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BioC 2.12: CHECK report for xps on george2

This page was generated on 2013-10-09 09:37:26 -0700 (Wed, 09 Oct 2013).

Package 669/671HostnameOS / ArchBUILDCHECKBUILD BIN
xps 1.20.3
Christian Stratowa
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/xps
Last Changed Rev: 79980 / Revision: 81334
Last Changed Date: 2013-08-31 11:59:57 -0700 (Sat, 31 Aug 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: xps
Version: 1.20.3
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings xps_1.20.3.tar.gz
StartedAt: 2013-10-09 05:35:31 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 05:39:39 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 247.7 seconds
RetCode: 0
Status:  OK 
CheckDir: xps.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/xps.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.20.3’
* 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 ... [139s/142s] 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 ... [24s/25s] 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.

xps.Rcheck/00install.out:

* 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++ -I/include -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++ -I/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c TStat.cxx
g++ -I/include -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++ -I/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSBase.cxx
g++ -I/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSUtils.cxx
g++ -I/include -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:7506:29: warning: variable ‘psetID’ set but not used [-Wunused-but-set-variable]
g++ -I/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSDataTypes.cxx
g++ -I/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSProjectHandler.cxx
g++ -I/include -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++ -I/include -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++ -I/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSHybridizer.cxx
g++ -I/include -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++ -I/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSNormalizer.cxx
g++ -I/include -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++ -I/include -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++ -I/include -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++ -I/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSAnalyzer.cxx
g++ -I/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSAnalysis.cxx
g++ -I/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c rwrapper.cxx
Generating dictionary xpsDict.cxx...
g++ -I/include -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
** testing if installed package can be loaded
* DONE (xps)

xps.Rcheck/xps-Ex.timings:

nameusersystemelapsed
AffyRNAdeg0.0960.0000.095
AnalysisTreeSet-class0.0080.0000.008
CallTreeSet-class0.0040.0000.006
DataTreeSet-class0.0200.0000.017
ExprTreeSet-class0.0080.0000.007
Filter-class0.0040.0000.006
FilterTreeSet-class0.0040.0000.007
PreFilter-class0.0640.0000.063
PreFilter-constructor0.0560.0000.054
ProcesSet-class0.0080.0000.006
ProjectInfo-class0.0320.0000.031
ProjectInfo-constructor0.0760.0000.076
QualTreeSet-class0.0920.0000.091
SchemeTreeSet-class0.0160.0000.015
TreeSet-class0.0080.0000.009
UniFilter-class0.0240.0040.027
UniFilter-constructor0.0400.0000.041
addData-methods0.2440.0240.412
attachCall-methods0.4320.0080.442
attachDataXY-methods0.2440.0360.277
attachExpr-methods1.2360.0041.247
attachInten-methods0.4840.0360.520
attachMask-methods0.1840.0160.200
attachProbe-methods0.2080.0320.241
attachUnitNames-methods0.1720.0000.173
bgcorrect0.5480.0840.639
borderplot-methods0.0040.0000.005
boxplot-methods0.6680.0920.761
callFilter-methods0.0320.0000.033
coiplot-methods0.0080.0000.004
cvFilter-methods0.0160.0000.016
dabg.call1.1840.0081.193
dfw0.2840.0000.286
diffFilter-methods0.0120.0040.017
existsROOTFile0.0080.0000.005
exonLevel0.0040.0000.007
export0.4200.0680.489
export.root0.4360.0720.511
express1.0440.0161.065
exprs-methods0.0240.0000.024
extenPart0.0160.0000.015
farms0.4320.0000.435
fcFilter-methods0.0200.0040.024
firma0.0160.0000.017
firma.expr0.0080.0000.007
firma.score0.0040.0000.005
fitQC0.0120.0000.011
fitRLM0.0120.0000.011
gapFilter-methods0.0200.0000.021
getChipName0.0080.0000.010
getChipType0.0120.0000.010
getDatatype0.0080.0000.005
getNameType0.0080.0000.010
getNumberTrees0.0080.0000.010
getProbeInfo0.0080.0000.007
getTreeNames0.0160.0000.014
highFilter-methods0.0240.0000.020
hist-methods0.0360.0000.038
image-methods0.0080.0000.009
import.data0.1840.0000.190
import.exon.scheme0.0120.0000.011
import.expr.scheme0.0080.0000.009
import.genome.scheme0.0040.0040.006
indexUnits-methods0.5880.1440.732
ini.call0.3840.0120.403
intensity-methods0.0080.0000.007
intensity2GCplot-methods0.3960.0760.472
isROOTFile0.0040.0000.004
lowFilter-methods0.0160.0000.019
madFilter-methods0.0160.0000.017
mas40.4880.0040.497
mas50.5600.0080.572
mas5.call0.2520.0000.254
mboxplot-methods0.5240.0520.576
metaProbesets0.0040.0000.004
namePart0.0040.0000.005
normalize1.0480.0121.068
nuseplot-methods0.0440.0000.043
plotImage0.0080.0000.012
pm-methods0.6480.0640.712
pmplot-methods0.4770.0720.548
prefilter0.0080.0000.009
presCall-methods0.0080.0000.009
probeContentGC-methods0.3200.0520.376
probeSequence-methods0.2600.0360.297
probesetID2unitID-methods0.1760.0000.176
probesetplot-methods0.4120.0520.462
qualify0.0120.0040.015
quantileFilter-methods0.0160.0000.017
ratioFilter-methods0.0160.0000.015
rawCELName-methods0.0280.0000.030
rleplot-methods0.0360.0040.041
rma1.0880.0081.131
root.call0.1640.0080.170
root.data0.1320.0040.138
root.density0.0080.0000.006
root.expr1.0160.0121.032
root.graph1D0.0080.0000.006
root.graph2D0.0040.0000.004
root.hist1D0.0040.0000.006
root.hist2D0.0080.0000.005
root.hist3D0.0040.0000.005
root.image0.0040.0000.006
root.merge.data0.1720.0000.173
root.mvaplot0.0080.0000.006
root.profile0.0040.0000.005
root.scheme0.0240.0080.031
summarize1.0440.0161.068
symbol2unitID-methods0.2040.0160.220
treeInfo-methods0.0520.0000.051
trma1.0680.0201.089
type2Exten0.0040.0000.005
uniTest-methods0.0160.0000.017
unifilter0.0080.0000.008
unitestFilter-methods0.0200.0000.018
validTreetype0.0040.0000.005
varFilter-methods0.0160.0000.017
xpsQAReport0.0080.0000.008