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BioC 3.0: CHECK report for xps on zin1

This page was generated on 2015-04-10 09:37:57 -0700 (Fri, 10 Apr 2015).

Package 930/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
xps 1.26.1
Christian Stratowa
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/xps
Last Changed Rev: 101499 / Revision: 102249
Last Changed Date: 2015-03-28 02:45:25 -0700 (Sat, 28 Mar 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: xps
Version: 1.26.1
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings xps_1.26.1.tar.gz
StartedAt: 2015-04-10 05:29:18 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 05:32:32 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 193.8 seconds
RetCode: 0
Status:  OK 
CheckDir: xps.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings xps_1.26.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/xps.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.26.1’
* 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 ... [103s/113s] 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 ... NOTE
'library' or 'require' call to ‘tools’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* 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-3.0-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, nor the system RNG.
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 ... [19s/26s] 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
* DONE

NOTE: There were 5 notes.
See
  ‘/home/biocbuild/bbs-3.0-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-3.0-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
AffyRNAdeg0.0040.0000.001
AnalysisTreeSet-class0.0040.0000.002
CallTreeSet-class0.0000.0000.001
DataTreeSet-class0.0000.0000.002
ExprTreeSet-class0.0040.0000.001
Filter-class000
FilterTreeSet-class0.0000.0000.001
NUSE0.0000.0000.001
PreFilter-class0.0400.0000.043
PreFilter-constructor0.0800.0000.081
ProcesSet-class0.0000.0000.002
ProjectInfo-class0.0120.0000.012
ProjectInfo-constructor0.0520.0040.057
QualTreeSet-class0.0040.0000.001
RLE0.0000.0000.001
SchemeTreeSet-class0.0000.0000.002
TreeSet-class0.0040.0000.001
UniFilter-class0.0160.0000.017
UniFilter-constructor0.0280.0000.029
addData-methods0.2520.0080.699
attachCall-methods0.2600.0040.397
attachDataXY-methods0.1520.0120.161
attachExpr-methods1.1520.0121.438
attachInten-methods0.2760.0400.318
attachMask-methods0.0960.0280.127
attachProbe-methods0.140.020.16
attachUnitNames-methods0.1000.0000.099
bgcorrect0.4840.0560.705
borderplot-methods0.0000.0000.001
boxplot-methods0.3720.0880.461
callFilter-methods0.0200.0000.021
coiplot-methods0.0000.0000.001
cvFilter-methods0.0120.0000.010
dabg.call0.9480.0001.100
dfw0.2600.0040.581
diffFilter-methods0.0080.0000.011
existsROOTFile0.0000.0000.001
exonLevel0.0040.0000.001
export0.3760.0320.431
export.root0.340.040.38
express1.0640.0081.509
exprs-methods0.0000.0000.001
extenPart0.0040.0000.001
farms0.2520.0120.584
fcFilter-methods0.0160.0000.013
firma0.0000.0000.002
firma.expr0.0000.0000.001
firma.score0.0000.0000.001
fitQC0.0000.0000.002
fitRLM0.0040.0000.001
gapFilter-methods0.0120.0000.012
getChipName0.0040.0000.003
getChipType0.0040.0000.003
getDatatype0.0040.0000.001
getNameType0.0040.0000.004
getNumberTrees0.0000.0040.003
getProbeInfo0.0040.0000.002
getTreeNames0.0040.0040.008
highFilter-methods0.0120.0000.011
hist-methods0.0680.0000.067
image-methods0.0000.0000.001
import.data0.1680.0040.518
import.exon.scheme0.0040.0000.001
import.expr.scheme0.0040.0000.001
import.genome.scheme0.0000.0000.001
indexUnits-methods0.3840.1280.511
ini.call0.3320.0040.622
intensity-methods0.0000.0000.001
intensity2GCplot-methods0.2600.0440.306
isROOTFile0.0000.0000.001
lowFilter-methods0.0080.0000.010
madFilter-methods0.0080.0000.010
mas40.4120.0040.844
mas50.4600.0040.856
mas5.call0.1760.0000.332
mboxplot-methods0.3800.0560.442
metaProbesets0.0000.0000.001
namePart0.0000.0000.001
normalize1.0640.0041.889
nuseplot-methods0.0320.0000.036
plotImage0.0040.0000.001
pm-methods0.4480.0480.513
pmplot-methods0.3640.0640.448
prefilter0.0000.0000.001
presCall-methods0.0000.0000.002
probeContentGC-methods0.2360.0480.292
probeSequence-methods0.1840.0240.217
probesetID2unitID-methods0.1080.0000.109
probesetplot-methods0.3400.0240.367
qualify0.0000.0000.002
quantileFilter-methods0.0080.0040.010
ratioFilter-methods0.0120.0000.010
rawCELName-methods0.0240.0000.024
rleplot-methods0.0320.0000.033
rma1.1120.0081.519
root.call0.1400.0120.288
root.data0.1120.0040.277
root.density0.0040.0000.000
root.expr0.9560.0081.261
root.graph1D000
root.graph2D0.0000.0000.001
root.hist1D000
root.hist2D0.0000.0000.001
root.hist3D0.0000.0000.001
root.image000
root.merge.data0.1440.0000.312
root.mvaplot0.0000.0000.001
root.profile0.0040.0000.001
root.scheme0.0200.0000.022
summarize0.9930.0041.715
symbol2unitID-methods0.1160.0040.125
treeInfo-methods0.0320.0000.103
trma0.9800.0121.473
type2Exten0.0000.0000.001
uniTest-methods0.0120.0000.011
unifilter000
unitestFilter-methods0.0120.0000.011
validTreetype000
varFilter-methods0.0120.0000.010
xpsQAReport0.0000.0000.001