Package: xps

Version: 1.10.2

Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings xps_1.10.2.tar.gz

StartedAt: 2011-03-31 09:09:54 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 09:12:47 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 173.1 seconds

RetCode: 0

Status:  OK

CheckDir: xps.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/xps.Rcheck’
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 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 for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* 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

* 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 5.27/04 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:240: warning: ‘his2sel’ may be used uninitialized in this function
XPSNormalizer.cxx:239: warning: ‘his2all’ 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 -lz -lGui -pthread -lm -ldl -rdynamic  -lRIO -lGed -lTreePlayer -lTreeViewer -o  xps.so 
installing to /loc/home/biocbuild/bbs-2.7-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 1.10.2 
    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	0.000	0.004	0.001
Filter-class	0.000	0.000	0.001
FilterTreeSet-class	0.000	0.000	0.001
PreFilter-class	0.084	0.000	0.086
PreFilter-constructor	0.036	0.000	0.037
ProcesSet-class	0.004	0.000	0.001
ProjectInfo-class	0.012	0.000	0.011
ProjectInfo-constructor	0.048	0.004	0.054
SchemeTreeSet-class	0.000	0.000	0.001
TreeSet-class	0.000	0.000	0.001
UniFilter-class	0.016	0.000	0.018
UniFilter-constructor	0.024	0.004	0.029
addData-methods	0.332	0.032	0.703
attachCall-methods	0.348	0.008	0.404
attachExpr-methods	1.072	0.008	1.234
attachInten-methods	0.292	0.060	0.359
attachMask-methods	0.116	0.036	0.155
bgcorrect	0.512	0.076	0.654
boxplot-methods	0.532	0.056	0.586
callFilter-methods	0.024	0.000	0.022
cvFilter-methods	0.012	0.000	0.010
dabg.call	0.988	0.008	1.000
dfw	0.296	0.016	0.525
diffFilter-methods	0.012	0.000	0.011
existsROOTFile	0	0	0
exonLevel	0	0	0
export	0.436	0.052	0.486
export.root	0.396	0.048	0.444
express	0.952	0.016	1.115
exprs-methods	0	0	0
extenPart	0.000	0.000	0.001
farms	0.348	0.004	0.407
fcFilter-methods	0.012	0.000	0.013
firma	0.000	0.000	0.001
firma.expr	0.000	0.000	0.001
firma.score	0	0	0
gapFilter-methods	0.012	0.000	0.011
getChipName	0.004	0.000	0.003
getChipType	0.004	0.000	0.003
getDatatype	0.000	0.000	0.001
getNameType	0.000	0.004	0.003
getNumberTrees	0.004	0.000	0.003
getProbeInfo	0.004	0.000	0.002
getTreeNames	0.008	0.000	0.007
highFilter-methods	0.008	0.000	0.010
hist-methods	0.460	0.116	0.580
image.dev	0.432	0.100	0.532
import.data	0.132	0.004	0.272
import.exon.scheme	0.000	0.004	0.000
import.expr.scheme	0	0	0
import.genome.scheme	0	0	0
ini.call	0.400	0.008	0.501
intensity-methods	0	0	0
isROOTFile	0	0	0
lowFilter-methods	0.012	0.000	0.010
madFilter-methods	0.008	0.000	0.009
mas4	0.508	0.008	0.630
mas5	0.552	0.016	0.777
mas5.call	0.224	0.004	0.310
mboxplot-methods	0.384	0.112	0.496
metaProbesets	0	0	0
namePart	0	0	0
normalize	0.976	0.020	1.158
nuseplot-methods	0.036	0.004	0.040
pm-methods	0.464	0.100	0.575
pmplot-methods	0.432	0.088	0.521
prefilter	0	0	0
presCall-methods	0	0	0
quantileFilter-methods	0.004	0.004	0.010
ratioFilter-methods	0.008	0.000	0.009
rawCELName-methods	0.028	0.000	0.028
rleplot-methods	0.040	0.000	0.037
rma	0.984	0.012	1.139
root.call	0.224	0.004	0.410
root.data	0.120	0.004	0.478
root.density	0.000	0.000	0.001
root.expr	0.944	0.024	1.354
root.graph1D	0	0	0
root.graph2D	0	0	0
root.hist1D	0	0	0
root.hist2D	0.000	0.000	0.001
root.hist3D	0	0	0
root.image	0	0	0
root.merge.data	0.152	0.004	0.303
root.mvaplot	0	0	0
root.profile	0	0	0
root.scheme	0.020	0.004	0.023
summarize	0.965	0.020	1.214
type2Exten	0.000	0.000	0.001
uniTest-methods	0.012	0.000	0.012
unifilter	0	0	0
unitestFilter-methods	0.016	0.000	0.015
validTreetype	0.000	0.000	0.001
varFilter-methods	0.012	0.000	0.010