* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* installing *source* package ‘CASMAP’ ...
** package ‘CASMAP’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-24) 13.2.0’
using C++11
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpeLGqUT/R.INSTALL167f6758ef06b6/CASMAP/src'
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c ArrayFile.cpp -o ArrayFile.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c CumulativeTimeMeasurement.cpp -o CumulativeTimeMeasurement.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Exception.cpp -o Exception.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c FeatureSet.cpp -o FeatureSet.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c FilterIntervals.cpp -o FilterIntervals.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Genotype.cpp -o Genotype.o
In file included from ../inst/include/Genotype.h:14,
                 from Genotype.cpp:8:
../inst/include/ArrayFile.h:80:28: warning: ‘virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)’ was hidden [-Woverloaded-virtual=]
   80 |         virtual ArrayFile& operator=(const ArrayFile& other);
      |                            ^~~~~~~~
In file included from ../inst/include/Genotype.h:15:
../inst/include/Phenotype.h:222:28: note:   by ‘virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)’
  222 |         virtual Phenotype& operator=(const Phenotype& other);
      |                            ^~~~~~~~
../inst/include/ArrayFile.h:80:28: warning: ‘virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)’ was hidden [-Woverloaded-virtual=]
   80 |         virtual ArrayFile& operator=(const ArrayFile& other);
      |                            ^~~~~~~~
../inst/include/Genotype.h:69:27: note:   by ‘virtual SignificantPattern::Genotype& SignificantPattern::Genotype::operator=(const SignificantPattern::Genotype&)’
   69 |         virtual Genotype& operator=(const Genotype& other);
      |                           ^~~~~~~~
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c PValues.cpp -o PValues.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Phenotype.cpp -o Phenotype.o
In file included from ../inst/include/Phenotype.h:16,
                 from Phenotype.cpp:8:
../inst/include/ArrayFile.h:80:28: warning: ‘virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)’ was hidden [-Woverloaded-virtual=]
   80 |         virtual ArrayFile& operator=(const ArrayFile& other);
      |                            ^~~~~~~~
../inst/include/Phenotype.h:222:28: note:   by ‘virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)’
  222 |         virtual Phenotype& operator=(const Phenotype& other);
      |                            ^~~~~~~~
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Profiler.cpp -o Profiler.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c SignificantFeaturesSearch.cpp -o SignificantFeaturesSearch.o
In file included from ../inst/include/Genotype.h:14,
                 from ../inst/include/SignificantFeaturesSearch.h:15,
                 from SignificantFeaturesSearch.cpp:9:
../inst/include/ArrayFile.h:80:28: warning: ‘virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)’ was hidden [-Woverloaded-virtual=]
   80 |         virtual ArrayFile& operator=(const ArrayFile& other);
      |                            ^~~~~~~~
In file included from ../inst/include/Genotype.h:15:
../inst/include/Phenotype.h:222:28: note:   by ‘virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)’
  222 |         virtual Phenotype& operator=(const Phenotype& other);
      |                            ^~~~~~~~
../inst/include/ArrayFile.h:80:28: warning: ‘virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)’ was hidden [-Woverloaded-virtual=]
   80 |         virtual ArrayFile& operator=(const ArrayFile& other);
      |                            ^~~~~~~~
../inst/include/Genotype.h:69:27: note:   by ‘virtual SignificantPattern::Genotype& SignificantPattern::Genotype::operator=(const SignificantPattern::Genotype&)’
   69 |         virtual Genotype& operator=(const Genotype& other);
      |                           ^~~~~~~~
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c SignificantFeaturesSearchTaroneCmh.cpp -o SignificantFeaturesSearchTaroneCmh.o
In file included from ../inst/include/Genotype.h:14,
                 from ../inst/include/SignificantFeaturesSearch.h:15,
                 from ../inst/include/SignificantFeaturesSearchWithCovariates.h:11,
                 from ../inst/include/SignificantFeaturesSearchTaroneCmh.h:16,
                 from SignificantFeaturesSearchTaroneCmh.cpp:8:
../inst/include/ArrayFile.h:80:28: warning: ‘virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)’ was hidden [-Woverloaded-virtual=]
   80 |         virtual ArrayFile& operator=(const ArrayFile& other);
      |                            ^~~~~~~~
In file included from ../inst/include/Genotype.h:15:
../inst/include/Phenotype.h:222:28: note:   by ‘virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)’
  222 |         virtual Phenotype& operator=(const Phenotype& other);
      |                            ^~~~~~~~
../inst/include/ArrayFile.h:80:28: warning: ‘virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)’ was hidden [-Woverloaded-virtual=]
   80 |         virtual ArrayFile& operator=(const ArrayFile& other);
      |                            ^~~~~~~~
../inst/include/Genotype.h:69:27: note:   by ‘virtual SignificantPattern::Genotype& SignificantPattern::Genotype::operator=(const SignificantPattern::Genotype&)’
   69 |         virtual Genotype& operator=(const Genotype& other);
      |                           ^~~~~~~~
SignificantFeaturesSearchTaroneCmh.cpp: In member function ‘virtual void SignificantPattern::SignificantFeaturesSearchTaroneCmh::freq_destructor()’:
SignificantFeaturesSearchTaroneCmh.cpp:104:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  104 |         if (freq_par_cov[0]) delete [] freq_par_cov[0]; freq_par_cov[0] = 0;
      |         ^~
SignificantFeaturesSearchTaroneCmh.cpp:104:57: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  104 |         if (freq_par_cov[0]) delete [] freq_par_cov[0]; freq_par_cov[0] = 0;
      |                                                         ^~~~~~~~~~~~
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c SignificantFeaturesSearchWithCovariates.cpp -o SignificantFeaturesSearchWithCovariates.o
In file included from ../inst/include/Genotype.h:14,
                 from ../inst/include/SignificantFeaturesSearch.h:15,
                 from ../inst/include/SignificantFeaturesSearchWithCovariates.h:11,
                 from SignificantFeaturesSearchWithCovariates.cpp:8:
../inst/include/ArrayFile.h:80:28: warning: ‘virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)’ was hidden [-Woverloaded-virtual=]
   80 |         virtual ArrayFile& operator=(const ArrayFile& other);
      |                            ^~~~~~~~
In file included from ../inst/include/Genotype.h:15:
../inst/include/Phenotype.h:222:28: note:   by ‘virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)’
  222 |         virtual Phenotype& operator=(const Phenotype& other);
      |                            ^~~~~~~~
../inst/include/ArrayFile.h:80:28: warning: ‘virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)’ was hidden [-Woverloaded-virtual=]
   80 |         virtual ArrayFile& operator=(const ArrayFile& other);
      |                            ^~~~~~~~
../inst/include/Genotype.h:69:27: note:   by ‘virtual SignificantPattern::Genotype& SignificantPattern::Genotype::operator=(const SignificantPattern::Genotype&)’
   69 |         virtual Genotype& operator=(const Genotype& other);
      |                           ^~~~~~~~
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c SignificantIntervalSearch.cpp -o SignificantIntervalSearch.o
In file included from ../inst/include/Genotype.h:14,
                 from ../inst/include/SignificantFeaturesSearch.h:15,
                 from ../inst/include/SignificantIntervalSearch.h:13,
                 from SignificantIntervalSearch.cpp:9:
../inst/include/ArrayFile.h:80:28: warning: ‘virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)’ was hidden [-Woverloaded-virtual=]
   80 |         virtual ArrayFile& operator=(const ArrayFile& other);
      |                            ^~~~~~~~
In file included from ../inst/include/Genotype.h:15:
../inst/include/Phenotype.h:222:28: note:   by ‘virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)’
  222 |         virtual Phenotype& operator=(const Phenotype& other);
      |                            ^~~~~~~~
../inst/include/ArrayFile.h:80:28: warning: ‘virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)’ was hidden [-Woverloaded-virtual=]
   80 |         virtual ArrayFile& operator=(const ArrayFile& other);
      |                            ^~~~~~~~
../inst/include/Genotype.h:69:27: note:   by ‘virtual SignificantPattern::Genotype& SignificantPattern::Genotype::operator=(const SignificantPattern::Genotype&)’
   69 |         virtual Genotype& operator=(const Genotype& other);
      |                           ^~~~~~~~
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c SignificantIntervalSearchChi.cpp -o SignificantIntervalSearchChi.o
In file included from ../inst/include/Genotype.h:14,
                 from ../inst/include/SignificantFeaturesSearch.h:15,
                 from ../inst/include/SignificantIntervalSearch.h:13,
                 from ../inst/include/SignificantIntervalSearchFais.h:11,
                 from ../inst/include/SignificantIntervalSearchChi.h:21,
                 from SignificantIntervalSearchChi.cpp:5:
../inst/include/ArrayFile.h:80:28: warning: ‘virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)’ was hidden [-Woverloaded-virtual=]
   80 |         virtual ArrayFile& operator=(const ArrayFile& other);
      |                            ^~~~~~~~
In file included from ../inst/include/Genotype.h:15:
../inst/include/Phenotype.h:222:28: note:   by ‘virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)’
  222 |         virtual Phenotype& operator=(const Phenotype& other);
      |                            ^~~~~~~~
../inst/include/ArrayFile.h:80:28: warning: ‘virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)’ was hidden [-Woverloaded-virtual=]
   80 |         virtual ArrayFile& operator=(const ArrayFile& other);
      |                            ^~~~~~~~
../inst/include/Genotype.h:69:27: note:   by ‘virtual SignificantPattern::Genotype& SignificantPattern::Genotype::operator=(const SignificantPattern::Genotype&)’
   69 |         virtual Genotype& operator=(const Genotype& other);
      |                           ^~~~~~~~
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c SignificantIntervalSearchExact.cpp -o SignificantIntervalSearchExact.o
In file included from ../inst/include/Genotype.h:14,
                 from ../inst/include/SignificantFeaturesSearch.h:15,
                 from ../inst/include/SignificantIntervalSearch.h:13,
                 from ../inst/include/SignificantIntervalSearchFais.h:11,
                 from ../inst/include/SignificantIntervalSearchExact.h:21,
                 from SignificantIntervalSearchExact.cpp:8:
../inst/include/ArrayFile.h:80:28: warning: ‘virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)’ was hidden [-Woverloaded-virtual=]
   80 |         virtual ArrayFile& operator=(const ArrayFile& other);
      |                            ^~~~~~~~
In file included from ../inst/include/Genotype.h:15:
../inst/include/Phenotype.h:222:28: note:   by ‘virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)’
  222 |         virtual Phenotype& operator=(const Phenotype& other);
      |                            ^~~~~~~~
../inst/include/ArrayFile.h:80:28: warning: ‘virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)’ was hidden [-Woverloaded-virtual=]
   80 |         virtual ArrayFile& operator=(const ArrayFile& other);
      |                            ^~~~~~~~
../inst/include/Genotype.h:69:27: note:   by ‘virtual SignificantPattern::Genotype& SignificantPattern::Genotype::operator=(const SignificantPattern::Genotype&)’
   69 |         virtual Genotype& operator=(const Genotype& other);
      |                           ^~~~~~~~
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c SignificantIntervalSearchFais.cpp -o SignificantIntervalSearchFais.o
In file included from ../inst/include/Genotype.h:14,
                 from ../inst/include/SignificantFeaturesSearch.h:15,
                 from ../inst/include/SignificantIntervalSearch.h:13,
                 from ../inst/include/SignificantIntervalSearchFais.h:11,
                 from SignificantIntervalSearchFais.cpp:8:
../inst/include/ArrayFile.h:80:28: warning: ‘virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)’ was hidden [-Woverloaded-virtual=]
   80 |         virtual ArrayFile& operator=(const ArrayFile& other);
      |                            ^~~~~~~~
In file included from ../inst/include/Genotype.h:15:
../inst/include/Phenotype.h:222:28: note:   by ‘virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)’
  222 |         virtual Phenotype& operator=(const Phenotype& other);
      |                            ^~~~~~~~
../inst/include/ArrayFile.h:80:28: warning: ‘virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)’ was hidden [-Woverloaded-virtual=]
   80 |         virtual ArrayFile& operator=(const ArrayFile& other);
      |                            ^~~~~~~~
../inst/include/Genotype.h:69:27: note:   by ‘virtual SignificantPattern::Genotype& SignificantPattern::Genotype::operator=(const SignificantPattern::Genotype&)’
   69 |         virtual Genotype& operator=(const Genotype& other);
      |                           ^~~~~~~~
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c SignificantIntervalSearchFastCmh.cpp -o SignificantIntervalSearchFastCmh.o
In file included from ../inst/include/Genotype.h:14,
                 from ../inst/include/SignificantFeaturesSearch.h:15,
                 from ../inst/include/SignificantIntervalSearch.h:13,
                 from ../inst/include/SignificantIntervalSearchFastCmh.h:11,
                 from SignificantIntervalSearchFastCmh.cpp:8:
../inst/include/ArrayFile.h:80:28: warning: ‘virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)’ was hidden [-Woverloaded-virtual=]
   80 |         virtual ArrayFile& operator=(const ArrayFile& other);
      |                            ^~~~~~~~
In file included from ../inst/include/Genotype.h:15:
../inst/include/Phenotype.h:222:28: note:   by ‘virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)’
  222 |         virtual Phenotype& operator=(const Phenotype& other);
      |                            ^~~~~~~~
../inst/include/ArrayFile.h:80:28: warning: ‘virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)’ was hidden [-Woverloaded-virtual=]
   80 |         virtual ArrayFile& operator=(const ArrayFile& other);
      |                            ^~~~~~~~
../inst/include/Genotype.h:69:27: note:   by ‘virtual SignificantPattern::Genotype& SignificantPattern::Genotype::operator=(const SignificantPattern::Genotype&)’
   69 |         virtual Genotype& operator=(const Genotype& other);
      |                           ^~~~~~~~
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c SignificantItemsetSearch.cpp -o SignificantItemsetSearch.o
In file included from ../inst/include/Genotype.h:14,
                 from ../inst/include/SignificantFeaturesSearch.h:15,
                 from ../inst/include/SignificantItemsetSearch.h:11,
                 from SignificantItemsetSearch.cpp:8:
../inst/include/ArrayFile.h:80:28: warning: ‘virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)’ was hidden [-Woverloaded-virtual=]
   80 |         virtual ArrayFile& operator=(const ArrayFile& other);
      |                            ^~~~~~~~
In file included from ../inst/include/Genotype.h:15:
../inst/include/Phenotype.h:222:28: note:   by ‘virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)’
  222 |         virtual Phenotype& operator=(const Phenotype& other);
      |                            ^~~~~~~~
../inst/include/ArrayFile.h:80:28: warning: ‘virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)’ was hidden [-Woverloaded-virtual=]
   80 |         virtual ArrayFile& operator=(const ArrayFile& other);
      |                            ^~~~~~~~
../inst/include/Genotype.h:69:27: note:   by ‘virtual SignificantPattern::Genotype& SignificantPattern::Genotype::operator=(const SignificantPattern::Genotype&)’
   69 |         virtual Genotype& operator=(const Genotype& other);
      |                           ^~~~~~~~
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c SignificantItemsetSearchFacs.cpp -o SignificantItemsetSearchFacs.o
In file included from ../inst/include/Genotype.h:14,
                 from ../inst/include/SignificantFeaturesSearch.h:15,
                 from ../inst/include/SignificantItemsetSearch.h:11,
                 from ../inst/include/SignificantItemsetSearchFacs.h:11,
                 from SignificantItemsetSearchFacs.cpp:8:
../inst/include/ArrayFile.h:80:28: warning: ‘virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)’ was hidden [-Woverloaded-virtual=]
   80 |         virtual ArrayFile& operator=(const ArrayFile& other);
      |                            ^~~~~~~~
In file included from ../inst/include/Genotype.h:15:
../inst/include/Phenotype.h:222:28: note:   by ‘virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)’
  222 |         virtual Phenotype& operator=(const Phenotype& other);
      |                            ^~~~~~~~
../inst/include/ArrayFile.h:80:28: warning: ‘virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)’ was hidden [-Woverloaded-virtual=]
   80 |         virtual ArrayFile& operator=(const ArrayFile& other);
      |                            ^~~~~~~~
../inst/include/Genotype.h:69:27: note:   by ‘virtual SignificantPattern::Genotype& SignificantPattern::Genotype::operator=(const SignificantPattern::Genotype&)’
   69 |         virtual Genotype& operator=(const Genotype& other);
      |                           ^~~~~~~~
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Summary.cpp -o Summary.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c TransactionsData.cpp -o TransactionsData.o
In file included from ../inst/include/Genotype.h:14,
                 from ../inst/include/TransactionsData.h:13,
                 from TransactionsData.cpp:14:
../inst/include/ArrayFile.h:80:28: warning: ‘virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)’ was hidden [-Woverloaded-virtual=]
   80 |         virtual ArrayFile& operator=(const ArrayFile& other);
      |                            ^~~~~~~~
In file included from ../inst/include/Genotype.h:15:
../inst/include/Phenotype.h:222:28: note:   by ‘virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)’
  222 |         virtual Phenotype& operator=(const Phenotype& other);
      |                            ^~~~~~~~
../inst/include/ArrayFile.h:80:28: warning: ‘virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)’ was hidden [-Woverloaded-virtual=]
   80 |         virtual ArrayFile& operator=(const ArrayFile& other);
      |                            ^~~~~~~~
../inst/include/Genotype.h:69:27: note:   by ‘virtual SignificantPattern::Genotype& SignificantPattern::Genotype::operator=(const SignificantPattern::Genotype&)’
   69 |         virtual Genotype& operator=(const Genotype& other);
      |                           ^~~~~~~~
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c double_comp.cpp -o double_comp.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c gamma.cpp -o gamma.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c pval.cpp -o pval.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c sigpatsearch.cpp -o sigpatsearch.o
In file included from ../inst/include/Genotype.h:14,
                 from ../inst/include/SignificantFeaturesSearch.h:15,
                 from sigpatsearch.cpp:6:
../inst/include/ArrayFile.h:80:28: warning: ‘virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)’ was hidden [-Woverloaded-virtual=]
   80 |         virtual ArrayFile& operator=(const ArrayFile& other);
      |                            ^~~~~~~~
In file included from ../inst/include/Genotype.h:15:
../inst/include/Phenotype.h:222:28: note:   by ‘virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)’
  222 |         virtual Phenotype& operator=(const Phenotype& other);
      |                            ^~~~~~~~
../inst/include/ArrayFile.h:80:28: warning: ‘virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)’ was hidden [-Woverloaded-virtual=]
   80 |         virtual ArrayFile& operator=(const ArrayFile& other);
      |                            ^~~~~~~~
../inst/include/Genotype.h:69:27: note:   by ‘virtual SignificantPattern::Genotype& SignificantPattern::Genotype::operator=(const SignificantPattern::Genotype&)’
   69 |         virtual Genotype& operator=(const Genotype& other);
      |                           ^~~~~~~~
g++-13 -std=gnu++11 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o CASMAP.so ArrayFile.o CumulativeTimeMeasurement.o Exception.o FeatureSet.o FilterIntervals.o Genotype.o PValues.o Phenotype.o Profiler.o RcppExports.o SignificantFeaturesSearch.o SignificantFeaturesSearchTaroneCmh.o SignificantFeaturesSearchWithCovariates.o SignificantIntervalSearch.o SignificantIntervalSearchChi.o SignificantIntervalSearchExact.o SignificantIntervalSearchFais.o SignificantIntervalSearchFastCmh.o SignificantItemsetSearch.o SignificantItemsetSearchFacs.o Summary.o TransactionsData.o double_comp.o gamma.o pval.o sigpatsearch.o -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpeLGqUT/R.INSTALL167f6758ef06b6/CASMAP/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpeLGqUT/R.INSTALL167f6758ef06b6/CASMAP/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpeLGqUT/R.INSTALL167f6758ef06b6/CASMAP/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/00LOCK-CASMAP/00new/CASMAP/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 (CASMAP)