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 working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.4-bioc/meat/xcms.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'xcms/DESCRIPTION' ... OK
* this is package 'xcms' version '1.16.3'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'xcms' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.onLoad : <anonymous>: no visible global function definition for
'mpi.comm.size'
.onLoad : <anonymous>: no visible global function definition for
'mpi.close.Rslaves'
.onLoad : <anonymous>: no visible global function definition for
'mpi.finalize'
KeggSearch: no visible binding for global variable 'masfile'
KeggSearch: no visible binding for global variable 'type'
patternVsRowScore: no visible global function definition for 'nn2'
running: multiple local function definitions for 'funct' with different
formal arguments
xcmsPapply: no visible global function definition for 'mpi.comm.size'
xcmsPapply: no visible global function definition for
'mpi.spawn.Rslaves'
xcmsPapply: no visible global function definition for 'mpi.comm.rank'
xcmsPapply : papply_int_slavefunction: no visible global function
definition for 'mpi.send.Robj'
xcmsPapply : papply_int_slavefunction: no visible global function
definition for 'mpi.recv.Robj'
xcmsPapply : papply_int_slavefunction: no visible global function
definition for 'mpi.any.source'
xcmsPapply : papply_int_slavefunction: no visible global function
definition for 'mpi.any.tag'
xcmsPapply : papply_int_slavefunction: no visible global function
definition for 'mpi.get.sourcetag'
xcmsPapply: no visible global function definition for
'mpi.bcast.Robj2slave'
xcmsPapply: no visible global function definition for 'mpi.bcast.cmd'
xcmsPapply: no visible global function definition for 'mpi.recv.Robj'
xcmsPapply: no visible global function definition for 'mpi.any.source'
xcmsPapply: no visible global function definition for 'mpi.any.tag'
xcmsPapply: no visible global function definition for
'mpi.get.sourcetag'
xcmsPapply: no visible global function definition for 'mpi.send.Robj'
xcmsSet: no visible global function definition for 'mpi.spawn.Rslaves'
xcmsSet: no visible global function definition for 'mpi.comm.size'
xcmsSet: no visible global function definition for 'mpi.comm.rank'
xcmsSet: no visible global function definition for 'mpi.close.Rslaves'
* checking Rd files ... OK
* checking Rd files against version 2 parser ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking tests ...
Running 'doRUnit.R'
OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* 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'
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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
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filtfft text html latex chm
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findPeaks.MS1-methods text html latex chm
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findPeaks.centWave-methods text html latex chm
findPeaks.matchedFilter-methods text html latex chm
getEIC-methods text html latex chm
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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-2~1.4-B\meat\XCMS~1.RCH\00_PKG~1\xcms\chm\xcms.chm
Compile time: 0 minutes, 1 second
78 Topics
413 Local links
22 Internet links
1 Graphic
Created e:\biocbld\BBS-2~1.4-B\meat\XCMS~1.RCH\00_PKG~1\xcms\chm\xcms.chm, 106,929 bytes
Compression decreased file by 177,024 bytes.
** building package indices ...
** MD5 sums
* DONE (xcms)