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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: /Library/Frameworks/R.framework/Versions/2.9/Resources/bin/R CMD check --no-vignettes xcms_1.16.3.tar.gz
StartedAt: 2009-10-20 19:06:44 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 19:08:37 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 112.3 seconds
RetCode: 0
Status: OK
CheckDir: xcms.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.4-bioc/meat/xcms.Rcheck'
* using R version 2.9.2 Patched (2009-08-24 r49420)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
** arch - i386
g++-4.0 -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  -g -O2 -Wall -fasm-blocks -c obiwarp/cmdparser.cpp -o obiwarp/cmdparser.o
obiwarp/cmdparser.cpp: In member function ‘void CmdParser::print_argv()’:
obiwarp/cmdparser.cpp:235: warning: unused variable ‘j’
g++-4.0 -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  -g -O2 -Wall -fasm-blocks -c obiwarp/mat.cpp -o obiwarp/mat.o
g++-4.0 -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  -g -O2 -Wall -fasm-blocks -c obiwarp/vec.cpp -o obiwarp/vec.o
g++-4.0 -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  -g -O2 -Wall -fasm-blocks -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
g++-4.0 -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  -g -O2 -Wall -fasm-blocks -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++-4.0 -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  -g -O2 -Wall -fasm-blocks -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:39: warning: unused variable ‘outfile’
gcc-4.2 -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  -g -O2 -Wall -c mzClust_hclust.c -o mzClust_hclust.o
gcc-4.2 -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  -g -O2 -Wall -c mzROI.c -o mzROI.o
gcc-4.2 -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  -g -O2 -Wall -c netCDF.c -o netCDF.o
g++-4.0 -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  -g -O2 -Wall -fasm-blocks -c ramp_base64.cpp -o ramp_base64.o
g++-4.0 -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  -g -O2 -Wall -fasm-blocks -c ramp.cpp -o ramp.o
ramp.cpp: In function ‘char* rampValidFileType(const char*)’:
ramp.cpp:1459: warning: ‘result’ may be used uninitialized in this function
g++-4.0 -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  -g -O2 -Wall -fasm-blocks -c rampR.cpp -o rampR.o
gcc-4.2 -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  -g -O2 -Wall -c util.c -o util.o
gcc-4.2 -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  -g -O2 -Wall -c xcms.c -o xcms.o
g++-4.2 -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -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
** arch - ppc
gcc-4.2 -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 -Wall -c mzClust_hclust.c -o mzClust_hclust.o
gcc-4.2 -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 -Wall -c mzROI.c -o mzROI.o
gcc-4.2 -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 -Wall -c netCDF.c -o netCDF.o
g++-4.0 -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 -Wall -fasm-blocks -c ramp_base64.cpp -o ramp_base64.o
g++-4.0 -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 -Wall -fasm-blocks -c ramp.cpp -o ramp.o
ramp.cpp: In function ‘char* rampValidFileType(const char*)’:
ramp.cpp:1459: warning: ‘result’ may be used uninitialized in this function
g++-4.0 -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 -Wall -fasm-blocks -c rampR.cpp -o rampR.o
gcc-4.2 -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 -Wall -c util.c -o util.o
gcc-4.2 -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 -Wall -c xcms.c -o xcms.o
g++-4.2 -arch ppc -dynamiclib -Wl,-headerpad_max_install_names -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
ld: warning in obiwarp/cmdparser.o, file is not of required architecture
ld: warning in obiwarp/mat.o, file is not of required architecture
ld: warning in obiwarp/vec.o, file is not of required architecture
ld: warning in obiwarp/xcms_dynprog.o, file is not of required architecture
ld: warning in obiwarp/xcms_lmat.o, file is not of required architecture
ld: warning in obiwarp/xcms_obiwarp.o, file is not of required architecture
** arch - ppc64
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c mzClust_hclust.c -o mzClust_hclust.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c mzROI.c -o mzROI.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c netCDF.c -o netCDF.o
g++-4.0 -arch ppc64 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c ramp_base64.cpp -o ramp_base64.o
g++-4.0 -arch ppc64 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c ramp.cpp -o ramp.o
ramp.cpp: In function ‘char* rampValidFileType(const char*)’:
ramp.cpp:1459: warning: ‘result’ may be used uninitialized in this function
g++-4.0 -arch ppc64 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c rampR.cpp -o rampR.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -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-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c xcms.c -o xcms.o
g++-4.2 -arch ppc64 -dynamiclib -Wl,-headerpad_max_install_names -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
ld: warning in obiwarp/cmdparser.o, file is not of required architecture
ld: warning in obiwarp/mat.o, file is not of required architecture
ld: warning in obiwarp/vec.o, file is not of required architecture
ld: warning in obiwarp/xcms_dynprog.o, file is not of required architecture
ld: warning in obiwarp/xcms_lmat.o, file is not of required architecture
ld: warning in obiwarp/xcms_obiwarp.o, file is not of required architecture
ld: warning in /usr/local/lib/libnetcdf.a, missing required architecture ppc64 in file
** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c mzClust_hclust.c -o mzClust_hclust.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c mzROI.c -o mzROI.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c netCDF.c -o netCDF.o
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c ramp_base64.cpp -o ramp_base64.o
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c ramp.cpp -o ramp.o
ramp.cpp: In function ‘char* rampValidFileType(const char*)’:
ramp.cpp:1459: warning: ‘result’ may be used uninitialized in this function
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c rampR.cpp -o rampR.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -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-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fPIC  -g -O2 -Wall -c xcms.c -o xcms.o
g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -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
ld: warning in obiwarp/cmdparser.o, file is not of required architecture
ld: warning in obiwarp/mat.o, file is not of required architecture
ld: warning in obiwarp/vec.o, file is not of required architecture
ld: warning in obiwarp/xcms_dynprog.o, file is not of required architecture
ld: warning in obiwarp/xcms_lmat.o, file is not of required architecture
ld: warning in obiwarp/xcms_obiwarp.o, file is not of required architecture
** 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
  simSearch                         text    html    latex
  specNoise                         text    html    latex
  specPeaks                         text    html    latex
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
  xcmsFragments                     text    html    latex
  xcmsPapply                        text    html    latex   example
  xcmsPeaks-class                   text    html    latex
  xcmsRaw-class                     text    html    latex
Note: removing empty section \note in file 'xcmsRaw.Rd'
  xcmsRaw                           text    html    latex
  xcmsSet-class                     text    html    latex
Note: removing empty section \note in file 'xcmsSet.Rd'
  xcmsSet                           text    html    latex
** building package indices ...
* DONE (xcms)