############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SAIGEgds ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘SAIGEgds’ ... ** this is package ‘SAIGEgds’ version ‘2.9.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c SPATest.cpp -o SPATest.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c saige_fitnull.cpp -o saige_fitnull.o In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from saige_fitnull.cpp:28: /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’ 66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.") | ^ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c saige_main.cpp -o saige_main.o In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from saige_main.cpp:29: /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’ 66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.") | ^ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c saige_misc.cpp -o saige_misc.o In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from saige_misc.cpp:24: /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’ 66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.") | ^ In file included from saige_misc.cpp:25: saige.h:80:33: error: ‘tbb::concurrent_vector’ has not been declared 80 | #define PARALLEL_VECTOR tbb::concurrent_vector | ^~~~~~~~~~~~~~~~~ saige_misc.cpp:518:9: note: in expansion of macro ‘PARALLEL_VECTOR’ 518 | PARALLEL_VECTOR &sp) | ^~~~~~~~~~~~~~~ saige_misc.cpp:518:24: error: expected ‘,’ or ‘...’ before ‘<’ token 518 | PARALLEL_VECTOR &sp) | ^ saige_misc.cpp: In lambda function: saige_misc.cpp:540:41: error: ‘sp’ was not declared in this scope 540 | sp.push_back(t_sp_i_j(i_b+i_st, j_b+j_st)); | ^~ saige_misc.cpp: In function ‘SEXPREC* saige_grm_sp_calc(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: saige.h:80:33: error: ‘concurrent_vector’ is not a member of ‘tbb’ 80 | #define PARALLEL_VECTOR tbb::concurrent_vector | ^~~~~~~~~~~~~~~~~ saige_misc.cpp:568:9: note: in expansion of macro ‘PARALLEL_VECTOR’ 568 | PARALLEL_VECTOR sp; | ^~~~~~~~~~~~~~~ saige_misc.cpp:568:33: error: expected primary-expression before ‘>’ token 568 | PARALLEL_VECTOR sp; | ^ saige_misc.cpp:568:35: error: ‘sp’ was not declared in this scope 568 | PARALLEL_VECTOR sp; | ^~ saige_misc.cpp: At global scope: saige_misc.cpp:515:13: warning: ‘void grm_sp_calc_block(double, int, int, int, int, size_t, const Rcpp::RawMatrix&, const Rcpp::NumericMatrix&, int)’ defined but not used [-Wunused-function] 515 | static void grm_sp_calc_block(const double rel, | ^~~~~~~~~~~~~~~~~ make: *** [/home/biocbuild/bbs-3.22-bioc/R/etc/Makeconf:209: saige_misc.o] Error 1 ERROR: compilation failed for package ‘SAIGEgds’ * removing ‘/home/biocbuild/bbs-3.22-bioc/R/site-library/SAIGEgds’