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Package 259/260HostnameOS / ArchBUILDCHECKBUILD BIN
xps 1.0.2
Christian Stratowa
Snapshot Date: 2008-10-16 00:10:09 -0700 (Thu, 16 Oct 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_2/madman/Rpacks/xps
Last Changed Rev: 32964 / Revision: 34573
Last Changed Date: 2008-07-29 14:50:16 -0700 (Tue, 29 Jul 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 
pitt Mac OS X Tiger (10.4.11) / i386  OK  WARNINGS  OK 
Package: xps
Version: 1.0.2
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD check xps_1.0.2.tar.gz
StartedAt: 2008-10-16 06:27:10 -0700 (Thu, 16 Oct 2008)
EndedAt: 2008-10-16 06:29:55 -0700 (Thu, 16 Oct 2008)
EllapsedTime: 165.7 seconds
RetCode: 0
Status: OK
CheckDir: xps.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/home/biocbuild/bbs-2.2-bioc/meat/xps.Rcheck'
* using R version 2.7.2 (2008-08-25)
* using session charset: ISO8859-1
* checking for file 'xps/DESCRIPTION' ... OK
* this is package 'xps' version '1.0.2'
* 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 5.17/05 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
TMLMath.cxx: In static member function 'static Double_t TMLMath::PBetaRaw(Double_t, Double_t, Double_t, Int_t)':
TMLMath.cxx:1397: warning: converting to 'Int_t' from 'Double_t'
TMLMath.cxx:1403: warning: converting to 'Int_t' from 'Double_t'
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
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'
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:230: warning: 'his2all' may be used uninitialized in this function
XPSNormalizer.cxx:231: warning: 'his2sel' 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::DoMedianPolish(Int_t, TTree**, Int_t, TTree**)':
XPSPreProcessing.cxx:4200: 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:4557: 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:4877: warning: unused variable 'scmleaf'
XPSPreProcessing.cxx: In member function 'virtual Int_t XGenomeProcesSet::DoMedianPolish(Int_t, TTree**, Int_t, TTree**)':
XPSPreProcessing.cxx:5697: 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:6086: warning: operation on 'numsels' may be undefined
XPSPreProcessing.cxx: In member function 'virtual Int_t XExonProcesSet::DoMedianPolish(Int_t, TTree**, Int_t, TTree**)':
XPSPreProcessing.cxx:7358: 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:7759: warning: operation on 'numsels' may be undefined
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
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
 >>> 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
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  existsROOTFile                    text    html    latex   example
  export                            text    html    latex   example
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  export.root                       text    html    latex   example
  express                           text    html    latex   example
  fcFilter-methods                  text    html    latex   example
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  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
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  hist-methods                      text    html    latex   example
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  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
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  mas4                              text    html    latex   example
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  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
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  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
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  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)