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###
### Running command:
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### rm -rf xcms.buildbin-libdir xcms.Rcheck && mkdir xcms.buildbin-libdir xcms.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=xcms.buildbin-libdir xcms_1.46.0.tar.gz >xcms.Rcheck\00install.out 2>&1 && cp xcms.Rcheck\00install.out xcms-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=xcms.buildbin-libdir --install="check:xcms-install.out" --force-multiarch --no-vignettes --timings xcms_1.46.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/xcms.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'xcms/DESCRIPTION' ... OK
* this is package 'xcms' version '1.46.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'xcms' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
GPL (>= 2) + file LICENSE
* checking top-level files ... OK
* checking for left-over 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
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
'Biobase' 'BiocGenerics'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'mzR:::rampCloseAll'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Calls with DUP:
.C("ColMax", x, as.integer(n), as.integer(prod(dn)), double(prod(dn)),
DUP = FALSE, PACKAGE = "xcms")
.C("continuousPtsAboveThreshold", y, as.integer(istart - 1),
length(y), threshold = as.double(threshold), num = as.integer(num),
n = integer(1), DUP = FALSE, PACKAGE = "xcms")
.C("continuousPtsAboveThresholdIdx", y, as.integer(istart - 1),
length(y), threshold = as.double(threshold), num = as.integer(num),
n = integer(length(y)), DUP = FALSE, PACKAGE = "xcms")
.C("DescendMin", y, length(y), as.integer(istart - 1), ilower = integer(1),
iupper = integer(1), DUP = FALSE, PACKAGE = "xcms")
.C("DescendValue", y, length(y), as.integer(istart - 1), as.double(value),
ilower = integer(1), iupper = integer(1), DUP = FALSE, PACKAGE = "xcms")
.C("DescendZero", y, length(y), as.integer(istart - 1), ilower = integer(1),
iupper = integer(1), DUP = FALSE, PACKAGE = "xcms")
.C("FindEqualGreater", x, length(x), as.double(value), index = integer(1),
DUP = FALSE, PACKAGE = "xcms")
.C("FindEqualGreaterM", x, length(x), values, length(values),
index = integer(length(values)), DUP = FALSE, PACKAGE = "xcms")
.C("FindEqualGreaterUnsorted", x, length(x), as.double(value),
index = integer(1), DUP = FALSE, PACKAGE = "xcms")
.C("FindEqualLess", x, length(x), as.double(value), index = integer(1),
DUP = FALSE, PACKAGE = "xcms")
.C("FindEqualGreater", x, length(x), as.double(values[1]), integer(1),
NAOK = NAOK, DUP = FALSE, PACKAGE = "xcms")
.C("FindEqualLess", x, length(x), as.double(values[2]), integer(1),
NAOK = NAOK, DUP = FALSE, PACKAGE = "xcms")
.C("MedianFilter", x, as.integer(dimx[1]), as.integer(dimx[2]),
as.integer(mrad), as.integer(nrad), out = doubleMatrix(dimx[1],
dimx[2]), DUP = FALSE, PACKAGE = "xcms")
.C("R_mzClust_hclust", x = as.double(x), num = N, d = as.double(d),
g = integer(length = N), eppm = as.double(eppm), eabs = as.double(eabs),
DUP = FALSE, NAOK = TRUE)
.C("NetCDFMSPoints", as.integer(ncid), as.integer(length(scanIndex)),
scanIndex, as.integer(len), massValues = double(len), intensityValues = double(len),
status = integer(1), DUP = FALSE, PACKAGE = "xcms")
.C("NetCDFVarDouble", as.integer(ncid), as.integer(var), data = double(len),
status = integer(1), DUP = FALSE, PACKAGE = "xcms")
.C("NetCDFVarInt", as.integer(ncid), as.integer(var), data = integer(len),
status = integer(1), DUP = FALSE, PACKAGE = "xcms")
.C("ProfBin", x, y, as.integer(length(x)), as.double(xstart),
as.double(xend), as.integer(num), out = double(num), DUP = FALSE,
PACKAGE = "xcms")
.C("ProfBinLin", x, y, as.integer(length(x)), as.double(xstart),
as.double(xend), as.integer(num), out = double(num), DUP = FALSE,
PACKAGE = "xcms")
.C("ProfBinLinBase", x, y, as.integer(length(x)), as.double(baselevel),
as.double(basespace), as.double(xstart), as.double(xend),
as.integer(num), out = double(num), DUP = FALSE, PACKAGE = "xcms")
.C("ProfBinLinBaseM", x, y, as.integer(length(x)), as.integer(zidx),
as.integer(length(zidx)), as.double(baselevel), as.double(basespace),
as.double(xstart), as.double(xend), as.integer(num), out = doubleMatrix(num,
length(zidx)), NAOK = NAOK, DUP = FALSE, PACKAGE = "xcms")
.C("ProfBinLinM", x, y, as.integer(length(x)), as.integer(zidx),
as.integer(length(zidx)), as.double(xstart), as.double(xend),
as.integer(num), out = doubleMatrix(num, length(zidx)), NAOK = NAOK,
DUP = FALSE, PACKAGE = "xcms")
.C("ProfBinM", x, y, as.integer(length(x)), as.integer(zidx),
as.integer(length(zidx)), as.double(xstart), as.double(xend),
as.integer(num), out = doubleMatrix(num, length(zidx)), NAOK = NAOK,
DUP = FALSE, PACKAGE = "xcms")
.C("ProfIntLin", x, y, as.integer(length(x)), as.double(xstart),
as.double(xend), as.integer(num), out = double(num), DUP = FALSE,
PACKAGE = "xcms")
.C("ProfIntLinM", x, y, as.integer(length(x)), as.integer(zidx),
as.integer(length(zidx)), as.double(xstart), as.double(xend),
as.integer(num), out = doubleMatrix(num, length(zidx)), NAOK = NAOK,
DUP = FALSE, PACKAGE = "xcms")
.C("ProfMaxIdx", x, y, as.integer(length(x)), as.double(xstart),
as.double(xend), as.integer(num), out = integer(num), DUP = FALSE,
PACKAGE = "xcms")
.C("ProfMaxIdxM", x, y, as.integer(length(x)), as.integer(zidx),
as.integer(length(zidx)), as.double(xstart), as.double(xend),
as.integer(num), out = matrix(as.integer(0), num, length(zidx)),
NAOK = NAOK, DUP = FALSE, PACKAGE = "xcms")
.C("RectUnique", m, as.integer(order - 1), nr, nc, as.double(xdiff),
as.double(ydiff), logical(nrow(m)), DUP = FALSE, PACKAGE = "xcms")
.C("RowMax", x, as.integer(prod(dn)), as.integer(p), double(prod(dn)),
DUP = FALSE, PACKAGE = "xcms")
.C("WhichColMax", x, as.integer(n), as.integer(prod(dn)), integer(prod(dn)),
DUP = FALSE, PACKAGE = "xcms")
.C("WhichRowMax", x, as.integer(prod(dn)), as.integer(p), integer(prod(dn)),
DUP = FALSE, PACKAGE = "xcms")
DUP is no longer supported and will be ignored.
* checking R code for possible problems ... NOTE
fitGauss: warning in nls(d ˜ SSgauss(td, mu, sigma, h), algo = "port"):
partial argument match of 'algo' to 'algorithm'
joinOverlappingPeaks: warning in which(upper.tri(matrix(0, Ngp, Ngp)),
arr = TRUE): partial argument match of 'arr' to 'arr.ind'
joinOverlappingPeaks: warning in which(upper.tri(matrix(0, lcc, lcc)),
arr = TRUE): partial argument match of 'arr' to 'arr.ind'
plot.xcmsEIC: warning in rgb(rgbvec[1], rgbvec[2], rgbvec[3], max =
255): partial argument match of 'max' to 'maxColorValue'
plotQC: warning in apply(deviation_mzs[, sampOrder], MAR = 2, FUN =
function(x) median(x, na.rm = TRUE)): partial argument match of 'MAR'
to 'MARGIN'
plotQC: warning in apply(deviation_rts[, sampOrder], MAR = 2, FUN =
function(x) median(x, na.rm = TRUE)): partial argument match of 'MAR'
to 'MARGIN'
findPeaks.centWave,xcmsRaw : .local: warning in which(m == max(m), arr
= T): partial argument match of 'arr' to 'arr.ind'
findPeaks.centWave,xcmsRaw : .local: warning in matrix(c(1, 2, 3), nr =
3, nc = 1, byrow = T): partial argument match of 'nr' to 'nrow'
findPeaks.centWave,xcmsRaw : .local: warning in matrix(c(1, 2, 3), nr =
3, nc = 1, byrow = T): partial argument match of 'nc' to 'ncol'
group.nearest,xcmsSet : .local: warning in assign("peakmat", peakmat,
env = mplenv): partial argument match of 'env' to 'envir'
plotrt,xcmsSet : .local: warning in close.screen(all = TRUE): partial
argument match of 'all' to 'all.screens'
retcor.peakgroups,xcmsSet : .local: warning in close.screen(all =
TRUE): partial argument match of 'all' to 'all.screens'
.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'
.xcmsFragments.plotTree: no visible global function definition for
'edgemode<-'
.xcmsFragments.plotTree: no visible global function definition for
'addEdge'
buildAnalysisSummary: no visible global function definition for
'newXMLNode'
buildAssayList : <anonymous>: no visible global function definition for
'newXMLNode'
buildAssayList: no visible global function definition for 'newXMLNode'
buildAuditCollection: no visible global function definition for
'newXMLNode'
buildCVlist: no visible global function definition for 'newXMLNode'
buildCVlist: no visible global function definition for 'addChildren'
buildCvParams : <anonymous>: no visible global function definition for
'newXMLNode'
buildDataProcessingList: no visible global function definition for
'newXMLNode'
buildFeatureList : <anonymous>: no visible global function definition
for 'newXMLNode'
buildInputFiles : <anonymous>: no visible global function definition
for 'newXMLNode'
buildInputFiles: no visible global function definition for 'newXMLNode'
buildMzq: no visible global function definition for 'xmlTree'
buildSmallMoleculeList : <anonymous>: no visible global function
definition for 'newXMLNode'
buildSmallMoleculeList: no visible global function definition for
'newXMLNode'
buildSoftwareList: no visible global function definition for
'newXMLNode'
buildStudyVariableList : <anonymous>: no visible global function
definition for 'newXMLNode'
buildStudyVariableList : <anonymous> : <anonymous>: no visible global
function definition for 'newXMLNode'
buildStudyVariableList: no visible global function definition for
'newXMLNode'
fillPeaksChromPar: no visible binding for global variable 'i'
fillPeaksChromPar: no visible binding for global variable 'object'
patternVsRowScore: no visible global function definition for 'nn2'
rampRawData: no visible global function definition for
'rampScanHeaders'
rampRawData: no visible global function definition for 'rampSIPeaks'
rampRawDataMSn: no visible global function definition for
'rampScanHeaders'
rampRawDataMSn: no visible global function definition for 'rampSIPeaks'
running: multiple local function definitions for 'funct' with different
formal arguments
verify.mzQuantML: no visible global function definition for
'xmlTreeParse'
verify.mzQuantML: no visible global function definition for
'xmlInternalTreeParse'
verify.mzQuantML: no visible global function definition for
'xmlSchemaValidate'
xcmsClusterApply: no visible global function definition for
'checkCluster'
xcmsClusterApply : submit: no visible global function definition for
'sendCall'
xcmsClusterApply: no visible global function definition for
'recvOneResult'
xcmsClusterApply: no visible global function definition for
'checkForRemoteErrors'
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'
xcmsParallelSetup: no visible global function definition for
'mpi.spawn.Rslaves'
xcmsParallelSetup: no visible global function definition for
'mpi.comm.size'
xcmsParallelSetup: no visible global function definition for
'mpi.comm.rank'
xcmsParallelSetup: no visible global function definition for
'makeCluster'
xcmsSet: no visible global function definition for 'mpi.close.Rslaves'
xcmsSet: no visible global function definition for 'stopCluster'
diffreport,xcmsSet : .local: no visible global function definition for
'mt.teststat'
fillPeaks.chrom,xcmsSet : .local: no visible global function definition
for 'mpi.close.Rslaves'
fillPeaks.chrom,xcmsSet : .local: no visible global function definition
for 'stopCluster'
findPeaks.MSW,xcmsRaw : .local: no visible global function definition
for 'peakDetectionCWT'
findPeaks.MSW,xcmsRaw : .local: no visible global function definition
for 'tuneInPeakInfo'
getEICNew,xcmsRaw : .local: no visible binding for global variable
'mclapply'
getXcmsRaw,xcmsSet : .local: no visible binding for global variable
'mclapply'
group.nearest,xcmsSet : .local : <anonymous>: no visible binding for
global variable 's'
group.nearest,xcmsSet : .local : <anonymous>: no visible binding for
global variable 'coreList'
group.nearest,xcmsSet : .local : <anonymous>: no visible binding for
global variable 'peakIdxList'
levelplot,xcmsSet : .local: no visible binding for global variable
'xset'
plotSurf,xcmsRaw : .local: no visible global function definition for
'rgl.clear'
plotSurf,xcmsRaw : .local: no visible global function definition for
'rgl.surface'
plotSurf,xcmsRaw : .local: no visible global function definition for
'rgl.points'
plotSurf,xcmsRaw : .local: no visible global function definition for
'rgl.bbox'
plotTree,xcmsFragments : .local: no visible global function definition
for 'edgemode<-'
plotTree,xcmsFragments : .local: no visible global function definition
for 'addEdge'
write.cdf,xcmsRaw : .local: no visible global function definition for
'dim.def.ncdf'
write.cdf,xcmsRaw : .local: no visible global function definition for
'var.def.ncdf'
write.cdf,xcmsRaw : .local: no visible global function definition for
'create.ncdf'
write.cdf,xcmsRaw : .local: no visible global function definition for
'put.var.ncdf'
write.cdf,xcmsRaw : .local: no visible global function definition for
'att.put.ncdf'
write.cdf,xcmsRaw : .local: no visible global function definition for
'close.ncdf'
write.mzQuantML,xcmsSet : .local: no visible global function definition
for 'saveXML'
write.mzdata,xcmsRaw : .local: no visible global function definition
for 'base64encode'
* checking Rd files ... NOTE
prepare_Rd: split.xcmsRaw.Rd:18-20: Dropping empty section \usage
prepare_Rd: split.xcmsSet.Rd:19-21: Dropping empty section \usage
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.2-bioc/meat/xcms.buildbin-libdir/xcms/libs/i386/xcms.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'rand', possibly from 'rand' (C)
File 'D:/biocbld/bbs-3.2-bioc/meat/xcms.buildbin-libdir/xcms/libs/x64/xcms.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'rand', possibly from 'rand' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [72s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
findPeaks.massifquant-methods 54.1 0.16 54.62
msn2xcmsRaw 1.7 0.03 9.27
** running examples for arch 'x64' ... [55s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
findPeaks.massifquant-methods 44.27 0.05 44.31
msn2xcmsRaw 1.21 0.03 5.62
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'doRUnit.R'
