BioC 3.2: CHECK report for xps on perceval

Package: xps

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings xps_1.30.0.tar.gz

StartedAt: 2015-11-10 10:41:03 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 10:44:18 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 195.0 seconds

RetCode: 0

Status:  OK

CheckDir: xps.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings xps_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/xps.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘xps/DESCRIPTION’ ... OK
* this is package ‘xps’ version ‘1.30.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘xps’ can be installed ... [94s/101s] OK
* checking installed package size ... NOTE
  installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   5.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking 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 GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* 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-3.2-bioc/meat/xps.Rcheck/xps/libs/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 entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/21s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/xps.Rcheck/00check.log’
for details.

* installing *source* package ‘xps’ ...
checking for gcc... llvm-gcc-4.2 -arch x86_64 -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 llvm-gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes
checking for llvm-gcc-4.2 -arch x86_64 -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... llvm-gcc-4.2 -arch x86_64 -std=gnu99 -E
checking for gcc... (cached) llvm-gcc-4.2 -arch x86_64 -std=gnu99
checking whether we are using the GNU C compiler... (cached) yes
checking whether llvm-gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... (cached) yes
checking for llvm-gcc-4.2 -arch x86_64 -std=gnu99 option to accept ANSI C... (cached) none needed
checking for root-config... yes
found ROOT version 5.34/05 in directory /usr/local/root
** libs
** arch - 
g++ -I/include -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m64 -I/usr/local/root/include -c TMLMath.cxx
TMLMath.cxx:1111:1: warning: "xmax" redefined
TMLMath.cxx:1062:1: warning: this is the location of the previous definition
g++ -I/include -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m64 -I/usr/local/root/include -c TStat.cxx
In file included from TStat.cxx:55:
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++ -I/include -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m64 -I/usr/local/root/include -c StatUtils.cxx
In file included from StatUtils.cxx:60:
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:242: warning: unused parameter ‘df’
StatUtils.cxx:266: warning: unused parameter ‘df’
g++ -I/include -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m64 -I/usr/local/root/include -c XPSBase.cxx
In file included from XPSBase.cxx:103:
/usr/local/root/include/TObject.h:127: warning: ‘virtual const Option_t* TObject::GetOption() const’ was hidden
XPSBase.h:208: warning:   by ‘virtual const Option_t* XTreeInfo::GetOption()’
g++ -I/include -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m64 -I/usr/local/root/include -c XPSUtils.cxx
In file included from XPSUtils.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’
XPSUtils.cxx:1335: warning: unused parameter ‘canvasname’
XPSUtils.cxx:1335: warning: unused parameter ‘treename’
XPSUtils.cxx:1335: warning: unused parameter ‘varexp’
XPSUtils.cxx:1335: warning: unused parameter ‘selection’
XPSUtils.cxx:1335: warning: unused parameter ‘opt’
XPSUtils.cxx:1724: warning: unused parameter ‘min’
XPSUtils.cxx:1724: warning: unused parameter ‘max’
XPSUtils.cxx:2119: warning: unused parameter ‘n’
XPSUtils.cxx:2119: warning: unused parameter ‘x’
XPSUtils.cxx:2119: warning: unused parameter ‘y’
XPSUtils.cxx:2119: warning: unused parameter ‘z’
XPSUtils.cxx:2119: warning: unused parameter ‘opt’
XPSUtils.cxx:2627: warning: unused parameter ‘index’
XPSUtils.cxx:3080: warning: unused parameter ‘n’
XPSUtils.cxx:3080: warning: unused parameter ‘colors’
XPSUtils.cxx:3080: warning: unused parameter ‘priority’
g++ -I/include -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m64 -I/usr/local/root/include -c XPSSchemes.cxx
In file included from XPSSchemes.h:41,
                 from XPSSchemes.cxx:74:
/usr/local/root/include/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:10096: warning: unused parameter ‘index’
XPSSchemes.cxx:10107: warning: unused parameter ‘index’
g++ -I/include -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m64 -I/usr/local/root/include -c XPSDataTypes.cxx
g++ -I/include -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m64 -I/usr/local/root/include -c XPSProjectHandler.cxx
In file included from XPSProjectHandler.cxx:49:
XPSProjectHandler.h:84: warning: unused parameter ‘name’
g++ -I/include -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m64 -I/usr/local/root/include -c XPSData.cxx
In file included from XPSSchemes.h:41,
                 from XPSData.h:43,
                 from XPSData.cxx:82:
/usr/local/root/include/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:82:
XPSProjectHandler.h:84: warning: unused parameter ‘name’
In file included from XPSData.cxx:82:
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:84:
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:506: 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:1799: warning: unused variable ‘err’
XPSData.cxx: At global scope:
XPSData.cxx:1794: warning: unused parameter ‘n’
XPSData.cxx:1794: warning: unused parameter ‘names’
XPSData.cxx:1794: warning: unused parameter ‘varlist’
XPSData.cxx:1794: warning: unused parameter ‘output’
XPSData.cxx:1794: warning: unused parameter ‘sep’
XPSData.cxx: In member function ‘virtual Int_t XGeneChipHyb::ReadXMLHeader(std::ifstream&, const char*, char)’:
XPSData.cxx:2812: warning: unused variable ‘fNMasked’
XPSData.cxx:2822: warning: unused variable ‘fNOutlier’
XPSData.cxx:2832: warning: unused variable ‘fNModified’
g++ -I/include -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m64 -I/usr/local/root/include -c XPSProcessing.cxx
In file included from XPSSchemes.h:41,
                 from XPSProcessing.h:42,
                 from XPSProcessing.cxx:71:
/usr/local/root/include/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:71:
XPSProjectHandler.h:84: warning: unused parameter ‘name’
In file included from XPSProcessing.h:46,
                 from XPSProcessing.cxx:71:
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: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’
XPSProcessing.cxx:788: 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:1532: warning: unused variable ‘err’
XPSProcessing.cxx: At global scope:
XPSProcessing.cxx:1527: warning: unused parameter ‘n’
XPSProcessing.cxx:1527: warning: unused parameter ‘names’
XPSProcessing.cxx:1527: warning: unused parameter ‘varlist’
XPSProcessing.cxx:1527: warning: unused parameter ‘output’
XPSProcessing.cxx:1527: warning: unused parameter ‘sep’
g++ -I/include -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m64 -I/usr/local/root/include -c XPSHybridizer.cxx
In file included from XPSHybridizer.cxx:66:
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:67:
/usr/local/root/include/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:67:
XPSProjectHandler.h:84: warning: unused parameter ‘name’
In file included from XPSProcessing.h:46,
                 from XPSHybridizer.h:42,
                 from XPSHybridizer.cxx:67:
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:67:
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:750: warning: unused parameter ‘msk’
XPSHybridizer.cxx:1874: warning: unused parameter ‘num’
XPSHybridizer.cxx:1987: warning: unused parameter ‘num’
XPSHybridizer.cxx:2170: warning: unused parameter ‘value1’
XPSHybridizer.cxx:2170: warning: unused parameter ‘value2’
XPSHybridizer.cxx:2170: warning: unused parameter ‘num’
XPSHybridizer.cxx:2294: warning: unused parameter ‘num’
XPSHybridizer.cxx:2554: warning: unused parameter ‘msk’
XPSHybridizer.cxx:2598: warning: unused parameter ‘x’
XPSHybridizer.cxx:2598: warning: unused parameter ‘scale’
XPSHybridizer.cxx:2786: warning: unused parameter ‘x’
XPSHybridizer.cxx:2786: warning: unused parameter ‘scale’
XPSHybridizer.cxx:3833: warning: unused parameter ‘msk’
XPSHybridizer.cxx:3893: warning: unused parameter ‘msk’
XPSHybridizer.cxx:4466: warning: unused parameter ‘msk’
g++ -I/include -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m64 -I/usr/local/root/include -c XPSSelector.cxx
In file included from XPSSchemes.h:41,
                 from XPSProcessing.h:42,
                 from XPSSelector.h:42,
                 from XPSSelector.cxx:54:
/usr/local/root/include/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:54:
XPSProjectHandler.h:84: warning: unused parameter ‘name’
In file included from XPSProcessing.h:46,
                 from XPSSelector.h:42,
                 from XPSSelector.cxx:54:
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:54:
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:318: warning: unused parameter ‘max’
XPSSelector.cxx:318: warning: unused parameter ‘showGraph’
g++ -I/include -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m64 -I/usr/local/root/include -c XPSNormalizer.cxx
In file included from XPSSchemes.h:41,
                 from XPSProcessing.h:42,
                 from XPSNormalizer.h:42,
                 from XPSNormalizer.cxx:65:
/usr/local/root/include/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:65:
XPSProjectHandler.h:84: warning: unused parameter ‘name’
In file included from XPSProcessing.h:46,
                 from XPSNormalizer.h:42,
                 from XPSNormalizer.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 XPSNormalizer.cxx:66:
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:536: warning: unused parameter ‘xout’
XPSNormalizer.cxx:613: warning: unused parameter ‘xout’
XPSNormalizer.cxx:692: warning: unused parameter ‘xout’
XPSNormalizer.cxx:1132: warning: unused parameter ‘n’
XPSNormalizer.cxx:1163: warning: unused parameter ‘n’
XPSNormalizer.cxx:1300: warning: unused parameter ‘x’
XPSNormalizer.cxx:1300: warning: unused parameter ‘msk’
g++ -I/include -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m64 -I/usr/local/root/include -c XPSPreProcessing.cxx
In file included from XPSSchemes.h:41,
                 from XPSProcessing.h:42,
                 from XPSPreProcessing.h:42,
                 from XPSPreProcessing.cxx:95:
/usr/local/root/include/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:95:
XPSProjectHandler.h:84: warning: unused parameter ‘name’
In file included from XPSProcessing.h:46,
                 from XPSPreProcessing.h:42,
                 from XPSPreProcessing.cxx:95:
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:95:
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:96:
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:97:
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:99:
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::DoBorderElements(Int_t, TTree**, TTree**, XDNAChip*, TFile*)’:
XPSPreProcessing.cxx:3524: warning: unused variable ‘idxhi’
XPSPreProcessing.cxx:3524: warning: unused variable ‘idxlo’
XPSPreProcessing.cxx: At global scope:
XPSPreProcessing.cxx:3511: warning: unused parameter ‘file’
XPSPreProcessing.cxx: In member function ‘virtual Int_t XGCProcesSet::DoBgrdQualityControl(Int_t, TTree**, XDNAChip*, TFile*)’:
XPSPreProcessing.cxx:3679: warning: unused variable ‘numunits’
XPSPreProcessing.cxx:3680: warning: unused variable ‘size’
XPSPreProcessing.cxx: At global scope:
XPSPreProcessing.cxx:3670: warning: unused parameter ‘numbgrd’
XPSPreProcessing.cxx:3670: warning: unused parameter ‘bgrdtree’
XPSPreProcessing.cxx:3670: warning: unused parameter ‘file’
XPSPreProcessing.cxx: In member function ‘virtual Int_t XGCProcesSet::ExportQualTrees(Int_t, TString*, const char*, std::ofstream&, const char*)’:
XPSPreProcessing.cxx:6771: warning: unused variable ‘idxstr’
XPSPreProcessing.cxx: At global scope:
XPSPreProcessing.cxx:7990: warning: unused parameter ‘bgrd’
XPSPreProcessing.cxx:7990: warning: unused parameter ‘bgdev’
XPSPreProcessing.cxx:8086: warning: unused parameter ‘algorithm’
XPSPreProcessing.cxx:8106: warning: unused parameter ‘algorithm’
XPSPreProcessing.cxx:8608: 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:8746: 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:9791: warning: unused variable ‘numatoms’
XPSPreProcessing.cxx:9398: warning: unused variable ‘x’
XPSPreProcessing.cxx:9399: warning: unused variable ‘y’
XPSPreProcessing.cxx:9404: warning: unused variable ‘stepout’
XPSPreProcessing.cxx: In member function ‘virtual TTree* XExonProcesSet::SchemeTree(XAlgorithm*, void*, TLeaf**)’:
XPSPreProcessing.cxx:10358: warning: unused variable ‘scheme_ptr_ptr’
g++ -I/include -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m64 -I/usr/local/root/include -c XPSNormation.cxx
In file included from XPSSchemes.h:41,
                 from XPSProcessing.h:42,
                 from XPSNormation.h:42,
                 from XPSNormation.cxx:72:
/usr/local/root/include/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:72:
XPSProjectHandler.h:84: warning: unused parameter ‘name’
In file included from XPSProcessing.h:46,
                 from XPSNormation.h:42,
                 from XPSNormation.cxx:72:
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:73:
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:75:
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:184: warning: unused parameter ‘infile’
XPSNormation.cxx:1021: warning: unused parameter ‘method’
g++ -I/include -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m64 -I/usr/local/root/include -c XPSFilter.cxx
In file included from XPSFilter.h:49,
                 from XPSFilter.cxx:46:
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:46:
/usr/local/root/include/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:46:
XPSProjectHandler.h:84: warning: unused parameter ‘name’
In file included from XPSProcessing.h:46,
                 from XPSFilter.h:52,
                 from XPSFilter.cxx:46:
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:46:
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:623: warning: unused parameter ‘sepo’
XPSFilter.cxx:1353: warning: unused parameter ‘table’
XPSFilter.cxx:1632: warning: unused parameter ‘infile’
XPSFilter.cxx:1632: warning: unused parameter ‘outfile’
XPSFilter.cxx:1632: warning: unused parameter ‘varlist’
XPSFilter.cxx:1632: warning: unused parameter ‘nrows’
XPSFilter.cxx:1632: warning: unused parameter ‘sepi’
XPSFilter.cxx:1632: warning: unused parameter ‘sepo’
XPSFilter.cxx:1632: warning: unused parameter ‘delim’
XPSFilter.cxx: In member function ‘virtual Int_t XUniFilter::Calculate(TTree*, const char*, TTree*, const char*, Int_t)’:
XPSFilter.cxx:1789: warning: unused variable ‘brchUnit’
XPSFilter.cxx: At global scope:
XPSFilter.cxx:1659: warning: unused parameter ‘leafname’
XPSFilter.cxx:1841: warning: unused parameter ‘outtree’
g++ -I/include -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m64 -I/usr/local/root/include -c XPSAnalyzer.cxx
In file included from XPSSchemes.h:41,
                 from XPSProcessing.h:42,
                 from XPSAnalyzer.h:45,
                 from XPSAnalyzer.cxx:44:
/usr/local/root/include/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:44:
XPSProjectHandler.h:84: warning: unused parameter ‘name’
In file included from XPSProcessing.h:46,
                 from XPSAnalyzer.h:45,
                 from XPSAnalyzer.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’
XPSAnalyzer.cxx:215: warning: unused parameter ‘type’
XPSAnalyzer.cxx:215: warning: unused parameter ‘options’
XPSAnalyzer.cxx:215: warning: unused parameter ‘npars’
XPSAnalyzer.cxx:215: warning: unused parameter ‘pars’
XPSAnalyzer.cxx:229: warning: unused parameter ‘infile’
XPSAnalyzer.cxx:229: warning: unused parameter ‘outfile’
XPSAnalyzer.cxx:229: warning: unused parameter ‘varlist’
XPSAnalyzer.cxx:229: warning: unused parameter ‘nrows’
XPSAnalyzer.cxx:229: warning: unused parameter ‘nperm’
XPSAnalyzer.cxx:229: warning: unused parameter ‘mu’
XPSAnalyzer.cxx:229: warning: unused parameter ‘sepi’
XPSAnalyzer.cxx:229: warning: unused parameter ‘sepo’
XPSAnalyzer.cxx:229: warning: unused parameter ‘delim’
XPSAnalyzer.cxx:229: warning: unused parameter ‘linebuf’
XPSAnalyzer.cxx:241: warning: unused parameter ‘n’
XPSAnalyzer.cxx:241: warning: unused parameter ‘gid’
XPSAnalyzer.cxx:241: warning: unused parameter ‘intree’
XPSAnalyzer.cxx:241: warning: unused parameter ‘leafname’
XPSAnalyzer.cxx:241: warning: unused parameter ‘outtree’
XPSAnalyzer.cxx:241: warning: unused parameter ‘varlist’
XPSAnalyzer.cxx:241: warning: unused parameter ‘nperm’
XPSAnalyzer.cxx:241: warning: unused parameter ‘mu’
XPSAnalyzer.cxx:290: warning: unused parameter ‘type’
XPSAnalyzer.cxx:290: warning: unused parameter ‘options’
XPSAnalyzer.cxx:290: warning: unused parameter ‘npars’
XPSAnalyzer.cxx:290: warning: unused parameter ‘pars’
XPSAnalyzer.cxx:304: warning: unused parameter ‘infile’
XPSAnalyzer.cxx:304: warning: unused parameter ‘outfile’
XPSAnalyzer.cxx:304: warning: unused parameter ‘varlist’
XPSAnalyzer.cxx:304: warning: unused parameter ‘nrows’
XPSAnalyzer.cxx:304: warning: unused parameter ‘nperm’
XPSAnalyzer.cxx:304: warning: unused parameter ‘mu’
XPSAnalyzer.cxx:304: warning: unused parameter ‘sepi’
XPSAnalyzer.cxx:304: warning: unused parameter ‘sepo’
XPSAnalyzer.cxx:304: warning: unused parameter ‘delim’
XPSAnalyzer.cxx:304: warning: unused parameter ‘linebuf’
XPSAnalyzer.cxx:316: warning: unused parameter ‘n’
XPSAnalyzer.cxx:316: warning: unused parameter ‘gid’
XPSAnalyzer.cxx:316: warning: unused parameter ‘intree’
XPSAnalyzer.cxx:316: warning: unused parameter ‘leafname’
XPSAnalyzer.cxx:316: warning: unused parameter ‘outtree’
XPSAnalyzer.cxx:316: warning: unused parameter ‘varlist’
XPSAnalyzer.cxx:316: warning: unused parameter ‘nperm’
XPSAnalyzer.cxx:316: warning: unused parameter ‘mu’
XPSAnalyzer.cxx:365: warning: unused parameter ‘type’
XPSAnalyzer.cxx:365: warning: unused parameter ‘options’
XPSAnalyzer.cxx:365: warning: unused parameter ‘npars’
XPSAnalyzer.cxx:365: warning: unused parameter ‘pars’
XPSAnalyzer.cxx:379: warning: unused parameter ‘infile’
XPSAnalyzer.cxx:379: warning: unused parameter ‘outfile’
XPSAnalyzer.cxx:379: warning: unused parameter ‘varlist’
XPSAnalyzer.cxx:379: warning: unused parameter ‘nrows’
XPSAnalyzer.cxx:379: warning: unused parameter ‘nperm’
XPSAnalyzer.cxx:379: warning: unused parameter ‘mu’
XPSAnalyzer.cxx:379: warning: unused parameter ‘sepi’
XPSAnalyzer.cxx:379: warning: unused parameter ‘sepo’
XPSAnalyzer.cxx:379: warning: unused parameter ‘delim’
XPSAnalyzer.cxx:379: warning: unused parameter ‘linebuf’
XPSAnalyzer.cxx:391: warning: unused parameter ‘n’
XPSAnalyzer.cxx:391: warning: unused parameter ‘gid’
XPSAnalyzer.cxx:391: warning: unused parameter ‘intree’
XPSAnalyzer.cxx:391: warning: unused parameter ‘leafname’
XPSAnalyzer.cxx:391: warning: unused parameter ‘outtree’
XPSAnalyzer.cxx:391: warning: unused parameter ‘varlist’
XPSAnalyzer.cxx:391: warning: unused parameter ‘nperm’
XPSAnalyzer.cxx:391: warning: unused parameter ‘mu’
g++ -I/include -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m64 -I/usr/local/root/include -c XPSAnalysis.cxx
In file included from XPSSchemes.h:41,
                 from XPSAnalysis.h:41,
                 from XPSAnalysis.cxx:65:
/usr/local/root/include/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:65:
XPSProjectHandler.h:84: warning: unused parameter ‘name’
In file included from XPSProcessing.h:46,
                 from XPSAnalysis.h:44,
                 from XPSAnalysis.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 XPSFilter.h:49,
                 from XPSAnalysis.cxx:66:
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:66:
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:268: warning: unused parameter ‘infile’
XPSAnalysis.cxx:446: warning: unused parameter ‘type’
XPSAnalysis.cxx:966: warning: unused parameter ‘ntree’
XPSAnalysis.cxx:966: warning: unused parameter ‘tree’
XPSAnalysis.cxx:966: warning: unused parameter ‘n’
XPSAnalysis.cxx:966: warning: unused parameter ‘msk’
XPSAnalysis.cxx:1711: warning: unused parameter ‘exten’
XPSAnalysis.cxx:1711: warning: unused parameter ‘n’
XPSAnalysis.cxx:1711: warning: unused parameter ‘names’
XPSAnalysis.cxx:1711: warning: unused parameter ‘varlist’
XPSAnalysis.cxx:1711: warning: unused parameter ‘output’
XPSAnalysis.cxx:1711: warning: unused parameter ‘sep’
XPSAnalysis.cxx:2003: warning: unused parameter ‘exten’
XPSAnalysis.cxx:2003: warning: unused parameter ‘n’
XPSAnalysis.cxx:2003: warning: unused parameter ‘names’
XPSAnalysis.cxx:2003: warning: unused parameter ‘varlist’
XPSAnalysis.cxx:2003: warning: unused parameter ‘output’
XPSAnalysis.cxx:2003: warning: unused parameter ‘sep’
XPSAnalysis.cxx:2656: warning: unused parameter ‘n’
XPSAnalysis.cxx:2656: warning: unused parameter ‘tree’
XPSAnalysis.cxx:2793: warning: unused parameter ‘leafname’
XPSAnalysis.cxx:2793: warning: unused parameter ‘outtree’
XPSAnalysis.cxx:2793: warning: unused parameter ‘varlist’
XPSAnalysis.cxx:2821: warning: unused parameter ‘exten’
XPSAnalysis.cxx:2821: warning: unused parameter ‘n’
XPSAnalysis.cxx:2821: warning: unused parameter ‘names’
XPSAnalysis.cxx:2821: warning: unused parameter ‘varlist’
XPSAnalysis.cxx:2821: warning: unused parameter ‘output’
XPSAnalysis.cxx:2821: warning: unused parameter ‘sep’
XPSAnalysis.cxx:2869: warning: unused parameter ‘n’
XPSAnalysis.cxx:2869: warning: unused parameter ‘names’
XPSAnalysis.cxx:2869: warning: unused parameter ‘varlist’
XPSAnalysis.cxx:2869: warning: unused parameter ‘output’
XPSAnalysis.cxx:2869: warning: unused parameter ‘sep’
XPSAnalysis.cxx:2938: warning: unused parameter ‘leafname’
XPSAnalysis.cxx:2938: warning: unused parameter ‘outtree’
XPSAnalysis.cxx:2938: warning: unused parameter ‘varlist’
XPSAnalysis.cxx:2966: warning: unused parameter ‘exten’
XPSAnalysis.cxx:2966: warning: unused parameter ‘n’
XPSAnalysis.cxx:2966: warning: unused parameter ‘names’
XPSAnalysis.cxx:2966: warning: unused parameter ‘varlist’
XPSAnalysis.cxx:2966: warning: unused parameter ‘output’
XPSAnalysis.cxx:2966: warning: unused parameter ‘sep’
XPSAnalysis.cxx:3008: warning: unused parameter ‘n’
XPSAnalysis.cxx:3008: warning: unused parameter ‘names’
XPSAnalysis.cxx:3008: warning: unused parameter ‘varlist’
XPSAnalysis.cxx:3008: warning: unused parameter ‘output’
XPSAnalysis.cxx:3008: warning: unused parameter ‘sep’
XPSAnalysis.cxx:3077: warning: unused parameter ‘leafname’
XPSAnalysis.cxx:3077: warning: unused parameter ‘outtree’
XPSAnalysis.cxx:3077: warning: unused parameter ‘varlist’
XPSAnalysis.cxx:3105: warning: unused parameter ‘exten’
XPSAnalysis.cxx:3105: warning: unused parameter ‘n’
XPSAnalysis.cxx:3105: warning: unused parameter ‘names’
XPSAnalysis.cxx:3105: warning: unused parameter ‘varlist’
XPSAnalysis.cxx:3105: warning: unused parameter ‘output’
XPSAnalysis.cxx:3105: warning: unused parameter ‘sep’
XPSAnalysis.cxx:3147: warning: unused parameter ‘n’
XPSAnalysis.cxx:3147: warning: unused parameter ‘names’
XPSAnalysis.cxx:3147: warning: unused parameter ‘varlist’
XPSAnalysis.cxx:3147: warning: unused parameter ‘output’
XPSAnalysis.cxx:3147: warning: unused parameter ‘sep’
g++ -I/include -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m64 -I/usr/local/root/include -c rwrapper.cxx
In file included from rwrapper.cxx:44:
/usr/local/root/include/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:47:
XPSProjectHandler.h:84: warning: unused parameter ‘name’
In file included from rwrapper.cxx:47:
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:48:
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:1559: warning: unused parameter ‘level’
Generating dictionary xpsDict.cxx...
g++ -I/include -O2 -pipe -Wall -W -Woverloaded-virtual -pthread -m64 -I/usr/local/root/include -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/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-3.2-bioc/meat/xps.Rcheck/00_pkg_src/xps/src/xps.so -O2 -m64 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 -lGui -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -lpthread -Wl,-rpath,/usr/local/root/lib -lm -ldl  -lRIO -lGed -lTreePlayer -lTreeViewer -o  xps.so
installing to /Users/biocbuild/bbs-3.2-bioc/meat/xps.Rcheck/xps/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (xps)

name	user	system	elapsed
AffyRNAdeg	0.001	0.000	0.001
AnalysisTreeSet-class	0.002	0.000	0.002
CallTreeSet-class	0.001	0.000	0.002
DataTreeSet-class	0.002	0.000	0.003
ExprTreeSet-class	0.002	0.001	0.002
Filter-class	0.001	0.000	0.001
FilterTreeSet-class	0.002	0.001	0.002
NUSE	0.001	0.000	0.001
PreFilter-class	0.086	0.002	0.087
PreFilter-constructor	0.038	0.005	0.042
ProcesSet-class	0.001	0.001	0.002
ProjectInfo-class	0.011	0.001	0.012
ProjectInfo-constructor	0.056	0.002	0.058
QualTreeSet-class	0.002	0.000	0.002
RLE	0.001	0.000	0.001
SchemeTreeSet-class	0.002	0.000	0.002
TreeSet-class	0.002	0.000	0.001
UniFilter-class	0.016	0.000	0.016
UniFilter-constructor	0.029	0.001	0.030
addData-methods	0.266	0.021	0.396
attachCall-methods	0.318	0.011	0.332
attachDataXY-methods	0.159	0.038	0.198
attachExpr-methods	1.071	0.017	1.111
attachInten-methods	0.266	0.052	0.319
attachMask-methods	0.119	0.038	0.157
attachProbe-methods	0.153	0.042	0.197
attachUnitNames-methods	0.115	0.002	0.117
bgcorrect	0.508	0.097	0.623
borderplot-methods	0.001	0.000	0.000
boxplot-methods	0.417	0.088	0.506
callFilter-methods	0.023	0.001	0.024
coiplot-methods	0.001	0.000	0.001
cvFilter-methods	0.010	0.001	0.012
dabg.call	1.266	0.008	1.277
dfw	0.291	0.008	0.312
diffFilter-methods	0.012	0.000	0.013
existsROOTFile	0.001	0.000	0.001
exonLevel	0.001	0.000	0.002
export	0.336	0.059	0.400
export.root	0.307	0.054	0.365
express	0.977	0.014	1.013
exprs-methods	0.001	0.000	0.001
extenPart	0.001	0.000	0.001
farms	0.314	0.009	0.331
fcFilter-methods	0.013	0.000	0.013
firma	0.002	0.000	0.002
firma.expr	0.001	0.000	0.001
firma.score	0.001	0.000	0.001
fitQC	0.001	0.000	0.002
fitRLM	0.001	0.001	0.001
gapFilter-methods	0.015	0.001	0.015
getChipName	0.003	0.000	0.004
getChipType	0.003	0.001	0.004
getDatatype	0.001	0.000	0.001
getNameType	0.004	0.000	0.003
getNumberTrees	0.003	0.000	0.004
getProbeInfo	0.002	0.000	0.002
getTreeNames	0.009	0.001	0.009
highFilter-methods	0.011	0.000	0.012
hist-methods	0.023	0.001	0.023
image-methods	0.001	0.000	0.001
import.data	0.188	0.007	0.208
import.exon.scheme	0.002	0.000	0.002
import.expr.scheme	0.001	0.000	0.002
import.genome.scheme	0.001	0.000	0.001
indexUnits-methods	0.518	0.191	0.711
ini.call	0.380	0.011	0.398
intensity-methods	0.001	0.001	0.002
intensity2GCplot-methods	0.307	0.079	0.388
isROOTFile	0.001	0.001	0.001
lowFilter-methods	0.011	0.000	0.011
madFilter-methods	0.01	0.00	0.01
mas4	0.479	0.013	0.514
mas5	0.539	0.013	0.575
mas5.call	0.200	0.007	0.216
mboxplot-methods	0.367	0.088	0.457
metaProbesets	0.001	0.000	0.001
namePart	0.001	0.000	0.001
normalize	1.011	0.016	1.056
nuseplot-methods	0.034	0.002	0.037
plotImage	0.002	0.000	0.002
pm-methods	0.469	0.096	0.569
pmplot-methods	0.379	0.092	0.473
prefilter	0.001	0.000	0.001
presCall-methods	0.001	0.000	0.001
probeContentGC-methods	0.266	0.078	0.347
probeSequence-methods	0.208	0.044	0.254
probesetID2unitID-methods	0.122	0.004	0.127
probesetplot-methods	0.319	0.052	0.373
qualify	0.002	0.001	0.002
quantileFilter-methods	0.01	0.00	0.01
ratioFilter-methods	0.009	0.000	0.010
rawCELName-methods	0.023	0.001	0.024
rleplot-methods	0.032	0.002	0.034
rma	1.022	0.014	1.063
root.call	0.181	0.011	0.200
root.data	0.146	0.007	0.155
root.density	0.001	0.000	0.001
root.expr	1.035	0.016	1.059
root.graph1D	0.000	0.000	0.001
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	0.001	0.001
root.merge.data	0.166	0.006	0.176
root.mvaplot	0.000	0.001	0.001
root.profile	0.001	0.000	0.001
root.scheme	0.024	0.001	0.025
summarize	1.007	0.016	1.049
symbol2unitID-methods	0.150	0.012	0.164
treeInfo-methods	0.036	0.003	0.039
trma	1.013	0.013	1.034
type2Exten	0.001	0.000	0.001
uniTest-methods	0.011	0.001	0.012
unifilter	0.001	0.000	0.001
unitestFilter-methods	0.013	0.001	0.013
validTreetype	0.001	0.000	0.001
varFilter-methods	0.011	0.001	0.011
xpsQAReport	0.001	0.000	0.001