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BioC 3.2: CHECK report for xps on zin1

This page was generated on 2016-04-23 10:10:52 -0700 (Sat, 23 Apr 2016).

Package 1100/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
xps 1.30.0
Christian Stratowa
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/xps
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  WARNINGS  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: 2016-04-23 06:34:24 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 06:37:45 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 201.7 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 3.2.4 Revised (2016-03-16 r70336)
* 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 ... [116s/125s] OK
* checking installed package size ... NOTE
  installed size is 12.2Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    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 sizes of PDF files under ‘inst/doc’ ... OK
* 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

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 5.32/01 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: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-class0.0080.0000.008
DataTreeSet-class0.0020.0000.001
ExprTreeSet-class0.0010.0000.002
Filter-class0.0010.0000.000
FilterTreeSet-class0.0010.0000.001
NUSE0.0010.0000.001
PreFilter-class0.0710.0000.073
PreFilter-constructor0.0280.0080.036
ProcesSet-class0.0020.0000.001
ProjectInfo-class0.010.000.01
ProjectInfo-constructor0.0460.0040.050
QualTreeSet-class0.0010.0000.001
RLE0.0010.0000.001
SchemeTreeSet-class0.0020.0000.001
TreeSet-class0.0010.0000.002
UniFilter-class0.0100.0040.015
UniFilter-constructor0.0260.0000.025
addData-methods0.2240.0120.770
attachCall-methods0.2310.0040.387
attachDataXY-methods0.1120.0280.140
attachExpr-methods1.3490.0121.639
attachInten-methods0.2260.0400.265
attachMask-methods0.0880.0160.105
attachProbe-methods0.1130.0200.132
attachUnitNames-methods0.0820.0000.082
bgcorrect0.3840.0720.662
borderplot-methods0.0010.0000.001
boxplot-methods0.3430.0640.406
callFilter-methods0.0190.0000.020
coiplot-methods000
cvFilter-methods0.0090.0000.009
dabg.call0.9270.0041.087
dfw0.2300.0040.511
diffFilter-methods0.0090.0000.009
existsROOTFile0.0010.0000.001
exonLevel0.0010.0000.001
export0.3240.0280.352
export.root0.2840.0360.320
express1.3270.0061.651
exprs-methods0.0010.0010.001
extenPart0.0010.0000.001
farms0.2480.0070.529
fcFilter-methods0.0080.0000.012
firma0.0020.0000.002
firma.expr0.0010.0000.000
firma.score0.0000.0000.001
fitQC0.0010.0000.001
fitRLM0.0000.0000.001
gapFilter-methods0.0130.0000.014
getChipName0.0030.0000.003
getChipType0.0030.0000.003
getDatatype0.0000.0000.001
getNameType0.0040.0000.004
getNumberTrees0.0040.0000.003
getProbeInfo0.0010.0000.002
getTreeNames0.0060.0000.007
highFilter-methods0.0090.0000.010
hist-methods0.020.000.02
image-methods0.0010.0000.001
import.data0.1640.0040.512
import.exon.scheme0.0020.0000.001
import.expr.scheme0.0010.0000.001
import.genome.scheme0.0010.0000.001
indexUnits-methods0.3970.1320.529
ini.call0.2910.0090.583
intensity-methods0.0000.0000.001
intensity2GCplot-methods0.2530.0320.284
isROOTFile000
lowFilter-methods0.0090.0000.009
madFilter-methods0.0080.0000.008
mas40.3830.0030.819
mas50.4070.0160.820
mas5.call0.1470.0040.283
mboxplot-methods0.2980.0560.354
metaProbesets0.0010.0000.000
namePart0.0010.0000.001
normalize1.2330.0081.961
nuseplot-methods0.0250.0000.025
plotImage0.0020.0000.001
pm-methods0.3710.0640.434
pmplot-methods0.3030.0640.367
prefilter0.0010.0000.001
presCall-methods0.0010.0000.001
probeContentGC-methods0.2120.0400.251
probeSequence-methods0.1610.0280.189
probesetID2unitID-methods0.0970.0000.100
probesetplot-methods0.2670.0480.315
qualify0.0010.0000.001
quantileFilter-methods0.0090.0000.009
ratioFilter-methods0.0070.0000.007
rawCELName-methods0.0190.0000.018
rleplot-methods0.0260.0000.026
rma1.2630.0031.537
root.call0.1430.0040.296
root.data0.1140.0080.292
root.density0.0010.0000.001
root.expr1.3000.0081.599
root.graph1D000
root.graph2D000
root.hist1D0.0010.0000.001
root.hist2D000
root.hist3D000
root.image0.0000.0040.001
root.merge.data0.1240.0000.291
root.mvaplot0.0010.0000.001
root.profile000
root.scheme0.0190.0000.019
summarize1.2450.0051.941
symbol2unitID-methods0.1120.0040.119
treeInfo-methods0.0270.0000.027
trma1.2390.0001.491
type2Exten0.0010.0000.000
uniTest-methods0.0090.0000.009
unifilter0.0010.0000.001
unitestFilter-methods0.0100.0000.009
validTreetype0.0000.0000.001
varFilter-methods0.0090.0000.008
xpsQAReport0.0010.0000.001