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Package 349/353HostnameOS / ArchBUILDCHECKBUILD BIN
xcms 1.20.1
Colin A. Smith
Snapshot Date: 2009-12-13 23:30:35 -0800 (Sun, 13 Dec 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_5/madman/Rpacks/xcms
Last Changed Rev: 43253 / Revision: 43539
Last Changed Date: 2009-11-25 03:28:51 -0800 (Wed, 25 Nov 2009)
wilson2 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: 1.20.1
Command: /home/biocbuild/bbs-2.5-bioc/R/bin/R CMD check --no-vignettes xcms_1.20.1.tar.gz
StartedAt: 2009-12-14 06:49:10 -0800 (Mon, 14 Dec 2009)
EndedAt: 2009-12-14 06:51:24 -0800 (Mon, 14 Dec 2009)
EllapsedTime: 134.5 seconds
RetCode: 0
Status: OK
CheckDir: xcms.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.5-bioc/meat/xcms.Rcheck'
* using R version 2.10.0 (2009-10-26)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'xcms/DESCRIPTION' ... OK
* this is package 'xcms' version '1.20.1'
* 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 ... NOTE
prepare_Rd: collect-methods.Rd:63-64: Dropping empty section \seealso
prepare_Rd: split.xcmsRaw.Rd:18-20: Dropping empty section \usage
prepare_Rd: split.xcmsSet.Rd:19-21: Dropping empty section \usage
prepare_Rd: xcmsRaw.Rd:46-48: Dropping empty section \note
prepare_Rd: xcmsSet.Rd:41-43: 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 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:

* install options are ' --no-html'

* installing *source* package ‘xcms’ ...
** libs
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fpic  -g -O2 -Wall -c obiwarp/mat.cpp -o obiwarp/mat.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fpic  -g -O2 -Wall -c obiwarp/vec.cpp -o obiwarp/vec.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fpic  -g -O2 -Wall -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fpic  -g -O2 -Wall -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fpic  -g -O2 -Wall -c obiwarp/xcms_obiwarp.cpp -o obiwarp/xcms_obiwarp.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -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 -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -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 -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -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++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fpic  -g -O2 -Wall -c ramp_base64.cpp -o ramp_base64.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fpic  -g -O2 -Wall -c ramp.cpp -o ramp.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include    -fpic  -g -O2 -Wall -c rampR.cpp -o rampR.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -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 -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -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++ -shared -L/usr/local/lib64 -o xcms.so 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 -L/home/biocbuild/bbs-2.5-bioc/R/lib -lR
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
* DONE (xcms)