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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: E:\biocbld\bbs-2.4-bioc\R\bin\R.exe CMD check --no-vignettes xcms_1.16.3.tar.gz
StartedAt: 2009-10-20 18:39:38 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 18:41:10 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 91.6 seconds
RetCode: 0
Status: OK
CheckDir: xcms.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.4-bioc/meat/xcms.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'xcms/DESCRIPTION' ... OK
* this is package 'xcms' version '1.16.3'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'xcms' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.onLoad : <anonymous>: no visible global function definition for
  'mpi.comm.size'
.onLoad : <anonymous>: no visible global function definition for
  'mpi.close.Rslaves'
.onLoad : <anonymous>: no visible global function definition for
  'mpi.finalize'
KeggSearch: no visible binding for global variable 'masfile'
KeggSearch: no visible binding for global variable 'type'
patternVsRowScore: no visible global function definition for 'nn2'
running: multiple local function definitions for 'funct' with different
  formal arguments
xcmsPapply: no visible global function definition for 'mpi.comm.size'
xcmsPapply: no visible global function definition for
  'mpi.spawn.Rslaves'
xcmsPapply: no visible global function definition for 'mpi.comm.rank'
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for 'mpi.send.Robj'
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for 'mpi.recv.Robj'
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for 'mpi.any.source'
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for 'mpi.any.tag'
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for 'mpi.get.sourcetag'
xcmsPapply: no visible global function definition for
  'mpi.bcast.Robj2slave'
xcmsPapply: no visible global function definition for 'mpi.bcast.cmd'
xcmsPapply: no visible global function definition for 'mpi.recv.Robj'
xcmsPapply: no visible global function definition for 'mpi.any.source'
xcmsPapply: no visible global function definition for 'mpi.any.tag'
xcmsPapply: no visible global function definition for
  'mpi.get.sourcetag'
xcmsPapply: no visible global function definition for 'mpi.send.Robj'
xcmsSet: no visible global function definition for 'mpi.spawn.Rslaves'
xcmsSet: no visible global function definition for 'mpi.comm.size'
xcmsSet: no visible global function definition for 'mpi.comm.rank'
xcmsSet: no visible global function definition for 'mpi.close.Rslaves'
* checking Rd files ... OK
* checking Rd files against version 2 parser ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking tests ...
  Running 'doRUnit.R'
 OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

xcms.Rcheck/00install.out:

* Installing *source* package 'xcms' ...
** libs
  making DLL ...
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN       -O2 -Wall  -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*'
obiwarp/cmdparser.cpp: In member function 'void CmdParser::print_argv()':
obiwarp/cmdparser.cpp:235: warning: unused variable 'j'
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN       -O2 -Wall  -c obiwarp/mat.cpp -o obiwarp/mat.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN       -O2 -Wall  -c obiwarp/vec.cpp -o obiwarp/vec.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN       -O2 -Wall  -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN       -O2 -Wall  -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN       -O2 -Wall  -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*'
obiwarp/xcms_obiwarp.cpp:39: warning: unused variable 'outfile'
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN       -O3 -Wall  -std=gnu99 -c mzClust_hclust.c -o mzClust_hclust.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN       -O3 -Wall  -std=gnu99 -c mzROI.c -o mzROI.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN       -O3 -Wall  -std=gnu99 -c netCDF.c -o netCDF.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN       -O2 -Wall  -c ramp_base64.cpp -o ramp_base64.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN       -O2 -Wall  -c ramp.cpp -o ramp.o
ramp.cpp:64:1: warning: "S_ISDIR" redefined
In file included from ramp.h:59,
                 from ramp.cpp:34:
c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include/sys/stat.h:68:1: warning: this is the location of the previous definition
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN       -O2 -Wall  -c rampR.cpp -o rampR.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN       -O3 -Wall  -std=gnu99 -c util.c -o util.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN       -O3 -Wall  -std=gnu99 -c xcms.c -o xcms.o
g++ -shared -s -o xcms.dll tmp.def 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./win -lws2_32 -lnetcdf -lz -Le:/biocbld/bbs-2.4-bioc/R/bin -lR
  ... done
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
 >>> Building/Updating help pages for package 'xcms'
     Formats: text html latex example chm 
  SSgauss                           text    html    latex           chm
  c.xcmsSet                         text    html    latex           chm
  calibrate                         text    html    latex           chm
  colMax                            text    html    latex           chm
Note: removing empty section \seealso in file 'collect-methods.Rd'
Note: removing empty section \seealso in file 'collect-methods.Rd'
  collect-methods                   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
  fillPeaks.MSW-methods             text    html    latex           chm
  fillPeaks.chrom-methods           text    html    latex           chm
  filtfft                           text    html    latex           chm
  findEqualGreater                  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.density                     text    html    latex           chm
  group.mzClust                     text    html    latex   example chm
  group.nearest                     text    html    latex           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
  rawMat-methods                    text    html    latex           chm
  rectUnique                        text    html    latex   example chm
  retcor-methods                    text    html    latex           chm
  retcor.obiwarp-methods            text    html    latex           chm
  retcor.peakgroups-methods         text    html    latex           chm
  retexp                            text    html    latex           chm
  sampnames-methods                 text    html    latex           chm
  score_fun                         text    html    latex           chm
  score_fun.cor                     text    html    latex   example chm
  score_fun.distMatrix              text    html    latex   example chm
  searchMetlin                      text    html    latex           chm
  simSearch                         text    html    latex           chm
  specNoise                         text    html    latex           chm
  specPeaks                         text    html    latex           chm
Note: removing empty section \usage in file 'split.xcmsRaw.Rd'
Note: removing empty section \usage in file 'split.xcmsRaw.Rd'
  split.xcmsRaw                     text    html    latex           chm
Note: removing empty section \usage in file 'split.xcmsSet.Rd'
Note: removing empty section \usage in file 'split.xcmsSet.Rd'
  split.xcmsSet                     text    html    latex           chm
  write.cdf-methods                 text    html    latex           chm
  xcmsEIC-class                     text    html    latex           chm
  xcmsFragments-class               text    html    latex           chm
  xcmsFragments                     text    html    latex           chm
  xcmsPapply                        text    html    latex   example chm
  xcmsPeaks-class                   text    html    latex           chm
  xcmsRaw-class                     text    html    latex           chm
Note: removing empty section \note in file 'xcmsRaw.Rd'
Note: removing empty section \note in file 'xcmsRaw.Rd'
  xcmsRaw                           text    html    latex           chm
  xcmsSet-class                     text    html    latex           chm
Note: removing empty section \note in file 'xcmsSet.Rd'
Note: removing empty section \note in file 'xcmsSet.Rd'
  xcmsSet                           text    html    latex           chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\BBS-2~1.4-B\meat\XCMS~1.RCH\00_PKG~1\xcms\chm\xcms.chm


Compile time: 0 minutes, 1 second
78	Topics
413	Local links
22	Internet links
1	Graphic


Created e:\biocbld\BBS-2~1.4-B\meat\XCMS~1.RCH\00_PKG~1\xcms\chm\xcms.chm, 106,929 bytes
Compression decreased file by 177,024 bytes.
** building package indices ...
** MD5 sums
* DONE (xcms)