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Package 462/467HostnameOS / ArchBUILDCHECKBUILD BIN
xcms 1.26.1
Ralf Tautenhahn
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/xcms
Last Changed Rev: 55277 / Revision: 59457
Last Changed Date: 2011-05-05 11:43:13 -0700 (Thu, 05 May 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: xcms
Version: 1.26.1
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch xcms_1.26.1.tar.gz
StartedAt: 2011-10-20 17:51:03 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 17:58:24 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 440.7 seconds
RetCode: 0
Status:  OK 
CheckDir: xcms.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/xcms.Rcheck'
* using R version 2.13.2 (2011-09-30)
* 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 '1.26.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'xcms' can be installed ... OK
* checking installed package size ... 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 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
.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'
read.metlin: no visible binding for global variable 'MS2_data'
read.metlinMS: no visible binding for global variable 'ans'
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:52-54: 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 sizes of PDF files under inst/doc ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'xcmsPreprocess.pdf' from 940Kb to 549Kb
  consider running tools::compactPDF() on these files
* 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 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++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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++-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/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 -lnetcdf -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/xcms.Rcheck/xcms/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (xcms)

xcms.Rcheck/xcms-Ex.timings:

nameusersystemelapsed
descendZero0.0010.0010.002
findMZ000
findneutral0.0000.0000.001
group.mzClust000
medianFilter0.0010.0000.001
peakTable-methods0.0010.0000.001
profGenerate0.0010.0000.000
profStep-methods0.0010.0010.000
ramp000
rectUnique0.0040.0010.005
score_fun.cor0.0000.0000.001
score_fun.distMatrix0.0000.0010.000
searchMetlin000
stitch0.0000.0000.001
xcmsPapply000
xcmsRaw0.0000.0000.001