BioC 3.4: CHECK report for xps on malbec1

Package: xps

Version: 1.34.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings xps_1.34.0.tar.gz

StartedAt: 2017-04-15 01:53:44 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 01:56:40 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 175.5 seconds

RetCode: 0

Status:  OK

CheckDir: xps.Rcheck

Warnings: 0

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###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings xps_1.34.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/xps.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘xps/DESCRIPTION’ ... OK
* this is package ‘xps’ version ‘1.34.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is 11.9Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   5.9Mb
* 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 ... NOTE
.onAttach: no visible global function definition for
  ‘packageDescription’
AffyRNAdeg : lm.stats: no visible global function definition for ‘lm’
dabgCall.DataTreeSet: no visible global function definition for
  ‘read.table’
distMAD: no visible global function definition for ‘mad’
export.root: no visible global function definition for ‘read.table’
exportProcesSet: no visible global function definition for ‘read.table’
exportSchemeTreeSet: no visible global function definition for
  ‘read.table’
firma.DataTreeSet: no visible global function definition for
  ‘read.table’
iniCall.DataTreeSet: no visible global function definition for
  ‘read.table’
mas4.DataTreeSet: no visible global function definition for
  ‘read.table’
mas5.DataTreeSet: no visible global function definition for
  ‘read.table’
mas5Call.DataTreeSet: no visible global function definition for
  ‘read.table’
normalize.ExprTreeSet: no visible global function definition for
  ‘read.table’
plotBorder: no visible global function definition for ‘x11’
plotBorder: no visible global function definition for ‘jpeg’
plotBorder: no visible global function definition for ‘png’
plotBorder: no visible global function definition for ‘pdf’
plotBorder: no visible global function definition for ‘postscript’
plotBorder: no visible global function definition for ‘dev.off’
plotBoxplot: no visible global function definition for ‘x11’
plotBoxplot: no visible global function definition for ‘jpeg’
plotBoxplot: no visible global function definition for ‘png’
plotBoxplot: no visible global function definition for ‘pdf’
plotBoxplot: no visible global function definition for ‘postscript’
plotBoxplot: no visible global function definition for ‘dev.off’
plotCOI: no visible global function definition for ‘x11’
plotCOI: no visible global function definition for ‘jpeg’
plotCOI: no visible global function definition for ‘png’
plotCOI: no visible global function definition for ‘pdf’
plotCOI: no visible global function definition for ‘postscript’
plotCOI: no visible global function definition for ‘dev.off’
plotCall: no visible global function definition for ‘x11’
plotCall: no visible global function definition for ‘jpeg’
plotCall: no visible global function definition for ‘png’
plotCall: no visible global function definition for ‘pdf’
plotCall: no visible global function definition for ‘postscript’
plotCall: no visible global function definition for ‘dev.off’
plotCorr: no visible global function definition for ‘x11’
plotCorr: no visible global function definition for ‘jpeg’
plotCorr: no visible global function definition for ‘png’
plotCorr: no visible global function definition for ‘pdf’
plotCorr: no visible global function definition for ‘postscript’
plotCorr: no visible global function definition for ‘dev.off’
plotDensities: no visible binding for global variable ‘density’
plotDensity: no visible global function definition for ‘x11’
plotDensity: no visible global function definition for ‘jpeg’
plotDensity: no visible global function definition for ‘png’
plotDensity: no visible global function definition for ‘pdf’
plotDensity: no visible global function definition for ‘postscript’
plotDensity: no visible global function definition for ‘dev.off’
plotImage: no visible global function definition for ‘x11’
plotImage: no visible global function definition for ‘jpeg’
plotImage: no visible global function definition for ‘png’
plotImage: no visible global function definition for ‘pdf’
plotImage: no visible global function definition for ‘postscript’
plotImage: no visible global function definition for ‘dev.off’
plotIntensity2GC: no visible global function definition for ‘x11’
plotIntensity2GC: no visible global function definition for ‘jpeg’
plotIntensity2GC: no visible global function definition for ‘png’
plotIntensity2GC: no visible global function definition for ‘pdf’
plotIntensity2GC: no visible global function definition for
  ‘postscript’
plotIntensity2GC: no visible global function definition for ‘dev.off’
plotMA: no visible binding for global variable ‘median’
plotMA: no visible global function definition for ‘x11’
plotMA: no visible global function definition for ‘jpeg’
plotMA: no visible global function definition for ‘png’
plotMA: no visible global function definition for ‘pdf’
plotMA: no visible global function definition for ‘postscript’
plotMA: no visible global function definition for ‘gray’
plotMA: no visible global function definition for ‘dev.off’
plotMAD: no visible global function definition for ‘x11’
plotMAD: no visible global function definition for ‘jpeg’
plotMAD: no visible global function definition for ‘png’
plotMAD: no visible global function definition for ‘pdf’
plotMAD: no visible global function definition for ‘postscript’
plotMAD: no visible global function definition for ‘dev.off’
plotNUSE: no visible global function definition for ‘x11’
plotNUSE: no visible global function definition for ‘jpeg’
plotNUSE: no visible global function definition for ‘png’
plotNUSE: no visible global function definition for ‘pdf’
plotNUSE: no visible global function definition for ‘postscript’
plotNUSE: no visible global function definition for ‘dev.off’
plotPCA: no visible global function definition for ‘x11’
plotPCA: no visible global function definition for ‘jpeg’
plotPCA: no visible global function definition for ‘png’
plotPCA: no visible global function definition for ‘pdf’
plotPCA: no visible global function definition for ‘postscript’
plotPCA: no visible global function definition for ‘dev.off’
plotPM: no visible global function definition for ‘x11’
plotPM: no visible global function definition for ‘jpeg’
plotPM: no visible global function definition for ‘png’
plotPM: no visible global function definition for ‘pdf’
plotPM: no visible global function definition for ‘postscript’
plotPM: no visible global function definition for ‘dev.off’
plotProbeset: no visible global function definition for ‘x11’
plotProbeset: no visible global function definition for ‘jpeg’
plotProbeset: no visible global function definition for ‘png’
plotProbeset: no visible global function definition for ‘pdf’
plotProbeset: no visible global function definition for ‘postscript’
plotProbeset: no visible global function definition for ‘dev.off’
plotRLE: no visible global function definition for ‘x11’
plotRLE: no visible global function definition for ‘jpeg’
plotRLE: no visible global function definition for ‘png’
plotRLE: no visible global function definition for ‘pdf’
plotRLE: no visible global function definition for ‘postscript’
plotRLE: no visible global function definition for ‘dev.off’
plotVolcano: no visible global function definition for ‘x11’
plotVolcano: no visible global function definition for ‘jpeg’
plotVolcano: no visible global function definition for ‘png’
plotVolcano: no visible global function definition for ‘pdf’
plotVolcano: no visible global function definition for ‘postscript’
plotVolcano: no visible global function definition for ‘dev.off’
prefilter.ExprTreeSet: no visible global function definition for
  ‘read.table’
preprocess.DataTreeSet: no visible global function definition for
  ‘read.table’
pseudoPalette: no visible global function definition for ‘col2rgb’
pseudoPalette: no visible global function definition for ‘rgb’
qc.DataTreeSet: no visible global function definition for ‘read.table’
qualify.DataTreeSet: no visible global function definition for
  ‘read.table’
rma.DataTreeSet: no visible global function definition for ‘read.table’
root.call: no visible global function definition for ‘read.table’
root.expr: no visible global function definition for ‘read.table’
summarize.DataTreeSet: no visible global function definition for
  ‘read.table’
unifilter.ExprTreeSet: no visible global function definition for
  ‘read.table’
xpsQAReport: no visible global function definition for ‘write.table’
xpsQAReport: no visible global function definition for ‘png’
xpsQAReport: no visible global function definition for ‘dev.off’
xpsQAReport: no visible global function definition for ‘Sweave’
corplot,ExprTreeSet: no visible global function definition for ‘cor’
corplot,ExprTreeSet: no visible global function definition for
  ‘heat.colors’
export,ProcesSet: no visible global function definition for
  ‘read.table’
export,SchemeTreeSet: no visible global function definition for
  ‘read.table’
hist,DataTreeSet: no visible global function definition for ‘density’
image,ProcesSet: no visible global function definition for ‘gray’
image,QualTreeSet: no visible global function definition for
  ‘terrain.colors’
intensity2GCplot,DataTreeSet: no visible global function definition for
  ‘colorRampPalette’
intensity<-,DataTreeSet-data.frame: no visible global function
  definition for ‘write.table’
madplot,ExprTreeSet: no visible global function definition for
  ‘colorRampPalette’
madplot,ExprTreeSet: no visible global function definition for ‘rgb’
mboxplot,ProcesSet: no visible binding for global variable ‘median’
mvaplot,ExprTreeSet: no visible binding for global variable ‘median’
nuseplot,ExprTreeSet: no visible binding for global variable ‘median’
pcaplot,ExprTreeSet: no visible global function definition for ‘prcomp’
pcaplot,ExprTreeSet: no visible global function definition for ‘cor’
xpsDABGCall,DataTreeSet: no visible global function definition for
  ‘read.table’
xpsFIRMA,DataTreeSet: no visible global function definition for
  ‘read.table’
xpsINICall,DataTreeSet: no visible global function definition for
  ‘read.table’
xpsMAS4,DataTreeSet: no visible global function definition for
  ‘read.table’
xpsMAS5,DataTreeSet: no visible global function definition for
  ‘read.table’
xpsMAS5Call,DataTreeSet: no visible global function definition for
  ‘read.table’
xpsNormalize,ExprTreeSet: no visible global function definition for
  ‘read.table’
xpsPreFilter,ExprTreeSet: no visible global function definition for
  ‘read.table’
xpsPreprocess,DataTreeSet: no visible global function definition for
  ‘read.table’
xpsQualify,DataTreeSet: no visible global function definition for
  ‘read.table’
xpsQualityControl,DataTreeSet: no visible global function definition
  for ‘read.table’
xpsRMA,DataTreeSet: no visible global function definition for
  ‘read.table’
xpsSummarize,DataTreeSet: no visible global function definition for
  ‘read.table’
xpsUniFilter,ExprTreeSet: no visible global function definition for
  ‘read.table’
Undefined global functions or variables:
  Sweave col2rgb colorRampPalette cor density dev.off gray heat.colors
  jpeg lm mad median packageDescription pdf png postscript prcomp
  read.table rgb terrain.colors write.table x11
Consider adding
  importFrom("grDevices", "col2rgb", "colorRampPalette", "dev.off",
             "gray", "heat.colors", "jpeg", "pdf", "png", "postscript",
             "rgb", "terrain.colors", "x11")
  importFrom("stats", "cor", "density", "lm", "mad", "median", "prcomp")
  importFrom("utils", "Sweave", "packageDescription", "read.table",
             "write.table")
to your NAMESPACE file.
* 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-3.4-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 ... 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

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/xps.Rcheck/00check.log’
for details.

* installing *source* package ‘xps’ ...
checking for gcc... gcc
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 accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -E
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ANSI C... (cached) none needed
found ROOT version 5.34/36 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:1111:0: warning: "xmax" redefined
 #define xmax  2.5327372760800758e+305
 ^
TMLMath.cxx:1062:0: note: this is the location of the previous definition
 # define xmax  3.745194030963158e306
 ^
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:766:40: warning: variable ‘pval’ set but not used [-Wunused-but-set-variable]
       Double_t mn1, mn2, se, df, stat, pval, pcha, padj;
                                        ^
g++ -I/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSBase.cxx
XPSBase.cxx: In member function ‘virtual Option_t* XAlgorithm::GetOptions(const char*)’:
XPSBase.cxx:1492:34: warning: function may return address of local variable [-Wreturn-local-addr]
    return (Option_t*)option.Data();
                                  ^
XPSBase.cxx:1490:12: note: declared here
    TString option = SubString(fOption.Data(), sep, 0);
            ^
XPSBase.cxx: In member function ‘virtual Option_t* XAlgorithm::GetOptions(TString&, const char*)’:
XPSBase.cxx:1512:34: warning: function may return address of local variable [-Wreturn-local-addr]
    return (Option_t*)option.Data();
                                  ^
XPSBase.cxx:1504:12: note: declared here
    TString option;
            ^
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:2802:12: warning: variable ‘order’ set but not used [-Wunused-but-set-variable]
    Int_t   order, x, y, position, id;
            ^
XPSSchemes.cxx: In member function ‘virtual Int_t XGeneChip::ReadBinaryData(std::ifstream&, Option_t*, const char*, char, Int_t)’:
XPSSchemes.cxx:3454:22: warning: variable ‘flag’ set but not used [-Wunused-but-set-variable]
    Int_t x, y, plen, flag;
                      ^
XPSSchemes.cxx: In member function ‘virtual Int_t XGenomeChip::ImportTransAnnotation(std::ifstream&, Option_t*, const char*, char, Int_t)’:
XPSSchemes.cxx:6215:13: warning: variable ‘nprobes’ set but not used [-Wunused-but-set-variable]
    Int_t    nprobes;
             ^
XPSSchemes.cxx: In member function ‘virtual Int_t XExonChip::ReadData(std::ifstream&, Option_t*, const char*, char, Int_t)’:
XPSSchemes.cxx:7508:29: warning: variable ‘psetID’ set but not used [-Wunused-but-set-variable]
    Int_t    geneID, exonID, psetID;
                             ^
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:1605:11: warning: variable ‘hasMaxNPix’ set but not used [-Wunused-but-set-variable]
    Bool_t hasMaxNPix   = kFALSE;
           ^
XPSData.cxx: In member function ‘virtual Int_t XGeneChipHyb::ExportMaskTreeInfo(Int_t, TString*, const char*, std::ofstream&, const char*)’:
XPSData.cxx:1799:10: warning: unused variable ‘err’ [-Wunused-variable]
    Int_t err = errNoErr;
          ^
XPSData.cxx: In member function ‘virtual Int_t XGeneChipHyb::ReadXMLHeader(std::ifstream&, const char*, char)’:
XPSData.cxx:2812:10: warning: unused variable ‘fNMasked’ [-Wunused-variable]
    Int_t fNMasked = atoi(strtok(&nextline[dif], "\""));
          ^
XPSData.cxx:2822:10: warning: unused variable ‘fNOutlier’ [-Wunused-variable]
    Int_t fNOutlier = atoi(strtok(&nextline[dif], "\""));
          ^
XPSData.cxx:2832:10: warning: unused variable ‘fNModified’ [-Wunused-variable]
    Int_t fNModified = atoi(strtok(&nextline[dif], "\""));
          ^
XPSData.cxx: In member function ‘virtual Int_t XGeneChipPivot::ReadData(std::ifstream&, Option_t*, const char*, char, Int_t)’:
XPSData.cxx:3760:10: warning: variable ‘numunits’ set but not used [-Wunused-but-set-variable]
    Int_t numunits = 0;
          ^
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:1532:10: warning: unused variable ‘err’ [-Wunused-variable]
    Int_t err = errNoErr;
          ^
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:224:10: warning: variable ‘err’ set but not used [-Wunused-but-set-variable]
    Int_t err    = errNoErr;
          ^
XPSSelector.cxx: In member function ‘Double_t XRankSelector::Cutoff(Int_t, const Double_t*, Double_t, Bool_t)’:
XPSSelector.cxx:336:19: warning: variable ‘par1’ set but not used [-Wunused-but-set-variable]
    Double_t par0, par1;
                   ^
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:3524:10: warning: unused variable ‘idxhi’ [-Wunused-variable]
    Int_t idxhi, idxlo;
          ^
XPSPreProcessing.cxx:3524:17: warning: unused variable ‘idxlo’ [-Wunused-variable]
    Int_t idxhi, idxlo;
                 ^
XPSPreProcessing.cxx:3529:13: warning: variable ‘mnhi’ set but not used [-Wunused-but-set-variable]
    Double_t mnhi, lmnhi, rmnhi, tmnhi, bmnhi;
             ^
XPSPreProcessing.cxx:3530:13: warning: variable ‘mnlo’ set but not used [-Wunused-but-set-variable]
    Double_t mnlo, lmnlo, rmnlo, tmnlo, bmnlo;
             ^
XPSPreProcessing.cxx: In member function ‘virtual Int_t XGCProcesSet::DoBgrdQualityControl(Int_t, TTree**, XDNAChip*, TFile*)’:
XPSPreProcessing.cxx:3679:10: warning: unused variable ‘numunits’ [-Wunused-variable]
    Int_t numunits = chip->GetNumUnits();
          ^
XPSPreProcessing.cxx:3680:10: warning: unused variable ‘size’ [-Wunused-variable]
    Int_t size     = numrows*numcols;
          ^
XPSPreProcessing.cxx: In member function ‘virtual Int_t XGCProcesSet::ExportResdTrees(Int_t, TString*, const char*, std::ofstream&, const char*)’:
XPSPreProcessing.cxx:5782:10: warning: variable ‘err’ set but not used [-Wunused-but-set-variable]
    Int_t err = errNoErr;
          ^
XPSPreProcessing.cxx: In member function ‘virtual Int_t XGCProcesSet::ExportQualTrees(Int_t, TString*, const char*, std::ofstream&, const char*)’:
XPSPreProcessing.cxx:6771:16: warning: unused variable ‘idxstr’ [-Wunused-variable]
    XIdxString *idxstr = 0;
                ^
XPSPreProcessing.cxx: In member function ‘TTree* XGCProcesSet::FillDataTree(TTree*, const char*, XAlgorithm*, Int_t, Int_t, Double_t*, Double_t*)’:
XPSPreProcessing.cxx:8746:1: warning: label ‘cleanup’ defined but not used [-Wunused-label]
 cleanup:
 ^
XPSPreProcessing.cxx: In member function ‘virtual Int_t XExonProcesSet::DoSpliceExpress(Int_t, TTree**, Int_t, TTree**, TFile*)’:
XPSPreProcessing.cxx:9791:14: warning: unused variable ‘numatoms’ [-Wunused-variable]
       Int_t  numatoms = unit->GetNumAtoms();
              ^
XPSPreProcessing.cxx:9398:10: warning: unused variable ‘x’ [-Wunused-variable]
    Int_t x   = 0;
          ^
XPSPreProcessing.cxx:9399:10: warning: unused variable ‘y’ [-Wunused-variable]
    Int_t y   = 0;
          ^
XPSPreProcessing.cxx:9404:10: warning: unused variable ‘stepout’ [-Wunused-variable]
    Int_t stepout = (Int_t)((100000.0 + 10.0*numdata)/(Float_t)numdata); //step size for verbose output
          ^
XPSPreProcessing.cxx: In member function ‘virtual TTree* XExonProcesSet::SchemeTree(XAlgorithm*, void*, TLeaf**)’:
XPSPreProcessing.cxx:10358:18: warning: unused variable ‘scheme_ptr_ptr’ [-Wunused-variable]
    XExonScheme **scheme_ptr_ptr = (XExonScheme**)scheme;
                  ^
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:1352:10: warning: variable ‘err’ set but not used [-Wunused-but-set-variable]
    Int_t err = errNoErr;
          ^
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:1789:13: warning: unused variable ‘brchUnit’ [-Wunused-variable]
    TBranch *brchUnit = intree->GetBranch("fUnitID"); //prevent crash SafeDelete(fDataFile)
             ^
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-3.4-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)

name	user	system	elapsed
AffyRNAdeg	0.000	0.000	0.001
AnalysisTreeSet-class	0.000	0.000	0.001
CallTreeSet-class	0.000	0.000	0.001
DataTreeSet-class	0.000	0.000	0.002
ExprTreeSet-class	0	0	0
Filter-class	0.000	0.000	0.001
FilterTreeSet-class	0.000	0.000	0.001
NUSE	0	0	0
PreFilter-class	0.032	0.000	0.034
PreFilter-constructor	0.060	0.000	0.057
ProcesSet-class	0.000	0.000	0.001
ProjectInfo-class	0.004	0.004	0.008
ProjectInfo-constructor	0.040	0.000	0.039
QualTreeSet-class	0.000	0.000	0.001
RLE	0	0	0
SchemeTreeSet-class	0.000	0.000	0.001
TreeSet-class	0.000	0.000	0.001
UniFilter-class	0.012	0.000	0.011
UniFilter-constructor	0.020	0.000	0.019
addData-methods	0.204	0.000	0.303
attachCall-methods	0.224	0.008	0.234
attachDataXY-methods	0.100	0.028	0.127
attachExpr-methods	1.036	0.012	1.049
attachInten-methods	0.304	0.048	0.352
attachMask-methods	0.132	0.020	0.151
attachProbe-methods	0.120	0.016	0.136
attachUnitNames-methods	0.084	0.000	0.086
bgcorrect	0.384	0.028	0.412
borderplot-methods	0	0	0
boxplot-methods	0.328	0.032	0.358
callFilter-methods	0.016	0.000	0.016
coiplot-methods	0	0	0
cvFilter-methods	0.008	0.000	0.007
dabg.call	0.964	0.000	0.967
dfw	0.196	0.012	0.206
diffFilter-methods	0.008	0.000	0.007
existsROOTFile	0	0	0
exonLevel	0.000	0.000	0.001
export	0.244	0.020	0.263
export.root	0.248	0.008	0.256
express	0.940	0.000	0.944
exprs-methods	0.000	0.000	0.001
extenPart	0.000	0.000	0.001
farms	0.216	0.008	0.224
fcFilter-methods	0.008	0.000	0.008
firma	0.004	0.000	0.001
firma.expr	0	0	0
firma.score	0	0	0
fitQC	0.000	0.000	0.001
fitRLM	0.000	0.000	0.001
gapFilter-methods	0.004	0.004	0.007
getChipName	0.004	0.000	0.003
getChipType	0.004	0.000	0.003
getDatatype	0	0	0
getNameType	0.004	0.000	0.002
getNumberTrees	0.000	0.000	0.002
getProbeInfo	0.000	0.000	0.001
getTreeNames	0.008	0.000	0.008
highFilter-methods	0.004	0.000	0.007
hist-methods	0.012	0.000	0.015
image-methods	0.000	0.000	0.001
import.data	0.120	0.008	0.129
import.exon.scheme	0.000	0.000	0.001
import.expr.scheme	0.004	0.000	0.000
import.genome.scheme	0.000	0.000	0.001
indexUnits-methods	0.336	0.080	0.417
ini.call	0.248	0.004	0.254
intensity-methods	0.000	0.000	0.001
intensity2GCplot-methods	0.204	0.040	0.244
isROOTFile	0.004	0.000	0.000
lowFilter-methods	0.008	0.000	0.007
madFilter-methods	0.004	0.000	0.007
mas4	0.312	0.012	0.353
mas5	0.348	0.004	0.352
mas5.call	0.132	0.004	0.138
mboxplot-methods	0.260	0.040	0.302
metaProbesets	0	0	0
namePart	0	0	0
normalize	0.936	0.004	0.945
nuseplot-methods	0.020	0.000	0.022
plotImage	0.000	0.000	0.001
pm-methods	0.292	0.028	0.321
pmplot-methods	0.268	0.024	0.290
prefilter	0.000	0.000	0.001
presCall-methods	0.000	0.004	0.001
probeContentGC-methods	0.176	0.036	0.212
probeSequence-methods	0.136	0.020	0.156
probesetID2unitID-methods	0.092	0.000	0.090
probesetplot-methods	0.228	0.028	0.254
qualify	0.000	0.000	0.001
quantileFilter-methods	0.008	0.000	0.007
ratioFilter-methods	0.008	0.000	0.007
rawCELName-methods	0.016	0.000	0.015
rleplot-methods	0.020	0.000	0.021
rma	0.940	0.008	0.951
root.call	0.108	0.004	0.111
root.data	0.088	0.004	0.092
root.density	0	0	0
root.expr	0.896	0.004	0.904
root.graph1D	0	0	0
root.graph2D	0.004	0.000	0.000
root.hist1D	0	0	0
root.hist2D	0	0	0
root.hist3D	0	0	0
root.image	0.004	0.000	0.000
root.merge.data	0.108	0.004	0.114
root.mvaplot	0.000	0.000	0.001
root.profile	0.000	0.000	0.001
root.scheme	0.012	0.004	0.016
summarize	0.936	0.004	0.944
symbol2unitID-methods	0.116	0.004	0.123
treeInfo-methods	0.024	0.000	0.024
trma	0.936	0.008	0.946
type2Exten	0	0	0
uniTest-methods	0.008	0.000	0.007
unifilter	0	0	0
unitestFilter-methods	0.008	0.000	0.009
validTreetype	0.000	0.000	0.001
varFilter-methods	0.008	0.000	0.008
xpsQAReport	0.000	0.000	0.001