Package: xps

Version: 1.14.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings xps_1.14.0.tar.gz

StartedAt: 2012-03-24 03:11:02 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 03:14:47 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 225.3 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 2.14.2 (2012-02-29)
* 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 ‘1.14.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package ‘xps’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.2Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 ... NOTE
File ‘xps/R/zzz.R’:
  .onLoad calls:
    require(methods)
    require(utils)

Package startup functions should not change the search path.
See section ‘Good practice’ in ?.onAttach.

* 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 compiled code ... NOTE
File ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/xps.Rcheck/xps/libs/xps.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
  Found ‘printf’, possibly from ‘printf’ (C)

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.  The detected symbols
are linked into the code but might come from libraries and not actually
be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* 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 5.30/00 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

* DONE (xps)

name	user	system	elapsed
AffyRNAdeg	0	0	0
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	0	0
Filter-class	0	0	0
FilterTreeSet-class	0	0	0
PreFilter-class	0.040	0.004	0.042
PreFilter-constructor	0.036	0.000	0.038
ProcesSet-class	0.004	0.000	0.001
ProjectInfo-class	0.016	0.000	0.015
ProjectInfo-constructor	0.112	0.000	0.111
QualTreeSet-class	0.000	0.000	0.001
SchemeTreeSet-class	0.000	0.000	0.001
TreeSet-class	0	0	0
UniFilter-class	0.016	0.000	0.017
UniFilter-constructor	0.024	0.000	0.027
addData-methods	0.332	0.008	0.545
attachCall-methods	0.332	0.000	0.407
attachDataXY-methods	0.188	0.024	0.211
attachExpr-methods	1.020	0.016	1.153
attachInten-methods	0.268	0.056	0.322
attachMask-methods	0.132	0.020	0.150
attachProbe-methods	0.152	0.036	0.189
attachUnitNames-methods	0.136	0.000	0.136
bgcorrect	0.452	0.084	0.596
borderplot-methods	0	0	0
boxplot-methods	0.484	0.092	0.576
callFilter-methods	0.020	0.000	0.021
coiplot-methods	0.004	0.000	0.000
cvFilter-methods	0.008	0.000	0.011
dabg.call	0.976	0.020	1.031
dfw	0.256	0.004	0.329
diffFilter-methods	0.008	0.000	0.009
existsROOTFile	0	0	0
exonLevel	0	0	0
export	0.348	0.032	0.383
export.root	0.380	0.024	0.407
express	0.876	0.004	0.931
exprs-methods	0.004	0.000	0.001
extenPart	0.000	0.000	0.001
farms	0.284	0.004	0.382
fcFilter-methods	0.012	0.000	0.012
firma	0.000	0.000	0.001
firma.expr	0	0	0
firma.score	0	0	0
fitQC	0.000	0.000	0.001
fitRLM	0	0	0
gapFilter-methods	0.012	0.000	0.011
getChipName	0.004	0.000	0.007
getChipType	0.000	0.000	0.003
getDatatype	0.000	0.000	0.001
getNameType	0.000	0.000	0.002
getNumberTrees	0.004	0.000	0.002
getProbeInfo	0.000	0.000	0.001
getTreeNames	0.004	0.000	0.006
highFilter-methods	0.012	0.000	0.010
hist-methods	0.012	0.008	0.020
image-methods	0	0	0
import.data	0.172	0.000	0.424
import.exon.scheme	0.000	0.004	0.001
import.expr.scheme	0.000	0.000	0.001
import.genome.scheme	0	0	0
indexUnits-methods	0.508	0.148	0.660
ini.call	0.356	0.008	0.472
intensity-methods	0	0	0
intensity2GCplot-methods	0.356	0.040	0.395
isROOTFile	0	0	0
lowFilter-methods	0.008	0.004	0.010
madFilter-methods	0.008	0.000	0.009
mas4	0.452	0.000	0.567
mas5	0.500	0.008	0.685
mas5.call	0.180	0.008	0.270
mboxplot-methods	0.380	0.072	0.454
metaProbesets	0	0	0
namePart	0.000	0.000	0.001
normalize	0.960	0.008	1.300
nuseplot-methods	0.028	0.000	0.031
plotImage	0.004	0.000	0.000
pm-methods	0.532	0.072	0.606
pmplot-methods	0.392	0.072	0.461
prefilter	0.000	0.000	0.001
presCall-methods	0	0	0
probeContentGC-methods	0.252	0.076	0.325
probeSequence-methods	0.224	0.028	0.251
probesetID2unitID-methods	0.144	0.000	0.143
probesetplot-methods	0.356	0.028	0.383
qualify	0	0	0
quantileFilter-methods	0.008	0.000	0.009
ratioFilter-methods	0.008	0.000	0.008
rawCELName-methods	0.020	0.000	0.022
rleplot-methods	0.024	0.004	0.030
rma	0.964	0.004	1.097
root.call	0.148	0.000	0.193
root.data	0.128	0.000	0.187
root.density	0	0	0
root.expr	0.908	0.004	1.029
root.graph1D	0.000	0.000	0.001
root.graph2D	0	0	0
root.hist1D	0	0	0
root.hist2D	0	0	0
root.hist3D	0	0	0
root.image	0	0	0
root.merge.data	0.148	0.008	0.650
root.mvaplot	0	0	0
root.profile	0	0	0
root.scheme	0.021	0.000	0.021
summarize	0.968	0.012	1.174
symbol2unitID-methods	0.180	0.000	0.181
treeInfo-methods	0.032	0.000	0.033
trma	0.952	0.004	1.077
type2Exten	0.004	0.000	0.000
uniTest-methods	0.008	0.000	0.010
unifilter	0	0	0
unitestFilter-methods	0.008	0.000	0.011
validTreetype	0	0	0
varFilter-methods	0.008	0.000	0.010
xpsQAReport	0	0	0