* installing *source* package ‘ProFAST’ ... ** package ‘ProFAST’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (GCC) 14.2.0’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/ProFAST/src' g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 "-DARMA_64BIT_WORD=1" -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 DR_removebatch.cpp -o DR_removebatch.o DR_removebatch.cpp: In function 'void runICM_sp_embed(const arma::field<arma::Mat<double> >&, arma::field<arma::Col<long long int> >&, arma::field<arma::Mat<double> >&, const arma::mat&, const arma::mat&, const arma::cube&, arma::cube&, const arma::field<arma::SpMat<double> >&, const arma::vec&, const arma::vec&, int, double&, arma::field<arma::Mat<double> >&, arma::field<arma::Mat<double> >&, arma::field<arma::Cube<double> >&, arma::field<arma::Cube<double> >&, arma::field<arma::Cube<double> >&, arma::field<arma::Cube<double> >&, arma::field<arma::Cube<double> >&, arma::field<arma::Cube<double> >&, const bool&)': DR_removebatch.cpp:432:7: warning: unused variable 'i' [-Wunused-variable] 432 | int i, iter, k, n; | ^ g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 "-DARMA_64BIT_WORD=1" -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++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 "-DARMA_64BIT_WORD=1" -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 alignExp.cpp -o alignExp.o g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 "-DARMA_64BIT_WORD=1" -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 alignExps.cpp -o alignExps.o alignExp.cpp: In function 'Rcpp::List correct_one_gene(const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const arma::mat&, const Rcpp::List&, const arma::vec&, const arma::vec&, const arma::vec&, const arma::vec&, const arma::vec&, const int&, const double&, const bool&)': alignExp.cpp:165:8: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare] 165 | if(M != Tm.n_rows){ | ~~^~~~~~~~~~~~ alignExp.cpp:180:7: warning: unused variable 'n' [-Wunused-variable] 180 | int n; | ^ g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 "-DARMA_64BIT_WORD=1" -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 cofast_util.cpp -o cofast_util.o alignExps.cpp: In function 'Rcpp::List correct_genes(const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const arma::mat&, const Rcpp::List&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const int&, const double&, const bool&)': alignExps.cpp:255:8: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const long long unsigned int'} [-Wsign-compare] 255 | if(M != Tm.n_rows){ | ~~^~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 "-DARMA_64BIT_WORD=1" -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 profast.cpp -o profast.o profast.cpp: In function 'Rcpp::List profast_g_cpp(const Rcpp::List&, const Rcpp::List&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::cube&, const Rcpp::List&, const int&, const double&, const bool&, const bool&, const bool&)': profast.cpp:408:7: warning: variable 'n' set but not used [-Wunused-but-set-variable] 408 | int n; | ^ alignExps.cpp:287:18: warning: 'p' may be used uninitialized [-Wmaybe-uninitialized] 287 | Eu(r) = zeros(Xf(r).n_rows, p); | ~~~~~^~~~~~~~~~~~~~~~~ alignExps.cpp:270:8: note: 'p' was declared here 270 | int p; | ^ g++-14 -std=gnu++17 -shared -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o ProFAST.so DR_removebatch.o RcppExports.o alignExp.o alignExps.o cofast_util.o profast.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/ProFAST/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/ProFAST/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/ProFAST/src' installing to /data/gannet/ripley/R/packages/tests-devel/ProFAST.Rcheck/00LOCK-ProFAST/00new/ProFAST/libs ** R ** data *** moving datasets to lazyload DB ** 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 (ProFAST)