* installing *source* package ‘milorGWAS’ ... ** package ‘milorGWAS’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-13 (GCC) 13.2.0’ make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-LTO/milorGWAS/src' g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/milorGWAS/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/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 -flto=10 -c RcppExports.cpp -o RcppExports.o In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/routines.h:26, from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:128, from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp.h:27, from /data/gannet/ripley/R/test-dev/gaston/include/gaston/matrix4.h:2, from ../inst/include/milorGWAS.h:1, from RcppExports.cpp:4: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = true; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 53 | Rprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = false; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 57 | REprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/milorGWAS/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/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 -flto=10 -c chr_convert.cpp -o chr_convert.o In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/routines.h:26, from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:128, from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp.h:27, from chr_convert.cpp:1: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = true; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 53 | Rprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = false; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 57 | REprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} chr_convert.cpp: In function 'int chr_to_int(std::string&)': chr_convert.cpp:10:7: warning: unused variable 'c' [-Wunused-variable] 10 | int c = chr_ids.size(); | ^ g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/milorGWAS/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/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 -flto=10 -c dosage_files.cpp -o dosage_files.o In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/routines.h:26, from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:128, from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp.h:27, from dosage_files.cpp:1: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = true; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 53 | Rprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = false; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 57 | REprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} dosage_files.cpp: In member function 'void dosages::start()': dosage_files.cpp:76:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 76 | for(int i = 5; i < splitted.size(); i++) | ~~^~~~~~~~~~~~~~~~~ g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/milorGWAS/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/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 -flto=10 -c genotype_probas.cpp -o genotype_probas.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/milorGWAS/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/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 -flto=10 -c gwas_approx_pql_bed.cpp -o gwas_approx_pql_bed.o In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/routines.h:26, from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:128, from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp.h:27, from gwas_approx_pql_bed.cpp:1: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = true; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 53 | Rprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = false; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 57 | REprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/milorGWAS/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/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 -flto=10 -c gwas_approx_pql_dosages.cpp -o gwas_approx_pql_dosages.o In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/routines.h:26, from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:128, from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp.h:27, from gwas_approx_pql_dosages.cpp:1: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = true; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 53 | Rprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = false; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 57 | REprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} In file included from gwas_approx_pql_dosages.cpp:2: ../inst/include/milorGWAS/snp_filler_dosages.h: In instantiation of 'bool snp_filler_dosages::snp_fill(scalar_t*) [with scalar_t = float]': ../inst/include/milorGWAS/snp_filler_dosages.h:33:8: required from here ../inst/include/milorGWAS/snp_filler_dosages.h:54:22: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 54 | if(dosage.size() != nb_inds) { | ~~~~~~~~~~~~~~^~~~~~~~~~ g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/milorGWAS/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/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 -flto=10 -c gwas_logit_offset_bed.cpp -o gwas_logit_offset_bed.o In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/routines.h:26, from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:128, from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp.h:27, from gwas_logit_offset_bed.cpp:1: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = true; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 53 | Rprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = false; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 57 | REprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/milorGWAS/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/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 -flto=10 -c gwas_logit_offset_dosages.cpp -o gwas_logit_offset_dosages.o In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/routines.h:26, from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:128, from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp.h:27, from gwas_logit_offset_dosages.cpp:1: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = true; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 53 | Rprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = false; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 57 | REprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} In file included from gwas_logit_offset_dosages.cpp:2: ../inst/include/milorGWAS/snp_filler_dosages.h: In instantiation of 'bool snp_filler_dosages::snp_fill(scalar_t*) [with scalar_t = float]': ../inst/include/milorGWAS/snp_filler_dosages.h:33:8: required from here ../inst/include/milorGWAS/snp_filler_dosages.h:54:22: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 54 | if(dosage.size() != nb_inds) { | ~~~~~~~~~~~~~~^~~~~~~~~~ g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/milorGWAS/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/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 -flto=10 -c manhattan_thinning.cpp -o manhattan_thinning.o In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/routines.h:26, from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:128, from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp.h:27, from manhattan_thinning.cpp:1: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = true; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 53 | Rprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = false; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 57 | REprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/milorGWAS/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/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 -flto=10 -c matrix-varia.cpp -o matrix-varia.o In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/routines.h:26, from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:128, from /data/gannet/ripley/R/test-dev/RcppEigen/include/RcppEigenForward.h:26, from /data/gannet/ripley/R/test-dev/RcppEigen/include/RcppEigen.h:25, from matrix-varia.cpp:2: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = true; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 53 | Rprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = false; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 57 | REprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/milorGWAS/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/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 -flto=10 -c matrix4.cpp -o matrix4.o In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/routines.h:26, from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:128, from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp.h:27, from matrix4.cpp:1: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = true; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 53 | Rprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = false; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 57 | REprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/milorGWAS/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/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 -flto=10 -c read_dose_file.cpp -o read_dose_file.o In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/routines.h:26, from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:128, from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp.h:27, from read_dose_file.cpp:1: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = true; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 53 | Rprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = false; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 57 | REprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} read_dose_file.cpp: In function 'Rcpp::NumericVector dose_file_dim(Rcpp::CharacterVector)': read_dose_file.cpp:61:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 61 | if(nb_inds != dosage.size()) { | ~~~~~~~~^~~~~~~~~~~~~~~~ g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/milorGWAS/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/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 -flto=10 -c read_vcf_header.cpp -o read_vcf_header.o In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/routines.h:26, from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:128, from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp.h:27, from /data/gannet/ripley/R/test-dev/gaston/include/gaston/matrix4.h:2, from ../inst/include/milorGWAS/read_vcf_header.h:4, from read_vcf_header.cpp:2: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = true; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 53 | Rprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = false; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 57 | REprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/milorGWAS/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/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 -flto=10 -c snp_filter.cpp -o snp_filter.o In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/routines.h:26, from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:128, from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp.h:27, from ../inst/include/milorGWAS/snp_filter.h:1, from snp_filter.cpp:1: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = true; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 53 | Rprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = false; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 57 | REprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I ../inst/include/milorGWAS/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/gaston/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 -flto=10 -c token.cpp -o token.o In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/routines.h:26, from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:128, from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp.h:27, from token.cpp:1: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = true; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 53 | Rprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function 'std::streamsize Rcpp::Rstreambuf::xsputn(const char*, std::streamsize) [with bool OUTPUT = false; std::streamsize = long int]': /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'std::streamsize' {aka 'long int'} [-Wformat=] 57 | REprintf("%.*s", num, s); | ~~^~ ~~~ | | | | int std::streamsize {aka long int} g++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o milorGWAS.so RcppExports.o chr_convert.o dosage_files.o genotype_probas.o gwas_approx_pql_bed.o gwas_approx_pql_dosages.o gwas_logit_offset_bed.o gwas_logit_offset_dosages.o manhattan_thinning.o matrix-varia.o matrix4.o read_dose_file.o read_vcf_header.o snp_filter.o token.o -lz RcppExports.cpp:167:17: warning: 'gg_manhattan_thinning' violates the C++ One Definition Rule [-Wodr] 167 | RcppExport SEXP gg_manhattan_thinning(void *, void *, void *, void *); | ^ manhattan_thinning.cpp:52:17: note: 'gg_manhattan_thinning' was previously declared here 52 | RcppExport SEXP gg_manhattan_thinning(SEXP xSEXP, SEXP ySEXP, SEXP mxSEXP, SEXP mySEXP) { | ^ make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-LTO/milorGWAS/src' installing to /data/gannet/ripley/R/packages/tests-LTO/Libs/milorGWAS-lib/00LOCK-milorGWAS/00new/milorGWAS/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 (milorGWAS) Time 9:08.60, 234.89 + 18.58