xcms 1.16.3
Colin A. Smith
| Bioconductor Changelog | | Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/xcms | | Last Changed Rev: 39338 / Revision: 42512 | | Last Changed Date: 2009-05-07 12:56:52 -0700 (Thu, 07 May 2009) |
| wilson1 | 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 |
INSTALLATION WITH 'R CMD INSTALL --preclean --library=xcms.buildbin-libdir xcms_1.16.3.tar.gz'
* Installing *source* package ‘xcms’ ...
** libs
** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c obiwarp/cmdparser.cpp -o obiwarp/cmdparser.o
obiwarp/cmdparser.cpp: In constructor ‘CmdParser::CmdParser(int, char**, char*)’:
obiwarp/cmdparser.cpp:32: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:52: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:60: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:61: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:62: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:63: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:64: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:65: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:66: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:67: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:68: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:69: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:70: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:71: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:72: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:73: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:74: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:75: warning: deprecated conversion from string constant to ‘char*’
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c obiwarp/mat.cpp -o obiwarp/mat.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c obiwarp/vec.cpp -o obiwarp/vec.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c obiwarp/xcms_obiwarp.cpp -o obiwarp/xcms_obiwarp.o
obiwarp/xcms_obiwarp.cpp: In function ‘SEXPREC* R_set_from_xcms(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
obiwarp/xcms_obiwarp.cpp:53: warning: deprecated conversion from string constant to ‘char*’
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c mzClust_hclust.c -o mzClust_hclust.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c mzROI.c -o mzROI.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c netCDF.c -o netCDF.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c ramp_base64.cpp -o ramp_base64.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c ramp.cpp -o ramp.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c rampR.cpp -o rampR.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c util.c -o util.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c xcms.c -o xcms.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o xcms.so obiwarp/cmdparser.o 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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
/usr/libexec/gcc/i686-apple-darwin8/4.2.1/ld: warning -L: directory name (/sw/lib) does not exist
** arch - ppc
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c obiwarp/cmdparser.cpp -o obiwarp/cmdparser.o
obiwarp/cmdparser.cpp: In constructor ‘CmdParser::CmdParser(int, char**, char*)’:
obiwarp/cmdparser.cpp:32: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:52: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:60: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:61: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:62: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:63: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:64: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:65: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:66: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:67: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:68: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:69: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:70: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:71: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:72: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:73: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:74: warning: deprecated conversion from string constant to ‘char*’
obiwarp/cmdparser.cpp:75: warning: deprecated conversion from string constant to ‘char*’
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -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++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -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++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -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++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -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++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -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
obiwarp/xcms_obiwarp.cpp: In function ‘SEXPREC* R_set_from_xcms(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
obiwarp/xcms_obiwarp.cpp:53: warning: deprecated conversion from string constant to ‘char*’
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -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 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c mzROI.c -o mzROI.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c netCDF.c -o netCDF.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -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++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c ramp.cpp -o ramp.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c rampR.cpp -o rampR.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c util.c -o util.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fPIC -g -O2 -c xcms.c -o xcms.o
g++ -arch ppc -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o xcms.so obiwarp/cmdparser.o 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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
/usr/libexec/gcc/powerpc-apple-darwin8/4.2.1/ld: warning -L: directory name (/sw/lib) does not exist
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
>>> 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
fillPeaks.MSW-methods text html latex
fillPeaks.chrom-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
group.nearest text html latex
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
rawMat-methods text html latex
rectUnique text html latex example
retcor-methods text html latex
retcor.obiwarp-methods text html latex
retcor.peakgroups-methods text html latex
retexp text html latex
sampnames-methods text html latex
score_fun text html latex
score_fun.cor text html latex example
score_fun.distMatrix text html latex example
searchMetlin text html latex
simSearch text html latex
specNoise text html latex
specPeaks text html latex
Note: removing empty section \usage in file 'split.xcmsRaw.Rd'
split.xcmsRaw 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
xcmsPeaks-class text html latex
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)