* checking for file 'xcms/DESCRIPTION' ... OK
* preparing 'xcms':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* Installing *source* package 'xcms' ...
** libs
gcc -I/home/biocbuild/1.9d/R/include -I/home/biocbuild/1.9d/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -std=gnu99 -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 -I/home/biocbuild/1.9d/R/include -I/home/biocbuild/1.9d/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c netCDF.c -o netCDF.o
gcc -I/home/biocbuild/1.9d/R/include -I/home/biocbuild/1.9d/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c ramp.c -o ramp.o
ramp.c: In function 'readPeaks':
ramp.c:998: warning: dereferencing type-punned pointer will break strict-aliasing rules
ramp.c:1011: warning: dereferencing type-punned pointer will break strict-aliasing rules
ramp.c:1109: warning: dereferencing type-punned pointer will break strict-aliasing rules
ramp.c:1120: warning: dereferencing type-punned pointer will break strict-aliasing rules
ramp.c: In function 'rampValidFileType':
ramp.c:805: warning: 'result' may be used uninitialized in this function
ramp.c: In function 'readIndex':
ramp.c:225: warning: 'n' may be used uninitialized in this function
gcc -I/home/biocbuild/1.9d/R/include -I/home/biocbuild/1.9d/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c rampR.c -o rampR.o
gcc -I/home/biocbuild/1.9d/R/include -I/home/biocbuild/1.9d/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c util.c -o util.o
gcc -I/home/biocbuild/1.9d/R/include -I/home/biocbuild/1.9d/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -std=gnu99 -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 -shared -L/usr/local/lib64 -o xcms.so base64.o netCDF.o ramp.o rampR.o util.o xcms.o -L/usr/local/lib -L/sw/lib -lnetcdf
** 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
clustunique text html latex
colMax 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
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
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-methods 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
rectUnique text html latex example
retcor-methods text html latex
retexp text html latex
sampnames-methods text html latex
specNoise text html latex
specPeaks text html latex
split.xcmsSet text html latex
xcmsEIC-class text html latex
xcmsRaw-class text html latex
xcmsRaw text html latex
xcmsSet-class text html latex
xcmsSet text html latex
** building package indices ...
* DONE (xcms)
* creating vignettes ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source files
* checking for empty or unneeded directories
* building 'xcms_1.6.0.tar.gz'