xcms 1.11.16
Colin A. Smith
| Snapshot Date: 2008-04-09 00:13:10 -0700 (Wed, 09 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms | | Last Changed Rev: 30928 / Revision: 30951 | | Last Changed Date: 2008-04-08 12:41:03 -0700 (Tue, 08 Apr 2008) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | ERROR | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | ERROR | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | ERROR | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.1) / i386 | OK | ERROR | [ OK ] |
INSTALLATION WITH 'R CMD INSTALL xcms_1.11.16.tar.gz'
* Installing to library 'xcms.buildbin-libdir'
* Installing *source* package 'xcms' ...
** libs
** arch - i386
gcc-4.2 -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 -march=nocona -Wall -c base64.c -o base64.o
base64.c:18: warning: 'encode_group' defined but not used
base64.c:46: warning: 'decode_group' defined but not used
gcc-4.2 -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 -march=nocona -Wall -c mzClust_hclust.c -o mzClust_hclust.o
gcc-4.2 -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 -march=nocona -Wall -c mzboxes.c -o mzboxes.o
gcc-4.2 -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 -march=nocona -Wall -c netCDF.c -o netCDF.o
gcc-4.2 -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 -march=nocona -Wall -c ramp.c -o ramp.o
ramp.c: In function 'readPeaks':
ramp.c:1546: warning: 'multiplier' may be used uninitialized in this function
ramp.c:1545: warning: 'deltaMass' may be used uninitialized in this function
ramp.c:1544: warning: 'lastMass' may be used uninitialized in this function
gcc-4.2 -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 -march=nocona -Wall -c rampR.c -o rampR.o
gcc-4.2 -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 -march=nocona -Wall -c util.c -o util.o
gcc-4.2 -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 -march=nocona -Wall -c xcms.c -o xcms.o
xcms.c: In function 'ProfBinLin':
xcms.c:11: warning: 'ypre' may be used uninitialized in this function
xcms.c:11: warning: 'xpre' may be used uninitialized in this function
xcms.c: In function 'ProfBinLinBase':
xcms.c:62: warning: 'ipre' may be used uninitialized in this function
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o xcms.so base64.o mzClust_hclust.o mzboxes.o netCDF.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 -lintl -liconv -lc -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -Wall -c base64.c -o base64.o
base64.c:18: warning: 'encode_group' defined but not used
base64.c:46: warning: 'decode_group' defined but not used
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -Wall -c mzboxes.c -o mzboxes.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/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
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -Wall -c ramp.c -o ramp.o
ramp.c: In function 'readPeaks':
ramp.c:1546: warning: 'multiplier' may be used uninitialized in this function
ramp.c:1545: warning: 'deltaMass' may be used uninitialized in this function
ramp.c:1544: warning: 'lastMass' may be used uninitialized in this function
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -Wall -c rampR.c -o rampR.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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
xcms.c: In function 'ProfBinLin':
xcms.c:11: warning: 'ypre' may be used uninitialized in this function
xcms.c:11: warning: 'xpre' may be used uninitialized in this function
xcms.c: In function 'ProfBinLinBase':
xcms.c:62: warning: 'ipre' may be used uninitialized in this function
gcc-4.2 -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o xcms.so base64.o mzClust_hclust.o mzboxes.o netCDF.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 -lintl -liconv -lc -Wl,-framework -Wl,CoreFoundation
** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -Wall -c base64.c -o base64.o
base64.c:18: warning: 'encode_group' defined but not used
base64.c:46: warning: 'decode_group' defined but not used
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -Wall -c mzboxes.c -o mzboxes.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/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
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -Wall -c ramp.c -o ramp.o
ramp.c: In function 'readPeaks':
ramp.c:1546: warning: 'multiplier' may be used uninitialized in this function
ramp.c:1545: warning: 'deltaMass' may be used uninitialized in this function
ramp.c:1544: warning: 'lastMass' may be used uninitialized in this function
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -Wall -c rampR.c -o rampR.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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
xcms.c: In function 'ProfBinLin':
xcms.c:11: warning: 'ypre' may be used uninitialized in this function
xcms.c:11: warning: 'xpre' may be used uninitialized in this function
xcms.c: In function 'ProfBinLinBase':
xcms.c:62: warning: 'ipre' may be used uninitialized in this function
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o xcms.so base64.o mzClust_hclust.o mzboxes.o netCDF.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
** R
** inst
** preparing package for lazy loading
Warning in namespaceImportFrom(ns, loadNamespace(i[[1]], c(lib.loc, .libPaths())), :
replacing previous import: plot
** help
Note: removing empty section \seealso
Note: removing empty section \description
Note: removing empty section \description
>>> Building/Updating help pages for package 'xcms'
Formats: text html latex example
SSgauss text html latex
c.xcmsSet text html latex
colMax text html latex
collect-methods text html latex
descendZero text html latex example
diffreport-methods text html latex
dispName-methods text html latex
doubleMatrix text html latex
etg text html latex
explore-methods text html latex
fillPeaks-methods text html latex
filtfft text html latex
findEqualGreater text html latex
findMZBoxes-methods 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
findProtocols-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.mzClust text html latex example
groupnames-methods text html latex
groupval-methods text html latex
image.xcmsRaw text html latex
inType-methods text html latex
medianFilter text html latex example
na.flatfill text html latex
netCDF text html latex
outType-methods text html latex
panel.cor text html latex
perform-methods text html latex
pipeline-methods 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
protocol-methods text html latex
pval text html latex
ramp text html latex
rawEIC-methods text html latex
rawMat-methods text html latex
rectUnique text html latex example
retcor-methods text html latex
retexp text html latex
sampnames-methods text html latex
setProtocol text html latex example
setStage text html latex
missing link(s): defaultMethod
specNoise text html latex
specPeaks text html latex
split.xcmsSet text html latex
widget-methods text html latex
xcmsData-class text html latex
xcmsEIC-class Note: removing empty section \note
text html latex
xcmsFragments-class text html latex
xcmsFragments text html latex
xcmsPeaks-class text html latex
xcmsPipeline-class text html latex
xcmsPipelineProfile-class text html latex
xcmsProfile-class text html latex
missing link(s): profileMatrix
xcmsProtocol-class text html latex
xcmsProtocol text html latex example
xcmsRaw-class text html latex
xcmsRaw text html latex
missing link(s): profileMatrix genProfile genProfile
xcmsSet-class text html latex
xcmsSet text html latex
missing link(s): processRaws
xcmsStage-class text html latex
missing link(s): defaultMethod defaultMethod<-
xcmsStage text html latex example
** building package indices ...
* DONE (xcms)