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BioC 3.6: CHECK report for xps on malbec1

This page was generated on 2017-08-16 13:18:06 -0400 (Wed, 16 Aug 2017).

Package 1402/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
xps 1.37.1
Christian Stratowa
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xps
Last Changed Rev: 129248 / Revision: 131943
Last Changed Date: 2017-04-28 05:17:11 -0400 (Fri, 28 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: xps
Version: 1.37.1
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings xps_1.37.1.tar.gz
StartedAt: 2017-08-16 03:03:45 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 03:06:28 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 162.8 seconds
RetCode: 0
Status:  OK 
CheckDir: xps.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings xps_1.37.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/xps.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.37.1’
* 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 ... 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 ... 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-3.6-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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/xps.Rcheck/00check.log’
for details.

xps.Rcheck/00install.out:

* 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-3.6-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
AffyRNAdeg000
AnalysisTreeSet-class0.0000.0000.001
CallTreeSet-class0.0040.0000.001
DataTreeSet-class0.0000.0000.002
ExprTreeSet-class0.0000.0000.001
Filter-class000
FilterTreeSet-class0.0000.0000.001
NUSE000
PreFilter-class0.0320.0000.033
PreFilter-constructor0.1160.0040.120
ProcesSet-class0.0000.0000.001
ProjectInfo-class0.0040.0000.007
ProjectInfo-constructor0.0480.0040.055
QualTreeSet-class0.0000.0000.001
RLE0.0000.0000.001
SchemeTreeSet-class0.0040.0000.001
TreeSet-class0.0000.0000.001
UniFilter-class0.040.000.04
UniFilter-constructor0.0360.0000.035
addData-methods0.2360.0040.392
attachCall-methods0.3480.0040.351
attachDataXY-methods0.1480.0160.165
attachExpr-methods1.0280.0001.026
attachInten-methods0.1960.0160.213
attachMask-methods0.1040.0080.111
attachProbe-methods0.1320.0120.144
attachUnitNames-methods0.1000.0040.105
bgcorrect0.3320.0160.352
borderplot-methods0.0000.0000.001
boxplot-methods0.4040.0200.425
callFilter-methods0.0120.0040.016
coiplot-methods0.0000.0000.001
cvFilter-methods0.0080.0000.008
dabg.call0.9960.0000.998
dfw0.2320.0040.236
diffFilter-methods0.0080.0000.007
existsROOTFile0.0000.0000.001
exonLevel0.0040.0000.001
export0.3000.0240.326
export.root0.2160.0360.252
express1.0280.0081.037
exprs-methods0.0000.0000.001
extenPart0.0000.0000.001
farms0.2080.0000.209
fcFilter-methods0.0080.0000.010
firma0.0000.0000.002
firma.expr0.0000.0000.001
firma.score0.0000.0000.001
fitQC0.0040.0000.001
fitRLM0.0000.0000.001
gapFilter-methods0.0080.0000.008
getChipName0.0040.0000.003
getChipType0.0040.0000.002
getDatatype000
getNameType0.0040.0000.002
getNumberTrees0.0040.0000.002
getProbeInfo0.0000.0000.001
getTreeNames0.0080.0000.005
highFilter-methods0.0080.0000.008
hist-methods0.0160.0000.016
image-methods0.0000.0000.001
import.data0.2320.0040.241
import.exon.scheme0.0000.0000.001
import.expr.scheme000
import.genome.scheme0.0040.0000.001
indexUnits-methods0.4080.0680.478
ini.call0.2480.0080.255
intensity-methods0.0000.0000.001
intensity2GCplot-methods0.2320.0320.264
isROOTFile0.0000.0000.001
lowFilter-methods0.0080.0000.007
madFilter-methods0.0080.0000.007
mas40.3320.0080.361
mas50.4920.0000.494
mas5.call0.2120.0080.220
mboxplot-methods0.2920.0280.319
metaProbesets0.0000.0000.001
namePart000
normalize0.9280.0040.938
nuseplot-methods0.0240.0000.024
plotImage0.0040.0000.001
pm-methods0.3120.0320.346
pmplot-methods0.2800.0320.311
prefilter000
presCall-methods0.0000.0000.001
probeContentGC-methods0.2120.0360.250
probeSequence-methods0.1640.0240.189
probesetID2unitID-methods0.1200.0000.122
probesetplot-methods0.2320.0360.267
qualify0.0040.0000.001
quantileFilter-methods0.0080.0000.007
ratioFilter-methods0.0040.0000.007
rawCELName-methods0.0240.0000.026
rleplot-methods0.0600.0000.059
rma1.0280.0001.034
root.call0.1200.0000.122
root.data0.0960.0040.102
root.density000
root.expr0.9800.0000.985
root.graph1D0.0000.0000.001
root.graph2D0.0000.0000.001
root.hist1D0.0000.0000.001
root.hist2D000
root.hist3D0.0000.0000.001
root.image0.0000.0000.001
root.merge.data0.1200.0000.123
root.mvaplot000
root.profile000
root.scheme0.0160.0000.018
summarize1.0560.0081.068
symbol2unitID-methods0.2000.0040.202
treeInfo-methods0.0360.0000.037
trma0.9560.0160.972
type2Exten0.0000.0000.001
uniTest-methods0.0080.0000.008
unifilter0.0000.0000.001
unitestFilter-methods0.0080.0000.009
validTreetype000
varFilter-methods0.0040.0000.007
xpsQAReport000