############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/SAIGEgds_1.8.1.tar.gz && rm -rf SAIGEgds.buildbin-libdir && mkdir SAIGEgds.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SAIGEgds.buildbin-libdir SAIGEgds_1.8.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL SAIGEgds_1.8.1.zip && rm SAIGEgds_1.8.1.tar.gz SAIGEgds_1.8.1.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 31 1502k 31 466k 0 0 543k 0 0:00:02 --:--:-- 0:00:02 543k 100 1502k 100 1502k 0 0 916k 0 0:00:01 0:00:01 --:--:-- 917k install for i386 * installing *source* package 'SAIGEgds' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=0 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SPATest.cpp -o SPATest.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=0 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c saige_fitnull.cpp -o saige_fitnull.o saige_fitnull.cpp: In function 'SEXPREC* saige_store_2b_geno(SEXP, SEXP, SEXP, SEXP, SEXP)': saige_fitnull.cpp:71:13: warning: unused variable 'th_idx' [-Wunused-variable] const int th_idx = 0; \ ^~~~~~ saige_fitnull.cpp:71:13: note: in definition of macro 'PARALLEL_FOR' const int th_idx = 0; \ ^~~~~~ saige_fitnull.cpp: In function 'SEXPREC* saige_get_sparse(SEXP)': saige_fitnull.cpp:249:10: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_len_t' {aka 'int'} [-Wsign-compare] if (num > Rf_length(geno)) ~~~~^~~~~~~~~~~~~~~~~ saige_fitnull.cpp: In function 'SEXPREC* saige_store_sp_geno(SEXP, SEXP, SEXP, SEXP, SEXP)': saige_fitnull.cpp:71:13: warning: unused variable 'th_idx' [-Wunused-variable] const int th_idx = 0; \ ^~~~~~ saige_fitnull.cpp:71:13: note: in definition of macro 'PARALLEL_FOR' const int th_idx = 0; \ ^~~~~~ saige_fitnull.cpp: In function 'void get_crossprod_b_grm(const dcolvec&, arma::dvec&)': saige_fitnull.cpp:75:13: warning: unused variable 'th_idx' [-Wunused-variable] const int th_idx = 0; \ ^~~~~~ saige_fitnull.cpp:75:13: note: in definition of macro 'PARALLEL_RANGE' const int th_idx = 0; \ ^~~~~~ saige_fitnull.cpp: In function 'void get_diag_sigma(const dvec&, const dvec&, arma::dvec&)': saige_fitnull.cpp:75:13: warning: unused variable 'th_idx' [-Wunused-variable] const int th_idx = 0; \ ^~~~~~ saige_fitnull.cpp:75:13: note: in definition of macro 'PARALLEL_RANGE' const int th_idx = 0; \ ^~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=0 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c saige_main.cpp -o saige_main.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=0 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vectorization.cpp -o vectorization.o C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o SAIGEgds.dll tmp.def SPATest.o saige_fitnull.o saige_main.o vectorization.o -lm -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/lib/i386 -ltbb -ltbbmalloc -lgcc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/SAIGEgds.buildbin-libdir/00LOCK-SAIGEgds/00new/SAIGEgds/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'SAIGEgds' finding HTML links ... done SAIGEgds-package html glmmHeritability html pACAT html seqAssocGLMM_SPA html finding level-2 HTML links ... done seqAssocGLMM_spaACAT_O html seqAssocGLMM_spaACAT_V html seqAssocGLMM_spaBurden html seqFitNullGLMM_SPA html seqGLMM_GxG_spa html seqSAIGE_LoadPval html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'SAIGEgds' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=0 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SPATest.cpp -o SPATest.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=0 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c saige_fitnull.cpp -o saige_fitnull.o saige_fitnull.cpp: In function 'SEXPREC* saige_store_2b_geno(SEXP, SEXP, SEXP, SEXP, SEXP)': saige_fitnull.cpp:71:13: warning: unused variable 'th_idx' [-Wunused-variable] const int th_idx = 0; \ ^~~~~~ saige_fitnull.cpp:71:13: note: in definition of macro 'PARALLEL_FOR' const int th_idx = 0; \ ^~~~~~ saige_fitnull.cpp: In function 'SEXPREC* saige_get_sparse(SEXP)': saige_fitnull.cpp:249:10: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_len_t' {aka 'int'} [-Wsign-compare] if (num > Rf_length(geno)) ~~~~^~~~~~~~~~~~~~~~~ saige_fitnull.cpp: In function 'SEXPREC* saige_store_sp_geno(SEXP, SEXP, SEXP, SEXP, SEXP)': saige_fitnull.cpp:71:13: warning: unused variable 'th_idx' [-Wunused-variable] const int th_idx = 0; \ ^~~~~~ saige_fitnull.cpp:71:13: note: in definition of macro 'PARALLEL_FOR' const int th_idx = 0; \ ^~~~~~ saige_fitnull.cpp: In function 'void get_crossprod_b_grm(const dcolvec&, arma::dvec&)': saige_fitnull.cpp:75:13: warning: unused variable 'th_idx' [-Wunused-variable] const int th_idx = 0; \ ^~~~~~ saige_fitnull.cpp:75:13: note: in definition of macro 'PARALLEL_RANGE' const int th_idx = 0; \ ^~~~~~ saige_fitnull.cpp: In function 'void get_diag_sigma(const dvec&, const dvec&, arma::dvec&)': saige_fitnull.cpp:75:13: warning: unused variable 'th_idx' [-Wunused-variable] const int th_idx = 0; \ ^~~~~~ saige_fitnull.cpp:75:13: note: in definition of macro 'PARALLEL_RANGE' const int th_idx = 0; \ ^~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=0 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c saige_main.cpp -o saige_main.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=0 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vectorization.cpp -o vectorization.o C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o SAIGEgds.dll tmp.def SPATest.o saige_fitnull.o saige_main.o vectorization.o -lm -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -lgcc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/SAIGEgds.buildbin-libdir/SAIGEgds/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'SAIGEgds' as SAIGEgds_1.8.1.zip * DONE (SAIGEgds) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'SAIGEgds' successfully unpacked and MD5 sums checked