Package: xps

Version: 1.19.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings xps_1.19.1.tar.gz

StartedAt: 2013-01-16 07:07:45 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 07:11:21 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 215.9 seconds

RetCode: 0

Status:  OK

CheckDir: xps.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/xps.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.19.1’
* 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 for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 ... 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 compiled code ... NOTE
Note: information on .o files is not available
File ‘/loc/home/biocbuild/bbs-2.12-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 installed files from ‘inst/doc’ ... 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

NOTE: There were 3 notes.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/xps.Rcheck/00check.log’
for details.

* 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 5.32/01 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 -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -pthread -lm -ldl -rdynamic  -lRIO -lGed -lTreePlayer -lTreeViewer -o  xps.so 
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/xps.Rcheck/xps/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘APTvsXPS.Rnw’ 
   ‘xps.Rnw’ 
   ‘xpsClasses.Rnw’ 
   ‘xpsPreprocess.Rnw’ 
** testing if installed package can be loaded

* DONE (xps)

name	user	system	elapsed
AffyRNAdeg	0.072	0.000	0.070
AnalysisTreeSet-class	0.008	0.000	0.005
CallTreeSet-class	0.000	0.004	0.005
DataTreeSet-class	0.008	0.004	0.011
ExprTreeSet-class	0.008	0.000	0.008
Filter-class	0.000	0.004	0.003
FilterTreeSet-class	0.004	0.004	0.006
PreFilter-class	0.048	0.004	0.054
PreFilter-constructor	0.048	0.000	0.048
ProcesSet-class	0.008	0.000	0.006
ProjectInfo-class	0.020	0.008	0.029
ProjectInfo-constructor	0.060	0.004	0.067
QualTreeSet-class	0.008	0.000	0.007
SchemeTreeSet-class	0.008	0.000	0.008
TreeSet-class	0.004	0.000	0.007
UniFilter-class	0.020	0.000	0.022
UniFilter-constructor	0.036	0.000	0.035
addData-methods	0.212	0.028	0.494
attachCall-methods	0.344	0.008	0.356
attachDataXY-methods	0.188	0.028	0.215
attachExpr-methods	0.980	0.012	1.104
attachInten-methods	0.300	0.036	0.337
attachMask-methods	0.140	0.020	0.159
attachProbe-methods	0.232	0.028	0.263
attachUnitNames-methods	0.152	0.000	0.152
bgcorrect	0.464	0.072	0.669
borderplot-methods	0.004	0.000	0.005
boxplot-methods	0.480	0.068	0.548
callFilter-methods	0.032	0.000	0.031
coiplot-methods	0.004	0.000	0.005
cvFilter-methods	0.016	0.000	0.016
dabg.call	0.988	0.000	1.033
dfw	0.244	0.008	0.316
diffFilter-methods	0.016	0.000	0.016
existsROOTFile	0.004	0.004	0.004
exonLevel	0.004	0.000	0.006
export	0.352	0.044	0.395
export.root	0.48	0.02	0.50
express	0.836	0.020	0.923
exprs-methods	0.008	0.000	0.008
extenPart	0.004	0.000	0.004
farms	0.276	0.008	0.347
fcFilter-methods	0.016	0.000	0.017
firma	0.012	0.000	0.013
firma.expr	0.004	0.000	0.006
firma.score	0.004	0.000	0.005
fitQC	0.008	0.000	0.010
fitRLM	0.012	0.000	0.010
gapFilter-methods	0.016	0.000	0.017
getChipName	0.008	0.000	0.008
getChipType	0.008	0.000	0.008
getDatatype	0.004	0.000	0.005
getNameType	0.008	0.000	0.008
getNumberTrees	0.008	0.000	0.008
getProbeInfo	0.004	0.000	0.005
getTreeNames	0.012	0.000	0.011
highFilter-methods	0.016	0.000	0.016
hist-methods	0.028	0.000	0.029
image-methods	0.008	0.000	0.008
import.data	0.168	0.004	0.309
import.exon.scheme	0.008	0.000	0.010
import.expr.scheme	0.012	0.000	0.010
import.genome.scheme	0.004	0.000	0.006
indexUnits-methods	0.464	0.120	0.582
ini.call	0.348	0.008	0.463
intensity-methods	0.008	0.000	0.008
intensity2GCplot-methods	0.312	0.080	0.392
isROOTFile	0.004	0.000	0.004
lowFilter-methods	0.016	0.000	0.016
madFilter-methods	0.016	0.000	0.015
mas4	0.436	0.000	0.610
mas5	0.484	0.008	0.697
mas5.call	0.200	0.000	0.299
mboxplot-methods	0.424	0.044	0.469
metaProbesets	0.008	0.000	0.004
namePart	0.004	0.000	0.004
normalize	0.872	0.012	1.097
nuseplot-methods	0.040	0.000	0.038
plotImage	0.012	0.000	0.011
pm-methods	0.560	0.056	0.616
pmplot-methods	0.404	0.072	0.476
prefilter	0.004	0.000	0.006
presCall-methods	0.008	0.000	0.007
probeContentGC-methods	0.268	0.068	0.337
probeSequence-methods	0.228	0.040	0.266
probesetID2unitID-methods	0.160	0.004	0.162
probesetplot-methods	0.368	0.040	0.406
qualify	0.012	0.000	0.012
quantileFilter-methods	0.012	0.000	0.015
ratioFilter-methods	0.012	0.000	0.013
rawCELName-methods	0.028	0.000	0.030
rleplot-methods	0.040	0.000	0.038
rma	0.920	0.004	1.062
root.call	0.148	0.008	0.157
root.data	0.189	0.000	0.238
root.density	0.004	0.000	0.005
root.expr	0.856	0.004	0.970
root.graph1D	0.004	0.000	0.004
root.graph2D	0.004	0.000	0.006
root.hist1D	0.004	0.000	0.004
root.hist2D	0.004	0.000	0.005
root.hist3D	0.004	0.000	0.005
root.image	0.004	0.000	0.005
root.merge.data	0.156	0.000	0.259
root.mvaplot	0.004	0.000	0.006
root.profile	0.004	0.000	0.004
root.scheme	0.028	0.000	0.030
summarize	0.876	0.016	1.110
symbol2unitID-methods	0.192	0.000	0.192
treeInfo-methods	0.044	0.000	0.045
trma	0.908	0.012	1.015
type2Exten	0.004	0.000	0.004
uniTest-methods	0.08	0.00	0.08
unifilter	0.008	0.000	0.007
unitestFilter-methods	0.016	0.000	0.016
validTreetype	0.004	0.000	0.004
varFilter-methods	0.012	0.000	0.016
xpsQAReport	0.004	0.000	0.006