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Package 34/319HostnameOS / ArchBUILDCHECKBUILD BIN
beadarray 1.12.1
Mark Dunning
Bioconductor Changelog
Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/beadarray
Last Changed Rev: 42135 / Revision: 42512
Last Changed Date: 2009-10-02 09:48:47 -0700 (Fri, 02 Oct 2009)
wilson1 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  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386 [ OK ] OK  OK 
Package: beadarray
Version: 1.12.1
Command: /Library/Frameworks/R.framework/Versions/2.9/Resources/bin/R CMD build beadarray
StartedAt: 2009-10-20 15:37:58 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 15:38:25 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 26.8 seconds
RetCode: 0
Status: OK
PackageFile: beadarray_1.12.1.tar.gz
PackageFileSize: 9.737 MiB

Command output

* checking for file 'beadarray/DESCRIPTION' ... OK
* preparing 'beadarray':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* Installing *source* package ‘beadarray’ ...
** libs
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -c BASH.c -o BASH.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -c BLImagePlot.c -o BLImagePlot.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -c HULK.c -o HULK.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -c createBeadSummaryData.c -o createBeadSummaryData.o
createBeadSummaryData.c: In function ‘findAllOutliers’:
createBeadSummaryData.c:223: warning: ‘status’ may be used uninitialized in this function
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -c findProbeIndices.c -o findProbeIndices.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -c readBeadImages.c -o readBeadImages.o
readBeadImages.c: In function ‘getPixelIntensities’:
readBeadImages.c:368: warning: unused variable ‘result’
readBeadImages.c: In function ‘readBeadImage’:
readBeadImages.c:578: warning: ‘offset’ may be used uninitialized in this function
readBeadImages.c:578: warning: ‘records’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘StripOffset’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘ImageHeight’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘ImageWidth’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘BeginData’ may be used uninitialized in this function
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o beadarray.so BASH.o BLImagePlot.o HULK.o createBeadSummaryData.o findProbeIndices.o readBeadImages.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c BASH.c -o BASH.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c BLImagePlot.c -o BLImagePlot.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c HULK.c -o HULK.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c createBeadSummaryData.c -o createBeadSummaryData.o
createBeadSummaryData.c: In function ‘findAllOutliers’:
createBeadSummaryData.c:223: warning: ‘status’ may be used uninitialized in this function
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c findProbeIndices.c -o findProbeIndices.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c readBeadImages.c -o readBeadImages.o
readBeadImages.c: In function ‘getPixelIntensities’:
readBeadImages.c:368: warning: unused variable ‘result’
readBeadImages.c: In function ‘readBeadImage’:
readBeadImages.c:578: warning: ‘offset’ may be used uninitialized in this function
readBeadImages.c:578: warning: ‘records’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘StripOffset’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘ImageHeight’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘ImageWidth’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘BeginData’ may be used uninitialized in this function
gcc-4.2 -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o beadarray.so BASH.o BLImagePlot.o HULK.o createBeadSummaryData.o findProbeIndices.o readBeadImages.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc64
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c BASH.c -o BASH.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c BLImagePlot.c -o BLImagePlot.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c HULK.c -o HULK.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c createBeadSummaryData.c -o createBeadSummaryData.o
createBeadSummaryData.c: In function ‘findAllOutliers’:
createBeadSummaryData.c:223: warning: ‘status’ may be used uninitialized in this function
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c findProbeIndices.c -o findProbeIndices.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c readBeadImages.c -o readBeadImages.o
readBeadImages.c: In function ‘getPixelIntensities’:
readBeadImages.c:368: warning: unused variable ‘result’
readBeadImages.c: In function ‘readBeadImage’:
readBeadImages.c:578: warning: ‘offset’ may be used uninitialized in this function
readBeadImages.c:578: warning: ‘records’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘StripOffset’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘ImageHeight’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘ImageWidth’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘BeginData’ may be used uninitialized in this function
gcc-4.2 -arch ppc64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o beadarray.so BASH.o BLImagePlot.o HULK.o createBeadSummaryData.o findProbeIndices.o readBeadImages.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c BASH.c -o BASH.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c BLImagePlot.c -o BLImagePlot.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c HULK.c -o HULK.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c createBeadSummaryData.c -o createBeadSummaryData.o
createBeadSummaryData.c: In function ‘findAllOutliers’:
createBeadSummaryData.c:223: warning: ‘status’ may be used uninitialized in this function
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c findProbeIndices.c -o findProbeIndices.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c readBeadImages.c -o readBeadImages.o
readBeadImages.c: In function ‘getPixelIntensities’:
readBeadImages.c:368: warning: unused variable ‘result’
readBeadImages.c: In function ‘readBeadImage’:
readBeadImages.c:578: warning: ‘offset’ may be used uninitialized in this function
readBeadImages.c:578: warning: ‘records’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘StripOffset’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘ImageHeight’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘ImageWidth’ may be used uninitialized in this function
readBeadImages.c:577: warning: ‘BeginData’ may be used uninitialized in this function
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o beadarray.so BASH.o BLImagePlot.o HULK.o createBeadSummaryData.o findProbeIndices.o readBeadImages.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

** help
*** installing help indices
 >>> Building/Updating help pages for package 'beadarray'
     Formats: text html latex example 
  BASH                              text    html    latex   example
  BASHCompact                       text    html    latex   example
  BASHDiffuse                       text    html    latex   example
  BASHExtended                      text    html    latex   example
  BGFilter                          text    html    latex   example
  BGFilterWeighted                  text    html    latex   example
  BLData                            text    html    latex
  BSData                            text    html    latex
  ExpressionControlData             text    html    latex   example
  HULK                              text    html    latex   example
  HULKResids                        text    html    latex   example
  addArrayMask                      text    html    latex   example
  arrayNames                        text    html    latex   example
  backgroundControlPlot             text    html    latex
  backgroundCorrect                 text    html    latex   example
  beadResids                        text    html    latex   example
  beadarrayUsersGuide               text    html    latex   example
  boxplotBeads                      text    html    latex   example
  calculateBeadLevelScores          text    html    latex
  calculateDetection                text    html    latex   example
  chooseClusters                    text    html    latex   example
  class-BeadLevelList               text    html    latex
  class.ExpressionSetIllumina       text    html    latex
  closeImage                        text    html    latex   example
  combineBeadLevelLists             text    html    latex
  copyBeadLevelLists                text    html    latex   example
  createBeadSummaryData             text    html    latex   example
  denseRegions                      text    html    latex   example
  findAllOutliers                   text    html    latex   example
  findBeadStatus                    text    html    latex   example
  generateE                         text    html    latex   example
  generateNeighbours                text    html    latex   example
  getAnnotation                     text    html    latex   example
  getArrayData                      text    html    latex   example
  getVariance                       text    html    latex   example
  imageplot                         text    html    latex   example
  interactivePlots                  text    html    latex
  lmhPlot                           text    html    latex
  medianNormalise                   text    html    latex   example
  normaliseIllumina                 text    html    latex   example
  numBeads                          text    html    latex   example
  outlierplot                       text    html    latex
  plotBeadDensities                 text    html    latex   example
  plotBeadIntensities               text    html    latex   example
  plotBeadLocations                 text    html    latex   example
  plotMA                            text    html    latex   example
  plotMAXY                          text    html    latex   example
  plotOnSAM                         text    html    latex
  plotRG                            text    html    latex
  plotXY                            text    html    latex   example
  poscontPlot                       text    html    latex
  probePairsPlot                    text    html    latex
  qcBeadLevel                       text    html    latex   example
  rankInvariantNormalise            text    html    latex   example
  readBGX                           text    html    latex   example
  readBeadSummaryData               text    html    latex   example
  readIllumina                      text    html    latex   example
  readQC                            text    html    latex   example
  setWeights                        text    html    latex   example
  viewBeads                         text    html    latex   example
** building package indices ...
* DONE (beadarray)
* 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 'beadarray_1.12.1.tar.gz'