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Package 257/260HostnameOS / ArchBUILDCHECKBUILD BIN
xcms 1.12.1
Colin A. Smith
Snapshot Date: 2008-08-08 00:12:03 -0700 (Fri, 08 Aug 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_2/madman/Rpacks/xcms
Last Changed Rev: 31623 / Revision: 33132
Last Changed Date: 2008-05-12 04:39:45 -0700 (Mon, 12 May 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 ] OK  OK 
Package: xcms
Version: 1.12.1
Command: /Library/Frameworks/R.framework/Versions/2.7/Resources/bin/R CMD build xcms
StartedAt: 2008-08-08 02:58:54 -0700 (Fri, 08 Aug 2008)
EndedAt: 2008-08-08 03:01:05 -0700 (Fri, 08 Aug 2008)
EllapsedTime: 130.3 seconds
RetCode: 0
Status: OK
PackageFile: xcms_1.12.1.tar.gz
PackageFileSize: 1.355 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 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -msse3    -fPIC  -g -O2 -march=nocona -c base64.c -o base64.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -msse3    -fPIC  -g -O2 -march=nocona -c mzROI.c -o mzROI.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -msse3    -fPIC  -g -O2 -march=nocona -c netCDF.c -o netCDF.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -msse3    -fPIC  -g -O2 -march=nocona -c ramp.c -o ramp.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -msse3    -fPIC  -g -O2 -march=nocona -c rampR.c -o rampR.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -msse3    -fPIC  -g -O2 -march=nocona -c util.c -o util.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -msse3    -fPIC  -g -O2 -march=nocona -c xcms.c -o xcms.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o xcms.so base64.o mzROI.o netCDF.o ramp.o rampR.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
ld: warning -L: directory name (/sw/lib) does not exist
** arch - ppc
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -c base64.c -o base64.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -c mzROI.c -o mzROI.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -c netCDF.c -o netCDF.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -c ramp.c -o ramp.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -c rampR.c -o rampR.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -c util.c -o util.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -c xcms.c -o xcms.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o xcms.so base64.o mzROI.o netCDF.o ramp.o rampR.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
ld: warning -L: directory name (/sw/lib) does not exist
** R
** inst
** preparing package for lazy loading
** help
Note: removing empty section \usage
Note: removing empty section \note
Note: removing empty section \note
 >>> Building/Updating help pages for package 'xcms'
     Formats: text html latex example 
  SSgauss                           text    html    latex
  c.xcmsSet                         text    html    latex
  colMax                            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.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
  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
  specNoise                         text    html    latex
  specPeaks                         text    html    latex
  split.xcmsSet                     text    html    latex
  xcmsEIC-class                     text    html    latex
  xcmsRaw-class                     text    html    latex
  xcmsRaw                           text    html    latex
  xcmsSet-class                     text    html    latex
  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_1.12.1.tar.gz'