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Package 290/294HostnameOS / ArchBUILDCHECKBUILD BIN
xcms 1.14.1
Colin A. Smith
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/xcms
Last Changed Rev: 36077 / Revision: 38965
Last Changed Date: 2008-12-17 07:40:02 -0800 (Wed, 17 Dec 2008)
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  OK  OK 
pelham Mac OS X Leopard (10.5.6) / i386 [ OK ] OK  OK 
Package: xcms
Version: 1.14.1
Command: /Library/Frameworks/R.framework/Versions/2.8/Resources/bin/R CMD build xcms
StartedAt: 2009-04-18 15:19:39 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 15:25:46 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 367.1 seconds
RetCode: 0
Status: OK
PackageFile: xcms_1.14.1.tar.gz
PackageFileSize: 1.843 MiB

Command output

* checking for file 'xcms/DESCRIPTION' ... OK
* preparing 'xcms':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* Installing *source* package 'xcms' ...
** libs
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c mzClust_hclust.c -o mzClust_hclust.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c mzROI.c -o mzROI.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c netCDF.c -o netCDF.o
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c ramp.cpp -o ramp.o
ramp.cpp: In function 'char* rampValidFileType(const char*)':
ramp.cpp:1382: warning: 'result' may be used uninitialized in this function
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c rampR.cpp -o rampR.o
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c ramp_base64.cpp -o ramp_base64.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c util.c -o util.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c xcms.c -o xcms.o
g++-4.2 -arch i386 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o xcms.so mzClust_hclust.o mzROI.o netCDF.o ramp.o rampR.o ramp_base64.o util.o xcms.o -L/usr/local/lib -L/sw/lib -lnetcdf -lz  -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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c mzClust_hclust.c -o mzClust_hclust.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c mzROI.c -o mzROI.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c netCDF.c -o netCDF.o
g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c ramp.cpp -o ramp.o
ramp.cpp: In function 'char* rampValidFileType(const char*)':
ramp.cpp:1382: warning: 'result' may be used uninitialized in this function
g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c rampR.cpp -o rampR.o
g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c ramp_base64.cpp -o ramp_base64.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c util.c -o util.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c xcms.c -o xcms.o
g++-4.2 -arch ppc -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o xcms.so mzClust_hclust.o mzROI.o netCDF.o ramp.o rampR.o ramp_base64.o util.o xcms.o -L/usr/local/lib -L/sw/lib -lnetcdf -lz  -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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c mzClust_hclust.c -o mzClust_hclust.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c mzROI.c -o mzROI.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c netCDF.c -o netCDF.o
g++-4.0 -arch ppc64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c ramp.cpp -o ramp.o
ramp.cpp: In function 'char* rampValidFileType(const char*)':
ramp.cpp:1382: warning: 'result' may be used uninitialized in this function
g++-4.0 -arch ppc64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c rampR.cpp -o rampR.o
g++-4.0 -arch ppc64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c ramp_base64.cpp -o ramp_base64.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c util.c -o util.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c xcms.c -o xcms.o
g++-4.2 -arch ppc64 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o xcms.so mzClust_hclust.o mzROI.o netCDF.o ramp.o rampR.o ramp_base64.o util.o xcms.o -L/usr/local/lib -L/sw/lib -lnetcdf -lz  -L/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc64 -lR -dylib_file libRblas.dylib:/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc64/libRblas.dylib -Wl,-framework -Wl,CoreFoundation
ld: warning in /usr/local/lib/libnetcdf.a, missing required architecture ppc64 in file
** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c mzClust_hclust.c -o mzClust_hclust.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c mzROI.c -o mzROI.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c netCDF.c -o netCDF.o
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c ramp.cpp -o ramp.o
ramp.cpp: In function 'char* rampValidFileType(const char*)':
ramp.cpp:1382: warning: 'result' may be used uninitialized in this function
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c rampR.cpp -o rampR.o
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c ramp_base64.cpp -o ramp_base64.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c util.c -o util.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c xcms.c -o xcms.o
g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o xcms.so mzClust_hclust.o mzROI.o netCDF.o ramp.o rampR.o ramp_base64.o util.o xcms.o -L/usr/local/lib -L/sw/lib -lnetcdf -lz  -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** inst
** preparing package for lazy loading
** help
 >>> Building/Updating help pages for package 'xcms'
     Formats: text html latex example 
  SSgauss                           text    html    latex
  c.xcmsSet                         text    html    latex
  calibrate                         text    html    latex
  colMax                            text    html    latex
Note: removing empty section \seealso in file 'collect-methods.Rd'
  collect-methods                   text    html    latex
  descendZero                       text    html    latex   example
  diffreport-methods                text    html    latex
  doubleMatrix                      text    html    latex
  etg                               text    html    latex
  fillPeaks-methods                 text    html    latex
  filtfft                           text    html    latex
  findEqualGreater                  text    html    latex
  findPeaks-methods                 text    html    latex
  findPeaks.MS1-methods             text    html    latex
  findPeaks.MSW-methods             text    html    latex
  findPeaks.centWave-methods        text    html    latex
  findPeaks.matchedFilter-methods   text    html    latex
  getEIC-methods                    text    html    latex
  getPeaks-methods                  text    html    latex
  getScan-methods                   text    html    latex
  getSpec-methods                   text    html    latex
  group-methods                     text    html    latex
  group.density                     text    html    latex
  group.mzClust                     text    html    latex   example
  groupnames-methods                text    html    latex
  groupval-methods                  text    html    latex
  image.xcmsRaw                     text    html    latex
  medianFilter                      text    html    latex   example
  na.flatfill                       text    html    latex
  netCDF                            text    html    latex
  panel.cor                         text    html    latex
  plot.xcmsEIC                      text    html    latex
  plotChrom-methods                 text    html    latex
  plotPeaks-methods                 text    html    latex
  plotRaw-methods                   text    html    latex
  plotScan-methods                  text    html    latex
  plotSpec-methods                  text    html    latex
  plotSurf-methods                  text    html    latex
  plotTIC-methods                   text    html    latex
  plotrt-methods                    text    html    latex
  profGenerate                      text    html    latex
  profMedFilt-methods               text    html    latex
  profMethod-methods                text    html    latex
  profRange-methods                 text    html    latex
  profStep-methods                  text    html    latex
  pval                              text    html    latex
  ramp                              text    html    latex
  rawEIC-methods                    text    html    latex
  rectUnique                        text    html    latex   example
  retcor-methods                    text    html    latex
  retexp                            text    html    latex
  sampnames-methods                 text    html    latex
  score_fun                         text    html    latex
  searchMetlin                      text    html    latex
  simSearch                         text    html    latex
  specNoise                         text    html    latex
  specPeaks                         text    html    latex
Note: removing empty section \usage in file 'split.xcmsSet.Rd'
  split.xcmsSet                     text    html    latex
  write.cdf-methods                 text    html    latex
  xcmsEIC-class                     text    html    latex
  xcmsFragments-class               text    html    latex
  xcmsFragments                     text    html    latex
  xcmsPapply                        text    html    latex   example
  xcmsRaw-class                     text    html    latex
Note: removing empty section \note in file 'xcmsRaw.Rd'
  xcmsRaw                           text    html    latex
  xcmsSet-class                     text    html    latex
Note: removing empty section \note in file 'xcmsSet.Rd'
  xcmsSet                           text    html    latex
** building package indices ...
* DONE (xcms)
* 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 'xcms_1.14.1.tar.gz'