* checking for file 'xps/DESCRIPTION' ... OK
* preparing 'xps':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* Installing *source* package 'xps' ...
checking for gcc... gcc -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 -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for gcc... (cached) gcc -std=gnu99
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc -std=gnu99 accepts -g... (cached) yes
checking for gcc -std=gnu99 option to accept ANSI C... (cached) none needed
checking for root-config... yes
found ROOT version 5.18/00 in directory /usr/local
** libs
** arch -
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/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 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c TStat.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c StatUtils.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSBase.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSUtils.cxx
XPSUtils.cxx: In function 'char* FirstPath(const char*)':
XPSUtils.cxx:3804: warning: deprecated conversion from string constant to 'char*'
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSSchemes.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSDataTypes.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSProjectHandler.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSData.cxx
XPSData.cxx: In member function 'virtual Int_t XGeneChipHyb::ReadXMLHeader(std::ifstream&, const char*, char)':
XPSData.cxx:2442: warning: unused variable 'fNMasked'
XPSData.cxx:2452: warning: unused variable 'fNOutlier'
XPSData.cxx:2462: warning: unused variable 'fNModified'
XPSData.cxx: In member function 'virtual Int_t XGeneChipPivot::ExportCallTrees(Int_t, TString*, const char*, std::ofstream&, const char*)':
XPSData.cxx:3242: warning: deprecated conversion from string constant to 'char*'
XPSData.cxx:3243: warning: deprecated conversion from string constant to 'char*'
XPSData.cxx:3244: warning: deprecated conversion from string constant to 'char*'
XPSData.cxx:3245: warning: deprecated conversion from string constant to 'char*'
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSProcessing.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSHybridizer.cxx
XPSHybridizer.cxx: In member function 'Double_t XDetectionCall::WilcoxTest(Int_t, Double_t*, Double_t)':
XPSHybridizer.cxx:1710: warning: 'pval' may be used uninitialized in this function
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSSelector.cxx
XPSSelector.cxx: In member function 'Double_t XRankSelector::Cutoff(Int_t, const Double_t*, Double_t, Bool_t)':
XPSSelector.cxx:333: warning: 'par0' may be used uninitialized in this function
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSNormalizer.cxx
XPSNormalizer.cxx: In member function 'virtual Int_t XNormalizer::Calculate(Int_t, Double_t*, Double_t*, Int_t*)':
XPSNormalizer.cxx:221: warning: 'his2sel' may be used uninitialized in this function
XPSNormalizer.cxx:220: warning: 'his2all' may be used uninitialized in this function
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSPreProcessing.cxx
XPSPreProcessing.cxx: In member function 'virtual Int_t XGCProcesSet::ExportCallTrees(Int_t, TString*, const char*, std::ofstream&, const char*)':
XPSPreProcessing.cxx:3162: warning: deprecated conversion from string constant to 'char*'
XPSPreProcessing.cxx:3163: warning: deprecated conversion from string constant to 'char*'
XPSPreProcessing.cxx:3164: warning: deprecated conversion from string constant to 'char*'
XPSPreProcessing.cxx:3165: warning: deprecated conversion from string constant to 'char*'
XPSPreProcessing.cxx: In member function 'virtual Int_t XGCProcesSet::DoMedianPolish(Int_t, TTree**, Int_t, TTree**)':
XPSPreProcessing.cxx:4204: warning: operation on 'numsels' may be undefined
XPSPreProcessing.cxx: In member function 'virtual Int_t XGCProcesSet::DoMedianPolish(Int_t, TTree**, Int_t, TTree**, TFile*)':
XPSPreProcessing.cxx:4562: warning: operation on 'numsels' may be undefined
XPSPreProcessing.cxx: In member function 'virtual Int_t XGenomeProcesSet::DetectCall(Int_t, TTree**, Int_t&, TTree**)':
XPSPreProcessing.cxx:4908: warning: unused variable 'scmleaf'
XPSPreProcessing.cxx: In member function 'virtual Int_t XGenomeProcesSet::DoMedianPolish(Int_t, TTree**, Int_t, TTree**)':
XPSPreProcessing.cxx:5708: warning: operation on 'numsels' may be undefined
XPSPreProcessing.cxx: In member function 'virtual Int_t XGenomeProcesSet::DoMedianPolish(Int_t, TTree**, Int_t, TTree**, TFile*)':
XPSPreProcessing.cxx:6098: warning: operation on 'numsels' may be undefined
XPSPreProcessing.cxx: In member function 'virtual Int_t XGenomeProcesSet::ExportCallTrees(Int_t, TString*, const char*, std::ofstream&, const char*)':
XPSPreProcessing.cxx:6844: warning: deprecated conversion from string constant to 'char*'
XPSPreProcessing.cxx:6845: warning: deprecated conversion from string constant to 'char*'
XPSPreProcessing.cxx:6846: warning: deprecated conversion from string constant to 'char*'
XPSPreProcessing.cxx:6847: warning: deprecated conversion from string constant to 'char*'
XPSPreProcessing.cxx: In member function 'virtual Int_t XExonProcesSet::DoMedianPolish(Int_t, TTree**, Int_t, TTree**)':
XPSPreProcessing.cxx:7923: warning: operation on 'numsels' may be undefined
XPSPreProcessing.cxx: In member function 'virtual Int_t XExonProcesSet::DoMedianPolish(Int_t, TTree**, Int_t, TTree**, TFile*)':
XPSPreProcessing.cxx:8325: warning: operation on 'numsels' may be undefined
XPSPreProcessing.cxx: In member function 'virtual Int_t XExonProcesSet::ExportCallTrees(Int_t, TString*, const char*, std::ofstream&, const char*)':
XPSPreProcessing.cxx:9129: warning: deprecated conversion from string constant to 'char*'
XPSPreProcessing.cxx:9130: warning: deprecated conversion from string constant to 'char*'
XPSPreProcessing.cxx:9131: warning: deprecated conversion from string constant to 'char*'
XPSPreProcessing.cxx:9132: warning: deprecated conversion from string constant to 'char*'
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSNormation.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSFilter.cxx
XPSFilter.cxx: In member function 'virtual Int_t XUniFilter::Calculate(TTree*, const char*, TTree*, const char*, Int_t)':
XPSFilter.cxx:1800: warning: unused variable 'id'
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSAnalyzer.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSAnalysis.cxx
XPSAnalysis.cxx: In member function 'virtual Int_t XUnivarSet::ExportUnivarTrees(Int_t, TString*, const char*, std::ofstream&, const char*)':
XPSAnalysis.cxx:2174: warning: unused variable 'option'
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c rwrapper.cxx
rwrapper.cxx: In function 'void PreprocessRMA(char**, char**, char**, char**, char**, char**, char**, char**, char**, char**, int*, int*, int*, int*, char**)':
rwrapper.cxx:373: warning: deprecated conversion from string constant to 'char*'
rwrapper.cxx:381: warning: deprecated conversion from string constant to 'char*'
rwrapper.cxx:389: warning: deprecated conversion from string constant to 'char*'
rwrapper.cxx: In function 'void PreprocessMAS4(char**, char**, char**, char**, char**, char**, char**, char**, char**, int*, int*, int*, char**)':
rwrapper.cxx:493: warning: deprecated conversion from string constant to 'char*'
rwrapper.cxx: In function 'void PreprocessMAS5(char**, char**, char**, char**, char**, char**, char**, char**, char**, int*, int*, int*, char**)':
rwrapper.cxx:573: warning: deprecated conversion from string constant to 'char*'
rwrapper.cxx: In function 'void PreprocessMAS5Call(char**, char**, char**, char**, char**, char**, char**, char**, char**, int*, double*, double*, double*, int*, int*, int*, char**)':
rwrapper.cxx:654: warning: deprecated conversion from string constant to 'char*'
rwrapper.cxx: In function 'void Preprocess(char**, char**, char**, char**, char**, char**, int*, char**, char**, char**, int*, double*, char**, char**, char**, int*, double*, char**, char**, char**, int*, double*, char**, char**, double*, char**, char**, int*, int*, int*, char**)':
rwrapper.cxx:819: warning: deprecated conversion from string constant to 'char*'
rwrapper.cxx:827: warning: deprecated conversion from string constant to 'char*'
rwrapper.cxx:835: warning: deprecated conversion from string constant to 'char*'
rwrapper.cxx: In function 'void BgCorrect(char**, char**, char**, char**, char**, char**, char**, char**, int*, double*, char**, char**, int*, int*, int*, int*, char**)':
rwrapper.cxx:984: warning: deprecated conversion from string constant to 'char*'
rwrapper.cxx: In function 'void Normalize(char**, char**, char**, char**, char**, char**, char**, char**, int*, double*, int*, char**, char**, int*, char**, char**, int*, int*, char**)':
rwrapper.cxx:1106: warning: deprecated conversion from string constant to 'char*'
rwrapper.cxx: In function 'void Summarize(char**, char**, char**, char**, char**, char**, char**, char**, char**, int*, double*, int*, char**, char**, int*, int*, int*, char**)':
rwrapper.cxx:1194: warning: deprecated conversion from string constant to 'char*'
rwrapper.cxx: In function 'void Normxpress(char**, char**, char**, char**, char**, char**, double*, char**, char**, int*, double*, int*, char**, char**, int*, char**, char**, int*, int*, char**)':
rwrapper.cxx:1289: warning: deprecated conversion from string constant to 'char*'
rwrapper.cxx: In function 'void ChipNameType(char**, char**)':
rwrapper.cxx:1566: warning: deprecated conversion from string constant to 'char*'
rwrapper.cxx:1574: warning: deprecated conversion from string constant to 'char*'
rwrapper.cxx: In function 'void GetTreeNames4Exten(char**, char**, int*, char**)':
rwrapper.cxx:1823: warning: deprecated conversion from string constant to 'char*'
Generating dictionary xpsDict.cxx...
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c xpsDict.cxx
g++ -shared -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 -o xps.so -L/usr/local/lib/root -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lGui -pthread -lm -ldl -rdynamic
** R
** inst
** preparing package for lazy loading
** help
Note: removing empty section \examples
>>> Building/Updating help pages for package 'xps'
Formats: text html latex example
AnalysisTreeSet-class text html latex example
CallTreeSet-class text html latex example
DataTreeSet-class text html latex example
ExprTreeSet-class text html latex example
Filter-class text html latex example
FilterTreeSet-class text html latex example
PreFilter-class text html latex example
PreFilter-constructor text html latex example
ProcesSet-class text html latex example
ProjectInfo-class text html latex example
ProjectInfo-constructor text html latex example
ROOT text html latex
SchemeTreeSet-class text html latex example
TreeSet-class text html latex example
UniFilter-class text html latex example
UniFilter-constructor text html latex example
addData-methods text html latex example
attachBgrd-methods text html latex
attachInten-methods text html latex example
attachMask-methods text html latex example
bgcorrect text html latex example
boxplot-methods text html latex example
boxplot.dev text html latex
callFilter-methods text html latex example
callplot-methods text html latex
cvFilter-methods text html latex example
dabg.call text html latex example
diffFilter-methods text html latex example
existsROOTFile text html latex example
export text html latex example
export.filter text html latex
export.root text html latex example
express text html latex example
fcFilter-methods text html latex example
gapFilter-methods text html latex example
getChipName text html latex example
getChipType text html latex example
getDatatype text html latex example
getNameType text html latex example
getNumberTrees text html latex example
getProbeInfo text html latex example
getTreeData-methods text html latex
getTreeNames text html latex example
highFilter-methods text html latex example
hist-methods text html latex example
image-methods text html latex
image.dev text html latex example
import.data text html latex example
import.exon.scheme text html latex example
import.expr.scheme text html latex example
import.genome.scheme text html latex example
initialize-methods text html latex
isROOTFile text html latex example
lowFilter-methods text html latex example
madFilter-methods text html latex example
mas4 text html latex example
mas5 text html latex example
mas5.call text html latex example
mboxplot-methods text html latex example
mvaplot-methods text html latex
mvaplot.dev text html latex
normalize text html latex example
pm-methods text html latex example
pmplot-methods text html latex example
prefilter text html latex example
quantileFilter-methods text html latex example
ratioFilter-methods text html latex example
rawCELName-methods text html latex example
rma text html latex example
root.browser-methods text html latex
root.data text html latex example
root.density text html latex example
root.graph1D text html latex example
root.graph2D text html latex example
root.hist1D text html latex example
root.hist2D text html latex example
root.hist3D text html latex example
root.image text html latex example
root.mvaplot text html latex example
root.scheme text html latex example
summarize text html latex example
type2Exten text html latex example
uniTest-methods text html latex example
unifilter text html latex example
unitestFilter-methods text html latex example
validData-methods text html latex
validTreetype text html latex example
varFilter-methods text html latex example
volcanoplot-methods text html latex
xps-package text html latex
xpsOptions text html latex
** building package indices ...
* DONE (xps)
* creating vignettes ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'xps_0.99.8.tar.gz'