xcms 1.25.4
Colin A. Smith
| Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms | | Last Changed Rev: 52578 / Revision: 53255 | | Last Changed Date: 2011-02-10 15:00:20 -0800 (Thu, 10 Feb 2011) |
| lamb2 | Linux (openSUSE 11.2) / x86_64 | OK | [ OK ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.4) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/xcms.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘xcms/DESCRIPTION’ ... OK
* this is package ‘xcms’ version ‘1.25.4’
* 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space 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’
searchMetlin,xcmsFragments: no visible binding for global variable
‘MS1data’
* 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 ... 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 package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK
* installing *source* package ‘xcms’ ...
** libs
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++ -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c obiwarp/mat.cpp -o obiwarp/mat.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c obiwarp/vec.cpp -o obiwarp/vec.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c obiwarp/xcms_obiwarp.cpp -o obiwarp/xcms_obiwarp.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c fastMatch.c -o fastMatch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c mzClust_hclust.c -o mzClust_hclust.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c mzROI.c -o mzROI.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c netCDF.c -o netCDF.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c ramp_base64.cpp -o ramp_base64.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c ramp.cpp -o ramp.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c rampR.cpp -o rampR.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -c util.c -o util.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -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 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 -L/home/biocbuild/bbs-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/xcms.Rcheck/xcms/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (xcms)