* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘CASMAP’ ...
** package ‘CASMAP’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-8) 14.2.0’
using C++11
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpUTdqoU/R.INSTALL3212fe6ef133fd/CASMAP/src'
g++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I../inst/include -I'/home/hornik/tmp/R.check/r-patched-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++-14 -std=gnu++11 -shared -L/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpUTdqoU/R.INSTALL3212fe6ef133fd/CASMAP/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpUTdqoU/R.INSTALL3212fe6ef133fd/CASMAP/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpUTdqoU/R.INSTALL3212fe6ef133fd/CASMAP/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-CASMAP/00new/CASMAP/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘CASMAP’
finding HTML links ... done
CASMAP-class html
CASMAPenv html
SignificantIntervalSearchChi-class html
SignificantIntervalSearchExact-class html
SignificantIntervalSearchFastCmh-class
html
SignificantItemsetSearchFacs-class html
checkIsBoolean html
getExampleCovariatesFilename html
getExampleDataFilename html
getExampleLabelsFilename html
getExampleSignificantRegionsFilename html
getHigherOrderEpistasisString html
getMinModeLength html
getParentFunctionName html
getRegionGWASString html
isHigherOrderEpistasisString html
isInOpenInterval html
isRegionGWASString html
lib_delete_search_chi html
lib_delete_search_e html
lib_delete_search_facs html
lib_delete_search_fastcmh html
lib_execute_int html
lib_execute_iset html
lib_filter_intervals_write_to_file html
lib_get_filtered_intervals html
lib_get_result_facs html
lib_get_result_fais html
lib_get_result_int html
lib_get_result_iset html
lib_get_significant_intervals html
lib_get_significant_itemsets html
lib_new_search_chi html
lib_new_search_e html
lib_new_search_facs html
lib_new_search_fastcmh html
lib_profiler_write_to_file html
lib_pvals_significant_ints_write_to_file
html
lib_pvals_significant_isets_write_to_file
html
lib_pvals_testable_ints_write_to_file html
lib_pvals_testable_isets_write_to_file
html
lib_read_covariates_file_facs html
lib_read_covariates_file_fastcmh html
lib_read_eth_files html
lib_read_eth_files_with_cov_facs html
lib_read_eth_files_with_cov_fastcmh html
lib_read_plink_files html
lib_read_plink_files_with_cov_facs html
lib_read_plink_files_with_cov_fastcmh html
lib_summary_write_to_file_facs html
lib_summary_write_to_file_fais html
lib_summary_write_to_file_fastcmh html
lib_write_eth_files_int html
lib_write_eth_files_iset html
lib_write_eth_files_with_cov_facs html
lib_write_eth_files_with_cov_fastcmh html
m_SignificantFeaturesSearch-class html
m_SignificantFeaturesSearchWithCovariates-class
html
m_SignificantIntervalSearch-class html
m_SignificantIntervalSearchFais-class html
m_SignificantItemsetSearch-class html
modeErrorMessage html
modeLengthErrorMessage html
modeNeedsMoreChars html
** 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)