Package: xps

Version: 1.13.2

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings xps_1.13.2.tar.gz

StartedAt: 2011-07-07 02:36:25 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 02:39:42 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 197.0 seconds

RetCode: 1

Status:  ERROR

CheckDir: xps.Rcheck

Warnings: NA

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/xps.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* 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 ‘1.13.2’
* 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 installed package size ... NOTE
  installed size is 14.6Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs   6.2Mb
* 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 ... ERROR
Running examples in ‘xps-Ex.R’ failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: probesetID2unitID-methods
> ### Title: Conversion between Probeset IDs and UnitIDs
> ### Aliases: probesetID2unitID-methods probesetID2unitID
> ###   transcriptID2unitID-methods transcriptID2unitID
> ###   unitID2probesetID-methods unitID2probesetID
> ###   unitID2transcriptID-methods unitID2transcriptID
> ### Keywords: methods
> 
> ### ** Examples
> 
> ## load ROOT scheme file
> scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
> 
> ## unitNames not attached
> id <- unitID2probesetID(scheme.test3, c(2,34,229))
slot ‘unitname’ is empty, importing data from ‘Test3.idx’ ...
Error in parse(text = paste("id", sQuote(x), sep = "$")) : 
  1:4: unexpected input
1: id$â
      ^
Calls: unitID2probesetID ... .local -> unitID2affyID -> lapply -> FUN -> eval -> parse
Execution halted

* 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 5.30/00 in directory /usr/local/root
** libs
** arch - 
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/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/root/include/root -c TStat.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c StatUtils.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSBase.cxx
XPSBase.cxx: In member function ‘XFolder* XFolder::AddFolder(const char*, const char*, const char*, TCollection*)’:
XPSBase.cxx:183:76: warning: too many arguments for format
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSUtils.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSSchemes.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSDataTypes.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSProjectHandler.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/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/root/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/root/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/root/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/root/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/root/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/root/include/root -c XPSNormation.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/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/root/include/root -c XPSAnalyzer.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSAnalysis.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c rwrapper.cxx
Generating dictionary xpsDict.cxx...
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/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/root/lib/root -lGui -lGpad -lHist -lGraf -lGraf3d -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lRIO -lNet -lThread -lCore -lCint -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 1.13.2 
    an R wrapper for XPS - eXpression Profiling System
    (c) Copyright 2001-2011 by Christian Stratowa
    

* DONE (xps)

name	user	system	elapsed
AffyRNAdeg	0	0	0
AnalysisTreeSet-class	0.000	0.000	0.002
CallTreeSet-class	0.000	0.000	0.001
DataTreeSet-class	0.000	0.000	0.002
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	0.100	0.000	0.101
PreFilter-constructor	0.048	0.000	0.047
ProcesSet-class	0.000	0.000	0.001
ProjectInfo-class	0.012	0.000	0.013
ProjectInfo-constructor	0.072	0.000	0.076
QualTreeSet-class	0.004	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	0.028	0.008	0.034
addData-methods	0.364	0.016	0.595
attachCall-methods	0.384	0.008	0.478
attachDataXY-methods	0.188	0.028	0.217
attachExpr-methods	1.068	0.056	1.245
attachInten-methods	0.288	0.036	0.323
attachMask-methods	0.128	0.028	0.155
attachUnitNames-methods	0.112	0.000	0.113
bgcorrect	0.468	0.080	0.610
borderplot-methods	0	0	0
boxplot-methods	0.528	0.076	0.611
callFilter-methods	0.024	0.000	0.026
coiplot-methods	0	0	0
cvFilter-methods	0.012	0.000	0.013
dabg.call	1.040	0.000	1.088
dfw	0.288	0.020	0.369
diffFilter-methods	0.012	0.000	0.011
existsROOTFile	0.000	0.000	0.001
exonLevel	0	0	0
export	0.372	0.044	0.417
export.root	0.408	0.060	0.467
express	0.908	0.040	1.175
exprs-methods	0	0	0
extenPart	0	0	0
farms	0.396	0.004	0.479
fcFilter-methods	0.016	0.000	0.017
firma	0	0	0
firma.expr	0	0	0
firma.score	0	0	0
fitQC	0	0	0
fitRLM	0.000	0.000	0.001
gapFilter-methods	0.016	0.000	0.014
getChipName	0.004	0.000	0.004
getChipType	0.004	0.000	0.003
getDatatype	0	0	0
getNameType	0.004	0.000	0.002
getNumberTrees	0.004	0.000	0.003
getProbeInfo	0.000	0.000	0.002
getTreeNames	0.008	0.000	0.008
highFilter-methods	0.012	0.000	0.012
hist-methods	0.024	0.000	0.028
image-methods	0	0	0
import.data	0.196	0.000	0.936
import.exon.scheme	0.000	0.000	0.001
import.expr.scheme	0.000	0.004	0.001
import.genome.scheme	0	0	0
indexUnits-methods	0.436	0.144	0.580
ini.call	0.400	0.004	0.516
intensity-methods	0	0	0
isROOTFile	0	0	0
lowFilter-methods	0.012	0.000	0.011
madFilter-methods	0.012	0.000	0.011
mas4	0.480	0.008	0.671
mas5	0.544	0.016	0.732
mas5.call	0.208	0.004	0.288
mboxplot-methods	0.436	0.068	0.500
metaProbesets	0	0	0
namePart	0	0	0
normalize	0.964	0.008	1.626
nuseplot-methods	0.048	0.000	0.045
plotImage	0.000	0.000	0.001
pm-methods	0.480	0.072	0.551
pmplot-methods	0.448	0.064	0.513
prefilter	0.000	0.000	0.001
presCall-methods	0.000	0.000	0.001