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Package 263/264HostnameOS / ArchBUILDCHECKBUILD BIN
xps 0.99.8
Christian Stratowa
Snapshot Date: 2008-04-09 00:13:10 -0700 (Wed, 09 Apr 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xps
Last Changed Rev: 30930 / Revision: 30951
Last Changed Date: 2008-04-08 13:13:49 -0700 (Tue, 08 Apr 2008)
lamb1 Linux (SUSE 10.1) / x86_64  OK  OK 
wilson2 Linux (openSUSE 10.3) / x86_64  OK  OK 
wellington Linux (openSUSE 10.3) / i686  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.1) / i386  OK  WARNINGS  OK 
Package: xps
Version: 0.99.8
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD check xps_0.99.8.tar.gz
StartedAt: 2008-04-09 11:26:26 -0700 (Wed, 09 Apr 2008)
EndedAt: 2008-04-09 11:35:33 -0700 (Wed, 09 Apr 2008)
EllapsedTime: 546.6 seconds
RetCode: 0
Status: OK
CheckDir: xps.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.2-bioc/meat/xps.Rcheck'
* using R version 2.7.0 beta (2008-04-07 r45159)
* using session charset: ISO8859-1
* checking for file 'xps/DESCRIPTION' ... OK
* this is package 'xps' version '0.99.8'
* 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 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 name space can be loaded with stated dependencies ... 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 cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating xps-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating xps-manual.tex ... OK
* checking xps-manual.tex using pdflatex ... OK

xps.Rcheck/00install.out:

* 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 -m32 -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 -m32 -I/usr/local/include/root -c TStat.cxx
g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/local/include/root -c StatUtils.cxx
g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/local/include/root -c XPSBase.cxx
g++ -O2 -Wall -fPIC -pthread -m32 -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 -m32 -I/usr/local/include/root -c XPSSchemes.cxx
g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/local/include/root -c XPSDataTypes.cxx
g++ -O2 -Wall -fPIC -pthread -m32 -I/usr/local/include/root -c XPSProjectHandler.cxx
g++ -O2 -Wall -fPIC -pthread -m32 -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 -m32 -I/usr/local/include/root -c XPSProcessing.cxx
g++ -O2 -Wall -fPIC -pthread -m32 -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 -m32 -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 -m32 -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 -m32 -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 -m32 -I/usr/local/include/root -c XPSNormation.cxx
g++ -O2 -Wall -fPIC -pthread -m32 -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 -m32 -I/usr/local/include/root -c XPSAnalyzer.cxx
g++ -O2 -Wall -fPIC -pthread -m32 -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 -m32 -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 -m32 -I/usr/local/include/root -c xpsDict.cxx
g++ -shared -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 -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)