.0'
* 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 whether package 'xps' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   5.4Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File 'xps/R/zzz.R':
  .onLoad calls:
    require(methods)
    require(utils)

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

.onLoad: warning in packageDescription(pkgname, field = "Version"):
  partial argument match of 'field' to 'fields'
CELHeader: warning in matrix(nr = 23, nc = 1): partial argument match
  of 'nr' to 'nrow'
CELHeader: warning in matrix(nr = 23, nc = 1): partial argument match
  of 'nc' to 'ncol'
dabgCall.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial
  argument match of 'nr' to 'nrow'
dabgCall.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial
  argument match of 'nc' to 'ncol'
firma.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial argument
  match of 'nr' to 'nrow'
firma.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial argument
  match of 'nc' to 'ncol'
iniCall.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial
  argument match of 'nr' to 'nrow'
iniCall.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial
  argument match of 'nc' to 'ncol'
mas4.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial argument
  match of 'nr' to 'nrow'
mas4.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial argument
  match of 'nc' to 'ncol'
mas5.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial argument
  match of 'nr' to 'nrow'
mas5.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial argument
  match of 'nc' to 'ncol'
mas5Call.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial
  argument match of 'nr' to 'nrow'
mas5Call.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial
  argument match of 'nc' to 'ncol'
normalize.ExprTreeSet: warning in matrix(nr = 0, nc = 0): partial
  argument match of 'nr' to 'nrow'
normalize.ExprTreeSet: warning in matrix(nr = 0, nc = 0): partial
  argument match of 'nc' to 'ncol'
plotBorder: warning in jpeg(file = outfile, width = w, height = h):
  partial argument match of 'file' to 'filename'
plotBorder: warning in png(file = outfile, width = w, height = h):
  partial argument match of 'file' to 'filename'
plotBoxplot: warning in jpeg(file = outfile, width = w, height = h):
  partial argument match of 'file' to 'filename'
plotBoxplot: warning in png(file = outfile, width = w, height = h):
  partial argument match of 'file' to 'filename'
plotCOI: warning in jpeg(file = outfile, width = w, height = h):
  partial argument match of 'file' to 'filename'
plotCOI: warning in png(file = outfile, width = w, height = h): partial
  argument match of 'file' to 'filename'
plotCall: warning in jpeg(file = outfile, width = w, height = h):
  partial argument match of 'file' to 'filename'
plotCall: warning in png(file = outfile, width = w, height = h):
  partial argument match of 'file' to 'filename'
plotCorr: warning in jpeg(file = outfile, width = w, height = h):
  partial argument match of 'file' to 'filename'
plotCorr: warning in png(file = outfile, width = w, height = h):
  partial argument match of 'file' to 'filename'
plotDensity: warning in jpeg(file = outfile, width = w, height = h):
  partial argument match of 'file' to 'filename'
plotDensity: warning in png(file = outfile, width = w, height = h):
  partial argument match of 'file' to 'filename'
plotImage: warning in jpeg(file = outfile, width = w, height = h):
  partial argument match of 'file' to 'filename'
plotImage: warning in png(file = outfile, width = w, height = h):
  partial argument match of 'file' to 'filename'
plotIntensity2GC: warning in jpeg(file = outfile, width = w, height =
  h): partial argument match of 'file' to 'filename'
plotIntensity2GC: warning in png(file = outfile, width = w, height =
  h): partial argument match of 'file' to 'filename'
plotMA: warning in jpeg(file = outfile, width = w, height = h): partial
  argument match of 'file' to 'filename'
plotMA: warning in png(file = outfile, width = w, height = h): partial
  argument match of 'file' to 'filename'
plotMAD: warning in jpeg(file = outfile, width = w, height = h):
  partial argument match of 'file' to 'filename'
plotMAD: warning in png(file = outfile, width = w, height = h): partial
  argument match of 'file' to 'filename'
plotNUSE: warning in jpeg(file = outfile, width = w, height = h):
  partial argument match of 'file' to 'filename'
plotNUSE: warning in png(file = outfile, width = w, height = h):
  partial argument match of 'file' to 'filename'
plotPCA: warning in jpeg(file = outfile, width = w, height = h):
  partial argument match of 'file' to 'filename'
plotPCA: warning in png(file = outfile, width = w, height = h): partial
  argument match of 'file' to 'filename'
plotPM: warning in jpeg(file = outfile, width = w, height = h): partial
  argument match of 'file' to 'filename'
plotPM: warning in png(file = outfile, width = w, height = h): partial
  argument match of 'file' to 'filename'
plotProbeset: warning in jpeg(file = outfile, width = w, height = h):
  partial argument match of 'file' to 'filename'
plotProbeset: warning in png(file = outfile, width = w, height = h):
  partial argument match of 'file' to 'filename'
plotRLE: warning in jpeg(file = outfile, width = w, height = h):
  partial argument match of 'file' to 'filename'
plotRLE: warning in png(file = outfile, width = w, height = h): partial
  argument match of 'file' to 'filename'
plotVolcano: warning in jpeg(file = outfile, width = w, height = h):
  partial argument match of 'file' to 'filename'
plotVolcano: warning in png(file = outfile, width = w, height = h):
  partial argument match of 'file' to 'filename'
prefilter.ExprTreeSet: warning in matrix(nr = 0, nc = 0): partial
  argument match of 'nr' to 'nrow'
prefilter.ExprTreeSet: warning in matrix(nr = 0, nc = 0): partial
  argument match of 'nc' to 'ncol'
preprocess.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial
  argument match of 'nr' to 'nrow'
preprocess.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial
  argument match of 'nc' to 'ncol'
qc.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial argument
  match of 'nr' to 'nrow'
qc.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial argument
  match of 'nc' to 'ncol'
qualify.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial
  argument match of 'nr' to 'nrow'
qualify.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial
  argument match of 'nc' to 'ncol'
rma.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial argument
  match of 'nr' to 'nrow'
rma.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial argument
  match of 'nc' to 'ncol'
summarize.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial
  argument match of 'nr' to 'nrow'
summarize.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial
  argument match of 'nc' to 'ncol'
unifilter.ExprTreeSet: warning in matrix(nr = 0, nc = 0): partial
  argument match of 'nr' to 'nrow'
unifilter.ExprTreeSet: warning in matrix(nr = 0, nc = 0): partial
  argument match of 'nc' to 'ncol'
xpsQAReport: warning in png(file = file.path(docdir,
  "RNADegradationPlot.png"), width = 540, height = 540): partial
  argument match of 'file' to 'filename'
xpsQAReport: warning in png(file = file.path(docdir,
  "RNADegradationSlope.png"), width = 540, height = 440): partial
  argument match of 'file' to 'filename'
* 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 for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File '/Users/biocbuild/bbs-2.10-bioc/meat/xps.Rcheck/xps/libs/i386/xps.so':
  Found '__ZSt4cerr', possibly from 'std::cerr' (C++)
  Found '__ZSt4cout', possibly from 'std::cout' (C++)
  Found '_printf', possibly from 'printf' (C)

Compiled code should not call functions 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.10-bioc/meat/xps.Rcheck/00check.log'
for details.

* installing *source* package 'xps' ...
checking for gcc... gcc -arch i386 -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -arch i386 -std=gnu99 accepts -g... yes
checking for gcc -arch i386 -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -arch i386 -std=gnu99 -E
checking for gcc... (cached) gcc -arch i386 -std=gnu99
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc -arch i386 -std=gnu99 accepts -g... (cached) yes
checking for gcc -arch i386 -std=gnu99 option to accept ANSI C... (cached) none needed
checking for root-config... yes
found ROOT version 5.32/01 in directory /usr/local/root
** libs
** arch - i386
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m32 -I/usr/local/root/include/root -c TMLMath.cxx
TMLMath.cxx:1109:1: warning: "xmax" redefined
TMLMath.cxx:1060:1: warning: this is the location of the previous definition
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m32 -I/usr/local/root/include/root -c TStat.cxx
In file included from TStat.cxx:53:
TStat.h:332: warning: unused parameter 'x'
TStat.h:333: warning: unused parameter 'x'
TStat.h:334: warning: unused parameter 'x'
TStat.h:335: warning: unused parameter 'x'
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m32 -I/usr/local/root/include/root -c StatUtils.cxx
In file included from StatUtils.cxx:58:
TStat.h:332: warning: unused parameter 'x'
TStat.h:333: warning: unused parameter 'x'
TStat.h:334: warning: unused parameter 'x'
TStat.h:335: warning: unused parameter 'x'
StatUtils.cxx:240: warning: unused parameter 'df'
StatUtils.cxx:264: warning: unused parameter 'df'
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m32 -I/usr/local/root/include/root -c XPSBase.cxx
In file included from XPSBase.cxx:101:
/usr/local/root/include/root/TObject.h:127: warning: 'virtual const Option_t* TObject::GetOption() const' was hidden
XPSBase.h:208: warning:   by 'virtual const Option_t* XTreeInfo::GetOption()'
XPSBase.cxx: In member function 'XFolder* XFolder::AddFolder(const char*, const char*, const char*, TCollection*)':
XPSBase.cxx:183: warning: too many arguments for format
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m32 -I/usr/local/root/include/root -c XPSUtils.cxx
In file included from XPSUtils.cxx:79:
TStat.h:332: warning: unused parameter 'x'
TStat.h:333: warning: unused parameter 'x'
TStat.h:334: warning: unused parameter 'x'
TStat.h:335: warning: unused parameter 'x'
XPSUtils.cxx:1332: warning: unused parameter 'canvasname'
XPSUtils.cxx:1332: warning: unused parameter 'treename'
XPSUtils.cxx:1332: warning: unused parameter 'varexp'
XPSUtils.cxx:1332: warning: unused parameter 'selection'
XPSUtils.cxx:1332: warning: unused parameter 'opt'
XPSUtils.cxx:1721: warning: unused parameter 'min'
XPSUtils.cxx:1721: warning: unused parameter 'max'
XPSUtils.cxx:2116: warning: unused parameter 'n'
XPSUtils.cxx:2116: warning: unused parameter 'x'
XPSUtils.cxx:2116: warning: unused parameter 'y'
XPSUtils.cxx:2116: warning: unused parameter 'z'
XPSUtils.cxx:2116: warning: unused parameter 'opt'
XPSUtils.cxx:2624: warning: unused parameter 'index'
XPSUtils.cxx:3077: warning: unused parameter 'n'
XPSUtils.cxx:3077: warning: unused parameter 'colors'
XPSUtils.cxx:3077: warning: unused parameter 'priority'
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m32 -I/usr/local/root/include/root -c XPSSchemes.cxx
In file included from XPSSchemes.h:41,
                 from XPSSchemes.cxx:71:
/usr/local/root/include/root/TObject.h:127: warning: 'virtual const Option_t* TObject::GetOption() const' was hidden
XPSBase.h:208: warning:   by 'virtual const Option_t* XTreeInfo::GetOption()'
XPSSchemes.cxx:10004: warning: unused parameter 'index'
XPSSchemes.cxx:10015: warning: unused parameter 'index'
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m32 -I/usr/local/root/include/root -c XPSDataTypes.cxx
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m32 -I/usr/local/root/include/root -c XPSProjectHandler.cxx
In file included from XPSProjectHandler.cxx:47:
XPSProjectHandler.h:84: warning: unused parameter 'name'
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m32 -I/usr/local/root/include/root -c XPSData.cxx
In file included from XPSSchemes.h:41,
                 from XPSData.h:43,
                 from XPSData.cxx:80:
/usr/local/root/include/root/TObject.h:127: warning: 'virtual const Option_t* TObject::GetOption() const' was hidden
XPSBase.h:208: warning:   by 'virtual const Option_t* XTreeInfo::GetOption()'
In file included from XPSData.h:47,
                 from XPSData.cxx:80:
XPSProjectHandler.h:84: warning: unused parameter 'name'
In file included from XPSData.cxx:80:
XPSData.h:700: warning: unused parameter 'min'
XPSData.h:700: warning: unused parameter 'max'
XPSData.h:700: warning: unused parameter 'var2sort'
XPSData.h:700: warning: unused parameter 'down'
In file included from XPSData.cxx:82:
TStat.h:332: warning: unused parameter 'x'
TStat.h:333: warning: unused parameter 'x'
TStat.h:334: warning: unused parameter 'x'
TStat.h:335: warning: unused parameter 'x'
XPSData.cxx:504: warning: unused parameter 'name'
XPSData.cxx: In member function 'virtual Int_t XGeneChipHyb::ExportMaskTreeInfo(Int_t, TString*, const char*, std::ofstream&, const char*)':
XPSData.cxx:1797: warning: unused variable 'err'
XPSData.cxx: At global scope:
XPSData.cxx:1792: warning: unused parameter 'n'
XPSData.cxx:1792: warning: unused parameter 'names'
XPSData.cxx:1792: warning: unused parameter 'varlist'
XPSData.cxx:1792: warning: unused parameter 'output'
XPSData.cxx:1792: warning: unused parameter 'sep'
XPSData.cxx: In member function 'virtual Int_t XGeneChipHyb::ReadXMLHeader(std::ifstream&, const char*, char)':
XPSData.cxx:2810: warning: unused variable 'fNMasked'
XPSData.cxx:2820: warning: unused variable 'fNOutlier'
XPSData.cxx:2830: warning: unused variable 'fNModified'
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m32 -I/usr/local/root/include/root -c XPSProcessing.cxx
In file included from XPSSchemes.h:41,
                 from XPSProcessing.h:42,
                 from XPSProcessing.cxx:69:
/usr/local/root/include/root/TObject.h:127: warning: 'virtual const Option_t* TObject::GetOption() const' was hidden
XPSBase.h:208: warning:   by 'virtual const Option_t* XTreeInfo::GetOption()'
In file included from XPSData.h:47,
                 from XPSProcessing.h:46,
                 from XPSProcessing.cxx:69:
XPSProjectHandler.h:84: warning: unused parameter 'name'
In file included from XPSProcessing.h:46,
                 from XPSProcessing.cxx:69:
XPSData.h:700: warning: unused parameter 'min'
XPSData.h:700: warning: unused parameter 'max'
XPSData.h:700: warning: unused parameter 'var2sort'
XPSData.h:700: warning: unused parameter 'down'
In file included from XPSProcessing.cxx:71:
TStat.h:332: warning: unused parameter 'x'
TStat.h:333: warning: unused parameter 'x'
TStat.h:334: warning: unused parameter 'x'
TStat.h:335: warning: unused parameter 'x'
XPSProcessing.cxx:786: warning: unused parameter 'name'
XPSProcessing.cxx: In member function 'virtual Int_t XProcesSet::ExportMaskTreeInfo(Int_t, TString*, const char*, std::ofstream&, const char*)':
XPSProcessing.cxx:1530: warning: unused variable 'err'
XPSProcessing.cxx: At global scope:
XPSProcessing.cxx:1525: warning: unused parameter 'n'
XPSProcessing.cxx:1525: warning: unused parameter 'names'
XPSProcessing.cxx:1525: warning: unused parameter 'varlist'
XPSProcessing.cxx:1525: warning: unused parameter 'output'
XPSProcessing.cxx:1525: warning: unused parameter 'sep'
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m32 -I/usr/local/root/include/root -c XPSHybridizer.cxx
In file included from XPSHybridizer.cxx:64:
TStat.h:332: warning: unused parameter 'x'
TStat.h:333: warning: unused parameter 'x'
TStat.h:334: warning: unused parameter 'x'
TStat.h:335: warning: unused parameter 'x'
In file included from XPSSchemes.h:41,
                 from XPSProcessing.h:42,
                 from XPSHybridizer.h:42,
                 from XPSHybridizer.cxx:65:
/usr/local/root/include/root/TObject.h:127: warning: 'virtual const Option_t* TObject::GetOption() const' was hidden
XPSBase.h:208: warning:   by 'virtual const Option_t* XTreeInfo::GetOption()'
In file included from XPSData.h:47,
                 from XPSProcessing.h:46,
                 from XPSHybridizer.h:42,
                 from XPSHybridizer.cxx:65:
XPSProjectHandler.h:84: warning: unused parameter 'name'
In file included from XPSProcessing.h:46,
                 from XPSHybridizer.h:42,
                 from XPSHybridizer.cxx:65:
XPSData.h:700: warning: unused parameter 'min'
XPSData.h:700: warning: unused parameter 'max'
XPSData.h:700: warning: unused parameter 'var2sort'
XPSData.h:700: warning: unused parameter 'down'
In file included from XPSHybridizer.cxx:65:
XPSHybridizer.h:178: warning: unused parameter 'n'
XPSHybridizer.h:178: warning: unused parameter 'x'
XPSHybridizer.h:178: warning: unused parameter 'y'
XPSHybridizer.h:178: warning: unused parameter 'z'
XPSHybridizer.h:178: warning: unused parameter 'dx'
XPSHybridizer.h:178: warning: unused parameter 'dy'
XPSHybridizer.h:178: warning: unused parameter 'idx'
XPSHybridizer.h:178: warning: unused parameter 'nsub'
XPSHybridizer.h:178: warning: 'virtual Int_t XExpressor::Calculate(Int_t, Double_t*, Double_t*, Double_t*, Double_t*, Double_t*, Int_t*, Int_t)' was hidden
XPSBase.h:438: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:178: warning: 'virtual Int_t XExpressor::Calculate(Int_t, Double_t*, Double_t*, Double_t*, Double_t*, Double_t*, Int_t*, Int_t)' was hidden
XPSBase.h:438: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:178: warning: 'virtual Int_t XExpressor::Calculate(Int_t, Double_t*, Double_t*, Double_t*, Double_t*, Double_t*, Int_t*, Int_t)' was hidden
XPSBase.h:438: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:178: warning: 'virtual Int_t XExpressor::Calculate(Int_t, Double_t*, Double_t*, Double_t*, Double_t*, Double_t*, Int_t*, Int_t)' was hidden
XPSBase.h:437: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:178: warning: 'virtual Int_t XExpressor::Calculate(Int_t, Double_t*, Double_t*, Double_t*, Double_t*, Double_t*, Int_t*, Int_t)' was hidden
XPSBase.h:437: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:178: warning: 'virtual Int_t XExpressor::Calculate(Int_t, Double_t*, Double_t*, Double_t*, Double_t*, Double_t*, Int_t*, Int_t)' was hidden
XPSBase.h:437: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.cxx:748: warning: unused parameter 'msk'
XPSHybridizer.cxx:1872: warning: unused parameter 'num'
XPSHybridizer.cxx:1985: warning: unused parameter 'num'
XPSHybridizer.cxx:2168: warning: unused parameter 'value1'
XPSHybridizer.cxx:2168: warning: unused parameter 'value2'
XPSHybridizer.cxx:2168: warning: unused parameter 'num'
XPSHybridizer.cxx:2292: warning: unused parameter 'num'
XPSHybridizer.cxx:2552: warning: unused parameter 'msk'
XPSHybridizer.cxx:2596: warning: unused parameter 'x'
XPSHybridizer.cxx:2596: warning: unused parameter 'scale'
XPSHybridizer.cxx:2784: warning: unused parameter 'x'
XPSHybridizer.cxx:2784: warning: unused parameter 'scale'
XPSHybridizer.cxx:3831: warning: unused parameter 'msk'
XPSHybridizer.cxx:3891: warning: unused parameter 'msk'
XPSHybridizer.cxx:4464: warning: unused parameter 'msk'
XPSHybridizer.cxx: In member function 'Double_t XDetectionCall::WilcoxTest(Int_t, Double_t*, Double_t)':
XPSHybridizer.cxx:2066: warning: 'pval' may be used uninitialized in this function
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m32 -I/usr/local/root/include/root -c XPSSelector.cxx
In file included from XPSSchemes.h:41,
                 from XPSProcessing.h:42,
                 from XPSSelector.h:42,
                 from XPSSelector.cxx:52:
/usr/local/root/include/root/TObject.h:127: warning: 'virtual const Option_t* TObject::GetOption() const' was hidden
XPSBase.h:208: warning:   by 'virtual const Option_t* XTreeInfo::GetOption()'
In file included from XPSData.h:47,
                 from XPSProcessing.h:46,
                 from XPSSelector.h:42,
                 from XPSSelector.cxx:52:
XPSProjectHandler.h:84: warning: unused parameter 'name'
In file included from XPSProcessing.h:46,
                 from XPSSelector.h:42,
                 from XPSSelector.cxx:52:
XPSData.h:700: warning: unused parameter 'min'
XPSData.h:700: warning: unused parameter 'max'
XPSData.h:700: warning: unused parameter 'var2sort'
XPSData.h:700: warning: unused parameter 'down'
In file included from XPSSelector.cxx:52:
XPSSelector.h:152: warning: 'virtual Int_t XProbeSelector::Calculate(Int_t, Double_t*, Double_t*, Int_t*)' was hidden
XPSSelector.h:209: warning:   by 'XUnitSelector::Calculate'
XPSSelector.cxx:316: warning: unused parameter 'max'
XPSSelector.cxx:316: warning: unused parameter 'showGraph'
XPSSelector.cxx: In member function 'Double_t XRankSelector::Cutoff(Int_t, const Double_t*, Double_t, Bool_t)':
XPSSelector.cxx:334: warning: 'par0' may be used uninitialized in this function
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m32 -I/usr/local/root/include/root -c XPSNormalizer.cxx
In file included from XPSSchemes.h:41,
                 from XPSProcessing.h:42,
                 from XPSNormalizer.h:42,
                 from XPSNormalizer.cxx:63:
/usr/local/root/include/root/TObject.h:127: warning: 'virtual const Option_t* TObject::GetOption() const' was hidden
XPSBase.h:208: warning:   by 'virtual const Option_t* XTreeInfo::GetOption()'
In file included from XPSData.h:47,
                 from XPSProcessing.h:46,
                 from XPSNormalizer.h:42,
                 from XPSNormalizer.cxx:63:
XPSProjectHandler.h:84: warning: unused parameter 'name'
In file included from XPSProcessing.h:46,
                 from XPSNormalizer.h:42,
                 from XPSNormalizer.cxx:63:
XPSData.h:700: warning: unused parameter 'min'
XPSData.h:700: warning: unused parameter 'max'
XPSData.h:700: warning: unused parameter 'var2sort'
XPSData.h:700: warning: unused parameter 'down'
In file included from XPSNormalizer.cxx:64:
TStat.h:332: warning: unused parameter 'x'
TStat.h:333: warning: unused parameter 'x'
TStat.h:334: warning: unused parameter 'x'
TStat.h:335: warning: unused parameter 'x'
XPSNormalizer.cxx:533: warning: unused parameter 'xout'
XPSNormalizer.cxx:610: warning: unused parameter 'xout'
XPSNormalizer.cxx:689: warning: unused parameter 'xout'
XPSNormalizer.cxx:1129: warning: unused parameter 'n'
XPSNormalizer.cxx:1160: warning: unused parameter 'n'
XPSNormalizer.cxx:1297: warning: unused parameter 'x'
XPSNormalizer.cxx:1297: warning: unused parameter 'msk'
XPSNormalizer.cxx: In member function 'virtual Int_t XNormalizer::Calculate(Int_t, Double_t*, Double_t*, Int_t*)':
XPSNormalizer.cxx:240: warning: 'his2sel' may be used uninitialized in this function
XPSNormalizer.cxx:239: warning: 'his2all' may be used uninitialized in this function
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m32 -I/usr/local/root/include/root -c XPSPreProcessing.cxx
In file included from XPSSchemes.h:41,
                 from XPSProcessing.h:42,
                 from XPSPreProcessing.h:42,
                 from XPSPreProcessing.cxx:93:
/usr/local/root/include/root/TObject.h:127: warning: 'virtual const Option_t* TObject::GetOption() const' was hidden
XPSBase.h:208: warning:   by 'virtual const Option_t* XTreeInfo::GetOption()'
In file included from XPSData.h:47,
                 from XPSProcessing.h:46,
                 from XPSPreProcessing.h:42,
                 from XPSPreProcessing.cxx:93:
XPSProjectHandler.h:84: warning: unused parameter 'name'
In file included from XPSProcessing.h:46,
                 from XPSPreProcessing.h:42,
                 from XPSPreProcessing.cxx:93:
XPSData.h:700: warning: unused parameter 'min'
XPSData.h:700: warning: unused parameter 'max'
XPSData.h:700: warning: unused parameter 'var2sort'
XPSData.h:700: warning: unused parameter 'down'
In file included from XPSPreProcessing.cxx:93:
XPSPreProcessing.h:324: warning: 'virtual Int_t XPreProcesSet::QualityControl(Int_t, TTree**, Int_t&, TTree**)' was hidden
XPSPreProcessing.h:395: warning:   by 'virtual Int_t XGCProcesSet::QualityControl(Int_t, TTree**, Int_t, TTree**, const char*)'
In file included from XPSPreProcessing.cxx:94:
XPSHybridizer.h:178: warning: unused parameter 'n'
XPSHybridizer.h:178: warning: unused parameter 'x'
XPSHybridizer.h:178: warning: unused parameter 'y'
XPSHybridizer.h:178: warning: unused parameter 'z'
XPSHybridizer.h:178: warning: unused parameter 'dx'
XPSHybridizer.h:178: warning: unused parameter 'dy'
XPSHybridizer.h:178: warning: unused parameter 'idx'
XPSHybridizer.h:178: warning: unused parameter 'nsub'
XPSHybridizer.h:178: warning: 'virtual Int_t XExpressor::Calculate(Int_t, Double_t*, Double_t*, Double_t*, Double_t*, Double_t*, Int_t*, Int_t)' was hidden
XPSBase.h:438: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:178: warning: 'virtual Int_t XExpressor::Calculate(Int_t, Double_t*, Double_t*, Double_t*, Double_t*, Double_t*, Int_t*, Int_t)' was hidden
XPSBase.h:438: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:178: warning: 'virtual Int_t XExpressor::Calculate(Int_t, Double_t*, Double_t*, Double_t*, Double_t*, Double_t*, Int_t*, Int_t)' was hidden
XPSBase.h:438: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:178: warning: 'virtual Int_t XExpressor::Calculate(Int_t, Double_t*, Double_t*, Double_t*, Double_t*, Double_t*, Int_t*, Int_t)' was hidden
XPSBase.h:437: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:178: warning: 'virtual Int_t XExpressor::Calculate(Int_t, Double_t*, Double_t*, Double_t*, Double_t*, Double_t*, Int_t*, Int_t)' was hidden
XPSBase.h:437: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:178: warning: 'virtual Int_t XExpressor::Calculate(Int_t, Double_t*, Double_t*, Double_t*, Double_t*, Double_t*, Int_t*, Int_t)' was hidden
XPSBase.h:437: warning:   by 'XAlgorithm::Calculate'
In file included from XPSPreProcessing.cxx:95:
XPSSelector.h:152: warning: 'virtual Int_t XProbeSelector::Calculate(Int_t, Double_t*, Double_t*, Int_t*)' was hidden
XPSSelector.h:209: warning:   by 'XUnitSelector::Calculate'
In file included from XPSPreProcessing.cxx:97:
TStat.h:332: warning: unused parameter 'x'
TStat.h:333: warning: unused parameter 'x'
TStat.h:334: warning: unused parameter 'x'
TStat.h:335: warning: unused parameter 'x'
XPSPreProcessing.cxx: In member function 'virtual Int_t XGCProcesSet::DoDataQualityControl(Int_t, TTree**, TTree**, TTree**, XDNAChip*, TFile*)':
XPSPreProcessing.cxx:3026: warning: operation on 'numsels' may be undefined
XPSPreProcessing.cxx: In member function 'virtual Int_t XGCProcesSet::DoBorderElements(Int_t, TTree**, TTree**, XDNAChip*, TFile*)':
XPSPreProcessing.cxx:3515: warning: unused variable 'idxhi'
XPSPreProcessing.cxx:3515: warning: unused variable 'idxlo'
XPSPreProcessing.cxx: At global scope:
XPSPreProcessing.cxx:3502: warning: unused parameter 'file'
XPSPreProcessing.cxx: In member function 'virtual Int_t XGCProcesSet::DoBgrdQualityControl(Int_t, TTree**, XDNAChip*, TFile*)':
XPSPreProcessing.cxx:3670: warning: unused variable 'numunits'
XPSPreProcessing.cxx:3671: warning: unused variable 'size'
XPSPreProcessing.cxx: At global scope:
XPSPreProcessing.cxx:3661: warning: unused parameter 'numbgrd'
XPSPreProcessing.cxx:3661: warning: unused parameter 'bgrdtree'
XPSPreProcessing.cxx:3661: warning: unused parameter 'file'
XPSPreProcessing.cxx: In member function 'virtual Int_t XGCProcesSet::DoMultichipCall(Int_t, TTree**, Int_t&, TTree**, TFile*)':
XPSPreProcessing.cxx:4252: warning: operation on 'numsels' may be undefined
XPSPreProcessing.cxx: In member function 'virtual Int_t XGCProcesSet::DoMultichipExpress(Int_t, TTree**, Int_t, TTree**, TFile*)':
XPSPreProcessing.cxx:5135: warning: operation on 'numsels' may be undefined
XPSPreProcessing.cxx: In member function 'virtual Int_t XGCProcesSet::ExportQualTrees(Int_t, TString*, const char*, std::ofstream&, const char*)':
XPSPreProcessing.cxx:6762: warning: unused variable 'idxstr'
XPSPreProcessing.cxx: At global scope:
XPSPreProcessing.cxx:7981: warning: unused parameter 'bgrd'
XPSPreProcessing.cxx:7981: warning: unused parameter 'bgdev'
XPSPreProcessing.cxx:8077: warning: unused parameter 'algorithm'
XPSPreProcessing.cxx:8097: warning: unused parameter 'algorithm'
XPSPreProcessing.cxx:8599: warning: unused parameter 'nrow'
XPSPreProcessing.cxx: In member function 'TTree* XGCProcesSet::FillDataTree(TTree*, const char*, XAlgorithm*, Int_t, Int_t, Double_t*, Double_t*)':
XPSPreProcessing.cxx:8737: warning: label 'cleanup' defined but not used
XPSPreProcessing.cxx: In member function 'virtual Int_t XExonProcesSet::DoSpliceExpress(Int_t, TTree**, Int_t, TTree**, TFile*)':
XPSPreProcessing.cxx:9591: warning: operation on 'numsels' may be undefined
XPSPreProcessing.cxx:9782: warning: unused variable 'numatoms'
XPSPreProcessing.cxx:9389: warning: unused variable 'x'
XPSPreProcessing.cxx:9390: warning: unused variable 'y'
XPSPreProcessing.cxx:9395: warning: unused variable 'stepout'
XPSPreProcessing.cxx: In member function 'virtual TTree* XExonProcesSet::SchemeTree(XAlgorithm*, void*, TLeaf**)':
XPSPreProcessing.cxx:10349: warning: unused variable 'scheme_ptr_ptr'
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m32 -I/usr/local/root/include/root -c XPSNormation.cxx
In file included from XPSSchemes.h:41,
                 from XPSProcessing.h:42,
                 from XPSNormation.h:42,
                 from XPSNormation.cxx:70:
/usr/local/root/include/root/TObject.h:127: warning: 'virtual const Option_t* TObject::GetOption() const' was hidden
XPSBase.h:208: warning:   by 'virtual const Option_t* XTreeInfo::GetOption()'
In file included from XPSData.h:47,
                 from XPSProcessing.h:46,
                 from XPSNormation.h:42,
                 from XPSNormation.cxx:70:
XPSProjectHandler.h:84: warning: unused parameter 'name'
In file included from XPSProcessing.h:46,
                 from XPSNormation.h:42,
                 from XPSNormation.cxx:70:
XPSData.h:700: warning: unused parameter 'min'
XPSData.h:700: warning: unused parameter 'max'
XPSData.h:700: warning: unused parameter 'var2sort'
XPSData.h:700: warning: unused parameter 'down'
In file included from XPSNormation.cxx:71:
XPSSelector.h:152: warning: 'virtual Int_t XProbeSelector::Calculate(Int_t, Double_t*, Double_t*, Int_t*)' was hidden
XPSSelector.h:209: warning:   by 'XUnitSelector::Calculate'
In file included from XPSNormation.cxx:73:
TStat.h:332: warning: unused parameter 'x'
TStat.h:333: warning: unused parameter 'x'
TStat.h:334: warning: unused parameter 'x'
TStat.h:335: warning: unused parameter 'x'
XPSNormation.cxx:182: warning: unused parameter 'infile'
XPSNormation.cxx:1019: warning: unused parameter 'method'
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m32 -I/usr/local/root/include/root -c XPSFilter.cxx
In file included from XPSFilter.h:49,
                 from XPSFilter.cxx:44:
TStat.h:332: warning: unused parameter 'x'
TStat.h:333: warning: unused parameter 'x'
TStat.h:334: warning: unused parameter 'x'
TStat.h:335: warning: unused parameter 'x'
In file included from XPSSchemes.h:41,
                 from XPSProcessing.h:42,
                 from XPSFilter.h:52,
                 from XPSFilter.cxx:44:
/usr/local/root/include/root/TObject.h:127: warning: 'virtual const Option_t* TObject::GetOption() const' was hidden
XPSBase.h:208: warning:   by 'virtual const Option_t* XTreeInfo::GetOption()'
In file included from XPSData.h:47,
                 from XPSProcessing.h:46,
                 from XPSFilter.h:52,
                 from XPSFilter.cxx:44:
XPSProjectHandler.h:84: warning: unused parameter 'name'
In file included from XPSProcessing.h:46,
                 from XPSFilter.h:52,
                 from XPSFilter.cxx:44:
XPSData.h:700: warning: unused parameter 'min'
XPSData.h:700: warning: unused parameter 'max'
XPSData.h:700: warning: unused parameter 'var2sort'
XPSData.h:700: warning: unused parameter 'down'
In file included from XPSFilter.cxx:44:
XPSFilter.h:118: warning: 'virtual Int_t XFilter::Calculate(TTree*, const char*, TTree*, const char*)' was hidden
XPSBase.h:437: warning:   by 'XAlgorithm::Calculate'
XPSFilter.h:118: warning: 'virtual Int_t XFilter::Calculate(TTree*, const char*, TTree*, const char*)' was hidden
XPSBase.h:437: warning:   by 'XAlgorithm::Calculate'
XPSFilter.h:120: warning: 'virtual Int_t XFilter::Calculate(Int_t, TTree**, const char*, TTree*, const char*)' was hidden
XPSBase.h:437: warning:   by 'XAlgorithm::Calculate'
XPSFilter.cxx:621: warning: unused parameter 'sepo'
XPSFilter.cxx:1351: warning: unused parameter 'table'
XPSFilter.cxx:1630: warning: unused parameter 'infile'
XPSFilter.cxx:1630: warning: unused parameter 'outfile'
XPSFilter.cxx:1630: warning: unused parameter 'varlist'
XPSFilter.cxx:1630: warning: unused parameter 'nrows'
XPSFilter.cxx:1630: warning: unused parameter 'sepi'
XPSFilter.cxx:1630: warning: unused parameter 'sepo'
XPSFilter.cxx:1630: warning: unused parameter 'delim'
XPSFilter.cxx: In member function 'virtual Int_t XUniFilter::Calculate(TTree*, const char*, TTree*, const char*, Int_t)':
XPSFilter.cxx:1787: warning: unused variable 'brchUnit'
XPSFilter.cxx: At global scope:
XPSFilter.cxx:1657: warning: unused parameter 'leafname'
XPSFilter.cxx:1839: warning: unused parameter 'outtree'
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m32 -I/usr/local/root/include/root -c XPSAnalyzer.cxx
In file included from XPSSchemes.h:41,
                 from XPSProcessing.h:42,
                 from XPSAnalyzer.h:45,
                 from XPSAnalyzer.cxx:42:
/usr/local/root/include/root/TObject.h:127: warning: 'virtual const Option_t* TObject::GetOption() const' was hidden
XPSBase.h:208: warning:   by 'virtual const Option_t* XTreeInfo::GetOption()'
In file included from XPSData.h:47,
                 from XPSProcessing.h:46,
                 from XPSAnalyzer.h:45,
                 from XPSAnalyzer.cxx:42:
XPSProjectHandler.h:84: warning: unused parameter 'name'
In file included from XPSProcessing.h:46,
                 from XPSAnalyzer.h:45,
                 from XPSAnalyzer.cxx:42:
XPSData.h:700: warning: unused parameter 'min'
XPSData.h:700: warning: unused parameter 'max'
XPSData.h:700: warning: unused parameter 'var2sort'
XPSData.h:700: warning: unused parameter 'down'
XPSAnalyzer.cxx:213: warning: unused parameter 'type'
XPSAnalyzer.cxx:213: warning: unused parameter 'options'
XPSAnalyzer.cxx:213: warning: unused parameter 'npars'
XPSAnalyzer.cxx:213: warning: unused parameter 'pars'
XPSAnalyzer.cxx:227: warning: unused parameter 'infile'
XPSAnalyzer.cxx:227: warning: unused parameter 'outfile'
XPSAnalyzer.cxx:227: warning: unused parameter 'varlist'
XPSAnalyzer.cxx:227: warning: unused parameter 'nrows'
XPSAnalyzer.cxx:227: warning: unused parameter 'nperm'
XPSAnalyzer.cxx:227: warning: unused parameter 'mu'
XPSAnalyzer.cxx:227: warning: unused parameter 'sepi'
XPSAnalyzer.cxx:227: warning: unused parameter 'sepo'
XPSAnalyzer.cxx:227: warning: unused parameter 'delim'
XPSAnalyzer.cxx:227: warning: unused parameter 'linebuf'
XPSAnalyzer.cxx:239: warning: unused parameter 'n'
XPSAnalyzer.cxx:239: warning: unused parameter 'gid'
XPSAnalyzer.cxx:239: warning: unused parameter 'intree'
XPSAnalyzer.cxx:239: warning: unused parameter 'leafname'
XPSAnalyzer.cxx:239: warning: unused parameter 'outtree'
XPSAnalyzer.cxx:239: warning: unused parameter 'varlist'
XPSAnalyzer.cxx:239: warning: unused parameter 'nperm'
XPSAnalyzer.cxx:239: warning: unused parameter 'mu'
XPSAnalyzer.cxx:288: warning: unused parameter 'type'
XPSAnalyzer.cxx:288: warning: unused parameter 'options'
XPSAnalyzer.cxx:288: warning: unused parameter 'npars'
XPSAnalyzer.cxx:288: warning: unused parameter 'pars'
XPSAnalyzer.cxx:302: warning: unused parameter 'infile'
XPSAnalyzer.cxx:302: warning: unused parameter 'outfile'
XPSAnalyzer.cxx:302: warning: unused parameter 'varlist'
XPSAnalyzer.cxx:302: warning: unused parameter 'nrows'
XPSAnalyzer.cxx:302: warning: unused parameter 'nperm'
XPSAnalyzer.cxx:302: warning: unused parameter 'mu'
XPSAnalyzer.cxx:302: warning: unused parameter 'sepi'
XPSAnalyzer.cxx:302: warning: unused parameter 'sepo'
XPSAnalyzer.cxx:302: warning: unused parameter 'delim'
XPSAnalyzer.cxx:302: warning: unused parameter 'linebuf'
XPSAnalyzer.cxx:314: warning: unused parameter 'n'
XPSAnalyzer.cxx:314: warning: unused parameter 'gid'
XPSAnalyzer.cxx:314: warning: unused parameter 'intree'
XPSAnalyzer.cxx:314: warning: unused parameter 'leafname'
XPSAnalyzer.cxx:314: warning: unused parameter 'outtree'
XPSAnalyzer.cxx:314: warning: unused parameter 'varlist'
XPSAnalyzer.cxx:314: warning: unused parameter 'nperm'
XPSAnalyzer.cxx:314: warning: unused parameter 'mu'
XPSAnalyzer.cxx:363: warning: unused parameter 'type'
XPSAnalyzer.cxx:363: warning: unused parameter 'options'
XPSAnalyzer.cxx:363: warning: unused parameter 'npars'
XPSAnalyzer.cxx:363: warning: unused parameter 'pars'
XPSAnalyzer.cxx:377: warning: unused parameter 'infile'
XPSAnalyzer.cxx:377: warning: unused parameter 'outfile'
XPSAnalyzer.cxx:377: warning: unused parameter 'varlist'
XPSAnalyzer.cxx:377: warning: unused parameter 'nrows'
XPSAnalyzer.cxx:377: warning: unused parameter 'nperm'
XPSAnalyzer.cxx:377: warning: unused parameter 'mu'
XPSAnalyzer.cxx:377: warning: unused parameter 'sepi'
XPSAnalyzer.cxx:377: warning: unused parameter 'sepo'
XPSAnalyzer.cxx:377: warning: unused parameter 'delim'
XPSAnalyzer.cxx:377: warning: unused parameter 'linebuf'
XPSAnalyzer.cxx:389: warning: unused parameter 'n'
XPSAnalyzer.cxx:389: warning: unused parameter 'gid'
XPSAnalyzer.cxx:389: warning: unused parameter 'intree'
XPSAnalyzer.cxx:389: warning: unused parameter 'leafname'
XPSAnalyzer.cxx:389: warning: unused parameter 'outtree'
XPSAnalyzer.cxx:389: warning: unused parameter 'varlist'
XPSAnalyzer.cxx:389: warning: unused parameter 'nperm'
XPSAnalyzer.cxx:389: warning: unused parameter 'mu'
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m32 -I/usr/local/root/include/root -c XPSAnalysis.cxx
In file included from XPSSchemes.h:41,
                 from XPSAnalysis.h:41,
                 from XPSAnalysis.cxx:63:
/usr/local/root/include/root/TObject.h:127: warning: 'virtual const Option_t* TObject::GetOption() const' was hidden
XPSBase.h:208: warning:   by 'virtual const Option_t* XTreeInfo::GetOption()'
In file included from XPSData.h:47,
                 from XPSProcessing.h:46,
                 from XPSAnalysis.h:44,
                 from XPSAnalysis.cxx:63:
XPSProjectHandler.h:84: warning: unused parameter 'name'
In file included from XPSProcessing.h:46,
                 from XPSAnalysis.h:44,
                 from XPSAnalysis.cxx:63:
XPSData.h:700: warning: unused parameter 'min'
XPSData.h:700: warning: unused parameter 'max'
XPSData.h:700: warning: unused parameter 'var2sort'
XPSData.h:700: warning: unused parameter 'down'
In file included from XPSFilter.h:49,
                 from XPSAnalysis.cxx:64:
TStat.h:332: warning: unused parameter 'x'
TStat.h:333: warning: unused parameter 'x'
TStat.h:334: warning: unused parameter 'x'
TStat.h:335: warning: unused parameter 'x'
In file included from XPSAnalysis.cxx:64:
XPSFilter.h:118: warning: 'virtual Int_t XFilter::Calculate(TTree*, const char*, TTree*, const char*)' was hidden
XPSBase.h:437: warning:   by 'XAlgorithm::Calculate'
XPSFilter.h:118: warning: 'virtual Int_t XFilter::Calculate(TTree*, const char*, TTree*, const char*)' was hidden
XPSBase.h:437: warning:   by 'XAlgorithm::Calculate'
XPSFilter.h:120: warning: 'virtual Int_t XFilter::Calculate(Int_t, TTree**, const char*, TTree*, const char*)' was hidden
XPSBase.h:437: warning:   by 'XAlgorithm::Calculate'
XPSAnalysis.cxx:266: warning: unused parameter 'infile'
XPSAnalysis.cxx:444: warning: unused parameter 'type'
XPSAnalysis.cxx:964: warning: unused parameter 'ntree'
XPSAnalysis.cxx:964: warning: unused parameter 'tree'
XPSAnalysis.cxx:964: warning: unused parameter 'n'
XPSAnalysis.cxx:964: warning: unused parameter 'msk'
XPSAnalysis.cxx:1709: warning: unused parameter 'exten'
XPSAnalysis.cxx:1709: warning: unused parameter 'n'
XPSAnalysis.cxx:1709: warning: unused parameter 'names'
XPSAnalysis.cxx:1709: warning: unused parameter 'varlist'
XPSAnalysis.cxx:1709: warning: unused parameter 'output'
XPSAnalysis.cxx:1709: warning: unused parameter 'sep'
XPSAnalysis.cxx:2001: warning: unused parameter 'exten'
XPSAnalysis.cxx:2001: warning: unused parameter 'n'
XPSAnalysis.cxx:2001: warning: unused parameter 'names'
XPSAnalysis.cxx:2001: warning: unused parameter 'varlist'
XPSAnalysis.cxx:2001: warning: unused parameter 'output'
XPSAnalysis.cxx:2001: warning: unused parameter 'sep'
XPSAnalysis.cxx:2654: warning: unused parameter 'n'
XPSAnalysis.cxx:2654: warning: unused parameter 'tree'
XPSAnalysis.cxx:2791: warning: unused parameter 'leafname'
XPSAnalysis.cxx:2791: warning: unused parameter 'outtree'
XPSAnalysis.cxx:2791: warning: unused parameter 'varlist'
XPSAnalysis.cxx:2819: warning: unused parameter 'exten'
XPSAnalysis.cxx:2819: warning: unused parameter 'n'
XPSAnalysis.cxx:2819: warning: unused parameter 'names'
XPSAnalysis.cxx:2819: warning: unused parameter 'varlist'
XPSAnalysis.cxx:2819: warning: unused parameter 'output'
XPSAnalysis.cxx:2819: warning: unused parameter 'sep'
XPSAnalysis.cxx:2867: warning: unused parameter 'n'
XPSAnalysis.cxx:2867: warning: unused parameter 'names'
XPSAnalysis.cxx:2867: warning: unused parameter 'varlist'
XPSAnalysis.cxx:2867: warning: unused parameter 'output'
XPSAnalysis.cxx:2867: warning: unused parameter 'sep'
XPSAnalysis.cxx:2936: warning: unused parameter 'leafname'
XPSAnalysis.cxx:2936: warning: unused parameter 'outtree'
XPSAnalysis.cxx:2936: warning: unused parameter 'varlist'
XPSAnalysis.cxx:2964: warning: unused parameter 'exten'
XPSAnalysis.cxx:2964: warning: unused parameter 'n'
XPSAnalysis.cxx:2964: warning: unused parameter 'names'
XPSAnalysis.cxx:2964: warning: unused parameter 'varlist'
XPSAnalysis.cxx:2964: warning: unused parameter 'output'
XPSAnalysis.cxx:2964: warning: unused parameter 'sep'
XPSAnalysis.cxx:3006: warning: unused parameter 'n'
XPSAnalysis.cxx:3006: warning: unused parameter 'names'
XPSAnalysis.cxx:3006: warning: unused parameter 'varlist'
XPSAnalysis.cxx:3006: warning: unused parameter 'output'
XPSAnalysis.cxx:3006: warning: unused parameter 'sep'
XPSAnalysis.cxx:3075: warning: unused parameter 'leafname'
XPSAnalysis.cxx:3075: warning: unused parameter 'outtree'
XPSAnalysis.cxx:3075: warning: unused parameter 'varlist'
XPSAnalysis.cxx:3103: warning: unused parameter 'exten'
XPSAnalysis.cxx:3103: warning: unused parameter 'n'
XPSAnalysis.cxx:3103: warning: unused parameter 'names'
XPSAnalysis.cxx:3103: warning: unused parameter 'varlist'
XPSAnalysis.cxx:3103: warning: unused parameter 'output'
XPSAnalysis.cxx:3103: warning: unused parameter 'sep'
XPSAnalysis.cxx:3145: warning: unused parameter 'n'
XPSAnalysis.cxx:3145: warning: unused parameter 'names'
XPSAnalysis.cxx:3145: warning: unused parameter 'varlist'
XPSAnalysis.cxx:3145: warning: unused parameter 'output'
XPSAnalysis.cxx:3145: warning: unused parameter 'sep'
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m32 -I/usr/local/root/include/root -c rwrapper.cxx
In file included from rwrapper.cxx:42:
/usr/local/root/include/root/TObject.h:127: warning: 'virtual const Option_t* TObject::GetOption() const' was hidden
XPSBase.h:208: warning:   by 'virtual const Option_t* XTreeInfo::GetOption()'
In file included from XPSData.h:47,
                 from rwrapper.cxx:45:
XPSProjectHandler.h:84: warning: unused parameter 'name'
In file included from rwrapper.cxx:45:
XPSData.h:700: warning: unused parameter 'min'
XPSData.h:700: warning: unused parameter 'max'
XPSData.h:700: warning: unused parameter 'var2sort'
XPSData.h:700: warning: unused parameter 'down'
In file included from rwrapper.cxx:46:
XPSPreProcessing.h:324: warning: 'virtual Int_t XPreProcesSet::QualityControl(Int_t, TTree**, Int_t&, TTree**)' was hidden
XPSPreProcessing.h:395: warning:   by 'virtual Int_t XGCProcesSet::QualityControl(Int_t, TTree**, Int_t, TTree**, const char*)'
rwrapper.cxx:1557: warning: unused parameter 'level'
Generating dictionary xpsDict.cxx...
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m32 -I/usr/local/root/include/root -c xpsDict.cxx
In file included from xpsDict.h:35,
                 from xpsDict.cxx:17:
TStat.h:332: warning: unused parameter 'x'
TStat.h:333: warning: unused parameter 'x'
TStat.h:334: warning: unused parameter 'x'
TStat.h:335: warning: unused parameter 'x'
In file included from xpsDict.h:37,
                 from xpsDict.cxx:17:
/usr/local/root/include/root/TObject.h:127: warning: 'virtual const Option_t* TObject::GetOption() const' was hidden
XPSBase.h:208: warning:   by 'virtual const Option_t* XTreeInfo::GetOption()'
In file included from xpsDict.h:41,
                 from xpsDict.cxx:17:
XPSProjectHandler.h:84: warning: unused parameter 'name'
In file included from xpsDict.h:42,
                 from xpsDict.cxx:17:
XPSData.h:700: warning: unused parameter 'min'
XPSData.h:700: warning: unused parameter 'max'
XPSData.h:700: warning: unused parameter 'var2sort'
XPSData.h:700: warning: unused parameter 'down'
In file included from xpsDict.h:44,
                 from xpsDict.cxx:17:
XPSHybridizer.h:178: warning: unused parameter 'n'
XPSHybridizer.h:178: warning: unused parameter 'x'
XPSHybridizer.h:178: warning: unused parameter 'y'
XPSHybridizer.h:178: warning: unused parameter 'z'
XPSHybridizer.h:178: warning: unused parameter 'dx'
XPSHybridizer.h:178: warning: unused parameter 'dy'
XPSHybridizer.h:178: warning: unused parameter 'idx'
XPSHybridizer.h:178: warning: unused parameter 'nsub'
XPSHybridizer.h:178: warning: 'virtual Int_t XExpressor::Calculate(Int_t, Double_t*, Double_t*, Double_t*, Double_t*, Double_t*, Int_t*, Int_t)' was hidden
XPSBase.h:438: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:178: warning: 'virtual Int_t XExpressor::Calculate(Int_t, Double_t*, Double_t*, Double_t*, Double_t*, Double_t*, Int_t*, Int_t)' was hidden
XPSBase.h:438: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:178: warning: 'virtual Int_t XExpressor::Calculate(Int_t, Double_t*, Double_t*, Double_t*, Double_t*, Double_t*, Int_t*, Int_t)' was hidden
XPSBase.h:438: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:178: warning: 'virtual Int_t XExpressor::Calculate(Int_t, Double_t*, Double_t*, Double_t*, Double_t*, Double_t*, Int_t*, Int_t)' was hidden
XPSBase.h:437: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:178: warning: 'virtual Int_t XExpressor::Calculate(Int_t, Double_t*, Double_t*, Double_t*, Double_t*, Double_t*, Int_t*, Int_t)' was hidden
XPSBase.h:437: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:178: warning: 'virtual Int_t XExpressor::Calculate(Int_t, Double_t*, Double_t*, Double_t*, Double_t*, Double_t*, Int_t*, Int_t)' was hidden
XPSBase.h:437: warning:   by 'XAlgorithm::Calculate'
In file included from xpsDict.h:45,
                 from xpsDict.cxx:17:
XPSSelector.h:152: warning: 'virtual Int_t XProbeSelector::Calculate(Int_t, Double_t*, Double_t*, Int_t*)' was hidden
XPSSelector.h:209: warning:   by 'XUnitSelector::Calculate'
In file included from xpsDict.h:47,
                 from xpsDict.cxx:17:
XPSPreProcessing.h:324: warning: 'virtual Int_t XPreProcesSet::QualityControl(Int_t, TTree**, Int_t&, TTree**)' was hidden
XPSPreProcessing.h:395: warning:   by 'virtual Int_t XGCProcesSet::QualityControl(Int_t, TTree**, Int_t, TTree**, const char*)'
In file included from xpsDict.h:49,
                 from xpsDict.cxx:17:
XPSFilter.h:118: warning: 'virtual Int_t XFilter::Calculate(TTree*, const char*, TTree*, const char*)' was hidden
XPSBase.h:437: warning:   by 'XAlgorithm::Calculate'
XPSFilter.h:118: warning: 'virtual Int_t XFilter::Calculate(TTree*, const char*, TTree*, const char*)' was hidden
XPSBase.h:437: warning:   by 'XAlgorithm::Calculate'
XPSFilter.h:120: warning: 'virtual Int_t XFilter::Calculate(Int_t, TTree**, const char*, TTree*, const char*)' was hidden
XPSBase.h:437: warning:   by 'XAlgorithm::Calculate'
g++ -dynamiclib -single_module -undefined dynamic_lookup -install_name /Users/biocbuild/bbs-2.10-bioc/meat/xps.Rcheck/00_pkg_src/xps/src/xps.so -O2 -m32 TMLMath.o TStat.o StatUtils.o XPSBase.o XPSUtils.o XPSSchemes.o XPSDataTypes.o XPSProjectHandler.o XPSData.o XPSProcessing.o XPSHybridizer.o XPSSelector.o XPSNormalizer.o XPSPreProcessing.o XPSNormation.o XPSFilter.o XPSAnalyzer.o XPSAnalysis.o rwrapper.o xpsDict.o -L/usr/local/root/lib/root -lGui -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -lpthread -lm -ldl  -lRIO -lGed -lTreePlayer -lTreeViewer -o  xps.so
installing to /Users/biocbuild/bbs-2.10-bioc/meat/xps.Rcheck/xps/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'APTvsXPS.Rnw' 
   'xps.Rnw' 
   'xpsClasses.Rnw' 
   'xpsPreprocess.Rnw' 
** testing if installed package can be loaded

* DONE (xps)

name	user	system	elapsed
AffyRNAdeg	0.000	0.000	0.001
AnalysisTreeSet-class	0.002	0.001	0.001
CallTreeSet-class	0.001	0.000	0.001
DataTreeSet-class	0.000	0.001	0.001
ExprTreeSet-class	0.001	0.000	0.000
Filter-class	0.001	0.001	0.001
FilterTreeSet-class	0.001	0.000	0.001
PreFilter-class	0.047	0.002	0.048
PreFilter-constructor	0.043	0.002	0.045
ProcesSet-class	0.001	0.000	0.002
ProjectInfo-class	0.011	0.001	0.013
ProjectInfo-constructor	0.068	0.003	0.070
QualTreeSet-class	0.001	0.000	0.000
SchemeTreeSet-class	0.001	0.001	0.001
TreeSet-class	0.001	0.000	0.001
UniFilter-class	0.050	0.000	0.051
UniFilter-constructor	0.032	0.001	0.035
addData-methods	0.332	0.044	0.570
attachCall-methods	0.313	0.018	0.333
attachDataXY-methods	0.157	0.050	0.208
attachExpr-methods	1.417	0.103	1.527
attachInten-methods	0.296	0.065	0.362
attachMask-methods	0.132	0.052	0.184
attachProbe-methods	0.177	0.057	0.237
attachUnitNames-methods	0.085	0.003	0.088
bgcorrect	0.647	0.142	0.794
borderplot-methods	0.000	0.000	0.001
boxplot-methods	0.475	0.118	0.595
callFilter-methods	0.026	0.001	0.027
coiplot-methods	0.000	0.001	0.000
cvFilter-methods	0.013	0.000	0.013
dabg.call	1.420	0.023	1.455
dfw	0.385	0.038	0.433
diffFilter-methods	0.012	0.001	0.012
existsROOTFile	0.000	0.000	0.001
exonLevel	0.001	0.000	0.001
export	0.386	0.074	0.464
export.root	0.353	0.070	0.428
express	1.340	0.105	1.458
exprs-methods	0	0	0
extenPart	0.000	0.000	0.001
farms	0.418	0.038	0.476
fcFilter-methods	0.017	0.000	0.018
firma	0.000	0.000	0.001
firma.expr	0.000	0.000	0.001
firma.score	0.001	0.001	0.001
fitQC	0.000	0.000	0.001
fitRLM	0.000	0.000	0.001
gapFilter-methods	0.012	0.000	0.013
getChipName	0.003	0.001	0.003
getChipType	0.003	0.000	0.003
getDatatype	0	0	0
getNameType	0.003	0.000	0.003
getNumberTrees	0.003	0.001	0.003
getProbeInfo	0.002	0.000	0.002
getTreeNames	0.009	0.001	0.009
highFilter-methods	0.011	0.000	0.013
hist-methods	0.030	0.002	0.032
image-methods	0.000	0.000	0.001
import.data	0.245	0.030	0.296
import.exon.scheme	0	0	0
import.expr.scheme	0	0	0
import.genome.scheme	0.000	0.001	0.000
indexUnits-methods	0.601	0.270	0.874
ini.call	0.459	0.036	0.500
intensity-methods	0	0	0
intensity2GCplot-methods	0.329	0.111	0.497
isROOTFile	0.001	0.000	0.000
lowFilter-methods	0.012	0.000	0.012
madFilter-methods	0.012	0.000	0.012
mas4	0.640	0.055	0.764
mas5	0.984	0.079	1.076
mas5.call	0.252	0.018	0.272
mboxplot-methods	0.437	0.116	0.556
metaProbesets	0	0	0
namePart	0.000	0.000	0.001
normalize	1.428	0.102	1.556
nuseplot-methods	0.040	0.005	0.045
plotImage	0	0	0
pm-methods	0.495	0.132	0.629
pmplot-methods	0.408	0.119	0.528
prefilter	0	0	0
presCall-methods	0.000	0.001	0.001
probeContentGC-methods	0.296	0.108	0.406
probeSequence-methods	0.220	0.061	0.284
probesetID2unitID-methods	0.092	0.004	0.096
probesetplot-methods	0.337	0.066	0.406
qualify	0.001	0.000	0.001
quantileFilter-methods	0.012	0.001	0.012
ratioFilter-methods	0.011	0.000	0.011
rawCELName-methods	0.029	0.001	0.031
rleplot-methods	0.041	0.004	0.045
rma	1.374	0.093	1.482
root.call	0.209	0.021	0.234
root.data	0.177	0.016	0.197
root.density	0	0	0
root.expr	1.350	0.095	1.453
root.graph1D	0.000	0.001	0.000
root.graph2D	0	0	0
root.hist1D	0	0	0
root.hist2D	0	0	0
root.hist3D	0.001	0.000	0.000
root.image	0	0	0
root.merge.data	0.211	0.019	0.242
root.mvaplot	0.000	0.000	0.001
root.profile	0.000	0.000	0.001
root.scheme	0.028	0.001	0.029
summarize	1.378	0.094	1.496
symbol2unitID-methods	0.125	0.013	0.140
treeInfo-methods	0.039	0.003	0.043
trma	1.372	0.095	1.494
type2Exten	0.001	0.000	0.000
uniTest-methods	0.013	0.001	0.012
unifilter	0.000	0.000	0.001
unitestFilter-methods	0.013	0.001	0.014
validTreetype	0	0	0
varFilter-methods	0.013	0.001	0.013
xpsQAReport	0.000	0.000	0.001