Package: xps

Version: 1.8.3

Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes --timings xps_1.8.3.tar.gz

StartedAt: 2010-10-04 20:17:57 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 20:21:11 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 193.7 seconds

RetCode: 0

Status:  OK

CheckDir: xps.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/xps.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'xps/DESCRIPTION' ... OK
* this is package 'xps' version '1.8.3'
* 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 for sufficient/correct file permissions ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* installing *source* package 'xps' ...
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for gcc... (cached) gcc -std=gnu99
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc -std=gnu99 accepts -g... (cached) yes
checking for gcc -std=gnu99 option to accept ANSI C... (cached) none needed
checking for root-config... yes
found ROOT version 5.22/00 in directory /usr/local
** libs
** arch - 
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c TMLMath.cxx
TMLMath.cxx:1109:1: warning: "xmax" redefined
TMLMath.cxx:1060:1: warning: this is the location of the previous definition
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c TStat.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c StatUtils.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSBase.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSUtils.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSSchemes.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSDataTypes.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSProjectHandler.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSData.cxx
XPSData.cxx: In member function 'virtual Int_t XGeneChipHyb::ReadData(std::ifstream&, const Option_t*, const char*, char, Int_t)':
XPSData.cxx:1763: warning: label 'cleanup' defined but not used
XPSData.cxx: In member function 'virtual Int_t XGeneChipHyb::ReadXDAData(std::ifstream&, const Option_t*, const char*, char, Int_t)':
XPSData.cxx:1954: warning: label 'cleanup' defined but not used
XPSData.cxx: In member function 'virtual Int_t XGeneChipHyb::ReadXMLHeader(std::ifstream&, const char*, char)':
XPSData.cxx:2476: warning: unused variable 'fNMasked'
XPSData.cxx:2486: warning: unused variable 'fNOutlier'
XPSData.cxx:2496: warning: unused variable 'fNModified'
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSProcessing.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSHybridizer.cxx
XPSHybridizer.cxx: In member function 'Double_t XDetectionCall::WilcoxTest(Int_t, Double_t*, Double_t)':
XPSHybridizer.cxx:1857: warning: 'pval' may be used uninitialized in this function
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSSelector.cxx
XPSSelector.cxx: In member function 'Double_t XRankSelector::Cutoff(Int_t, const Double_t*, Double_t, Bool_t)':
XPSSelector.cxx:334: warning: 'par0' may be used uninitialized in this function
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSNormalizer.cxx
XPSNormalizer.cxx: In member function 'virtual Int_t XNormalizer::Calculate(Int_t, Double_t*, Double_t*, Int_t*)':
XPSNormalizer.cxx:239: warning: 'his2all' may be used uninitialized in this function
XPSNormalizer.cxx:240: warning: 'his2sel' may be used uninitialized in this function
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSPreProcessing.cxx
XPSPreProcessing.cxx: In member function 'virtual Int_t XGCProcesSet::DoMultichipCall(Int_t, TTree**, Int_t&, TTree**, TFile*)':
XPSPreProcessing.cxx:2651: warning: operation on 'numsels' may be undefined
XPSPreProcessing.cxx: In member function 'virtual Int_t XGCProcesSet::DoMultichipExpress(Int_t, TTree**, Int_t, TTree**, TFile*)':
XPSPreProcessing.cxx:3533: warning: operation on 'numsels' may be undefined
XPSPreProcessing.cxx: In member function 'virtual Int_t XExonProcesSet::DoSpliceExpress(Int_t, TTree**, Int_t, TTree**, TFile*)':
XPSPreProcessing.cxx:6184: warning: operation on 'numsels' may be undefined
XPSPreProcessing.cxx:6375: warning: unused variable 'numatoms'
XPSPreProcessing.cxx:5987: warning: unused variable 'x'
XPSPreProcessing.cxx:5988: warning: unused variable 'y'
XPSPreProcessing.cxx:5993: warning: unused variable 'stepout'
XPSPreProcessing.cxx: In member function 'virtual TTree* XExonProcesSet::SchemeTree(XAlgorithm*, void*, TLeaf**)':
XPSPreProcessing.cxx:6938: warning: unused variable 'scheme_ptr_ptr'
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSNormation.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSFilter.cxx
XPSFilter.cxx: In member function 'virtual Int_t XUniFilter::Calculate(TTree*, const char*, TTree*, const char*, Int_t)':
XPSFilter.cxx:1787: warning: unused variable 'brchUnit'
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSAnalyzer.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSAnalysis.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c rwrapper.cxx
Generating dictionary xpsDict.cxx...
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c xpsDict.cxx
g++ -shared -O2 -m64 TMLMath.o TStat.o StatUtils.o XPSBase.o XPSUtils.o XPSSchemes.o XPSDataTypes.o XPSProjectHandler.o XPSData.o XPSProcessing.o XPSHybridizer.o XPSSelector.o XPSNormalizer.o XPSPreProcessing.o XPSNormation.o XPSFilter.o XPSAnalyzer.o XPSAnalysis.o rwrapper.o xpsDict.o -L/usr/local/lib/root -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -lGui -pthread -lm -ldl -rdynamic  -lRIO -lGed -lTreePlayer -lTreeViewer -o  xps.so 
installing to /loc/home/biocbuild/bbs-2.6-bioc/meat/xps.Rcheck/xps/libs
** 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 1.8.3 
    an R wrapper for XPS - eXpression Profiling System
    (c) Copyright 2001-2010 by Christian Stratowa
    

* DONE (xps)

name	user	system	elapsed
AnalysisTreeSet-class	0.000	0.000	0.001
CallTreeSet-class	0.000	0.000	0.001
DataTreeSet-class	0.000	0.000	0.001
ExprTreeSet-class	0.004	0.000	0.001
Filter-class	0.000	0.000	0.001
FilterTreeSet-class	0.000	0.000	0.001
PreFilter-class	0.048	0.004	0.051
PreFilter-constructor	0.052	0.000	0.049
ProcesSet-class	0.000	0.000	0.001
ProjectInfo-class	0.016	0.000	0.014
ProjectInfo-constructor	0.108	0.008	0.116
SchemeTreeSet-class	0.000	0.004	0.001
TreeSet-class	0.000	0.000	0.001
UniFilter-class	0.020	0.000	0.021
UniFilter-constructor	0.032	0.000	0.034
addData-methods	0.260	0.008	0.773
attachCall-methods	0.384	0.028	0.618
attachExpr-methods	1.148	0.004	1.684
attachInten-methods	0.316	0.056	0.379
attachMask-methods	0.124	0.044	0.170
bgcorrect	0.528	0.092	0.909
boxplot-methods	0.548	0.084	0.634
callFilter-methods	0.024	0.004	0.028
cvFilter-methods	0.012	0.000	0.013
dabg.call	1.072	0.016	1.329
dfw	0.340	0.004	0.766
diffFilter-methods	0.012	0.000	0.014
existsROOTFile	0.000	0.004	0.001
exonLevel	0.000	0.000	0.001
export	0.388	0.056	0.442
export.root	0.392	0.112	0.503
express	1.020	0.008	1.553
exprs-methods	0.000	0.004	0.001
extenPart	0.000	0.000	0.001
farms	0.352	0.024	0.981
fcFilter-methods	0.016	0.000	0.014
firma	0.000	0.000	0.001
firma.expr	0	0	0
firma.score	0	0	0
gapFilter-methods	0.012	0.000	0.014
getChipName	0.000	0.000	0.003
getChipType	0.000	0.000	0.002
getDatatype	0	0	0
getNameType	0.000	0.000	0.002
getNumberTrees	0.004	0.000	0.003
getProbeInfo	0.004	0.000	0.002
getTreeNames	0.004	0.000	0.007
highFilter-methods	0.012	0.000	0.012
hist-methods	0.492	0.112	0.604
image.dev	0.440	0.100	0.541
import.data	0.152	0.000	0.717
import.exon.scheme	0	0	0
import.expr.scheme	0	0	0
import.genome.scheme	0	0	0
ini.call	0.480	0.004	0.916
intensity-methods	0	0	0
isROOTFile	0	0	0
lowFilter-methods	0.012	0.000	0.013
madFilter-methods	0.012	0.000	0.013
mas4	0.556	0.016	1.264
mas5	0.656	0.020	1.650
mas5.call	0.292	0.000	0.752
mboxplot-methods	0.420	0.108	0.539
metaProbesets	0	0	0
namePart	0	0	0
normalize	1.044	0.020	3.408
nuseplot-methods	0.040	0.004	0.047
pm-methods	0.476	0.104	0.578
pmplot-methods	0.440	0.116	0.553
prefilter	0	0	0
presCall-methods	0.000	0.000	0.001
quantileFilter-methods	0.012	0.000	0.012
ratioFilter-methods	0.008	0.000	0.011
rawCELName-methods	0.032	0.000	0.033
rleplot-methods	0.044	0.004	0.048
rma	1.076	0.004	1.897
root.call	0.260	0.008	0.543
root.data	0.128	0.004	0.400
root.density	0	0	0
root.expr	1.109	0.044	1.639
root.graph1D	0.000	0.000	0.001
root.graph2D	0.000	0.000	0.001
root.hist1D	0.000	0.004	0.001
root.hist2D	0.000	0.000	0.001
root.hist3D	0.000	0.000	0.001
root.image	0	0	0
root.merge.data	0.200	0.008	0.501
root.mvaplot	0	0	0
root.profile	0	0	0
root.scheme	0.032	0.000	0.030
summarize	1.072	0.008	2.227
type2Exten	0.000	0.000	0.001
uniTest-methods	0.016	0.000	0.017
unifilter	0	0	0
unitestFilter-methods	0.016	0.000	0.016
validTreetype	0	0	0
varFilter-methods	0.016	0.000	0.014