BioC 3.3: CHECK report for xps on moscato2

Package: xps

Version: 1.31.0

Command: E:\biocbld\bbs-3.3-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --no-vignettes --timings xps_1.31.0.tar.gz

StartedAt: 2016-03-29 13:21:42 -0700 (Tue, 29 Mar 2016)

EndedAt: 2016-03-29 13:29:48 -0700 (Tue, 29 Mar 2016)

EllapsedTime: 485.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: xps.Rcheck

Warnings: 2

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### Running command:
###
###   E:\biocbld\bbs-3.3-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --no-vignettes --timings xps_1.31.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/xps.Rcheck'
* using R version 3.3.0 alpha (2016-03-17 r70348)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'xps/DESCRIPTION' ... OK
* this is package 'xps' version '1.31.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... WARNING
Subdirectory 'xps/src' contains apparent object files/libraries
  xps.dll
Object files/libraries should not be included in a source package.
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'xps' can be installed ... [278s] OK
* checking installed package size ... NOTE
  installed size is 13.7Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   7.1Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 loading without being on the library search path ... OK
* checking 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
.onAttach: no visible global function definition for
  'packageDescription'
AffyRNAdeg : lm.stats: no visible global function definition for 'lm'
dabgCall.DataTreeSet: no visible global function definition for
  'read.table'
distMAD: no visible global function definition for 'mad'
export.root: no visible global function definition for 'read.table'
exportProcesSet: no visible global function definition for 'read.table'
exportSchemeTreeSet: no visible global function definition for
  'read.table'
firma.DataTreeSet: no visible global function definition for
  'read.table'
iniCall.DataTreeSet: no visible global function definition for
  'read.table'
mas4.DataTreeSet: no visible global function definition for
  'read.table'
mas5.DataTreeSet: no visible global function definition for
  'read.table'
mas5Call.DataTreeSet: no visible global function definition for
  'read.table'
normalize.ExprTreeSet: no visible global function definition for
  'read.table'
plotBorder: no visible global function definition for 'x11'
plotBorder: no visible global function definition for 'jpeg'
plotBorder: no visible global function definition for 'png'
plotBorder: no visible global function definition for 'pdf'
plotBorder: no visible global function definition for 'postscript'
plotBorder: no visible global function definition for 'dev.off'
plotBoxplot: no visible global function definition for 'x11'
plotBoxplot: no visible global function definition for 'jpeg'
plotBoxplot: no visible global function definition for 'png'
plotBoxplot: no visible global function definition for 'pdf'
plotBoxplot: no visible global function definition for 'postscript'
plotBoxplot: no visible global function definition for 'dev.off'
plotCOI: no visible global function definition for 'x11'
plotCOI: no visible global function definition for 'jpeg'
plotCOI: no visible global function definition for 'png'
plotCOI: no visible global function definition for 'pdf'
plotCOI: no visible global function definition for 'postscript'
plotCOI: no visible global function definition for 'dev.off'
plotCall: no visible global function definition for 'x11'
plotCall: no visible global function definition for 'jpeg'
plotCall: no visible global function definition for 'png'
plotCall: no visible global function definition for 'pdf'
plotCall: no visible global function definition for 'postscript'
plotCall: no visible global function definition for 'dev.off'
plotCorr: no visible global function definition for 'x11'
plotCorr: no visible global function definition for 'jpeg'
plotCorr: no visible global function definition for 'png'
plotCorr: no visible global function definition for 'pdf'
plotCorr: no visible global function definition for 'postscript'
plotCorr: no visible global function definition for 'dev.off'
plotDensities: no visible binding for global variable 'density'
plotDensity: no visible global function definition for 'x11'
plotDensity: no visible global function definition for 'jpeg'
plotDensity: no visible global function definition for 'png'
plotDensity: no visible global function definition for 'pdf'
plotDensity: no visible global function definition for 'postscript'
plotDensity: no visible global function definition for 'dev.off'
plotImage: no visible global function definition for 'x11'
plotImage: no visible global function definition for 'jpeg'
plotImage: no visible global function definition for 'png'
plotImage: no visible global function definition for 'pdf'
plotImage: no visible global function definition for 'postscript'
plotImage: no visible global function definition for 'dev.off'
plotIntensity2GC: no visible global function definition for 'x11'
plotIntensity2GC: no visible global function definition for 'jpeg'
plotIntensity2GC: no visible global function definition for 'png'
plotIntensity2GC: no visible global function definition for 'pdf'
plotIntensity2GC: no visible global function definition for
  'postscript'
plotIntensity2GC: no visible global function definition for 'dev.off'
plotMA: no visible binding for global variable 'median'
plotMA: no visible global function definition for 'x11'
plotMA: no visible global function definition for 'jpeg'
plotMA: no visible global function definition for 'png'
plotMA: no visible global function definition for 'pdf'
plotMA: no visible global function definition for 'postscript'
plotMA: no visible global function definition for 'gray'
plotMA: no visible global function definition for 'dev.off'
plotMAD: no visible global function definition for 'x11'
plotMAD: no visible global function definition for 'jpeg'
plotMAD: no visible global function definition for 'png'
plotMAD: no visible global function definition for 'pdf'
plotMAD: no visible global function definition for 'postscript'
plotMAD: no visible global function definition for 'dev.off'
plotNUSE: no visible global function definition for 'x11'
plotNUSE: no visible global function definition for 'jpeg'
plotNUSE: no visible global function definition for 'png'
plotNUSE: no visible global function definition for 'pdf'
plotNUSE: no visible global function definition for 'postscript'
plotNUSE: no visible global function definition for 'dev.off'
plotPCA: no visible global function definition for 'x11'
plotPCA: no visible global function definition for 'jpeg'
plotPCA: no visible global function definition for 'png'
plotPCA: no visible global function definition for 'pdf'
plotPCA: no visible global function definition for 'postscript'
plotPCA: no visible global function definition for 'dev.off'
plotPM: no visible global function definition for 'x11'
plotPM: no visible global function definition for 'jpeg'
plotPM: no visible global function definition for 'png'
plotPM: no visible global function definition for 'pdf'
plotPM: no visible global function definition for 'postscript'
plotPM: no visible global function definition for 'dev.off'
plotProbeset: no visible global function definition for 'x11'
plotProbeset: no visible global function definition for 'jpeg'
plotProbeset: no visible global function definition for 'png'
plotProbeset: no visible global function definition for 'pdf'
plotProbeset: no visible global function definition for 'postscript'
plotProbeset: no visible global function definition for 'dev.off'
plotRLE: no visible global function definition for 'x11'
plotRLE: no visible global function definition for 'jpeg'
plotRLE: no visible global function definition for 'png'
plotRLE: no visible global function definition for 'pdf'
plotRLE: no visible global function definition for 'postscript'
plotRLE: no visible global function definition for 'dev.off'
plotVolcano: no visible global function definition for 'x11'
plotVolcano: no visible global function definition for 'jpeg'
plotVolcano: no visible global function definition for 'png'
plotVolcano: no visible global function definition for 'pdf'
plotVolcano: no visible global function definition for 'postscript'
plotVolcano: no visible global function definition for 'dev.off'
prefilter.ExprTreeSet: no visible global function definition for
  'read.table'
preprocess.DataTreeSet: no visible global function definition for
  'read.table'
pseudoPalette: no visible global function definition for 'col2rgb'
pseudoPalette: no visible global function definition for 'rgb'
qc.DataTreeSet: no visible global function definition for 'read.table'
qualify.DataTreeSet: no visible global function definition for
  'read.table'
rma.DataTreeSet: no visible global function definition for 'read.table'
root.call: no visible global function definition for 'read.table'
root.expr: no visible global function definition for 'read.table'
summarize.DataTreeSet: no visible global function definition for
  'read.table'
unifilter.ExprTreeSet: no visible global function definition for
  'read.table'
xpsQAReport: no visible global function definition for 'write.table'
xpsQAReport: no visible global function definition for 'png'
xpsQAReport: no visible global function definition for 'dev.off'
xpsQAReport: no visible global function definition for 'Sweave'
corplot,ExprTreeSet: no visible global function definition for 'cor'
corplot,ExprTreeSet: no visible global function definition for
  'heat.colors'
export,ProcesSet: no visible global function definition for
  'read.table'
export,SchemeTreeSet: no visible global function definition for
  'read.table'
hist,DataTreeSet: no visible global function definition for 'density'
image,ProcesSet: no visible global function definition for 'gray'
image,QualTreeSet: no visible global function definition for
  'terrain.colors'
intensity2GCplot,DataTreeSet: no visible global function definition for
  'colorRampPalette'
intensity<-,DataTreeSet-data.frame: no visible global function
  definition for 'write.table'
madplot,ExprTreeSet: no visible global function definition for
  'colorRampPalette'
madplot,ExprTreeSet: no visible global function definition for 'rgb'
mboxplot,ProcesSet: no visible binding for global variable 'median'
mvaplot,ExprTreeSet: no visible binding for global variable 'median'
nuseplot,ExprTreeSet: no visible binding for global variable 'median'
pcaplot,ExprTreeSet: no visible global function definition for 'prcomp'
pcaplot,ExprTreeSet: no visible global function definition for 'cor'
xpsDABGCall,DataTreeSet: no visible global function definition for
  'read.table'
xpsFIRMA,DataTreeSet: no visible global function definition for
  'read.table'
xpsINICall,DataTreeSet: no visible global function definition for
  'read.table'
xpsMAS4,DataTreeSet: no visible global function definition for
  'read.table'
xpsMAS5,DataTreeSet: no visible global function definition for
  'read.table'
xpsMAS5Call,DataTreeSet: no visible global function definition for
  'read.table'
xpsNormalize,ExprTreeSet: no visible global function definition for
  'read.table'
xpsPreFilter,ExprTreeSet: no visible global function definition for
  'read.table'
xpsPreprocess,DataTreeSet: no visible global function definition for
  'read.table'
xpsQualify,DataTreeSet: no visible global function definition for
  'read.table'
xpsQualityControl,DataTreeSet: no visible global function definition
  for 'read.table'
xpsRMA,DataTreeSet: no visible global function definition for
  'read.table'
xpsSummarize,DataTreeSet: no visible global function definition for
  'read.table'
xpsUniFilter,ExprTreeSet: no visible global function definition for
  'read.table'
Undefined global functions or variables:
  Sweave col2rgb colorRampPalette cor density dev.off gray heat.colors
  jpeg lm mad median packageDescription pdf png postscript prcomp
  read.table rgb terrain.colors write.table x11
Consider adding
  importFrom("grDevices", "col2rgb", "colorRampPalette", "dev.off",
             "gray", "heat.colors", "jpeg", "pdf", "png", "postscript",
             "rgb", "terrain.colors", "x11")
  importFrom("stats", "cor", "density", "lm", "mad", "median", "prcomp")
  importFrom("utils", "Sweave", "packageDescription", "read.table",
             "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* 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 ... WARNING
Found the following sources/headers with CR or CRLF line endings:
  src/xpsDict.h
Some Unix compilers require LF line endings.
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* 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
File 'E:/biocbld/bbs-3.3-bioc/meat/xps.Rcheck/xps/libs/i386/xps.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'printf', possibly from 'printf' (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 ... [58s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
summarize 1.96   0.01    5.57
normalize 1.92   0.02    5.88
* 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: 2 WARNINGs, 5 NOTEs
See
  'E:/biocbld/bbs-3.3-bioc/meat/xps.Rcheck/00check.log'
for details.

* installing *source* package 'xps' ...
testing for presence of ROOT...
   found root.exe of ROOT in directory C:/root/bin...OK
** libs
  running 'src/Makefile.win' ...
g++ -pipe -mwindows  -IC:/root/include -include w32pragma.h -O2 -DWIN32 -c TMLMath.cxx
TMLMath.cxx:1111:0: warning: "xmax" redefined [enabled by default]
TMLMath.cxx:1062:0: note: this is the location of the previous definition
g++ -pipe -mwindows  -IC:/root/include -FIw32pragma.h   -O3 -DWIN32 -c TStat.cxx
g++ -pipe -mwindows  -IC:/root/include -FIw32pragma.h   -O3 -DWIN32 -c StatUtils.cxx
g++ -pipe -mwindows  -IC:/root/include -FIw32pragma.h   -O3 -DWIN32 -c XPSBase.cxx
g++ -pipe -mwindows  -IC:/root/include -FIw32pragma.h   -O3 -DWIN32 -c XPSUtils.cxx
g++ -pipe -mwindows  -IC:/root/include -FIw32pragma.h   -O3 -DWIN32 -c XPSSchemes.cxx
g++ -pipe -mwindows  -IC:/root/include -FIw32pragma.h   -O3 -DWIN32 -c XPSDataTypes.cxx
g++ -pipe -mwindows  -IC:/root/include -FIw32pragma.h   -O3 -DWIN32 -c XPSProjectHandler.cxx
g++ -pipe -mwindows  -IC:/root/include -FIw32pragma.h   -O3 -DWIN32 -c XPSData.cxx
g++ -pipe -mwindows  -IC:/root/include -FIw32pragma.h   -O3 -DWIN32 -c XPSProcessing.cxx
g++ -pipe -mwindows  -IC:/root/include -FIw32pragma.h   -O3 -DWIN32 -c XPSHybridizer.cxx
g++ -pipe -mwindows  -IC:/root/include -FIw32pragma.h   -O3 -DWIN32 -c XPSSelector.cxx
g++ -pipe -mwindows  -IC:/root/include -FIw32pragma.h   -O3 -DWIN32 -c XPSNormalizer.cxx
g++ -pipe -mwindows  -IC:/root/include -FIw32pragma.h   -O3 -DWIN32 -c XPSPreProcessing.cxx
g++ -pipe -mwindows  -IC:/root/include -FIw32pragma.h   -O3 -DWIN32 -c XPSNormation.cxx
g++ -pipe -mwindows  -IC:/root/include -FIw32pragma.h   -O3 -DWIN32 -c XPSFilter.cxx
g++ -pipe -mwindows  -IC:/root/include -FIw32pragma.h   -O3 -DWIN32 -c XPSAnalyzer.cxx
g++ -pipe -mwindows  -IC:/root/include -FIw32pragma.h   -O3 -DWIN32 -c XPSAnalysis.cxx
g++ -pipe -mwindows  -IC:/root/include -FIw32pragma.h   -O3 -DWIN32 -c rwrapper.cxx
Generating dictionary xpsDict.cxx...
#@rootcint -f xpsDict.cxx -c TMLMath.h TStat.h StatUtils.h XPSBase.h XPSUtils.h XPSSchemes.h XPSDataTypes.h XPSProjectHandler.h XPSData.h XPSProcessing.h XPSHybridizer.h XPSSelector.h XPSNormalizer.h XPSPreProcessing.h XPSNormation.h XPSFilter.h XPSAnalyzer.h XPSAnalysis.h rwrapper.h xpsLinkDef.h
g++ -pipe -mwindows  -IC:/root/include -include w32pragma.h -O3 -DWIN32 -c xpsDict.cxx
g++ -o xps.dll -mwindows -Wl,--subsystem,windows -Wl,--dll -shared  *.o "C:/root/lib/libCore.lib" "C:/root/lib/libCint.lib" "C:/root/lib/libHist.lib" "C:/root/lib/libGraf.lib" "C:/root/lib/libGraf3d.lib" "C:/root/lib/libGpad.lib" "C:/root/lib/libTree.lib" "C:/root/lib/libRint.lib" "C:/root/lib/libPostscript.lib" "C:/root/lib/libMatrix.lib" "C:/root/lib/libPhysics.lib" "C:/root/lib/libNet.lib" "C:/root/lib/libRIO.lib" "C:/root/lib/libMathCore.lib" "C:/root/lib/libGui.lib" "C:/root/lib/libGraf.lib" "C:/root/lib/libGpad.lib" "C:/root/lib/libGed.lib" "C:/root/lib/libTreePlayer.lib" "C:/root/lib/libTreeViewer.lib"
installing to E:/biocbld/bbs-3.3-bioc/meat/xps.Rcheck/xps/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (xps)

name	user	system	elapsed
AffyRNAdeg	0	0	0
AnalysisTreeSet-class	0	0	0
CallTreeSet-class	0	0	0
DataTreeSet-class	0	0	0
ExprTreeSet-class	0	0	0
Filter-class	0	0	0
FilterTreeSet-class	0	0	0
NUSE	0	0	0
PreFilter-class	0.04	0.00	0.04
PreFilter-constructor	0.05	0.00	0.05
ProcesSet-class	0	0	0
ProjectInfo-class	0.02	0.00	0.02
ProjectInfo-constructor	0.04	0.00	0.04
QualTreeSet-class	0	0	0
RLE	0	0	0
SchemeTreeSet-class	0	0	0
TreeSet-class	0	0	0
UniFilter-class	0	0	0
UniFilter-constructor	0.03	0.00	0.03
addData-methods	0.33	0.00	2.01
attachCall-methods	0.31	0.00	1.05
attachDataXY-methods	0.12	0.00	0.12
attachExpr-methods	1.44	0.00	2.53
attachInten-methods	0.37	0.00	0.37
attachMask-methods	0.10	0.03	0.13
attachProbe-methods	0.12	0.05	0.17
attachUnitNames-methods	0.05	0.01	0.06
bgcorrect	0.65	0.02	1.59
borderplot-methods	0	0	0
boxplot-methods	0.49	0.03	0.51
callFilter-methods	0.01	0.00	0.02
coiplot-methods	0	0	0
cvFilter-methods	0.02	0.00	0.01
dabg.call	1.36	0.00	2.36
dfw	0.31	0.01	1.95
diffFilter-methods	0.02	0.00	0.01
existsROOTFile	0	0	0
exonLevel	0	0	0
export	0.58	0.03	0.61
export.root	0.56	0.04	0.59
express	1.40	0.01	2.81
exprs-methods	0.02	0.00	0.02
extenPart	0	0	0
farms	0.34	0.03	1.42
fcFilter-methods	0.02	0.00	0.01
firma	0	0	0
firma.expr	0	0	0
firma.score	0	0	0
fitQC	0	0	0
fitRLM	0	0	0
gapFilter-methods	0.01	0.00	0.01
getChipName	0	0	0
getChipType	0.02	0.00	0.02
getDatatype	0	0	0
getNameType	0	0	0
getNumberTrees	0.01	0.00	0.02
getProbeInfo	0	0	0
getTreeNames	0.02	0.00	0.01
highFilter-methods	0.00	0.02	0.02
hist-methods	0.03	0.00	0.03
image-methods	0	0	0
import.data	0.30	0.03	1.98
import.exon.scheme	0	0	0
import.expr.scheme	0	0	0
import.genome.scheme	0	0	0
indexUnits-methods	0.71	0.12	0.83
ini.call	0.37	0.02	1.67
intensity-methods	0.02	0.00	0.02
intensity2GCplot-methods	0.35	0.05	0.40
isROOTFile	0	0	0
lowFilter-methods	0.02	0.00	0.02
madFilter-methods	0.02	0.00	0.01
mas4	0.71	0.01	2.78
mas5	0.80	0.03	2.98
mas5.call	0.25	0.00	0.84
mboxplot-methods	0.73	0.00	0.75
metaProbesets	0	0	0
namePart	0	0	0
normalize	1.92	0.02	5.88
nuseplot-methods	0.05	0.00	0.05
plotImage	0	0	0
pm-methods	0.73	0.03	0.76
pmplot-methods	0.41	0.05	0.46
prefilter	0.01	0.00	0.01
presCall-methods	0	0	0
probeContentGC-methods	0.25	0.01	0.27
probeSequence-methods	0.17	0.02	0.18
probesetID2unitID-methods	0.05	0.00	0.05
probesetplot-methods	0.38	0.00	0.37
qualify	0	0	0
quantileFilter-methods	0.01	0.00	0.02
ratioFilter-methods	0	0	0
rawCELName-methods	0.04	0.00	0.03
rleplot-methods	0.01	0.01	0.03
rma	1.56	0.03	2.76
root.call	0.25	0.04	1.33
root.data	0.24	0.01	0.84
root.density	0	0	0
root.expr	1.79	0.00	2.92
root.graph1D	0	0	0
root.graph2D	0	0	0
root.hist1D	0	0	0
root.hist2D	0	0	0
root.hist3D	0	0	0
root.image	0	0	0
root.merge.data	0.27	0.02	0.97
root.mvaplot	0	0	0
root.profile	0	0	0
root.scheme	0.03	0.00	0.03
summarize	1.96	0.01	5.57
symbol2unitID-methods	0.13	0.02	0.14
treeInfo-methods	0.03	0.01	0.05
trma	1.70	0.00	2.75
type2Exten	0	0	0
uniTest-methods	0.01	0.00	0.01
unifilter	0	0	0
unitestFilter-methods	0.02	0.00	0.02
validTreetype	0	0	0
varFilter-methods	0.02	0.00	0.01
xpsQAReport	0	0	0