* installing *source* package ‘CASMAP’ ... ** package ‘CASMAP’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-13 (GCC) 13.2.0’ using C++11 make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/CASMAP/src' g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c ArrayFile.cpp -o ArrayFile.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c CumulativeTimeMeasurement.cpp -o CumulativeTimeMeasurement.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c Exception.cpp -o Exception.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c FeatureSet.cpp -o FeatureSet.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c FilterIntervals.cpp -o FilterIntervals.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c PValues.cpp -o PValues.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c Profiler.cpp -o Profiler.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c SignificantFeaturesSearchTaroneCmh.cpp -o SignificantFeaturesSearchTaroneCmh.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -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 ../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); | ^~~~~~~~ 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); | ^~~~~~~~ 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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c SignificantIntervalSearchExact.cpp -o SignificantIntervalSearchExact.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -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); | ^~~~~~~~ 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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c SignificantItemsetSearch.cpp -o SignificantItemsetSearch.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -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); | ^~~~~~~~ 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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c Summary.cpp -o Summary.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c double_comp.cpp -o double_comp.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c gamma.cpp -o gamma.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c pval.cpp -o pval.o g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -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/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -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 make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/CASMAP/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/CASMAP/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/CASMAP/src' installing to /data/gannet/ripley/R/packages/tests-devel/CASMAP.Rcheck/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)