Package: xps

Version: 1.19.8

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings xps_1.19.8.tar.gz

StartedAt: 2013-03-25 05:12:21 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 05:17:48 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 326.7 seconds

RetCode: 0

Status:  OK

CheckDir: xps.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/xps.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘1.19.8’
* 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 ... [173s/195s] OK
* checking installed package size ... NOTE
  installed size is 12.3Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   6.1Mb
* 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 ‘/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++)

Compiled code should not call entry points 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 ... [27s/28s] 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
  ‘/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 [enabled by default]
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
StatUtils.cxx: In member function ‘Int_t TUnivariateTest::Test(const char*, const char*, const char*, Int_t, Int_t, Double_t, const char*, const char*, char)’:
StatUtils.cxx:764:40: warning: variable ‘pval’ set but not used [-Wunused-but-set-variable]
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 [-Wformat-extra-args]
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
XPSSchemes.cxx: In member function ‘virtual Int_t XGeneChip::ImportProbeInfo(std::ifstream&, Option_t*, const char*, char, Int_t)’:
XPSSchemes.cxx:2800:12: warning: variable ‘order’ set but not used [-Wunused-but-set-variable]
XPSSchemes.cxx: In member function ‘virtual Int_t XGeneChip::ReadBinaryData(std::ifstream&, Option_t*, const char*, char, Int_t)’:
XPSSchemes.cxx:3452:22: warning: variable ‘flag’ set but not used [-Wunused-but-set-variable]
XPSSchemes.cxx: In member function ‘virtual Int_t XGenomeChip::ImportTransAnnotation(std::ifstream&, Option_t*, const char*, char, Int_t)’:
XPSSchemes.cxx:6213:13: warning: variable ‘nprobes’ set but not used [-Wunused-but-set-variable]
XPSSchemes.cxx: In member function ‘virtual Int_t XExonChip::ReadData(std::ifstream&, Option_t*, const char*, char, Int_t)’:
XPSSchemes.cxx:7484:29: warning: variable ‘psetID’ set but not used [-Wunused-but-set-variable]
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::ExportDataTreeInfo(Int_t, TString*, const char*, std::ofstream&, const char*)’:
XPSData.cxx:1603:11: warning: variable ‘hasMaxNPix’ set but not used [-Wunused-but-set-variable]
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’ [-Wunused-variable]
XPSData.cxx: In member function ‘virtual Int_t XGeneChipHyb::ReadXMLHeader(std::ifstream&, const char*, char)’:
XPSData.cxx:2810:10: warning: unused variable ‘fNMasked’ [-Wunused-variable]
XPSData.cxx:2820:10: warning: unused variable ‘fNOutlier’ [-Wunused-variable]
XPSData.cxx:2830:10: warning: unused variable ‘fNModified’ [-Wunused-variable]
XPSData.cxx: In member function ‘virtual Int_t XGeneChipPivot::ReadData(std::ifstream&, Option_t*, const char*, char, Int_t)’:
XPSData.cxx:3758:10: warning: variable ‘numunits’ set but not used [-Wunused-but-set-variable]
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’ [-Wunused-variable]
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSHybridizer.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSSelector.cxx
XPSSelector.cxx: In member function ‘virtual Int_t XRankSelector::Calculate(Int_t, Double_t*, Double_t*, Int_t*)’:
XPSSelector.cxx:222:10: warning: variable ‘err’ set but not used [-Wunused-but-set-variable]
XPSSelector.cxx: In member function ‘Double_t XRankSelector::Cutoff(Int_t, const Double_t*, Double_t, Bool_t)’:
XPSSelector.cxx:334:19: warning: variable ‘par1’ set but not used [-Wunused-but-set-variable]
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:314:4: warning: ‘his2sel’ may be used uninitialized in this function [-Wuninitialized]
XPSNormalizer.cxx:313:4: warning: ‘his2all’ may be used uninitialized in this function [-Wuninitialized]
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 [-Wsequence-point]
XPSPreProcessing.cxx: In member function ‘virtual Int_t XGCProcesSet::DoBorderElements(Int_t, TTree**, TTree**, XDNAChip*, TFile*)’:
XPSPreProcessing.cxx:3515:10: warning: unused variable ‘idxhi’ [-Wunused-variable]
XPSPreProcessing.cxx:3515:17: warning: unused variable ‘idxlo’ [-Wunused-variable]
XPSPreProcessing.cxx:3520:13: warning: variable ‘mnhi’ set but not used [-Wunused-but-set-variable]
XPSPreProcessing.cxx:3521:13: warning: variable ‘mnlo’ set but not used [-Wunused-but-set-variable]
XPSPreProcessing.cxx: In member function ‘virtual Int_t XGCProcesSet::DoBgrdQualityControl(Int_t, TTree**, XDNAChip*, TFile*)’:
XPSPreProcessing.cxx:3670:10: warning: unused variable ‘numunits’ [-Wunused-variable]
XPSPreProcessing.cxx:3671:10: warning: unused variable ‘size’ [-Wunused-variable]
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 [-Wsequence-point]
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 [-Wsequence-point]
XPSPreProcessing.cxx: In member function ‘virtual Int_t XGCProcesSet::ExportResdTrees(Int_t, TString*, const char*, std::ofstream&, const char*)’:
XPSPreProcessing.cxx:5773:10: warning: variable ‘err’ set but not used [-Wunused-but-set-variable]
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’ [-Wunused-variable]
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 [-Wunused-label]
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 [-Wsequence-point]
XPSPreProcessing.cxx:9782:14: warning: unused variable ‘numatoms’ [-Wunused-variable]
XPSPreProcessing.cxx:9389:10: warning: unused variable ‘x’ [-Wunused-variable]
XPSPreProcessing.cxx:9390:10: warning: unused variable ‘y’ [-Wunused-variable]
XPSPreProcessing.cxx:9395:10: warning: unused variable ‘stepout’ [-Wunused-variable]
XPSPreProcessing.cxx: In member function ‘virtual TTree* XExonProcesSet::SchemeTree(XAlgorithm*, void*, TLeaf**)’:
XPSPreProcessing.cxx:10349:18: warning: unused variable ‘scheme_ptr_ptr’ [-Wunused-variable]
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSNormation.cxx
XPSNormation.cxx: In member function ‘virtual Int_t XNormedGCSet::ExportExprTrees(Int_t, TString*, const char*, std::ofstream&, const char*)’:
XPSNormation.cxx:1350:10: warning: variable ‘err’ set but not used [-Wunused-but-set-variable]
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’ [-Wunused-variable]
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 /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	0.116	0.000	0.121
AnalysisTreeSet-class	0.016	0.000	0.013
CallTreeSet-class	0.012	0.000	0.013
DataTreeSet-class	0.032	0.000	0.031
ExprTreeSet-class	0.016	0.000	0.017
Filter-class	0.004	0.004	0.011
FilterTreeSet-class	0.012	0.000	0.011
PreFilter-class	0.088	0.000	0.086
PreFilter-constructor	0.120	0.004	0.126
ProcesSet-class	0.044	0.000	0.042
ProjectInfo-class	0.052	0.000	0.053
ProjectInfo-constructor	0.212	0.004	0.216
QualTreeSet-class	0.008	0.004	0.014
SchemeTreeSet-class	0.016	0.000	0.019
TreeSet-class	0.008	0.000	0.011
UniFilter-class	0.032	0.000	0.033
UniFilter-constructor	0.052	0.000	0.052
addData-methods	0.396	0.004	0.561
attachCall-methods	0.584	0.008	0.618
attachDataXY-methods	0.316	0.048	0.366
attachExpr-methods	1.320	0.008	1.342
attachInten-methods	0.496	0.064	0.562
attachMask-methods	0.156	0.028	0.185
attachProbe-methods	0.224	0.032	0.254
attachUnitNames-methods	0.224	0.000	0.223
bgcorrect	0.700	0.068	0.773
borderplot-methods	0.016	0.000	0.019
boxplot-methods	0.920	0.068	0.989
callFilter-methods	0.072	0.000	0.073
coiplot-methods	0.016	0.000	0.012
cvFilter-methods	0.020	0.000	0.021
dabg.call	1.100	0.016	1.121
dfw	0.296	0.008	0.309
diffFilter-methods	0.104	0.004	0.108
existsROOTFile	0.008	0.000	0.008
exonLevel	0.004	0.004	0.008
export	0.436	0.072	0.510
export.root	0.472	0.068	0.539
express	1.128	0.016	1.149
exprs-methods	0.012	0.000	0.012
extenPart	0.008	0.000	0.009
farms	0.304	0.016	0.324
fcFilter-methods	0.020	0.000	0.023
firma	0.016	0.000	0.017
firma.expr	0.008	0.000	0.010
firma.score	0.004	0.000	0.007
fitQC	0.012	0.000	0.012
fitRLM	0.012	0.000	0.013
gapFilter-methods	0.02	0.00	0.02
getChipName	0.012	0.000	0.010
getChipType	0.008	0.000	0.011
getDatatype	0.004	0.000	0.005
getNameType	0.004	0.008	0.011
getNumberTrees	0.012	0.000	0.011
getProbeInfo	0.008	0.000	0.008
getTreeNames	0.012	0.004	0.014
highFilter-methods	0.020	0.004	0.021
hist-methods	0.032	0.000	0.033
image-methods	0.008	0.000	0.009
import.data	0.188	0.004	0.199
import.exon.scheme	0.012	0.004	0.016
import.expr.scheme	0.008	0.000	0.009
import.genome.scheme	0.008	0.000	0.008
indexUnits-methods	0.552	0.160	0.715
ini.call	0.432	0.004	0.439
intensity-methods	0.008	0.004	0.010
intensity2GCplot-methods	0.460	0.052	0.513
isROOTFile	0.008	0.000	0.007
lowFilter-methods	0.020	0.004	0.023
madFilter-methods	0.016	0.000	0.019
mas4	0.524	0.012	0.569
mas5	0.600	0.024	0.632
mas5.call	0.336	0.000	0.340
mboxplot-methods	0.621	0.112	0.740
metaProbesets	0.016	0.000	0.018
namePart	0.008	0.000	0.006
normalize	1.156	0.012	1.182
nuseplot-methods	0.048	0.008	0.055
plotImage	0.024	0.004	0.028
pm-methods	0.752	0.084	0.853
pmplot-methods	0.544	0.080	0.626
prefilter	0.016	0.000	0.015
presCall-methods	0.012	0.000	0.013
probeContentGC-methods	0.340	0.084	0.426
probeSequence-methods	0.280	0.040	0.323
probesetID2unitID-methods	0.188	0.000	0.189
probesetplot-methods	0.440	0.080	0.524
qualify	0.012	0.008	0.019
quantileFilter-methods	0.020	0.000	0.019
ratioFilter-methods	0.020	0.000	0.019
rawCELName-methods	0.036	0.000	0.034
rleplot-methods	0.044	0.000	0.044
rma	1.128	0.016	1.159
root.call	0.168	0.008	0.182
root.data	0.144	0.000	0.147
root.density	0.080	0.004	0.087
root.expr	1.060	0.004	1.069
root.graph1D	0.008	0.000	0.007
root.graph2D	0.004	0.000	0.005
root.hist1D	0.008	0.000	0.006
root.hist2D	0.004	0.000	0.006
root.hist3D	0.008	0.000	0.007
root.image	0.008	0.000	0.007
root.merge.data	0.164	0.008	0.179
root.mvaplot	0.008	0.000	0.007
root.profile	0.008	0.000	0.006
root.scheme	0.032	0.000	0.033
summarize	1.060	0.020	1.092
symbol2unitID-methods	0.220	0.012	0.234
treeInfo-methods	0.052	0.004	0.056
trma	1.136	0.012	1.154
type2Exten	0.004	0.000	0.006
uniTest-methods	0.020	0.000	0.019
unifilter	0.008	0.000	0.010
unitestFilter-methods	0.02	0.00	0.02
validTreetype	0.008	0.000	0.007
varFilter-methods	0.02	0.00	0.02
xpsQAReport	0.092	0.000	0.090