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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:xps.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings xps_1.48.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/xps.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.48.0’
* 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  9.7Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   5.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
* 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 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 shell scripts ... 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 use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.11-bioc/R/library/xps/libs/xps.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
  Found ‘__printf_chk’, possibly from ‘printf’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. 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 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-3.11-bioc/meat/xps.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL xps
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘xps’ ...
** using staged installation
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
 
TMLMath.cxx: In static member function ‘static Double_t TMLMath::PBetaRaw(Double_t, Double_t, Double_t, Int_t)’:
TMLMath.cxx:1421:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
    if (swap_tail == lower_tail)
    ^~
TMLMath.cxx:1423:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
       ans = FMax2(FMin2(ans, 1.), 0.);
       ^~~
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-3.11-bioc/R/library/00LOCK-xps/00new/xps/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (xps)