xcms 1.14.1
Colin A. Smith
| Bioconductor Changelog | | Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/xcms | | Last Changed Rev: 36077 / Revision: 38965 | | Last Changed Date: 2008-12-17 07:40:02 -0800 (Wed, 17 Dec 2008) |
| 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 (10.5.6) / i386 | OK | [ OK ] | OK |
* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.3-bioc/meat/xcms.Rcheck'
* using R version 2.8.1 Patched (2009-03-18 r48200)
* using session charset: ASCII
* checking for file 'xcms/DESCRIPTION' ... OK
* this is package 'xcms' version '1.14.1'
* 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'
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 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
* creating xcms-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating xcms-manual.tex ... OK
* checking xcms-manual.tex using pdflatex ... OK
* Installing *source* package 'xcms' ...
** libs
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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:1382: warning: 'result' may be used uninitialized in this function
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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 mzClust_hclust.o mzROI.o netCDF.o ramp.o rampR.o ramp_base64.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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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:1382: warning: 'result' may be used uninitialized in this function
g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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
g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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 mzClust_hclust.o mzROI.o netCDF.o ramp.o rampR.o ramp_base64.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 - ppc64
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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:1382: warning: 'result' may be used uninitialized in this function
g++-4.0 -arch ppc64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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
g++-4.0 -arch ppc64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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 mzClust_hclust.o mzROI.o netCDF.o ramp.o rampR.o ramp_base64.o util.o xcms.o -L/usr/local/lib -L/sw/lib -lnetcdf -lz -L/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc64 -lR -dylib_file libRblas.dylib:/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc64/libRblas.dylib -Wl,-framework -Wl,CoreFoundation
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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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:1382: warning: 'result' may be used uninitialized in this function
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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 mzClust_hclust.o mzROI.o netCDF.o ramp.o rampR.o ramp_base64.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
** R
** inst
** preparing package for lazy loading
** help
>>> 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
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
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
rectUnique text html latex example
retcor-methods text html latex
retexp text html latex
sampnames-methods text html latex
score_fun text html latex
searchMetlin text html latex
simSearch text html latex
specNoise text html latex
specPeaks 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
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)