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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
gcc -I/home/biocbuild/R-2.3.0/include -I/home/biocbuild/R-2.3.0/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -c base64.c -o base64.o
base64.c:18: warning: 'encode_group' defined but not used
base64.c:46: warning: 'decode_group' defined but not used
gcc -I/home/biocbuild/R-2.3.0/include -I/home/biocbuild/R-2.3.0/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -c netCDF.c -o netCDF.o
gcc -I/home/biocbuild/R-2.3.0/include -I/home/biocbuild/R-2.3.0/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -c ramp.c -o ramp.o
ramp.c: In function 'readPeaks':
ramp.c:990: warning: dereferencing type-punned pointer will break strict-aliasing rules
ramp.c:1003: warning: dereferencing type-punned pointer will break strict-aliasing rules
ramp.c:1101: warning: dereferencing type-punned pointer will break strict-aliasing rules
ramp.c:1112: warning: dereferencing type-punned pointer will break strict-aliasing rules
ramp.c: In function 'rampValidFileType':
ramp.c:797: warning: 'result' may be used uninitialized in this function
ramp.c: In function 'readIndex':
ramp.c:224: warning: 'n' may be used uninitialized in this function
gcc -I/home/biocbuild/R-2.3.0/include -I/home/biocbuild/R-2.3.0/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -c rampR.c -o rampR.o
gcc -I/home/biocbuild/R-2.3.0/include -I/home/biocbuild/R-2.3.0/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -c util.c -o util.o
gcc -I/home/biocbuild/R-2.3.0/include -I/home/biocbuild/R-2.3.0/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -c xcms.c -o xcms.o
xcms.c: In function 'ProfBinLin':
xcms.c:11: warning: 'ypre' may be used uninitialized in this function
xcms.c:11: warning: 'xpre' may be used uninitialized in this function
xcms.c: In function 'ProfBinLinBase':
xcms.c:62: warning: 'ipre' may be used uninitialized in this function
gcc -shared -L/usr/local/lib64 -o xcms.so base64.o netCDF.o ramp.o rampR.o util.o xcms.o -L/usr/local/lib -L/sw/lib -lnetcdf  
** R
** inst
** preparing package for lazy loading
** help
Warning message:
incomplete final line found by readLines on './man/medianFilter.Rd' 
 >>> Building/Updating help pages for package 'xcms'
     Formats: text html latex example 
  SSgauss                           text    html    latex
  c.xcmsSet                         text    html    latex
  clustunique                       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
  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-methods                      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
  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 files
* checking for empty or unneeded directories
* building 'xcms_1.4.0.tar.gz'