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Package 508/514HostnameOS / ArchBUILDCHECKBUILD BIN
xcms 1.30.3
Ralf Tautenhahn
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/xcms
Last Changed Rev: 60901 / Revision: 64395
Last Changed Date: 2011-11-27 08:24:47 -0800 (Sun, 27 Nov 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: xcms
Version: 1.30.3
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch xcms_1.30.3.tar.gz
StartedAt: 2012-03-24 04:49:53 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 04:57:22 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 448.9 seconds
RetCode: 0
Status:  OK 
CheckDir: xcms.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/xcms.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'xcms/DESCRIPTION' ... OK
* this is package 'xcms' version '1.30.3'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'xcms' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.2Mb
* 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 package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... 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
File 'xcms/R/unix/zzz.R':
  .onLoad calls:
    require(methods)

File 'xcms/R/windows/zzz.R':
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section 'Good practice' in ?.onAttach.

.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'
.xcmsFragments.plotTree: no visible global function definition for
  'edgemode<-'
.xcmsFragments.plotTree: no visible global function definition for
  'addEdge'
KeggSearch: no visible global function definition for
  'search.compounds.by.mass'
buildMzdata: no visible global function definition for 'xmlTree'
buildMzdata: no visible global function definition for 'base64encode'
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 ... NOTE
prepare_Rd: split.xcmsRaw.Rd:18-20: Dropping empty section \usage
prepare_Rd: split.xcmsSet.Rd:19-21: Dropping empty section \usage
prepare_Rd: xcmsSet.Rd:49-51: Dropping empty section \note
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File '/Users/biocbuild/bbs-2.9-bioc/meat/xcms.Rcheck/xcms/libs/i386/xcms.so':
  Found '__ZSt4cerr', possibly from 'std::cerr' (C++)
  Found '__ZSt4cout', possibly from 'std::cout' (C++)
  Found '___assert_rtn', possibly from 'assert' (C)
  Found '___stderrp', possibly from 'stderr' (C)
  Found '___stdoutp', possibly from 'stdout' (C)
  Found '_abort', possibly from 'abort' (C)
  Found '_exit', possibly from 'exit' (C)
  Found '_printf', possibly from 'printf' (C)
  Found '_puts', possibly from 'printf' (C), 'puts' (C)

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.  The detected symbols
are linked into the code but might come from libraries and not actually
be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... NOTE
'library' or 'require' call not declared from: 'RUnit'
* checking tests ...
  Running 'doRUnit.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

xcms.Rcheck/00install.out:

* installing *source* package 'xcms' ...
** libs
*** arch - i386
rm -f massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o obiwarp/xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o netCDF.o ramp_base64.o ramp.o rampR.o util.o xcms.o 
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
massifquant/xcms_massifquant.cpp: In function 'SEXPREC* massifquant(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
massifquant/xcms_massifquant.cpp:33: warning: unused variable 'list_names'
massifquant/xcms_massifquant.cpp:70: warning: unused variable 'maxScanNums'
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c massifquant/Tracker.cpp -o massifquant/Tracker.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c massifquant/SegProc.cpp -o massifquant/SegProc.o
massifquant/SegProc.cpp: In member function 'double SegProc::Rf_pt(double, double, int, int)':
massifquant/SegProc.cpp:358: warning: deprecated conversion from string constant to 'char*'
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/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++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/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++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/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++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/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++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/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
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c fastMatch.c -o fastMatch.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c mzClust_hclust.c -o mzClust_hclust.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c mzROI.c -o mzROI.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c netCDF.c -o netCDF.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/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++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/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
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/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 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c util.c -o util.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c xcms.c -o xcms.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o xcms.so massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o obiwarp/xcms_obiwarp.o fastMatch.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 -L/usr/local/lib -lnetcdf -lhdf5_hl -lhdf5 -lm -lz -lcurl -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/xcms.Rcheck/xcms/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'xcmsDirect.Rnw' 
   'xcmsInstall.Rnw' 
   'xcmsMSn.Rnw' 
   'xcmsPreprocess.Rnw' 
** testing if installed package can be loaded

* DONE (xcms)

xcms.Rcheck/xcms-Ex.timings:

nameusersystemelapsed
AutoLockMass-methods000
descendZero0.0030.0000.003
findMZ0.0010.0010.001
findneutral0.0010.0000.001
group.mzClust0.0000.0000.001
medianFilter0.0000.0010.001
peakTable-methods000
profGenerate0.0000.0000.001
profStep-methods0.0000.0000.001
ramp0.0010.0000.000
rectUnique0.0050.0010.006
stitch-methods0.0000.0000.001
xcmsPapply000
xcmsRaw0.0000.0000.001