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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: /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

Command output

* 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

xps.Rcheck/00install.out:

* 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)

xps.Rcheck/xps-Ex.timings:

nameusersystemelapsed
AnalysisTreeSet-class0.0000.0000.001
CallTreeSet-class0.0000.0000.001
DataTreeSet-class0.0000.0000.001
ExprTreeSet-class0.0000.0040.001
Filter-class0.0000.0000.001
FilterTreeSet-class0.0000.0000.001
PreFilter-class0.0840.0000.086
PreFilter-constructor0.0360.0000.037
ProcesSet-class0.0040.0000.001
ProjectInfo-class0.0120.0000.011
ProjectInfo-constructor0.0480.0040.054
SchemeTreeSet-class0.0000.0000.001
TreeSet-class0.0000.0000.001
UniFilter-class0.0160.0000.018
UniFilter-constructor0.0240.0040.029
addData-methods0.3320.0320.703
attachCall-methods0.3480.0080.404
attachExpr-methods1.0720.0081.234
attachInten-methods0.2920.0600.359
attachMask-methods0.1160.0360.155
bgcorrect0.5120.0760.654
boxplot-methods0.5320.0560.586
callFilter-methods0.0240.0000.022
cvFilter-methods0.0120.0000.010
dabg.call0.9880.0081.000
dfw0.2960.0160.525
diffFilter-methods0.0120.0000.011
existsROOTFile000
exonLevel000
export0.4360.0520.486
export.root0.3960.0480.444
express0.9520.0161.115
exprs-methods000
extenPart0.0000.0000.001
farms0.3480.0040.407
fcFilter-methods0.0120.0000.013
firma0.0000.0000.001
firma.expr0.0000.0000.001
firma.score000
gapFilter-methods0.0120.0000.011
getChipName0.0040.0000.003
getChipType0.0040.0000.003
getDatatype0.0000.0000.001
getNameType0.0000.0040.003
getNumberTrees0.0040.0000.003
getProbeInfo0.0040.0000.002
getTreeNames0.0080.0000.007
highFilter-methods0.0080.0000.010
hist-methods0.4600.1160.580
image.dev0.4320.1000.532
import.data0.1320.0040.272
import.exon.scheme0.0000.0040.000
import.expr.scheme000
import.genome.scheme000
ini.call0.4000.0080.501
intensity-methods000
isROOTFile000
lowFilter-methods0.0120.0000.010
madFilter-methods0.0080.0000.009
mas40.5080.0080.630
mas50.5520.0160.777
mas5.call0.2240.0040.310
mboxplot-methods0.3840.1120.496
metaProbesets000
namePart000
normalize0.9760.0201.158
nuseplot-methods0.0360.0040.040
pm-methods0.4640.1000.575
pmplot-methods0.4320.0880.521
prefilter000
presCall-methods000
quantileFilter-methods0.0040.0040.010
ratioFilter-methods0.0080.0000.009
rawCELName-methods0.0280.0000.028
rleplot-methods0.0400.0000.037
rma0.9840.0121.139
root.call0.2240.0040.410
root.data0.1200.0040.478
root.density0.0000.0000.001
root.expr0.9440.0241.354
root.graph1D000
root.graph2D000
root.hist1D000
root.hist2D0.0000.0000.001
root.hist3D000
root.image000
root.merge.data0.1520.0040.303
root.mvaplot000
root.profile000
root.scheme0.0200.0040.023
summarize0.9650.0201.214
type2Exten0.0000.0000.001
uniTest-methods0.0120.0000.012
unifilter000
unitestFilter-methods0.0160.0000.015
validTreetype0.0000.0000.001
varFilter-methods0.0120.0000.010