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BioC 2.14: CHECK report for xps on zin2

This page was generated on 2014-10-08 08:48:18 -0700 (Wed, 08 Oct 2014).

Package 821/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
xps 1.24.1
Christian Stratowa
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/xps
Last Changed Rev: 92881 / Revision: 95116
Last Changed Date: 2014-07-26 01:18:08 -0700 (Sat, 26 Jul 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: xps
Version: 1.24.1
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings xps_1.24.1.tar.gz
StartedAt: 2014-10-08 03:47:24 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 03:50:19 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 175.4 seconds
RetCode: 0
Status:  OK 
CheckDir: xps.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings xps_1.24.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/xps.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.24.1’
* 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 ... [98s/100s] 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 ‘build’ 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 loading without being on the library search path ... OK
* checking 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-2.14-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 files in ‘vignettes’ ... OK
* checking examples ... [17s/23s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.14-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
found ROOT version 5.32/01 in directory /usr/local/root
** libs
** arch - 
g++ -I/usr/local/root/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/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c TStat.cxx
g++ -I/usr/local/root/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/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSBase.cxx
g++ -I/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSUtils.cxx
g++ -I/usr/local/root/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/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSDataTypes.cxx
g++ -I/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSProjectHandler.cxx
g++ -I/usr/local/root/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/usr/local/root/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/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSHybridizer.cxx
g++ -I/usr/local/root/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/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSNormalizer.cxx
g++ -I/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSPreProcessing.cxx
XPSPreProcessing.cxx: In member function ‘virtual Int_t XGCProcesSet::DoBorderElements(Int_t, TTree**, TTree**, XDNAChip*, TFile*)’:
XPSPreProcessing.cxx:3522:10: warning: unused variable ‘idxhi’ [-Wunused-variable]
XPSPreProcessing.cxx:3522:17: warning: unused variable ‘idxlo’ [-Wunused-variable]
XPSPreProcessing.cxx:3527:13: warning: variable ‘mnhi’ set but not used [-Wunused-but-set-variable]
XPSPreProcessing.cxx:3528:13: 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:3677:10: warning: unused variable ‘numunits’ [-Wunused-variable]
XPSPreProcessing.cxx:3678:10: warning: unused variable ‘size’ [-Wunused-variable]
XPSPreProcessing.cxx: In member function ‘virtual Int_t XGCProcesSet::ExportResdTrees(Int_t, TString*, const char*, std::ofstream&, const char*)’:
XPSPreProcessing.cxx:5780:10: 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:6769:16: 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:8744:1: 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:9789:14: warning: unused variable ‘numatoms’ [-Wunused-variable]
XPSPreProcessing.cxx:9396:10: warning: unused variable ‘x’ [-Wunused-variable]
XPSPreProcessing.cxx:9397:10: warning: unused variable ‘y’ [-Wunused-variable]
XPSPreProcessing.cxx:9402:10: warning: unused variable ‘stepout’ [-Wunused-variable]
XPSPreProcessing.cxx: In member function ‘virtual TTree* XExonProcesSet::SchemeTree(XAlgorithm*, void*, TLeaf**)’:
XPSPreProcessing.cxx:10356:18: warning: unused variable ‘scheme_ptr_ptr’ [-Wunused-variable]
g++ -I/usr/local/root/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/usr/local/root/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/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSAnalyzer.cxx
g++ -I/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSAnalysis.cxx
g++ -I/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c rwrapper.cxx
Generating dictionary xpsDict.cxx...
g++ -I/usr/local/root/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-2.14-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
AffyRNAdeg0.0000.0000.001
AnalysisTreeSet-class0.0040.0000.001
CallTreeSet-class0.0000.0000.001
DataTreeSet-class0.0000.0000.002
ExprTreeSet-class0.0040.0000.001
Filter-class0.0000.0000.001
FilterTreeSet-class0.0040.0000.001
NUSE0.0000.0000.001
PreFilter-class0.0440.0000.040
PreFilter-constructor0.0640.0000.067
ProcesSet-class0.0000.0000.002
ProjectInfo-class0.0120.0000.010
ProjectInfo-constructor0.0480.0040.051
QualTreeSet-class0.0000.0000.001
RLE0.0000.0000.001
SchemeTreeSet-class0.0000.0000.001
TreeSet-class0.0000.0000.002
UniFilter-class0.0160.0000.013
UniFilter-constructor0.0240.0000.026
addData-methods0.2080.0200.775
attachCall-methods0.2480.0040.417
attachDataXY-methods0.1160.0320.146
attachExpr-methods0.9920.0081.374
attachInten-methods0.2360.0360.276
attachMask-methods0.0960.0120.108
attachProbe-methods0.1040.0320.135
attachUnitNames-methods0.0840.0040.088
bgcorrect0.4000.0600.618
borderplot-methods0.0000.0000.001
boxplot-methods0.3640.0360.404
callFilter-methods0.0160.0040.020
coiplot-methods000
cvFilter-methods0.0080.0000.009
dabg.call0.8680.0081.061
dfw0.2240.0040.475
diffFilter-methods0.0080.0000.009
existsROOTFile0.0040.0000.001
exonLevel0.0000.0000.001
export0.3320.0360.365
export.root0.3080.0320.340
express0.9160.0081.166
exprs-methods0.0000.0000.001
extenPart0.0040.0000.001
farms0.2440.0040.499
fcFilter-methods0.0120.0000.012
firma0.0000.0000.001
firma.expr0.0040.0000.001
firma.score0.0000.0000.001
fitQC0.0000.0000.001
fitRLM0.0000.0000.001
gapFilter-methods0.0120.0000.010
getChipName0.0040.0000.003
getChipType0.0040.0000.002
getDatatype0.0000.0000.001
getNameType0.0040.0000.002
getNumberTrees0.0040.0000.003
getProbeInfo0.0000.0000.002
getTreeNames0.0000.0040.006
highFilter-methods0.0080.0040.009
hist-methods0.0600.0000.059
image-methods000
import.data0.1400.0080.427
import.exon.scheme0.0040.0000.002
import.expr.scheme0.0000.0000.001
import.genome.scheme000
indexUnits-methods0.3120.1200.436
ini.call0.2800.0040.545
intensity-methods0.0000.0000.001
intensity2GCplot-methods0.2280.0280.259
isROOTFile0.0000.0000.001
lowFilter-methods0.0080.0000.009
madFilter-methods0.0080.0000.009
mas40.3480.0080.707
mas50.4080.0040.781
mas5.call0.1520.0000.287
mboxplot-methods0.3120.0640.373
metaProbesets000
namePart0.0000.0000.001
normalize0.9400.0121.564
nuseplot-methods0.0240.0040.028
plotImage0.0000.0000.001
pm-methods0.4000.0280.427
pmplot-methods0.3280.0480.374
prefilter0.0000.0000.001
presCall-methods0.0000.0000.001
probeContentGC-methods0.200.040.24
probeSequence-methods0.1520.0200.173
probesetID2unitID-methods0.0840.0040.095
probesetplot-methods0.2920.0200.311
qualify0.0000.0000.001
quantileFilter-methods0.0080.0000.009
ratioFilter-methods0.0080.0000.008
rawCELName-methods0.020.000.02
rleplot-methods0.0280.0000.026
rma0.9560.0001.228
root.call0.1280.0080.269
root.data0.1040.0040.255
root.density0.0000.0000.001
root.expr0.9200.0121.181
root.graph1D0.0000.0000.001
root.graph2D000
root.hist1D0.0000.0000.001
root.hist2D0.0000.0000.001
root.hist3D000
root.image0.0040.0000.001
root.merge.data0.1320.0000.274
root.mvaplot000
root.profile0.0000.0000.001
root.scheme0.0240.0000.021
summarize0.9400.0201.678
symbol2unitID-methods0.1080.0080.119
treeInfo-methods0.0320.0000.029
trma0.9560.0041.204
type2Exten0.0000.0000.001
uniTest-methods0.0040.0040.010
unifilter0.0000.0000.001
unitestFilter-methods0.0120.0040.011
validTreetype0.0000.0000.001
varFilter-methods0.0120.0000.009
xpsQAReport0.0000.0000.001