############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL fgsea ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’ * installing *source* package ‘fgsea’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c ScoreCalculation.cpp -o ScoreCalculation.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c ScoreRuler.cpp -o ScoreRuler.o In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/lexical_cast.hpp:30, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/math/tools/convert_from_string.hpp:15, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/math/constants/constants.hpp:14, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/math/special_functions/digamma.hpp:20, from util.h:5, from ScoreRuler.cpp:2: /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ 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"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c esCalculation.cpp -o esCalculation.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c fastGSEA.cpp -o fastGSEA.o In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/lexical_cast.hpp:30, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/math/tools/convert_from_string.hpp:15, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/math/constants/constants.hpp:14, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/math/special_functions/digamma.hpp:20, from util.h:5, from fastGSEA.cpp:13: /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ fastGSEA.cpp: In function ‘Rcpp::NumericVector calcGseaStatBatchCpp(const NumericVector&, const List&, const IntegerVector&)’: fastGSEA.cpp:446:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 446 | for (int j = 0; j < S.size(); ++j) { | ~~^~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c fgseaMultilevel.cpp -o fgseaMultilevel.o fgseaMultilevel.cpp: In function ‘Rcpp::DataFrame fgseaMultilevelCpp(const NumericVector&, const 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 unsigned int’} [-Wsign-compare] 10 | for (int i = 0; i < posRanks.size(); i++) { | ~~^~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/lexical_cast.hpp:30, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/math/tools/convert_from_string.hpp:15, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/math/constants/constants.hpp:14, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/math/special_functions/digamma.hpp:20, from util.h:5, from fgseaMultilevelSupplement.cpp:3: /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ 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, EsRuler::SampleChunks&, double, std::mt19937&)’: fgseaMultilevelSupplement.cpp:260:14: warning: unused variable ‘fl’ [-Wunused-variable] 260 | bool fl = false; | ^~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c geseca.cpp -o geseca.o geseca.cpp: In function ‘Rcpp::List gesecaCpp(const NumericMatrix&, const 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"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c util.cpp -o util.o In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/lexical_cast.hpp:30, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/math/tools/convert_from_string.hpp:15, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/math/constants/constants.hpp:14, from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/math/special_functions/digamma.hpp:20, from util.h:5, from util.cpp:1: /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o fgsea.so RcppExports.o ScoreCalculation.o ScoreRuler.o esCalculation.o fastGSEA.o fgseaMultilevel.o fgseaMultilevelSupplement.o geseca.o util.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-fgsea/00new/fgsea/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 (fgsea)