############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL cliqueMS ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'cliqueMS' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 12.2.0' using C++11 g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c findAnnotationR.cpp -o findAnnotationR.o In file included from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/functional/hash.hpp:6, from annotationCliqueMSR.h:18, from findAnnotationR.cpp:1: F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container_hash/hash.hpp:132:33: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\string:48, from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\locale_classes.h:40, from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\ios_base.h:41, from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\ios:42, from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\ostream:38, from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\iostream:39, from annotationCliqueMSR.h:5: c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ annotationCliqueMSR.h: In function 'std::vector > sortMass(annotData&, int, std::unordered_map >, int)': annotationCliqueMSR.h:440:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 440 | if(id < allM.size()) // not add more masses in case that for that feature are less than "n" top masses | ~~~^~~~~~~~~~~~~ annotationCliqueMSR.h: In function 'std::unordered_set getTopScoringMasses(annotData&, int, rawadList, int, int, double)': annotationCliqueMSR.h:476:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 476 | if(id < allM.size()) // not add more masses in case that there are less than "n" top masses | ~~~^~~~~~~~~~~~~ annotationCliqueMSR.h: In function 'std::vector sortAnnotations(std::unordered_map&, int)': annotationCliqueMSR.h:725:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 725 | if(id < allAn.size() ) | ~~~^~~~~~~~~~~~~~ annotationCliqueMSR.h: In function 'double computeMaxScore(std::vector&, int, double)': annotationCliqueMSR.h:747:25: warning: 'completeroundscore' may be used uninitialized [-Wmaybe-uninitialized] 747 | score = (completeround*completeroundscore) + remainderroundscore + (completeround*newmass); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ annotationCliqueMSR.h:733:10: note: 'completeroundscore' was declared here 733 | double completeroundscore,remainderroundscore = 0; | ^~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c findCliquesR.cpp -o findCliquesR.o In file included from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/functional/hash.hpp:6, from networkCliqueMSR.h:21, from findCliquesR.cpp:2: F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container_hash/hash.hpp:132:33: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | struct hash_base : std::unary_function {}; | ^~~~~~~~~~~~~~ In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\unordered_map:44, from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153, from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:62, from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:30, from F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25, from F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:29, from F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:25, from F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30, from networkCliqueMSR.h:7: c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c findIsotopesR.cpp -o findIsotopesR.o g++ -shared -s -static-libgcc -o cliqueMS.dll tmp.def RcppExports.o findAnnotationR.o findCliquesR.o findIsotopesR.o -fopenmp -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-cliqueMS/00new/cliqueMS/libs/x64 ** R ** data ** 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 (cliqueMS)