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 |
* checking for file 'xcms/DESCRIPTION' ... OK
* preparing 'xcms':
* checking DESCRIPTION meta-information ... OK
* cleaning src
rm -f 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
* installing the package to re-build vignettes
* Installing *source* package 'xcms' ...
** libs
making DLL ...
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN -O2 -Wall -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*'
obiwarp/cmdparser.cpp: In member function 'void CmdParser::print_argv()':
obiwarp/cmdparser.cpp:235: warning: unused variable 'j'
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN -O2 -Wall -c obiwarp/mat.cpp -o obiwarp/mat.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN -O2 -Wall -c obiwarp/vec.cpp -o obiwarp/vec.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN -O2 -Wall -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN -O2 -Wall -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN -O2 -Wall -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*'
obiwarp/xcms_obiwarp.cpp:39: warning: unused variable 'outfile'
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN -O3 -Wall -std=gnu99 -c mzClust_hclust.c -o mzClust_hclust.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN -O3 -Wall -std=gnu99 -c mzROI.c -o mzROI.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN -O3 -Wall -std=gnu99 -c netCDF.c -o netCDF.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN -O2 -Wall -c ramp_base64.cpp -o ramp_base64.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN -O2 -Wall -c ramp.cpp -o ramp.o
ramp.cpp:64:1: warning: "S_ISDIR" redefined
In file included from ramp.h:59,
from ramp.cpp:34:
c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include/sys/stat.h:68:1: warning: this is the location of the previous definition
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN -O2 -Wall -c rampR.cpp -o rampR.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN -O3 -Wall -std=gnu99 -c util.c -o util.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I./win -D_MSC_VER -DWIN32_LEAN_AND_MEAN -O3 -Wall -std=gnu99 -c xcms.c -o xcms.o
g++ -shared -s -o xcms.dll tmp.def 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./win -lws2_32 -lnetcdf -lz -Le:/biocbld/bbs-2.4-bioc/R/bin -lR
... done
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
>>> Building/Updating help pages for package 'xcms'
Formats: text html latex example chm
SSgauss text html latex chm
c.xcmsSet text html latex chm
calibrate text html latex chm
colMax text html latex chm
Note: removing empty section \seealso in file 'collect-methods.Rd'
Note: removing empty section \seealso in file 'collect-methods.Rd'
collect-methods text html latex chm
descendZero text html latex example chm
diffreport-methods text html latex chm
doubleMatrix text html latex chm
etg text html latex chm
fillPeaks-methods text html latex chm
fillPeaks.MSW-methods text html latex chm
fillPeaks.chrom-methods text html latex chm
filtfft text html latex chm
findEqualGreater text html latex chm
findPeaks-methods text html latex chm
findPeaks.MS1-methods text html latex chm
findPeaks.MSW-methods text html latex chm
findPeaks.centWave-methods text html latex chm
findPeaks.matchedFilter-methods text html latex chm
getEIC-methods text html latex chm
getPeaks-methods text html latex chm
getScan-methods text html latex chm
getSpec-methods text html latex chm
group-methods text html latex chm
group.density text html latex chm
group.mzClust text html latex example chm
group.nearest text html latex chm
groupnames-methods text html latex chm
groupval-methods text html latex chm
image.xcmsRaw text html latex chm
medianFilter text html latex example chm
na.flatfill text html latex chm
netCDF text html latex chm
panel.cor text html latex chm
plot.xcmsEIC text html latex chm
plotChrom-methods text html latex chm
plotPeaks-methods text html latex chm
plotRaw-methods text html latex chm
plotScan-methods text html latex chm
plotSpec-methods text html latex chm
plotSurf-methods text html latex chm
plotTIC-methods text html latex chm
plotrt-methods text html latex chm
profGenerate text html latex chm
profMedFilt-methods text html latex chm
profMethod-methods text html latex chm
profRange-methods text html latex chm
profStep-methods text html latex chm
pval text html latex chm
ramp text html latex chm
rawEIC-methods text html latex chm
rawMat-methods text html latex chm
rectUnique text html latex example chm
retcor-methods text html latex chm
retcor.obiwarp-methods text html latex chm
retcor.peakgroups-methods text html latex chm
retexp text html latex chm
sampnames-methods text html latex chm
score_fun text html latex chm
score_fun.cor text html latex example chm
score_fun.distMatrix text html latex example chm
searchMetlin text html latex chm
simSearch text html latex chm
specNoise text html latex chm
specPeaks text html latex chm
Note: removing empty section \usage in file 'split.xcmsRaw.Rd'
Note: removing empty section \usage in file 'split.xcmsRaw.Rd'
split.xcmsRaw text html latex chm
Note: removing empty section \usage in file 'split.xcmsSet.Rd'
Note: removing empty section \usage in file 'split.xcmsSet.Rd'
split.xcmsSet text html latex chm
write.cdf-methods text html latex chm
xcmsEIC-class text html latex chm
xcmsFragments-class text html latex chm
xcmsFragments text html latex chm
xcmsPapply text html latex example chm
xcmsPeaks-class text html latex chm
xcmsRaw-class text html latex chm
Note: removing empty section \note in file 'xcmsRaw.Rd'
Note: removing empty section \note in file 'xcmsRaw.Rd'
xcmsRaw text html latex chm
xcmsSet-class text html latex chm
Note: removing empty section \note in file 'xcmsSet.Rd'
Note: removing empty section \note in file 'xcmsSet.Rd'
xcmsSet text html latex chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.4-bioc\meat\xcms\chm\xcms.chm
Compile time: 0 minutes, 1 second
78 Topics
413 Local links
22 Internet links
1 Graphic
Created e:\biocbld\bbs-2.4-bioc\meat\xcms\chm\xcms.chm, 106,917 bytes
Compression decreased file by 177,036 bytes.
** building package indices ...
** MD5 sums
* DONE (xcms)
* creating vignettes ... OK
* cleaning src
rm -f 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
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'xcms_1.16.3.tar.gz'