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Package 315/319HostnameOS / ArchBUILDCHECKBUILD BIN
xcms 1.16.3
Colin A. Smith
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/xcms
Last Changed Rev: 39338 / Revision: 42512
Last Changed Date: 2009-05-07 12:56:52 -0700 (Thu, 07 May 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: xcms
Version: 1.16.3
Command: /Users/biocbuild/BBS/utils/build-universal.sh xcms_1.16.3.tar.gz /Library/Frameworks/R.framework/Versions/2.9/Resources/bin/R xcms.buildbin-libdir
StartedAt: 2009-10-20 19:39:16 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 19:39:54 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 38.1 seconds
RetCode: 0
Status: OK
PackageFile: xcms_1.16.3.tgz
PackageFileSize: 2.272 MiB

Command output

                INSTALLATION WITH 'R CMD INSTALL --preclean --library=xcms.buildbin-libdir xcms_1.16.3.tar.gz'

* Installing *source* package ‘xcms’ ...
** libs
** arch - i386
g++ -arch i386 -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c obiwarp/cmdparser.cpp -o obiwarp/cmdparser.o
obiwarp/cmdparser.cpp: In constructor ‘CmdParser::CmdParser(int, char**, char*)’:
obiwarp/cmdparser.cpp:32: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:52: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:60: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:61: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:62: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:63: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:64: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:65: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:66: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:67: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:68: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:69: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:70: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:71: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:72: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:73: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:74: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:75: warning: deprecated conversion from string constant to ‘char*’
g++ -arch i386 -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c obiwarp/mat.cpp -o obiwarp/mat.o
g++ -arch i386 -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c obiwarp/vec.cpp -o obiwarp/vec.o
g++ -arch i386 -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
g++ -arch i386 -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++ -arch i386 -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c obiwarp/xcms_obiwarp.cpp -o obiwarp/xcms_obiwarp.o
obiwarp/xcms_obiwarp.cpp: In function ‘SEXPREC* R_set_from_xcms(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
obiwarp/xcms_obiwarp.cpp:53: warning: deprecated conversion from string constant to ‘char*’
gcc -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c mzClust_hclust.c -o mzClust_hclust.o
gcc -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c mzROI.c -o mzROI.o
gcc -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c netCDF.c -o netCDF.o
g++ -arch i386 -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c ramp_base64.cpp -o ramp_base64.o
g++ -arch i386 -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c ramp.cpp -o ramp.o
g++ -arch i386 -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c rampR.cpp -o rampR.o
gcc -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c util.c -o util.o
gcc -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c xcms.c -o xcms.o
g++ -arch i386 -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 obiwarp/cmdparser.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o obiwarp/xcms_obiwarp.o mzClust_hclust.o mzROI.o netCDF.o ramp_base64.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
/usr/libexec/gcc/i686-apple-darwin8/4.2.1/ld: warning -L: directory name (/sw/lib) does not exist
** arch - ppc
g++ -arch ppc -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -c obiwarp/cmdparser.cpp -o obiwarp/cmdparser.o
obiwarp/cmdparser.cpp: In constructor ‘CmdParser::CmdParser(int, char**, char*)’:
obiwarp/cmdparser.cpp:32: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:52: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:60: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:61: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:62: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:63: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:64: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:65: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:66: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:67: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:68: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:69: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:70: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:71: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:72: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:73: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:74: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:75: warning: deprecated conversion from string constant to ‘char*’
g++ -arch ppc -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -c obiwarp/mat.cpp -o obiwarp/mat.o
g++ -arch ppc -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -c obiwarp/vec.cpp -o obiwarp/vec.o
g++ -arch ppc -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
g++ -arch ppc -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++ -arch ppc -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -c obiwarp/xcms_obiwarp.cpp -o obiwarp/xcms_obiwarp.o
obiwarp/xcms_obiwarp.cpp: In function ‘SEXPREC* R_set_from_xcms(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
obiwarp/xcms_obiwarp.cpp:53: warning: deprecated conversion from string constant to ‘char*’
gcc -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -c mzClust_hclust.c -o mzClust_hclust.o
gcc -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -c mzROI.c -o mzROI.o
gcc -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -c netCDF.c -o netCDF.o
g++ -arch ppc -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -c ramp_base64.cpp -o ramp_base64.o
g++ -arch ppc -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -c ramp.cpp -o ramp.o
g++ -arch ppc -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -c rampR.cpp -o rampR.o
gcc -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -c util.c -o util.o
gcc -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 -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -c xcms.c -o xcms.o
g++ -arch ppc -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 obiwarp/cmdparser.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o obiwarp/xcms_obiwarp.o mzClust_hclust.o mzROI.o netCDF.o ramp_base64.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
/usr/libexec/gcc/powerpc-apple-darwin8/4.2.1/ld: warning -L: directory name (/sw/lib) does not exist
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
 >>> 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
  fillPeaks.MSW-methods             text    html    latex
  fillPeaks.chrom-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
  group.nearest                     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
  rawMat-methods                    text    html    latex
  rectUnique                        text    html    latex   example
  retcor-methods                    text    html    latex
  retcor.obiwarp-methods            text    html    latex
  retcor.peakgroups-methods         text    html    latex
  retexp                            text    html    latex
  sampnames-methods                 text    html    latex
  score_fun                         text    html    latex
  score_fun.cor                     text    html    latex   example
  score_fun.distMatrix              text    html    latex   example
  searchMetlin                      text    html    latex
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Note: removing empty section \usage in file 'split.xcmsRaw.Rd'
  split.xcmsRaw                     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
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Note: removing empty section \note in file 'xcmsRaw.Rd'
  xcmsRaw                           text    html    latex
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Note: removing empty section \note in file 'xcmsSet.Rd'
  xcmsSet                           text    html    latex
** building package indices ...
* DONE (xcms)