Package: xps

Version: 1.13.1

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings xps_1.13.1.tar.gz

StartedAt: 2011-05-09 14:35:50 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 14:39:09 -0700 (Mon, 09 May 2011)

EllapsedTime: 199.0 seconds

RetCode: 0

Status:  OK

CheckDir: xps.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/xps.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* 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 ‘1.13.1’
* 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 15.8Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    libs   6.1Mb
* 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 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

* 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:1109:0: warning: "xmax" redefined
TMLMath.cxx:1060:0: note: 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::ExportMaskTreeInfo(Int_t, TString*, const char*, std::ofstream&, const char*)’:
XPSData.cxx:1797:10: warning: unused variable ‘err’
XPSData.cxx: In member function ‘virtual Int_t XGeneChipHyb::ReadXMLHeader(std::ifstream&, const char*, char)’:
XPSData.cxx:2810:10: warning: unused variable ‘fNMasked’
XPSData.cxx:2820:10: warning: unused variable ‘fNOutlier’
XPSData.cxx:2830:10: warning: unused variable ‘fNModified’
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSProcessing.cxx
XPSProcessing.cxx: In member function ‘virtual Int_t XProcesSet::ExportMaskTreeInfo(Int_t, TString*, const char*, std::ofstream&, const char*)’:
XPSProcessing.cxx:1530:10: warning: unused variable ‘err’
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:2066:36: 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:334:13: 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:239:10: warning: ‘his2all’ may be used uninitialized in this function
XPSNormalizer.cxx:240:10: 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::DoDataQualityControl(Int_t, TTree**, TTree**, TTree**, XDNAChip*, TFile*)’:
XPSPreProcessing.cxx:3026:56: warning: operation on ‘numsels’ may be undefined
XPSPreProcessing.cxx: In member function ‘virtual Int_t XGCProcesSet::DoBorderElements(Int_t, TTree**, TTree**, XDNAChip*, TFile*)’:
XPSPreProcessing.cxx:3515:10: warning: unused variable ‘idxhi’
XPSPreProcessing.cxx:3515:17: warning: unused variable ‘idxlo’
XPSPreProcessing.cxx: In member function ‘virtual Int_t XGCProcesSet::DoBgrdQualityControl(Int_t, TTree**, XDNAChip*, TFile*)’:
XPSPreProcessing.cxx:3670:10: warning: unused variable ‘numunits’
XPSPreProcessing.cxx:3671:10: warning: unused variable ‘size’
XPSPreProcessing.cxx: In member function ‘virtual Int_t XGCProcesSet::DoMultichipCall(Int_t, TTree**, Int_t&, TTree**, TFile*)’:
XPSPreProcessing.cxx:4252:56: 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:5135:56: warning: operation on ‘numsels’ may be undefined
XPSPreProcessing.cxx: In member function ‘virtual Int_t XGCProcesSet::ExportQualTrees(Int_t, TString*, const char*, std::ofstream&, const char*)’:
XPSPreProcessing.cxx:6762:16: warning: unused variable ‘idxstr’
XPSPreProcessing.cxx: In member function ‘TTree* XGCProcesSet::FillDataTree(TTree*, const char*, XAlgorithm*, Int_t, Int_t, Double_t*, Double_t*)’:
XPSPreProcessing.cxx:8737:1: warning: label ‘cleanup’ defined but not used
XPSPreProcessing.cxx: In member function ‘virtual Int_t XExonProcesSet::DoSpliceExpress(Int_t, TTree**, Int_t, TTree**, TFile*)’:
XPSPreProcessing.cxx:9591:56: warning: operation on ‘numsels’ may be undefined
XPSPreProcessing.cxx:9782:14: warning: unused variable ‘numatoms’
XPSPreProcessing.cxx:9389:10: warning: unused variable ‘x’
XPSPreProcessing.cxx:9390:10: warning: unused variable ‘y’
XPSPreProcessing.cxx:9395:10: warning: unused variable ‘stepout’
XPSPreProcessing.cxx: In member function ‘virtual TTree* XExonProcesSet::SchemeTree(XAlgorithm*, void*, TLeaf**)’:
XPSPreProcessing.cxx:10349:18: 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:1787:13: 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-2.9-bioc/meat/xps.Rcheck/xps/libs
** 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	0.000	0.000	0.001
AnalysisTreeSet-class	0.000	0.000	0.002
CallTreeSet-class	0.004	0.000	0.002
DataTreeSet-class	0.000	0.000	0.001
ExprTreeSet-class	0.000	0.000	0.001
Filter-class	0.004	0.000	0.000
FilterTreeSet-class	0.000	0.000	0.001
PreFilter-class	0.052	0.000	0.051
PreFilter-constructor	0.048	0.000	0.051
ProcesSet-class	0.000	0.004	0.001
ProjectInfo-class	0.012	0.000	0.012
ProjectInfo-constructor	0.064	0.000	0.063
QualTreeSet-class	0.000	0.000	0.001
SchemeTreeSet-class	0.000	0.000	0.001
TreeSet-class	0.000	0.000	0.001
UniFilter-class	0.02	0.00	0.02
UniFilter-constructor	0.036	0.000	0.036
addData-methods	0.392	0.016	0.601
attachCall-methods	0.484	0.012	0.547
attachExpr-methods	1.244	0.052	1.406
attachInten-methods	0.380	0.060	0.439
attachMask-methods	0.172	0.028	0.202
bgcorrect	0.608	0.108	0.787
borderplot-methods	0	0	0
boxplot-methods	0.680	0.064	0.744
callFilter-methods	0.020	0.008	0.027
coiplot-methods	0	0	0
cvFilter-methods	0.012	0.000	0.012
dabg.call	1.096	0.008	1.162
dfw	0.404	0.004	0.508
diffFilter-methods	0.012	0.000	0.013
existsROOTFile	0	0	0
exonLevel	0.000	0.000	0.001
export	0.456	0.052	0.506
export.root	0.440	0.044	0.486
express	1.076	0.032	1.230
exprs-methods	0	0	0
extenPart	0	0	0
farms	0.504	0.000	0.603
fcFilter-methods	0.012	0.000	0.014
firma	0.000	0.000	0.001
firma.expr	0	0	0
firma.score	0.000	0.000	0.001
fitQC	0.004	0.000	0.001
fitRLM	0	0	0
gapFilter-methods	0.016	0.000	0.016
getChipName	0.004	0.000	0.004
getChipType	0.004	0.000	0.004
getDatatype	0	0	0
getNameType	0.004	0.000	0.004
getNumberTrees	0.004	0.000	0.004
getProbeInfo	0.000	0.000	0.002
getTreeNames	0.008	0.000	0.011
highFilter-methods	0.012	0.000	0.012
hist-methods	0.468	0.112	0.583
image-methods	0	0	0
import.data	0.228	0.000	0.390
import.exon.scheme	0	0	0
import.expr.scheme	0	0	0
import.genome.scheme	0	0	0
ini.call	0.488	0.008	0.561
intensity-methods	0	0	0
isROOTFile	0	0	0
lowFilter-methods	0.008	0.000	0.011
madFilter-methods	0.008	0.000	0.010
mas4	0.652	0.000	0.839
mas5	0.724	0.012	0.919
mas5.call	0.272	0.008	0.363
mboxplot-methods	0.480	0.076	0.559
metaProbesets	0.000	0.000	0.001
namePart	0.000	0.000	0.001
normalize	1.144	0.008	1.434
nuseplot-methods	0.044	0.000	0.045
plotImage	0	0	0
pm-methods	0.424	0.116	0.549
pmplot-methods	0.404	0.088	0.491
prefilter	0	0	0
presCall-methods	0.004	0.000	0.001
qualify	0	0	0
quantileFilter-methods	0.008	0.000	0.010
ratioFilter-methods	0.008	0.000	0.008
rawCELName-methods	0.028	0.000	0.028
rleplot-methods	0.040	0.000	0.038
rma	1.108	0.008	1.215
root.call	0.200	0.008	0.287
root.data	0.149	0.004	0.208
root.density	0	0	0
root.expr	1.044	0.020	1.172
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	0.208	0.000	0.324
root.mvaplot	0	0	0
root.profile	0	0	0
root.scheme	0.032	0.000	0.032
summarize	1.140	0.024	1.386
treeInfo-methods	0.048	0.004	0.055
trma	1.216	0.032	1.312
type2Exten	0	0	0
uniTest-methods	0.016	0.000	0.016
unifilter	0	0	0
unitestFilter-methods	0.012	0.000	0.015
validTreetype	0.000	0.000	0.001
varFilter-methods	0.012	0.000	0.013