BioC 2.8: CHECK report for xps on petty

Package: xps

Version: 1.11.3

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch xps_1.11.3.tar.gz

StartedAt: 2011-03-17 17:46:55 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 17:50:46 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 231.7 seconds

RetCode: 0

Status: OK

CheckDir: xps.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/xps.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* 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 '1.11.3'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'xps' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 14.8Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    libs   5.2Mb
* 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... OK
* 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 examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* 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
found ROOT version 5.27/04 in directory /usr/local/root
** libs
** arch - i386
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -D_REENTRANT -pthread -m32 -I/usr/local/root/include -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 -D_REENTRANT -pthread -m32 -I/usr/local/root/include -c TStat.cxx
In file included from TStat.cxx:53:
TStat.h:327: warning: unused parameter 'x'
TStat.h:328: warning: unused parameter 'x'
TStat.h:329: warning: unused parameter 'x'
TStat.h:330: warning: unused parameter 'x'
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -D_REENTRANT -pthread -m32 -I/usr/local/root/include -c StatUtils.cxx
In file included from StatUtils.cxx:58:
TStat.h:327: warning: unused parameter 'x'
TStat.h:328: warning: unused parameter 'x'
TStat.h:329: warning: unused parameter 'x'
TStat.h:330: 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 -D_REENTRANT -pthread -m32 -I/usr/local/root/include -c XPSBase.cxx
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -D_REENTRANT -pthread -m32 -I/usr/local/root/include -c XPSUtils.cxx
In file included from XPSUtils.cxx:79:
TStat.h:327: warning: unused parameter 'x'
TStat.h:328: warning: unused parameter 'x'
TStat.h:329: warning: unused parameter 'x'
TStat.h:330: warning: unused parameter 'x'
XPSUtils.cxx:1324: warning: unused parameter 'canvasname'
XPSUtils.cxx:1324: warning: unused parameter 'treename'
XPSUtils.cxx:1324: warning: unused parameter 'varexp'
XPSUtils.cxx:1324: warning: unused parameter 'selection'
XPSUtils.cxx:1324: warning: unused parameter 'opt'
XPSUtils.cxx:1713: warning: unused parameter 'min'
XPSUtils.cxx:1713: warning: unused parameter 'max'
XPSUtils.cxx:2108: warning: unused parameter 'n'
XPSUtils.cxx:2108: warning: unused parameter 'x'
XPSUtils.cxx:2108: warning: unused parameter 'y'
XPSUtils.cxx:2108: warning: unused parameter 'z'
XPSUtils.cxx:2108: warning: unused parameter 'opt'
XPSUtils.cxx:2616: warning: unused parameter 'index'
XPSUtils.cxx:3069: warning: unused parameter 'n'
XPSUtils.cxx:3069: warning: unused parameter 'colors'
XPSUtils.cxx:3069: warning: unused parameter 'priority'
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -D_REENTRANT -pthread -m32 -I/usr/local/root/include -c XPSSchemes.cxx
XPSSchemes.cxx:10004: warning: unused parameter 'index'
XPSSchemes.cxx:10015: warning: unused parameter 'index'
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -D_REENTRANT -pthread -m32 -I/usr/local/root/include -c XPSDataTypes.cxx
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -D_REENTRANT -pthread -m32 -I/usr/local/root/include -c XPSProjectHandler.cxx
In file included from XPSProjectHandler.cxx:47:
XPSProjectHandler.h:84: warning: unused parameter 'name'
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -D_REENTRANT -pthread -m32 -I/usr/local/root/include -c XPSData.cxx
In file included from XPSData.h:47,
                 from XPSData.cxx:79:
XPSProjectHandler.h:84: warning: unused parameter 'name'
In file included from XPSData.cxx:79:
XPSData.h:678: warning: unused parameter 'min'
XPSData.h:678: warning: unused parameter 'max'
XPSData.h:678: warning: unused parameter 'var2sort'
XPSData.h:678: warning: unused parameter 'down'
XPSData.cxx:498: warning: unused parameter 'name'
XPSData.cxx: In member function 'virtual Int_t XGeneChipHyb::ReadData(std::ifstream&, const Option_t*, const char*, char, Int_t)':
XPSData.cxx:1763: warning: label 'cleanup' defined but not used
XPSData.cxx: In member function 'virtual Int_t XGeneChipHyb::ReadXDAData(std::ifstream&, const Option_t*, const char*, char, Int_t)':
XPSData.cxx:1954: warning: label 'cleanup' defined but not used
XPSData.cxx: In member function 'virtual Int_t XGeneChipHyb::ReadXMLHeader(std::ifstream&, const char*, char)':
XPSData.cxx:2476: warning: unused variable 'fNMasked'
XPSData.cxx:2486: warning: unused variable 'fNOutlier'
XPSData.cxx:2496: warning: unused variable 'fNModified'
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -D_REENTRANT -pthread -m32 -I/usr/local/root/include -c XPSProcessing.cxx
In file included from XPSData.h:47,
                 from XPSProcessing.h:46,
                 from XPSProcessing.cxx:68:
XPSProjectHandler.h:84: warning: unused parameter 'name'
In file included from XPSProcessing.h:46,
                 from XPSProcessing.cxx:68:
XPSData.h:678: warning: unused parameter 'min'
XPSData.h:678: warning: unused parameter 'max'
XPSData.h:678: warning: unused parameter 'var2sort'
XPSData.h:678: warning: unused parameter 'down'
XPSProcessing.cxx:745: warning: unused parameter 'name'
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -D_REENTRANT -pthread -m32 -I/usr/local/root/include -c XPSHybridizer.cxx
In file included from XPSHybridizer.cxx:63:
TStat.h:327: warning: unused parameter 'x'
TStat.h:328: warning: unused parameter 'x'
TStat.h:329: warning: unused parameter 'x'
TStat.h:330: warning: unused parameter 'x'
In file included from XPSData.h:47,
                 from XPSProcessing.h:46,
                 from XPSHybridizer.h:42,
                 from XPSHybridizer.cxx:64:
XPSProjectHandler.h:84: warning: unused parameter 'name'
In file included from XPSProcessing.h:46,
                 from XPSHybridizer.h:42,
                 from XPSHybridizer.cxx:64:
XPSData.h:678: warning: unused parameter 'min'
XPSData.h:678: warning: unused parameter 'max'
XPSData.h:678: warning: unused parameter 'var2sort'
XPSData.h:678: warning: unused parameter 'down'
In file included from XPSHybridizer.cxx:64:
XPSHybridizer.h:176: warning: unused parameter 'n'
XPSHybridizer.h:176: warning: unused parameter 'x'
XPSHybridizer.h:176: warning: unused parameter 'y'
XPSHybridizer.h:176: warning: unused parameter 'z'
XPSHybridizer.h:176: warning: unused parameter 'dx'
XPSHybridizer.h:176: warning: unused parameter 'dy'
XPSHybridizer.h:176: warning: unused parameter 'idx'
XPSHybridizer.h:176: warning: unused parameter 'nsub'
XPSHybridizer.h:176: 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:435: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:176: 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:435: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:176: 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:435: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:176: 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:434: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:176: 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:434: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:176: 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:434: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.cxx:1672: warning: unused parameter 'num'
XPSHybridizer.cxx:1785: warning: unused parameter 'num'
XPSHybridizer.cxx:1968: warning: unused parameter 'value1'
XPSHybridizer.cxx:1968: warning: unused parameter 'value2'
XPSHybridizer.cxx:1968: warning: unused parameter 'num'
XPSHybridizer.cxx:2092: warning: unused parameter 'num'
XPSHybridizer.cxx:2352: warning: unused parameter 'msk'
XPSHybridizer.cxx:2396: warning: unused parameter 'x'
XPSHybridizer.cxx:2396: warning: unused parameter 'scale'
XPSHybridizer.cxx:2584: warning: unused parameter 'x'
XPSHybridizer.cxx:2584: warning: unused parameter 'scale'
XPSHybridizer.cxx:3631: warning: unused parameter 'msk'
XPSHybridizer.cxx:3691: warning: unused parameter 'msk'
XPSHybridizer.cxx:4264: warning: unused parameter 'msk'
XPSHybridizer.cxx: In member function 'Double_t XDetectionCall::WilcoxTest(Int_t, Double_t*, Double_t)':
XPSHybridizer.cxx:1866: warning: 'pval' may be used uninitialized in this function
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -D_REENTRANT -pthread -m32 -I/usr/local/root/include -c XPSSelector.cxx
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:678: warning: unused parameter 'min'
XPSData.h:678: warning: unused parameter 'max'
XPSData.h:678: warning: unused parameter 'var2sort'
XPSData.h:678: 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 -D_REENTRANT -pthread -m32 -I/usr/local/root/include -c XPSNormalizer.cxx
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:678: warning: unused parameter 'min'
XPSData.h:678: warning: unused parameter 'max'
XPSData.h:678: warning: unused parameter 'var2sort'
XPSData.h:678: warning: unused parameter 'down'
In file included from XPSNormalizer.cxx:64:
TStat.h:327: warning: unused parameter 'x'
TStat.h:328: warning: unused parameter 'x'
TStat.h:329: warning: unused parameter 'x'
TStat.h:330: 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 -D_REENTRANT -pthread -m32 -I/usr/local/root/include -c XPSPreProcessing.cxx
In file included from XPSData.h:47,
                 from XPSProcessing.h:46,
                 from XPSPreProcessing.h:42,
                 from XPSPreProcessing.cxx:90:
XPSProjectHandler.h:84: warning: unused parameter 'name'
In file included from XPSProcessing.h:46,
                 from XPSPreProcessing.h:42,
                 from XPSPreProcessing.cxx:90:
XPSData.h:678: warning: unused parameter 'min'
XPSData.h:678: warning: unused parameter 'max'
XPSData.h:678: warning: unused parameter 'var2sort'
XPSData.h:678: warning: unused parameter 'down'
In file included from XPSPreProcessing.cxx:91:
XPSHybridizer.h:176: warning: unused parameter 'n'
XPSHybridizer.h:176: warning: unused parameter 'x'
XPSHybridizer.h:176: warning: unused parameter 'y'
XPSHybridizer.h:176: warning: unused parameter 'z'
XPSHybridizer.h:176: warning: unused parameter 'dx'
XPSHybridizer.h:176: warning: unused parameter 'dy'
XPSHybridizer.h:176: warning: unused parameter 'idx'
XPSHybridizer.h:176: warning: unused parameter 'nsub'
XPSHybridizer.h:176: 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:435: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:176: 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:435: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:176: 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:435: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:176: 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:434: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:176: 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:434: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:176: 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:434: warning:   by 'XAlgorithm::Calculate'
In file included from XPSPreProcessing.cxx:92:
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:94:
TStat.h:327: warning: unused parameter 'x'
TStat.h:328: warning: unused parameter 'x'
TStat.h:329: warning: unused parameter 'x'
TStat.h:330: warning: unused parameter 'x'
XPSPreProcessing.cxx: In member function 'virtual Int_t XGCProcesSet::DoMultichipCall(Int_t, TTree**, Int_t&, TTree**, TFile*)':
XPSPreProcessing.cxx:2653: 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:3535: warning: operation on 'numsels' may be undefined
XPSPreProcessing.cxx: At global scope:
XPSPreProcessing.cxx:4869: warning: unused parameter 'bgrd'
XPSPreProcessing.cxx:4869: warning: unused parameter 'bgdev'
XPSPreProcessing.cxx:4923: warning: unused parameter 'algorithm'
XPSPreProcessing.cxx:4943: warning: unused parameter 'algorithm'
XPSPreProcessing.cxx:5331: warning: unused parameter 'nrow'
XPSPreProcessing.cxx: In member function 'virtual Int_t XExonProcesSet::DoSpliceExpress(Int_t, TTree**, Int_t, TTree**, TFile*)':
XPSPreProcessing.cxx:6186: warning: operation on 'numsels' may be undefined
XPSPreProcessing.cxx:6377: warning: unused variable 'numatoms'
XPSPreProcessing.cxx:5989: warning: unused variable 'x'
XPSPreProcessing.cxx:5990: warning: unused variable 'y'
XPSPreProcessing.cxx:5995: warning: unused variable 'stepout'
XPSPreProcessing.cxx: In member function 'virtual TTree* XExonProcesSet::SchemeTree(XAlgorithm*, void*, TLeaf**)':
XPSPreProcessing.cxx:6940: warning: unused variable 'scheme_ptr_ptr'
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -D_REENTRANT -pthread -m32 -I/usr/local/root/include -c XPSNormation.cxx
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:678: warning: unused parameter 'min'
XPSData.h:678: warning: unused parameter 'max'
XPSData.h:678: warning: unused parameter 'var2sort'
XPSData.h:678: 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:327: warning: unused parameter 'x'
TStat.h:328: warning: unused parameter 'x'
TStat.h:329: warning: unused parameter 'x'
TStat.h:330: warning: unused parameter 'x'
XPSNormation.cxx:182: warning: unused parameter 'infile'
XPSNormation.cxx:988: warning: unused parameter 'method'
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -D_REENTRANT -pthread -m32 -I/usr/local/root/include -c XPSFilter.cxx
In file included from XPSFilter.h:49,
                 from XPSFilter.cxx:44:
TStat.h:327: warning: unused parameter 'x'
TStat.h:328: warning: unused parameter 'x'
TStat.h:329: warning: unused parameter 'x'
TStat.h:330: warning: unused parameter 'x'
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:678: warning: unused parameter 'min'
XPSData.h:678: warning: unused parameter 'max'
XPSData.h:678: warning: unused parameter 'var2sort'
XPSData.h:678: 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:434: warning:   by 'XAlgorithm::Calculate'
XPSFilter.h:118: warning: 'virtual Int_t XFilter::Calculate(TTree*, const char*, TTree*, const char*)' was hidden
XPSBase.h:434: 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:434: 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 -D_REENTRANT -pthread -m32 -I/usr/local/root/include -c XPSAnalyzer.cxx
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:678: warning: unused parameter 'min'
XPSData.h:678: warning: unused parameter 'max'
XPSData.h:678: warning: unused parameter 'var2sort'
XPSData.h:678: 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 -D_REENTRANT -pthread -m32 -I/usr/local/root/include -c XPSAnalysis.cxx
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:678: warning: unused parameter 'min'
XPSData.h:678: warning: unused parameter 'max'
XPSData.h:678: warning: unused parameter 'var2sort'
XPSData.h:678: warning: unused parameter 'down'
In file included from XPSFilter.h:49,
                 from XPSAnalysis.cxx:64:
TStat.h:327: warning: unused parameter 'x'
TStat.h:328: warning: unused parameter 'x'
TStat.h:329: warning: unused parameter 'x'
TStat.h:330: 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:434: warning:   by 'XAlgorithm::Calculate'
XPSFilter.h:118: warning: 'virtual Int_t XFilter::Calculate(TTree*, const char*, TTree*, const char*)' was hidden
XPSBase.h:434: 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:434: 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 -D_REENTRANT -pthread -m32 -I/usr/local/root/include -c rwrapper.cxx
In file included from XPSData.h:47,
                 from rwrapper.cxx:29:
XPSProjectHandler.h:84: warning: unused parameter 'name'
In file included from rwrapper.cxx:29:
XPSData.h:678: warning: unused parameter 'min'
XPSData.h:678: warning: unused parameter 'max'
XPSData.h:678: warning: unused parameter 'var2sort'
XPSData.h:678: warning: unused parameter 'down'
rwrapper.cxx:1541: warning: unused parameter 'level'
Generating dictionary xpsDict.cxx...
g++ -O2 -pipe -Wall -W -Woverloaded-virtual -D_REENTRANT -pthread -m32 -I/usr/local/root/include -c xpsDict.cxx
In file included from xpsDict.h:35,
                 from xpsDict.cxx:16:
TStat.h:327: warning: unused parameter 'x'
TStat.h:328: warning: unused parameter 'x'
TStat.h:329: warning: unused parameter 'x'
TStat.h:330: warning: unused parameter 'x'
In file included from xpsDict.h:41,
                 from xpsDict.cxx:16:
XPSProjectHandler.h:84: warning: unused parameter 'name'
In file included from xpsDict.h:42,
                 from xpsDict.cxx:16:
XPSData.h:678: warning: unused parameter 'min'
XPSData.h:678: warning: unused parameter 'max'
XPSData.h:678: warning: unused parameter 'var2sort'
XPSData.h:678: warning: unused parameter 'down'
In file included from xpsDict.h:44,
                 from xpsDict.cxx:16:
XPSHybridizer.h:176: warning: unused parameter 'n'
XPSHybridizer.h:176: warning: unused parameter 'x'
XPSHybridizer.h:176: warning: unused parameter 'y'
XPSHybridizer.h:176: warning: unused parameter 'z'
XPSHybridizer.h:176: warning: unused parameter 'dx'
XPSHybridizer.h:176: warning: unused parameter 'dy'
XPSHybridizer.h:176: warning: unused parameter 'idx'
XPSHybridizer.h:176: warning: unused parameter 'nsub'
XPSHybridizer.h:176: 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:435: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:176: 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:435: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:176: 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:435: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:176: 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:434: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:176: 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:434: warning:   by 'XAlgorithm::Calculate'
XPSHybridizer.h:176: 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:434: warning:   by 'XAlgorithm::Calculate'
In file included from xpsDict.h:45,
                 from xpsDict.cxx:16:
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:49,
                 from xpsDict.cxx:16:
XPSFilter.h:118: warning: 'virtual Int_t XFilter::Calculate(TTree*, const char*, TTree*, const char*)' was hidden
XPSBase.h:434: warning:   by 'XAlgorithm::Calculate'
XPSFilter.h:118: warning: 'virtual Int_t XFilter::Calculate(TTree*, const char*, TTree*, const char*)' was hidden
XPSBase.h:434: 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:434: warning:   by 'XAlgorithm::Calculate'
g++ -dynamiclib -single_module -undefined dynamic_lookup -install_name /Users/biocbuild/bbs-2.8-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 -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -lz -lGui -pthread -Wl,-rpath,/usr/local/root/lib -lm -ldl  -lRIO -lGed -lTreePlayer -lTreeViewer -o  xps.so
installing to /Users/biocbuild/bbs-2.8-bioc/meat/xps.Rcheck/xps/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

Welcome to xps version 1.11.3 
    an R wrapper for XPS - eXpression Profiling System
    (c) Copyright 2001-2010 by Christian Stratowa
    

* DONE (xps)

name	user	system	elapsed
AnalysisTreeSet-class	0.001	0.000	0.002
CallTreeSet-class	0.001	0.000	0.001
DataTreeSet-class	0.000	0.000	0.002
ExprTreeSet-class	0.001	0.000	0.001
Filter-class	0	0	0
FilterTreeSet-class	0.001	0.000	0.001
PreFilter-class	0.068	0.002	0.070
PreFilter-constructor	0.041	0.002	0.042
ProcesSet-class	0.001	0.001	0.002
ProjectInfo-class	0.013	0.000	0.013
ProjectInfo-constructor	0.063	0.002	0.065
SchemeTreeSet-class	0.000	0.000	0.001
TreeSet-class	0.001	0.001	0.001
UniFilter-class	0.020	0.001	0.022
UniFilter-constructor	0.033	0.001	0.034
addData-methods	0.526	0.020	0.585
attachCall-methods	0.391	0.011	0.404
attachExpr-methods	1.509	0.019	1.535
attachInten-methods	0.397	0.057	0.455
attachMask-methods	0.164	0.045	0.211
bgcorrect	0.815	0.105	0.927
boxplot-methods	0.589	0.101	0.753
callFilter-methods	0.026	0.001	0.028
cvFilter-methods	0.012	0.001	0.012
dabg.call	1.548	0.014	2.110
dfw	0.482	0.012	0.501
diffFilter-methods	0.012	0.000	0.013
existsROOTFile	0.001	0.000	0.000
exonLevel	0.001	0.000	0.001
export	0.560	0.068	0.781
export.root	0.501	0.059	0.595
express	1.485	0.018	1.525
exprs-methods	0.001	0.000	0.000
extenPart	0.001	0.000	0.001
farms	0.528	0.011	0.718
fcFilter-methods	0.015	0.000	0.016
firma	0	0	0
firma.expr	0.001	0.000	0.001
firma.score	0.001	0.000	0.000
gapFilter-methods	0.015	0.001	0.017
getChipName	0.004	0.000	0.004
getChipType	0.003	0.001	0.004
getDatatype	0	0	0
getNameType	0.003	0.001	0.004
getNumberTrees	0.004	0.000	0.004
getProbeInfo	0.002	0.001	0.002
getTreeNames	0.011	0.001	0.012
highFilter-methods	0.012	0.001	0.013
hist-methods	0.538	0.103	0.744
image.dev	0.526	0.103	1.192
import.data	0.213	0.009	0.226
import.exon.scheme	0.001	0.001	0.001
import.expr.scheme	0	0	0
import.genome.scheme	0.000	0.000	0.001
ini.call	0.559	0.011	0.575
intensity-methods	0	0	0
isROOTFile	0.000	0.000	0.001
lowFilter-methods	0.011	0.001	0.012
madFilter-methods	0.011	0.000	0.011
mas4	0.707	0.014	0.892
mas5	0.767	0.018	0.793
mas5.call	0.296	0.008	0.454
mboxplot-methods	0.534	0.100	0.637
metaProbesets	0.000	0.001	0.001
namePart	0	0	0
normalize	1.495	0.022	1.527
nuseplot-methods	0.049	0.003	0.052
pm-methods	0.571	0.098	0.818
pmplot-methods	0.523	0.098	0.625
prefilter	0.000	0.000	0.001
presCall-methods	0	0	0
quantileFilter-methods	0.011	0.000	0.012
ratioFilter-methods	0.010	0.001	0.011
rawCELName-methods	0.033	0.001	0.034
rleplot-methods	0.050	0.002	0.053
rma	1.468	0.016	1.491
root.call	0.311	0.011	0.326
root.data	0.160	0.005	0.168
root.density	0	0	0
root.expr	1.458	0.017	1.596
root.graph1D	0	0	0
root.graph2D	0	0	0
root.hist1D	0.000	0.001	0.001
root.hist2D	0	0	0
root.hist3D	0.001	0.000	0.000
root.image	0.001	0.000	0.001
root.merge.data	0.210	0.009	0.221
root.mvaplot	0	0	0
root.profile	0	0	0
root.scheme	0.026	0.001	0.027
summarize	1.499	0.021	1.691
trma	1.479	0.018	1.503
type2Exten	0.000	0.000	0.001
uniTest-methods	0.012	0.001	0.013
unifilter	0	0	0
unitestFilter-methods	0.014	0.001	0.014
validTreetype	0.000	0.001	0.001
varFilter-methods	0.011	0.000	0.012

Summary

Command output