* installing *source* package ‘CASMAP’ ...
** package ‘CASMAP’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (GCC) 14.2.0’
using C++11
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/CASMAP/src'
g++-14 -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 -DC99_INLINE_SEMANTICS=0   -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  -DR_NO_REMAP -c ArrayFile.cpp -o ArrayFile.o
g++-14 -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 -DC99_INLINE_SEMANTICS=0   -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  -DR_NO_REMAP -c CumulativeTimeMeasurement.cpp -o CumulativeTimeMeasurement.o
g++-14 -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 -DC99_INLINE_SEMANTICS=0   -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  -DR_NO_REMAP -c Exception.cpp -o Exception.o
g++-14 -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 -DC99_INLINE_SEMANTICS=0   -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  -DR_NO_REMAP -c FeatureSet.cpp -o FeatureSet.o
g++-14 -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 -DC99_INLINE_SEMANTICS=0   -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  -DR_NO_REMAP -c FilterIntervals.cpp -o FilterIntervals.o
g++-14 -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 -DC99_INLINE_SEMANTICS=0   -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  -DR_NO_REMAP -c Genotype.cpp -o Genotype.o
g++-14 -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 -DC99_INLINE_SEMANTICS=0   -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  -DR_NO_REMAP -c PValues.cpp -o PValues.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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0   -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  -DR_NO_REMAP -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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0   -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  -DR_NO_REMAP -c Profiler.cpp -o Profiler.o
g++-14 -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 -DC99_INLINE_SEMANTICS=0   -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  -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++-14 -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 -DC99_INLINE_SEMANTICS=0   -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  -DR_NO_REMAP -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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0   -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  -DR_NO_REMAP -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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0   -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  -DR_NO_REMAP -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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0   -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  -DR_NO_REMAP -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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0   -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  -DR_NO_REMAP -c SignificantIntervalSearchChi.cpp -o SignificantIntervalSearchChi.o
g++-14 -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 -DC99_INLINE_SEMANTICS=0   -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  -DR_NO_REMAP -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/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);
      |                           ^~~~~~~~
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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0   -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  -DR_NO_REMAP -c SignificantIntervalSearchFais.cpp -o SignificantIntervalSearchFais.o
g++-14 -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 -DC99_INLINE_SEMANTICS=0   -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  -DR_NO_REMAP -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/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/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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0   -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  -DR_NO_REMAP -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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0   -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  -DR_NO_REMAP -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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0   -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  -DR_NO_REMAP -c Summary.cpp -o Summary.o
g++-14 -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 -DC99_INLINE_SEMANTICS=0   -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  -DR_NO_REMAP -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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0   -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  -DR_NO_REMAP -c double_comp.cpp -o double_comp.o
g++-14 -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 -DC99_INLINE_SEMANTICS=0   -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  -DR_NO_REMAP -c gamma.cpp -o gamma.o
g++-14 -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 -DC99_INLINE_SEMANTICS=0   -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  -DR_NO_REMAP -c pval.cpp -o pval.o
g++-14 -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 -DC99_INLINE_SEMANTICS=0   -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  -DR_NO_REMAP -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/usr/local/gcc14/lib64 -L/usr/local/lib64 -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)