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Package 293/294HostnameOS / ArchBUILDCHECKBUILD BIN
xps 1.2.10
Christian Stratowa
Bioconductor Changelog
Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/xps
Last Changed Rev: 38744 / Revision: 38965
Last Changed Date: 2009-04-12 10:22:40 -0700 (Sun, 12 Apr 2009)
wilson2 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  WARNINGS  ERROR 
pelham Mac OS X Leopard (10.5.6) / i386  OK  WARNINGS [ OK ]
Package: xps
Version: 1.2.10
Command: /Users/biocbuild/BBS/utils/build-universal.sh xps_1.2.10.tar.gz /Library/Frameworks/R.framework/Versions/2.8/Resources/bin/R xps.buildbin-libdir
StartedAt: 2009-04-18 19:02:10 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 19:05:39 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 208.4 seconds
RetCode: 0
Status: OK
PackageFile: xps_1.2.10.tgz
PackageFileSize: 7.349 MiB

Command output

                INSTALLATION WITH 'R CMD INSTALL --library=xps.buildbin-libdir xps_1.2.10.tar.gz'

* Installing *source* package 'xps' ...
checking for gcc... gcc-4.2 -arch i386 -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc-4.2 -arch i386 -std=gnu99 accepts -g... yes
checking for gcc-4.2 -arch i386 -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc-4.2 -arch i386 -std=gnu99 -E
checking for gcc... (cached) gcc-4.2 -arch i386 -std=gnu99
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc-4.2 -arch i386 -std=gnu99 accepts -g... (cached) yes
checking for gcc-4.2 -arch i386 -std=gnu99 option to accept ANSI C... (cached) none needed
checking for root-config... yes
found ROOT version 5.22/00 in directory /usr/local
** libs
** arch - i386
Generating dictionary xpsDict.cxx...
c++ -O2 -pipe -Wall -W -Woverloaded-virtual -D_REENTRANT -pthread -I/usr/local/include/root -c xpsDict.cxx
In file included from xpsDict.h:40,
                 from xpsDict.cxx:16:
XPSProjectHandler.h:84: warning: unused parameter 'name'
In file included from xpsDict.h:41,
                 from xpsDict.cxx:16:
XPSData.h:677: warning: unused parameter 'min'
XPSData.h:677: warning: unused parameter 'max'
XPSData.h:677: warning: unused parameter 'var2sort'
XPSData.h:677: warning: unused parameter 'down'
In file included from xpsDict.h:46,
                 from xpsDict.cxx:16:
XPSProcessing.h:282: warning: 'virtual const char* XProcesSet::GetTranscriptID(XTransAnnotation*)' was hidden
XPSPreProcessing.h:371: warning:   by 'virtual const char* XExonProcesSet::GetTranscriptID(XUnit*, XTransAnnotation*, Int_t)'
In file included from xpsDict.h:47,
                 from xpsDict.cxx:16:
XPSProcessing.h:282: warning: 'virtual const char* XProcesSet::GetTranscriptID(XTransAnnotation*)' was hidden
XPSNormation.h:215: warning:   by 'virtual const char* XNormedExonSet::GetTranscriptID(XUnit*, XTransAnnotation*, Int_t)'
In file included from xpsDict.h:48,
                 from xpsDict.cxx:16:
XPSFilter.h:118: warning: 'virtual Int_t XFilter::Calculate(TTree*, const char*, TTree*, const char*)' was hidden
XPSBase.h:427: warning:   by 'XAlgorithm::Calculate'
XPSFilter.h:118: warning: 'virtual Int_t XFilter::Calculate(TTree*, const char*, TTree*, const char*)' was hidden
XPSBase.h:427: 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:427: warning:   by 'XAlgorithm::Calculate'
MACOSX_DEPLOYMENT_TARGET=10.5 c++ -dynamiclib -single_module -undefined dynamic_lookup 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/lib/root -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -lfreetype -lGui -pthread -lm -ldl  -lRIO -lGed -lTreePlayer -lTreeViewer -o  xps.dylib 
ln -sf xps.dylib xps.so
** 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
  UniFilter-constructor             text    html    latex   example
  addData-methods                   text    html    latex   example
  attachBgrd-methods                text    html    latex
  attachCall-methods                text    html    latex   example
  attachExpr-methods                text    html    latex   example
  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
  dfw                               text    html    latex   example
  diffFilter-methods                text    html    latex   example
  existsROOTFile                    text    html    latex   example
  exonLevel                         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
  exprs-methods                     text    html    latex   example
  farms                             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
  ini.call                          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
  metaProbesets                     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
  presCall-methods                  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.call                         text    html    latex   example
  root.data                         text    html    latex   example
  root.density                      text    html    latex   example
  root.expr                         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.profile                      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)

                INSTALLATION OF ppc LIBS WITH 'R_ARCH=/ppc R CMD INSTALL --library=xps.buildbin-libdir --libs-only xps_1.2.10.tar.gz'

* Installing *source* package 'xps' ...
checking for gcc... gcc-4.2 -arch ppc -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-4.2 -arch ppc -std=gnu99 accepts -g... yes
checking for gcc-4.2 -arch ppc -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc-4.2 -arch ppc -std=gnu99 -E
checking for gcc... (cached) gcc-4.2 -arch ppc -std=gnu99
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc-4.2 -arch ppc -std=gnu99 accepts -g... (cached) yes
checking for gcc-4.2 -arch ppc -std=gnu99 option to accept ANSI C... (cached) none needed
checking for root-config... yes
found ROOT version 5.22/00 in directory /usr/local
** libs
** arch - ppc
Generating dictionary xpsDict.cxx...
c++ -O2 -pipe -Wall -W -Woverloaded-virtual -D_REENTRANT -pthread -I/usr/local/include/root -c xpsDict.cxx
In file included from xpsDict.h:40,
                 from xpsDict.cxx:16:
XPSProjectHandler.h:84: warning: unused parameter 'name'
In file included from xpsDict.h:41,
                 from xpsDict.cxx:16:
XPSData.h:677: warning: unused parameter 'min'
XPSData.h:677: warning: unused parameter 'max'
XPSData.h:677: warning: unused parameter 'var2sort'
XPSData.h:677: warning: unused parameter 'down'
In file included from xpsDict.h:46,
                 from xpsDict.cxx:16:
XPSProcessing.h:282: warning: 'virtual const char* XProcesSet::GetTranscriptID(XTransAnnotation*)' was hidden
XPSPreProcessing.h:371: warning:   by 'virtual const char* XExonProcesSet::GetTranscriptID(XUnit*, XTransAnnotation*, Int_t)'
In file included from xpsDict.h:47,
                 from xpsDict.cxx:16:
XPSProcessing.h:282: warning: 'virtual const char* XProcesSet::GetTranscriptID(XTransAnnotation*)' was hidden
XPSNormation.h:215: warning:   by 'virtual const char* XNormedExonSet::GetTranscriptID(XUnit*, XTransAnnotation*, Int_t)'
In file included from xpsDict.h:48,
                 from xpsDict.cxx:16:
XPSFilter.h:118: warning: 'virtual Int_t XFilter::Calculate(TTree*, const char*, TTree*, const char*)' was hidden
XPSBase.h:427: warning:   by 'XAlgorithm::Calculate'
XPSFilter.h:118: warning: 'virtual Int_t XFilter::Calculate(TTree*, const char*, TTree*, const char*)' was hidden
XPSBase.h:427: 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:427: warning:   by 'XAlgorithm::Calculate'
MACOSX_DEPLOYMENT_TARGET=10.5 c++ -dynamiclib -single_module -undefined dynamic_lookup 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/lib/root -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -lfreetype -lGui -pthread -lm -ldl  -lRIO -lGed -lTreePlayer -lTreeViewer -o  xps.dylib 
ln -sf xps.dylib xps.so
* DONE (xps)

                INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --library=xps.buildbin-libdir --libs-only xps_1.2.10.tar.gz'

* Installing *source* package 'xps' ...
checking for gcc... 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 gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes
checking for gcc-4.2 -arch x86_64 -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc-4.2 -arch x86_64 -std=gnu99 -E
checking for gcc... (cached) gcc-4.2 -arch x86_64 -std=gnu99
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... (cached) yes
checking for gcc-4.2 -arch x86_64 -std=gnu99 option to accept ANSI C... (cached) none needed
checking for root-config... yes
found ROOT version 5.22/00 in directory /usr/local
** libs
** arch - x86_64
make: Nothing to be done for `all'.
* DONE (xps)