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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings xcms_1.46.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/xcms.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘xcms’ can be installed ... [17s/17s] 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
* 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
File ‘xcms/libs/xcms.so’:
Found ‘rand’, possibly from ‘rand’ (C)
Object: ‘massifquant/TrMgr.o’
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.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [29s/29s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
findPeaks.massifquant-methods 24.349 0.079 24.458
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘doRUnit.R’ [264s/268s]
[264s/269s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 6 NOTEs
See
‘/home/biocbuild/bbs-3.2-bioc/meat/xcms.Rcheck/00check.log’
for details.
