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Package 418/419HostnameOS / ArchBUILDCHECKBUILD BIN
xps 1.10.2
Christian Stratowa
Snapshot Date: 2011-03-30 23:22:56 -0700 (Wed, 30 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/xps
Last Changed Rev: 50493 / Revision: 54281
Last Changed Date: 2010-10-26 11:36:41 -0700 (Tue, 26 Oct 2010)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ WARNINGS ] OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64 N O T   S U P P O R T E D
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: xps
Version: 1.10.2
Command: E:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings xps_1.10.2.tar.gz
StartedAt: 2011-03-31 08:40:49 -0700 (Thu, 31 Mar 2011)
EndedAt: 2011-03-31 08:43:43 -0700 (Thu, 31 Mar 2011)
EllapsedTime: 174.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: xps.Rcheck
Warnings: 1

Command output

* using log directory 'E:/biocbld/bbs-2.7-bioc/meat/xps.Rcheck'
* using R version 2.12.2 (2011-02-25)
* 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 '1.10.2'
* 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 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 package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'E:/biocbld/bbs-2.7-bioc/meat/xps.Rcheck/00check.log'
for details

xps.Rcheck/00install.out:

* 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-2.7-bioc/meat/xps.Rcheck/xps/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

Welcome to xps version 1.10.2 
    an R wrapper for XPS - eXpression Profiling System
    (c) Copyright 2001-2010 by Christian Stratowa
    

* DONE (xps)

xps.Rcheck/xps-Ex.timings:

nameusersystemelapsed
AnalysisTreeSet-class000
CallTreeSet-class000
DataTreeSet-class000
ExprTreeSet-class000
Filter-class000
FilterTreeSet-class000
PreFilter-class0.080.000.08
PreFilter-constructor0.040.000.04
ProcesSet-class000
ProjectInfo-class0.020.000.02
ProjectInfo-constructor0.060.000.06
SchemeTreeSet-class000
TreeSet-class000
UniFilter-class0.010.000.01
UniFilter-constructor0.040.000.03
addData-methods0.460.031.21
attachCall-methods0.410.000.62
attachExpr-methods1.410.011.66
attachInten-methods0.450.040.48
attachMask-methods0.170.010.19
bgcorrect0.740.080.99
boxplot-methods0.640.060.73
callFilter-methods0.030.000.03
cvFilter-methods0.010.000.02
dabg.call1.380.063.31
dfw0.370.000.66
diffFilter-methods0.020.000.01
existsROOTFile000
exonLevel000
export0.640.100.74
export.root0.660.060.71
express1.280.031.83
exprs-methods000
extenPart000
farms0.430.000.91
fcFilter-methods0.020.000.01
firma000
firma.expr000
firma.score000
gapFilter-methods000
getChipName0.010.000.02
getChipType000
getDatatype000
getNameType000
getNumberTrees000
getProbeInfo0.020.000.01
getTreeNames000
highFilter-methods0.010.000.02
hist-methods0.580.060.64
image.dev0.550.080.62
import.data0.220.000.58
import.exon.scheme000
import.expr.scheme000
import.genome.scheme000
ini.call0.480.000.64
intensity-methods000
isROOTFile000
lowFilter-methods0.000.000.02
madFilter-methods0.020.000.01
mas40.560.020.99
mas50.610.051.03
mas5.call0.260.000.40
mboxplot-methods0.600.030.63
metaProbesets000
namePart000
normalize1.310.011.92
nuseplot-methods0.050.000.05
pm-methods0.620.030.65
pmplot-methods0.520.110.63
prefilter000
presCall-methods000
quantileFilter-methods0.010.000.01
ratioFilter-methods0.020.000.02
rawCELName-methods0.030.000.03
rleplot-methods0.050.000.05
rma1.310.021.62
root.call0.250.000.41
root.data0.120.030.31
root.density000
root.expr1.320.021.63
root.graph1D000
root.graph2D000
root.hist1D000
root.hist2D000
root.hist3D000
root.image000
root.merge.data0.220.000.39
root.mvaplot000
root.profile000
root.scheme0.030.000.03
summarize1.320.032.04
type2Exten000
uniTest-methods0.010.000.01
unifilter000
unitestFilter-methods0.020.000.02
validTreetype000
varFilter-methods0.010.000.01