############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL fgsea ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'fgsea' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' using C++11 g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ScoreCalculation.cpp -o ScoreCalculation.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ScoreRuler.cpp -o ScoreRuler.o In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11, from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29, from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:15, from util.h:5, from ScoreRuler.cpp:2: F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ ScoreRuler.cpp: In member function 'void ScoreRuler::extend(double, int, double)': ScoreRuler.cpp:76:31: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 76 | for (moves = 0; moves < sampleSize * genesetSize;) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c esCalculation.cpp -o esCalculation.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fastGSEA.cpp -o fastGSEA.o In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11, from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29, from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:15, from util.h:5, from fastGSEA.cpp:13: F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ fastGSEA.cpp: In function 'Rcpp::NumericVector calcGseaStatBatchCpp(const Rcpp::NumericVector&, const Rcpp::List&, const Rcpp::IntegerVector&)': fastGSEA.cpp:446:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 446 | for (int j = 0; j < S.size(); ++j) { | ~~^~~~~~~~~~ g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fgseaMultilevel.cpp -o fgseaMultilevel.o fgseaMultilevel.cpp: In function 'Rcpp::DataFrame fgseaMultilevelCpp(const Rcpp::NumericVector&, const Rcpp::NumericVector&, int, int, int, double, bool)': fgseaMultilevel.cpp:10:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 10 | for (int i = 0; i < posRanks.size(); i++) { | ~~^~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11, from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29, from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:15, from util.h:5, from fgseaMultilevelSupplement.cpp:3: F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ fgseaMultilevelSupplement.cpp: In member function 'void EsRuler::duplicateSamples()': fgseaMultilevelSupplement.cpp:40:37: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 40 | for (int sampleId = 0; sampleId < sampleSize; sampleId++) { | ~~~~~~~~~^~~~~~~~~~~~ fgseaMultilevelSupplement.cpp:50:41: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 50 | for (int sampleId = 0; 2 * sampleId < sampleSize; sampleId++) { | ~~~~~~~~~~~~~^~~~~~~~~~~~ fgseaMultilevelSupplement.cpp:59:41: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 59 | for (int sampleId = 0; 2 * sampleId < sampleSize - 2; sampleId++) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ fgseaMultilevelSupplement.cpp: In member function 'void EsRuler::extend(double, int, double)': fgseaMultilevelSupplement.cpp:73:37: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 73 | for (int sampleId = 0; sampleId < sampleSize; sampleId++) { | ~~~~~~~~~^~~~~~~~~~~~ fgseaMultilevelSupplement.cpp:77:16: warning: unused variable 'currentES' [-Wunused-variable] 77 | double currentES = calcES(ranks, currentSamples[sampleId]); | ^~~~~~~~~ fgseaMultilevelSupplement.cpp:90:31: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 90 | for (int j = 0; j < sampleSize; ++j) { | ~~^~~~~~~~~~~~ fgseaMultilevelSupplement.cpp:97:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 97 | for (int i = 0; i < sampleSize; ++i) { | ~~^~~~~~~~~~~~ fgseaMultilevelSupplement.cpp:112:35: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 112 | for (int moves = 0; moves < sampleSize * pathwaySize;) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ fgseaMultilevelSupplement.cpp:113:45: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 113 | for (int sampleId = 0; sampleId < sampleSize; sampleId++) { | ~~~~~~~~~^~~~~~~~~~~~ fgseaMultilevelSupplement.cpp:118:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 118 | for (int i = 0; i < sampleSize; ++i) { | ~~^~~~~~~~~~~~ fgseaMultilevelSupplement.cpp: In member function 'int EsRuler::perturbate(const std::vector&, int, SampleChunks&, double, std::mt19937&)': fgseaMultilevelSupplement.cpp:260:14: warning: unused variable 'fl' [-Wunused-variable] 260 | bool fl = false; | ^~ g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c geseca.cpp -o geseca.o geseca.cpp: In function 'Rcpp::List gesecaCpp(const Rcpp::NumericMatrix&, const Rcpp::NumericVector&, unsigned int, unsigned int, int, double)': geseca.cpp:9:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 9 | for (unsigned i = 0; i < E.nrow(); i++){ | ~~^~~~~~~~~~ g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c util.cpp -o util.o In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11, from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29, from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:15, from util.h:5, from util.cpp:1: F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ g++ -shared -s -static-libgcc -o fgsea.dll tmp.def RcppExports.o ScoreCalculation.o ScoreRuler.o esCalculation.o fastGSEA.o fgseaMultilevel.o fgseaMultilevelSupplement.o geseca.o util.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-fgsea/00new/fgsea/libs/x64 ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (fgsea)