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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: D:\biocbld\bbs-2.2-bioc\R\bin\R.exe CMD build xcms
StartedAt: 2007-12-11 03:47:43 -0700 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 03:50:48 -0700 (Tue, 11 Dec 2007)
EllapsedTime: 184.9 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
installing R.css in D:/biocbld/bbs-2.2-bioc/tmpdir/Rinst456446588


---------- Making package xcms ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making base64.d from base64.c
making hra_hclust.d from hra_hclust.c
making mzboxes.d from mzboxes.c
making netCDF.d from netCDF.c
making ramp.d from ramp.c
making rampR.d from rampR.c
making util.d from util.c
making xcms.d from xcms.c
gcc  -std=gnu99 -I./win -D_MSC_VER -Id:/biocbld/bbs-2.2-bioc/R/include     -O3 -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./win -D_MSC_VER -Id:/biocbld/bbs-2.2-bioc/R/include     -O3 -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./win -D_MSC_VER -Id:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c mzboxes.c -o mzboxes.o
gcc  -std=gnu99 -I./win -D_MSC_VER -Id:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c netCDF.c -o netCDF.o
gcc  -std=gnu99 -I./win -D_MSC_VER -Id:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c ramp.c -o ramp.o
ramp.c: In function 'readPeaks':
ramp.c:1540: warning: 'multiplier' may be used uninitialized in this function
ramp.c:1539: warning: 'deltaMass' may be used uninitialized in this function
ramp.c:1538: warning: 'lastMass' may be used uninitialized in this function
gcc  -std=gnu99 -I./win -D_MSC_VER -Id:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c rampR.c -o rampR.o
gcc  -std=gnu99 -I./win -D_MSC_VER -Id:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -c util.c -o util.o
gcc  -std=gnu99 -I./win -D_MSC_VER -Id:/biocbld/bbs-2.2-bioc/R/include     -O3 -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
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I d:/biocbld/bbs-2.2-bioc/R/include  -i xcms_res.rc -o xcms_res.o
gcc  -std=gnu99  -shared -s  -o xcms.dll xcms.def base64.o hra_hclust.o mzboxes.o netCDF.o ramp.o rampR.o util.o xcms.o xcms_res.o  -Ld:/biocbld/bbs-2.2-bioc/R/bin -L./win -lws2_32 -lnetcdf -lz   -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  preparing package xcms for lazy loading
  installing man source files
  installing indices
  installing 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 \description
Note: removing empty section \description
Note: removing empty section \description
Note: removing empty section \description
 >>> Building/Updating help pages for package 'xcms'
     Formats: text html latex example chm 
  SSgauss                           text    html    latex           chm
  c.xcmsSet                         text    html    latex           chm
  colMax                            text    html    latex           chm
  descendZero                       text    html    latex   example chm
  diffreport-methods                text    html    latex           chm
  doubleMatrix                      text    html    latex           chm
  etg                               text    html    latex           chm
  fillPeaks-methods                 text    html    latex           chm
  filtfft                           text    html    latex           chm
  findEqualGreater                  text    html    latex           chm
  findMZBoxes-methods               text    html    latex           chm
  findPeaks-methods                 text    html    latex           chm
  findPeaks.MS1-methods             text    html    latex           chm
  findPeaks.MSW-methods             text    html    latex           chm
  findPeaks.centWave-methods        text    html    latex           chm
  findPeaks.matchedFilter-methods   text    html    latex           chm
  getEIC-methods                    text    html    latex           chm
  getPeaks-methods                  text    html    latex           chm
  getScan-methods                   text    html    latex           chm
  getSpec-methods                   text    html    latex           chm
  group-methods                     text    html    latex           chm
  group.mzAlign                     text    html    latex   example chm
  groupnames-methods                text    html    latex           chm
  groupval-methods                  text    html    latex           chm
  image.xcmsRaw                     text    html    latex           chm
  medianFilter                      text    html    latex   example chm
  na.flatfill                       text    html    latex           chm
  netCDF                            text    html    latex           chm
  panel.cor                         text    html    latex           chm
  plot.xcmsEIC                      text    html    latex           chm
  plotChrom-methods                 text    html    latex           chm
  plotPeaks-methods                 text    html    latex           chm
  plotRaw-methods                   text    html    latex           chm
  plotScan-methods                  text    html    latex           chm
  plotSpec-methods                  text    html    latex           chm
  plotSurf-methods                  text    html    latex           chm
  plotTIC-methods                   text    html    latex           chm
  plotrt-methods                    text    html    latex           chm
  profGenerate                      text    html    latex           chm
  profMedFilt-methods               text    html    latex           chm
  profMethod-methods                text    html    latex           chm
  profRange-methods                 text    html    latex           chm
  profStep-methods                  text    html    latex           chm
  pval                              text    html    latex           chm
  ramp                              text    html    latex           chm
  rawEIC-methods                    text    html    latex           chm
  rectUnique                        text    html    latex   example chm
  retcor-methods                    text    html    latex           chm
  retexp                            text    html    latex           chm
  sampnames-methods                 text    html    latex           chm
  specNoise                         text    html    latex           chm
  specPeaks                         text    html    latex           chm
  split.xcmsSet                     text    html    latex           chm
  xcmsEIC-class                     text    html    latex           chm
  xcmsRaw-class                     text    html    lateNote: removing empty section \note
Note: removing empty section \note
Note: removing empty section \note
Note: removing empty section \note
x           chm
  xcmsRaw                           text    html    latex           chm
  xcmsSet-class                     text    html    latex           chm
  xcmsSet                           text    html    latex           chm
Microsoft HTML Help Compiler 4.74.8702



Compiling d:\biocbld\bbs-2.2-bioc\meat\xcms\chm\xcms.chm





Compile time: 0 minutes, 0 seconds

59	Topics

291	Local links

8	Internet links

1	Graphic





Created d:\biocbld\bbs-2.2-bioc\meat\xcms\chm\xcms.chm, 83,277 bytes

Compression decreased file by 133,784 bytes.

  adding MD5 sums

* DONE (xcms)
* creating vignettes ... ERROR
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