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Package 249/251HostnameOS / ArchBUILDCHECKBUILD BIN
xcms 1.11.11
Colin A. Smith
Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms
Last Changed Rev: 29091 / Revision: 29143
Last Changed Date: 2007-12-07 04:36:59 -0800 (Fri, 07 Dec 2007)
lamb1 Linux (SUSE 10.1) / x86_64  ERROR  skipped 
wilson2 Linux (openSUSE 10.3) / x86_64 [ ERROR ] skipped 
wellington Linux (openSUSE 10.3) / i686  ERROR  skipped 
liverpool Windows Server 2003 R2 (32-bit) / x64  ERROR  skipped  skipped 
lemming Windows Server 2003 (32-bit) / x64  ERROR  skipped  skipped 
Package: xcms
Version: 1.11.11
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD build xcms
StartedAt: 2007-12-11 02:11:50 -0700 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 02:12:39 -0700 (Tue, 11 Dec 2007)
EllapsedTime: 49.5 seconds
RetCode: 1
Status: ERROR
PackageFile: None
PackageFileSize: NA

Command output

* checking for file 'xcms/DESCRIPTION' ... OK
* preparing 'xcms':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
/tmp/Rinst1675576640
* Installing *source* package 'xcms' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fpic  -g -O2 -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 -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fpic  -g -O2 -Wall -c hra_hclust.c -o hra_hclust.o
hra_hclust.c: In function ‘R_hra_hclust’:
hra_hclust.c:22: warning: ‘minclust[0]’ may be used uninitialized in this function
hra_hclust.c:22: warning: ‘minclust[1]’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fpic  -g -O2 -Wall -c mzboxes.c -o mzboxes.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fpic  -g -O2 -Wall -c netCDF.c -o netCDF.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fpic  -g -O2 -Wall -c ramp.c -o ramp.o
ramp.c: In function ‘readPeaks’:
ramp.c:1538: warning: ‘lastMass’ may be used uninitialized in this function
ramp.c:1540: warning: ‘multiplier’ may be used uninitialized in this function
ramp.c:1539: warning: ‘deltaMass’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fpic  -g -O2 -Wall -c rampR.c -o rampR.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -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 -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fpic  -g -O2 -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 -std=gnu99 -shared -L/usr/local/lib64 -o xcms.so base64.o hra_hclust.o mzboxes.o netCDF.o ramp.o rampR.o util.o xcms.o -L/usr/local/lib -L/sw/lib -lnetcdf -lz  -L/home/biocbuild/bbs-2.2-bioc/R/lib -lR
** R
** inst
** preparing package for lazy loading
** help
Note: removing empty section \description
Note: removing empty section \description
Note: removing empty section \description
Note: removing empty section \description
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
  findMZBoxes-methods               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.mzAlign                     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
  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 ... ERROR
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './xcmsInstall.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './xcmsInstall.tex' ...
Loading required package: Biobase

Welcome to Bioconductor

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

Loading required package: survival
Loading required package: splines
Error in stop(gettextf("invalid names for slots of class \"%s\": %s",  : 
  no function to return from, jumping to top level
Calls: xcmsProtocol -> new -> initialize -> initialize
Execution halted