Package: xps

Version: 1.13.1

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings xps_1.13.1.tar.gz

StartedAt: 2011-05-09 16:01:17 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 16:04:15 -0700 (Mon, 09 May 2011)

EllapsedTime: 178.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: xps.Rcheck

Warnings: 1

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/xps.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'xps/DESCRIPTION' ... OK
* this is package 'xps' version '1.13.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'xps' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 13.1Mb
  sub-directories of 1Mb or more:
    doc    6.9Mb
    libs   3.3Mb
* 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 ... OK
* 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 portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'E:/biocbld/bbs-2.9-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
testing for presence of MSVC++...
   found Visual C++ compiler in directory C:\Program Files\Microsoft Visual Studio 9.0\VC/bin...OK
** libs
  running src/Makefile.win ...
"C:\Program Files\Microsoft Visual Studio 9.0\VC\bin/cl" /I"C:/root/include" /FIw32pragma.h /MT /EHsc /Ox /D "MSVC" /D "WIN32" /c TMLMath.cxx
Microsoft (R) 32-bit C/C++ Optimizing Compiler Version 15.00.21022.08 for 80x86
Copyright (C) Microsoft Corporation.  All rights reserved.

TMLMath.cxx
TMLMath.cxx(1109) : warning C4005: 'xmax' : macro redefinition
        TMLMath.cxx(1060) : see previous definition of 'xmax'
"C:\Program Files\Microsoft Visual Studio 9.0\VC\bin/cl" /I"C:/root/include" /FIw32pragma.h /MT /EHsc /Ox /D "MSVC" /D "WIN32" /c TStat.cxx
Microsoft (R) 32-bit C/C++ Optimizing Compiler Version 15.00.21022.08 for 80x86
Copyright (C) Microsoft Corporation.  All rights reserved.

TStat.cxx
"C:\Program Files\Microsoft Visual Studio 9.0\VC\bin/cl" /I"C:/root/include" /FIw32pragma.h /MT /EHsc /Ox /D "MSVC" /D "WIN32" /c StatUtils.cxx
Microsoft (R) 32-bit C/C++ Optimizing Compiler Version 15.00.21022.08 for 80x86
Copyright (C) Microsoft Corporation.  All rights reserved.

StatUtils.cxx
"C:\Program Files\Microsoft Visual Studio 9.0\VC\bin/cl" /I"C:/root/include" /FIw32pragma.h /MT /EHsc /Ox /D "MSVC" /D "WIN32" /c XPSBase.cxx
Microsoft (R) 32-bit C/C++ Optimizing Compiler Version 15.00.21022.08 for 80x86
Copyright (C) Microsoft Corporation.  All rights reserved.

XPSBase.cxx
"C:\Program Files\Microsoft Visual Studio 9.0\VC\bin/cl" /I"C:/root/include" /FIw32pragma.h /MT /EHsc /Ox /D "MSVC" /D "WIN32" /c XPSUtils.cxx
Microsoft (R) 32-bit C/C++ Optimizing Compiler Version 15.00.21022.08 for 80x86
Copyright (C) Microsoft Corporation.  All rights reserved.

XPSUtils.cxx
"C:\Program Files\Microsoft Visual Studio 9.0\VC\bin/cl" /I"C:/root/include" /FIw32pragma.h /MT /EHsc /Ox /D "MSVC" /D "WIN32" /c XPSSchemes.cxx
Microsoft (R) 32-bit C/C++ Optimizing Compiler Version 15.00.21022.08 for 80x86
Copyright (C) Microsoft Corporation.  All rights reserved.

XPSSchemes.cxx
"C:\Program Files\Microsoft Visual Studio 9.0\VC\bin/cl" /I"C:/root/include" /FIw32pragma.h /MT /EHsc /Ox /D "MSVC" /D "WIN32" /c XPSDataTypes.cxx
Microsoft (R) 32-bit C/C++ Optimizing Compiler Version 15.00.21022.08 for 80x86
Copyright (C) Microsoft Corporation.  All rights reserved.

XPSDataTypes.cxx
"C:\Program Files\Microsoft Visual Studio 9.0\VC\bin/cl" /I"C:/root/include" /FIw32pragma.h /MT /EHsc /Ox /D "MSVC" /D "WIN32" /c XPSProjectHandler.cxx
Microsoft (R) 32-bit C/C++ Optimizing Compiler Version 15.00.21022.08 for 80x86
Copyright (C) Microsoft Corporation.  All rights reserved.

XPSProjectHandler.cxx
"C:\Program Files\Microsoft Visual Studio 9.0\VC\bin/cl" /I"C:/root/include" /FIw32pragma.h /MT /EHsc /Ox /D "MSVC" /D "WIN32" /c XPSData.cxx
Microsoft (R) 32-bit C/C++ Optimizing Compiler Version 15.00.21022.08 for 80x86
Copyright (C) Microsoft Corporation.  All rights reserved.

XPSData.cxx
"C:\Program Files\Microsoft Visual Studio 9.0\VC\bin/cl" /I"C:/root/include" /FIw32pragma.h /MT /EHsc /Ox /D "MSVC" /D "WIN32" /c XPSProcessing.cxx
Microsoft (R) 32-bit C/C++ Optimizing Compiler Version 15.00.21022.08 for 80x86
Copyright (C) Microsoft Corporation.  All rights reserved.

XPSProcessing.cxx
"C:\Program Files\Microsoft Visual Studio 9.0\VC\bin/cl" /I"C:/root/include" /FIw32pragma.h /MT /EHsc /Ox /D "MSVC" /D "WIN32" /c XPSHybridizer.cxx
Microsoft (R) 32-bit C/C++ Optimizing Compiler Version 15.00.21022.08 for 80x86
Copyright (C) Microsoft Corporation.  All rights reserved.

XPSHybridizer.cxx
"C:\Program Files\Microsoft Visual Studio 9.0\VC\bin/cl" /I"C:/root/include" /FIw32pragma.h /MT /EHsc /Ox /D "MSVC" /D "WIN32" /c XPSSelector.cxx
Microsoft (R) 32-bit C/C++ Optimizing Compiler Version 15.00.21022.08 for 80x86
Copyright (C) Microsoft Corporation.  All rights reserved.

XPSSelector.cxx
"C:\Program Files\Microsoft Visual Studio 9.0\VC\bin/cl" /I"C:/root/include" /FIw32pragma.h /MT /EHsc /Ox /D "MSVC" /D "WIN32" /c XPSNormalizer.cxx
Microsoft (R) 32-bit C/C++ Optimizing Compiler Version 15.00.21022.08 for 80x86
Copyright (C) Microsoft Corporation.  All rights reserved.

XPSNormalizer.cxx
"C:\Program Files\Microsoft Visual Studio 9.0\VC\bin/cl" /I"C:/root/include" /FIw32pragma.h /MT /EHsc /Ox /D "MSVC" /D "WIN32" /c XPSPreProcessing.cxx
Microsoft (R) 32-bit C/C++ Optimizing Compiler Version 15.00.21022.08 for 80x86
Copyright (C) Microsoft Corporation.  All rights reserved.

XPSPreProcessing.cxx
"C:\Program Files\Microsoft Visual Studio 9.0\VC\bin/cl" /I"C:/root/include" /FIw32pragma.h /MT /EHsc /Ox /D "MSVC" /D "WIN32" /c XPSNormation.cxx
Microsoft (R) 32-bit C/C++ Optimizing Compiler Version 15.00.21022.08 for 80x86
Copyright (C) Microsoft Corporation.  All rights reserved.

XPSNormation.cxx
"C:\Program Files\Microsoft Visual Studio 9.0\VC\bin/cl" /I"C:/root/include" /FIw32pragma.h /MT /EHsc /Ox /D "MSVC" /D "WIN32" /c XPSFilter.cxx
Microsoft (R) 32-bit C/C++ Optimizing Compiler Version 15.00.21022.08 for 80x86
Copyright (C) Microsoft Corporation.  All rights reserved.

XPSFilter.cxx
"C:\Program Files\Microsoft Visual Studio 9.0\VC\bin/cl" /I"C:/root/include" /FIw32pragma.h /MT /EHsc /Ox /D "MSVC" /D "WIN32" /c XPSAnalyzer.cxx
Microsoft (R) 32-bit C/C++ Optimizing Compiler Version 15.00.21022.08 for 80x86
Copyright (C) Microsoft Corporation.  All rights reserved.

XPSAnalyzer.cxx
"C:\Program Files\Microsoft Visual Studio 9.0\VC\bin/cl" /I"C:/root/include" /FIw32pragma.h /MT /EHsc /Ox /D "MSVC" /D "WIN32" /c XPSAnalysis.cxx
Microsoft (R) 32-bit C/C++ Optimizing Compiler Version 15.00.21022.08 for 80x86
Copyright (C) Microsoft Corporation.  All rights reserved.

XPSAnalysis.cxx
"C:\Program Files\Microsoft Visual Studio 9.0\VC\bin/cl" /I"C:/root/include" /FIw32pragma.h /MT /EHsc /Ox /D "MSVC" /D "WIN32" /c rwrapper.cxx
Microsoft (R) 32-bit C/C++ Optimizing Compiler Version 15.00.21022.08 for 80x86
Copyright (C) Microsoft Corporation.  All rights reserved.

rwrapper.cxx
Generating dictionary xpsDict.cxx...
"C:\Program Files\Microsoft Visual Studio 9.0\VC\bin/cl" /I"C:/root/include" /FIw32pragma.h /MT /EHsc /Ox /D "MSVC" /D "WIN32" /c xpsDict.cxx
Microsoft (R) 32-bit C/C++ Optimizing Compiler Version 15.00.21022.08 for 80x86
Copyright (C) Microsoft Corporation.  All rights reserved.

xpsDict.cxx
"C:\Program Files\Microsoft Visual Studio 9.0\VC\bin/link" /dll /def:xps.def /out:xps.dll fp10.obj  -opt:noref  -nologo -include:_G__cpp_setupG__Hist -include:_G__cpp_setupG__Graf -include:_G__cpp_setupG__G3D -include:_G__cpp_setupG__GPad -include:_G__cpp_setupG__Tree -include:_G__cpp_setupG__Rint -include:_G__cpp_setupG__PostScript -include:_G__cpp_setupG__Matrix -include:_G__cpp_setupG__Physics -include:_G__cpp_setupG__Ged  "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" *.obj 
   Creating library xps.lib and object xps.exp
installing to E:/biocbld/bbs-2.9-bioc/meat/xps.Rcheck/xps/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'APTvsXPS.Rnw' 
   'xps.Rnw' 
   'xpsClasses.Rnw' 
   'xpsPreprocess.Rnw' 
** testing if installed package can be loaded

Welcome to xps version 1.13.1 
    an R wrapper for XPS - eXpression Profiling System
    (c) Copyright 2001-2011 by Christian Stratowa
    

* 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	0.02	0.00	0.02
Filter-class	0	0	0
FilterTreeSet-class	0	0	0
PreFilter-class	0.03	0.00	0.03
PreFilter-constructor	0.04	0.00	0.05
ProcesSet-class	0	0	0
ProjectInfo-class	0.02	0.00	0.01
ProjectInfo-constructor	0.05	0.00	0.05
QualTreeSet-class	0	0	0
SchemeTreeSet-class	0	0	0
TreeSet-class	0	0	0
UniFilter-class	0.02	0.00	0.01
UniFilter-constructor	0.03	0.00	0.03
addData-methods	0.51	0.02	1.10
attachCall-methods	0.36	0.01	0.64
attachExpr-methods	1.52	0.02	2.23
attachInten-methods	0.41	0.06	0.47
attachMask-methods	0.15	0.02	0.17
bgcorrect	0.83	0.08	1.07
borderplot-methods	0	0	0
boxplot-methods	0.66	0.04	0.70
callFilter-methods	0.03	0.00	0.03
coiplot-methods	0	0	0
cvFilter-methods	0.01	0.00	0.02
dabg.call	1.38	0.00	1.48
dfw	0.42	0.00	0.72
diffFilter-methods	0.02	0.00	0.02
existsROOTFile	0	0	0
exonLevel	0	0	0
export	0.67	0.03	0.70
export.root	0.73	0.00	0.73
express	1.41	0.05	1.69
exprs-methods	0	0	0
extenPart	0	0	0
farms	0.45	0.03	0.77
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	0.02
getChipName	0	0	0
getChipType	0.00	0.02	0.01
getDatatype	0	0	0
getNameType	0	0	0
getNumberTrees	0	0	0
getProbeInfo	0	0	0
getTreeNames	0.02	0.00	0.02
highFilter-methods	0.01	0.00	0.01
hist-methods	0.66	0.01	0.68
image-methods	0	0	0
import.data	0.27	0.00	0.92
import.exon.scheme	0	0	0
import.expr.scheme	0	0	0
import.genome.scheme	0	0	0
ini.call	0.51	0.07	1.00
intensity-methods	0	0	0
isROOTFile	0	0	0
lowFilter-methods	0	0	0
madFilter-methods	0.02	0.00	0.01
mas4	0.70	0.00	1.22
mas5	0.77	0.03	1.19
mas5.call	0.28	0.01	0.58
mboxplot-methods	0.62	0.05	0.76
metaProbesets	0	0	0
namePart	0	0	0
normalize	1.45	0.08	2.50
nuseplot-methods	0.05	0.00	0.05
plotImage	0	0	0
pm-methods	0.73	0.06	0.79
pmplot-methods	0.66	0.03	0.69
prefilter	0.00	0.02	0.02
presCall-methods	0	0	0
qualify	0	0	0
quantileFilter-methods	0	0	0
ratioFilter-methods	0.01	0.00	0.01
rawCELName-methods	0.03	0.00	0.03
rleplot-methods	0.05	0.00	0.05
rma	1.48	0.07	1.76
root.call	0.28	0.04	0.52
root.data	0.21	0.01	0.34
root.density	0	0	0
root.expr	1.42	0.06	1.67
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	0.22	0.00	0.44
root.mvaplot	0	0	0
root.profile	0	0	0
root.scheme	0.03	0.00	0.03
summarize	1.49	0.02	1.86
treeInfo-methods	0.06	0.00	0.06
trma	1.48	0.00	1.70
type2Exten	0	0	0
uniTest-methods	0.02	0.00	0.02
unifilter	0	0	0
unitestFilter-methods	0.02	0.00	0.01
validTreetype	0	0	0
varFilter-methods	0	0	0