Package: xps

Version: 1.18.1

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings xps_1.18.1.tar.gz

StartedAt: 2013-03-25 05:39:41 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 05:43:39 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 237.8 seconds

RetCode: 0

Status:  OK

CheckDir: xps.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/xps.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.18.1’
* 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 whether package ‘xps’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   6.1Mb
* 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 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-2.11-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 2 notes.
See
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/xps.Rcheck/00check.log’
for details.

* installing *source* package ‘xps’ ...
configure: loading site script /usr/share/site/x86_64-unknown-linux-gnu
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
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:7477:29: 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 /loc/home/biocbuild/bbs-2.11-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	0	0
AnalysisTreeSet-class	0.000	0.000	0.001
CallTreeSet-class	0.000	0.004	0.001
DataTreeSet-class	0.000	0.000	0.001
ExprTreeSet-class	0	0	0
Filter-class	0.000	0.000	0.001
FilterTreeSet-class	0	0	0
PreFilter-class	0.052	0.004	0.055
PreFilter-constructor	0.064	0.000	0.064
ProcesSet-class	0.000	0.000	0.001
ProjectInfo-class	0.016	0.004	0.020
ProjectInfo-constructor	0.160	0.004	0.165
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	0.024	0.000	0.022
UniFilter-constructor	0.044	0.000	0.045
addData-methods	0.280	0.016	0.453
attachCall-methods	0.404	0.000	0.439
attachDataXY-methods	0.236	0.020	0.256
attachExpr-methods	1.100	0.020	1.263
attachInten-methods	0.364	0.060	0.427
attachMask-methods	0.164	0.016	0.182
attachProbe-methods	0.192	0.032	0.224
attachUnitNames-methods	0.192	0.012	0.203
bgcorrect	0.544	0.048	0.633
borderplot-methods	0.000	0.000	0.001
boxplot-methods	0.716	0.064	0.778
callFilter-methods	0.028	0.000	0.027
coiplot-methods	0	0	0
cvFilter-methods	0.016	0.000	0.015
dabg.call	0.984	0.012	1.023
dfw	0.260	0.012	0.329
diffFilter-methods	0.004	0.004	0.011
existsROOTFile	0.004	0.000	0.001
exonLevel	0.000	0.000	0.001
export	0.392	0.048	0.440
export.root	0.432	0.036	0.465
express	0.876	0.004	0.947
exprs-methods	0	0	0
extenPart	0.000	0.000	0.001
farms	0.388	0.000	0.461
fcFilter-methods	0.016	0.000	0.016
firma	0	0	0
firma.expr	0	0	0
firma.score	0	0	0
fitQC	0	0	0
fitRLM	0	0	0
gapFilter-methods	0.012	0.004	0.013
getChipName	0.004	0.000	0.004
getChipType	0.004	0.000	0.004
getDatatype	0	0	0
getNameType	0.004	0.000	0.003
getNumberTrees	0.004	0.000	0.004
getProbeInfo	0.000	0.000	0.001
getTreeNames	0.004	0.004	0.009
highFilter-methods	0.012	0.000	0.013
hist-methods	0.032	0.000	0.030
image-methods	0	0	0
import.data	0.188	0.000	0.275
import.exon.scheme	0	0	0
import.expr.scheme	0.000	0.000	0.001
import.genome.scheme	0	0	0
indexUnits-methods	0.472	0.112	0.587
ini.call	0.360	0.004	0.433
intensity-methods	0.004	0.000	0.000
intensity2GCplot-methods	0.360	0.056	0.417
isROOTFile	0	0	0
lowFilter-methods	0.012	0.000	0.010
madFilter-methods	0.012	0.000	0.011
mas4	0.488	0.004	0.657
mas5	0.532	0.012	0.725
mas5.call	0.216	0.000	0.272
mboxplot-methods	0.432	0.076	0.508
metaProbesets	0	0	0
namePart	0	0	0
normalize	0.868	0.000	1.014
nuseplot-methods	0.028	0.008	0.035
plotImage	0.000	0.000	0.001
pm-methods	0.516	0.044	0.560
pmplot-methods	0.368	0.108	0.477
prefilter	0	0	0
presCall-methods	0	0	0
probeContentGC-methods	0.344	0.036	0.378
probeSequence-methods	0.284	0.032	0.317
probesetID2unitID-methods	0.180	0.008	0.188
probesetplot-methods	0.436	0.016	0.451
qualify	0.000	0.000	0.001
quantileFilter-methods	0.012	0.000	0.012
ratioFilter-methods	0.012	0.000	0.010
rawCELName-methods	0.028	0.000	0.028
rleplot-methods	0.036	0.000	0.036
rma	0.965	0.016	1.123
root.call	0.172	0.004	0.196
root.data	0.132	0.004	0.164
root.density	0	0	0
root.expr	0.948	0.008	1.066
root.graph1D	0	0	0
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	0.176	0.004	0.223
root.mvaplot	0	0	0
root.profile	0	0	0
root.scheme	0.024	0.000	0.023
summarize	0.960	0.024	1.083
symbol2unitID-methods	0.200	0.004	0.204
treeInfo-methods	0.036	0.004	0.041
trma	0.932	0.004	1.079
type2Exten	0	0	0
uniTest-methods	0.012	0.000	0.011
unifilter	0.000	0.000	0.001
unitestFilter-methods	0.012	0.000	0.012
validTreetype	0	0	0
varFilter-methods	0.008	0.000	0.011
xpsQAReport	0	0	0