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BioC 3.2: CHECK report for xps on linux1.bioconductor.org

This page was generated on 2015-10-27 17:24:09 -0400 (Tue, 27 Oct 2015).

Package 1101/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
xps 1.30.0
Christian Stratowa
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/xps
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: xps
Version: 1.30.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings xps_1.30.0.tar.gz
StartedAt: 2015-10-27 09:09:20 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 09:12:40 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 200.1 seconds
RetCode: 0
Status:  OK 
CheckDir: xps.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings xps_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/xps.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.30.0’
* 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 ... [120s/121s] OK
* checking installed package size ... NOTE
  installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    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 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-3.2-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/19s] 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-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 5.34/24 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 [enabled by default]
 #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
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-3.2-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
AffyRNAdeg0.0010.0000.001
AnalysisTreeSet-class0.0010.0000.002
CallTreeSet-class0.0010.0000.001
DataTreeSet-class0.0010.0000.001
ExprTreeSet-class0.0010.0000.001
Filter-class0.0000.0040.001
FilterTreeSet-class000
NUSE0.0000.0000.001
PreFilter-class0.0670.0000.067
PreFilter-constructor0.0290.0000.029
ProcesSet-class0.0010.0000.001
ProjectInfo-class0.0080.0000.007
ProjectInfo-constructor0.040.000.04
QualTreeSet-class0.0000.0000.001
RLE000
SchemeTreeSet-class0.0010.0000.001
TreeSet-class0.0010.0000.001
UniFilter-class0.0120.0000.011
UniFilter-constructor0.0220.0000.022
addData-methods0.1900.0170.253
attachCall-methods0.2280.0000.237
attachDataXY-methods0.1170.0150.132
attachExpr-methods1.6510.0091.675
attachInten-methods0.2390.0200.259
attachMask-methods0.1100.0160.126
attachProbe-methods0.1770.0120.189
attachUnitNames-methods0.1090.0000.110
bgcorrect0.5010.0440.553
borderplot-methods000
boxplot-methods0.3030.0320.336
callFilter-methods0.0150.0000.016
coiplot-methods0.0010.0000.001
cvFilter-methods0.0080.0000.007
dabg.call0.9510.0120.969
dfw0.3350.0000.346
diffFilter-methods0.0120.0000.011
existsROOTFile0.0010.0000.000
exonLevel0.0010.0000.001
export0.4440.0360.480
export.root0.3430.0240.367
express1.0550.0031.070
exprs-methods0.0000.0000.001
extenPart0.0010.0000.001
farms0.2110.0010.221
fcFilter-methods0.0070.0040.010
firma0.0020.0000.001
firma.expr0.0010.0000.001
firma.score000
fitQC0.0010.0000.001
fitRLM0.0000.0000.001
gapFilter-methods0.0110.0000.011
getChipName0.0020.0000.002
getChipType0.0020.0000.002
getDatatype000
getNameType0.0020.0000.002
getNumberTrees0.0020.0000.002
getProbeInfo0.0010.0000.001
getTreeNames0.0060.0000.005
highFilter-methods0.0080.0000.008
hist-methods0.0150.0000.016
image-methods0.0010.0000.000
import.data0.1290.0000.142
import.exon.scheme0.0010.0000.001
import.expr.scheme0.0010.0000.001
import.genome.scheme000
indexUnits-methods0.3150.1160.431
ini.call0.2430.0080.262
intensity-methods0.0010.0000.001
intensity2GCplot-methods0.2080.0320.240
isROOTFile0.0010.0000.001
lowFilter-methods0.0060.0000.007
madFilter-methods0.0070.0000.006
mas40.3150.0040.343
mas50.3630.0000.378
mas5.call0.1280.0040.137
mboxplot-methods0.2440.0520.296
metaProbesets0.0000.0000.001
namePart000
normalize1.0710.0041.099
nuseplot-methods0.0180.0040.023
plotImage0.0010.0000.001
pm-methods0.3010.0440.345
pmplot-methods0.2640.0320.296
prefilter0.0010.0000.000
presCall-methods0.0010.0000.001
probeContentGC-methods0.1770.0360.214
probeSequence-methods0.1410.0160.156
probesetID2unitID-methods0.0830.0000.086
probesetplot-methods0.2150.0280.244
qualify0.0000.0040.002
quantileFilter-methods0.0010.0040.007
ratioFilter-methods0.0050.0000.006
rawCELName-methods0.0160.0000.016
rleplot-methods0.0220.0000.022
rma1.4770.0081.498
root.call0.1610.0200.187
root.data0.1580.0000.165
root.density0.0010.0000.001
root.expr1.5690.0001.582
root.graph1D0.0010.0000.001
root.graph2D0.0010.0000.001
root.hist1D0.0000.0000.001
root.hist2D0.0010.0000.001
root.hist3D000
root.image000
root.merge.data0.1890.0000.196
root.mvaplot0.0010.0000.001
root.profile0.0010.0000.001
root.scheme0.0270.0000.027
summarize1.2450.0041.272
symbol2unitID-methods0.1050.0040.110
treeInfo-methods0.0240.0000.023
trma1.0920.0041.108
type2Exten0.0010.0000.001
uniTest-methods0.0080.0000.008
unifilter0.0010.0000.001
unitestFilter-methods0.0090.0000.009
validTreetype0.0010.0000.001
varFilter-methods0.0080.0000.008
xpsQAReport000