xcms 1.11.11
Colin A. Smith
| Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms | | Last Changed Rev: 29091 / Revision: 29143 | | Last Changed Date: 2007-12-07 04:36:59 -0800 (Fri, 07 Dec 2007) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | ERROR | skipped | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | [ ERROR ] | skipped | |
| wellington | Linux (openSUSE 10.3) / i686 | ERROR | skipped | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | ERROR | skipped | skipped |
| lemming | Windows Server 2003 (32-bit) / x64 | ERROR | skipped | skipped |
* checking for file 'xcms/DESCRIPTION' ... OK
* preparing 'xcms':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
/tmp/Rinst1675576640
* Installing *source* package 'xcms' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -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 -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/usr/local/include -fpic -g -O2 -Wall -c hra_hclust.c -o hra_hclust.o
hra_hclust.c: In function ‘R_hra_hclust’:
hra_hclust.c:22: warning: ‘minclust[0]’ may be used uninitialized in this function
hra_hclust.c:22: warning: ‘minclust[1]’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -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 -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -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 -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -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:1538: warning: ‘lastMass’ may be used uninitialized in this function
ramp.c:1540: warning: ‘multiplier’ may be used uninitialized in this function
ramp.c:1539: warning: ‘deltaMass’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -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 -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -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 -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -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 -std=gnu99 -shared -L/usr/local/lib64 -o xcms.so base64.o hra_hclust.o mzboxes.o netCDF.o ramp.o rampR.o util.o xcms.o -L/usr/local/lib -L/sw/lib -lnetcdf -lz -L/home/biocbuild/bbs-2.2-bioc/R/lib -lR
** R
** inst
** preparing package for lazy loading
** help
Note: removing empty section \description
Note: removing empty section \description
Note: removing empty section \description
Note: removing empty section \description
Note: removing empty section \note
Note: removing empty section \note
>>> 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
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
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
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.mzAlign 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
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 ... ERROR
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './xcmsInstall.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './xcmsInstall.tex' ...
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: survival
Loading required package: splines
Error in stop(gettextf("invalid names for slots of class \"%s\": %s", :
no function to return from, jumping to top level
Calls: xcmsProtocol -> new -> initialize -> initialize
Execution halted