############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/openCyto_2.6.0.tar.gz && rm -rf openCyto.buildbin-libdir && mkdir openCyto.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=openCyto.buildbin-libdir openCyto_2.6.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL openCyto_2.6.0.zip && rm openCyto_2.6.0.tar.gz openCyto_2.6.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 1101k 100 1101k 0 0 1400k 0 --:--:-- --:--:-- --:--:-- 1403k install for i386 * installing *source* package 'openCyto' ... ** 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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cpPmden.cpp -o cpPmden.o cpPmden.cpp: In function 'stringInfo cpPmden(const std::vector&)': cpPmden.cpp:88:22: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] for (auto i = 0; i < (nsamp-1); i++) { ~~^~~~~~~~~~~ cpPmden.cpp:100:17: warning: variable 'newaccx' set but not used [-Wunused-but-set-variable] double rhs, newaccx; ^~~~~~~ cpPmden.cpp:157:24: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] for (auto i = 0; i < nsamp; i++) { ~~^~~~~~~ cpPmden.cpp:164:22: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] for (auto i=0; i < (nsamp-2); i++) { ~~^~~~~~~~~~~ cpPmden.cpp:193:24: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] for (auto i = 0; i < nsamp; i++) { ~~^~~~~~~ cpPmden.cpp:219:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] for (auto i = 0; i < nsamp; i++) { ~~^~~~~~~ cpPmden.cpp:251:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] for (auto i = 0; i < nsamp; i++) { ~~^~~~~~~ "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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cppApprox.cpp -o cppApprox.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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cppdip.cpp -o cppdip.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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dynamic_prog.cpp -o dynamic_prog.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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fill_SMAWK.cpp -o fill_SMAWK.o fill_SMAWK.cpp: In function 'void reduce_in_place(int, int, int, int, const std::vector&, std::vector&, const std::vector >&, const std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, DISSIMILARITY)': fill_SMAWK.cpp:80:8: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] if(N >= js.size()) { ~~^~~~~~~~~~~~ fill_SMAWK.cpp:90:11: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] while(m > N) { // js_reduced has more than N positions / columns ~~^~~ fill_SMAWK.cpp:121:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] for(int r=(left+1); r < m; ++r) { ~~^~~ fill_SMAWK.cpp: In function 'void fill_even_positions(int, int, int, int, const std::vector&, std::vector >&, std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, DISSIMILARITY)': fill_SMAWK.cpp:164:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] for(++ r; r < n && js[r]<=jmax; r++) { ~~^~~ fill_SMAWK.cpp:164:29: warning: comparison of integer expressions of different signedness: 'const value_type' {aka 'const unsigned int'} and 'int' [-Wsign-compare] for(++ r; r < n && js[r]<=jmax; r++) { fill_SMAWK.cpp:168:15: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'int' [-Wsign-compare] if(jabs > i) break; ~~~~~^~~ fill_SMAWK.cpp: In function 'void find_min_from_candidates(int, int, int, int, const std::vector&, std::vector >&, std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, DISSIMILARITY)': fill_SMAWK.cpp:218:16: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'int' [-Wsign-compare] if(j_abs > i) break; ~~~~~~^~~ "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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c getTautStringApprox.cpp -o getTautStringApprox.o getTautStringApprox.cpp: In function 'Rcpp::List getTautStringApprox(std::vector)': getTautStringApprox.cpp:32:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i = 1; i != fullString.size(); ++i) { ~~^~~~~~~~~~~~~~~~~~~~ getTautStringApprox.cpp:56:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0; i != plotSpecs.size(); ++i) { ~~^~~~~~~~~~~~~~~~~~~ "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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c kMedDP.cpp -o kMedDP.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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c kkuiper.cpp -o kkuiper.o kkuiper.cpp: In function 'void difficultmax(std::vector&, long int, long int, long int, long int*, long int*, double*)': kkuiper.cpp:77:10: warning: variable 'min' set but not used [-Wunused-but-set-variable] double min, max; ^~~ kkuiper.cpp: In function 'void easymax(std::vector&, long int, long int, long int, long int*, long int*, double*)': kkuiper.cpp:64:10: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized] *erga=maxi; ~~~~~^~~~~ kkuiper.cpp:63:10: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized] *ergb=mini; ~~~~~^~~~~ kkuiper.cpp: In function 'void difficultmax(std::vector&, long int, long int, long int, long int*, long int*, double*)': kkuiper.cpp:161:23: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized] *erga=minis[maxi]; ^ kkuiper.cpp: In function 'std::vector kkuiper(std::vector&, long int, int)': kkuiper.cpp:64:10: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized] *erga=maxi; ~~~~~^~~~~ kkuiper.cpp:44:15: note: 'maxi' was declared here long i,mini,maxi; ^~~~ kkuiper.cpp:63:10: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized] *ergb=mini; ~~~~~^~~~~ kkuiper.cpp:44:10: note: 'mini' was declared here long i,mini,maxi; ^~~~ kkuiper.cpp:64:10: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized] *erga=maxi; ~~~~~^~~~~ kkuiper.cpp:44:15: note: 'maxi' was declared here long i,mini,maxi; ^~~~ kkuiper.cpp:63:10: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized] *ergb=mini; ~~~~~^~~~~ kkuiper.cpp:44:10: note: 'mini' was declared here long i,mini,maxi; ^~~~ kkuiper.cpp:58:3: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized] if(mini&)': medianAbsoluteDeviation.cpp:28:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (auto i = 0; i != devs.size(); ++i) ~~^~~~~~~~~~~~~~ "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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c misc.cpp -o misc.o misc.cpp: In function 'Rcpp::NumericMatrix collapseData(Rcpp::List, Rcpp::StringVector)': misc.cpp:10:24: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare] for(unsigned i = 0; i < mat_list.size(); i++){ ~~^~~~~~~~~~~~~~~~~ misc.cpp:21:31: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare] for(unsigned ind = 0; ind < mat_list.size(); ind++){ ~~~~^~~~~~~~~~~~~~~~~ "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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rQuantile.cpp -o rQuantile.o rQuantile.cpp: In function 'std::vector rQuantile(const std::vector&, std::vector)': rQuantile.cpp:35:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (auto i = 0; i != lowInd.size(); ++i) { ~~^~~~~~~~~~~~~~~~ rQuantile.cpp:41:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (auto i = 0; i != lowInd.size(); ++i) { ~~^~~~~~~~~~~~~~~~ rQuantile.cpp:47:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (auto i = 0; i != offSet.size(); ++i) ~~^~~~~~~~~~~~~~~~ "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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c singleDip.cpp -o singleDip.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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tautstring.cpp -o tautstring.o tautstring.cpp: In function 'stringInfo tautString(const std::vector&, const std::vector&, const std::vector&, const std::vector&, double, double, long int, int)': tautstring.cpp:148:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (auto i = 0; i < knotst.size(); i++) { ~~^~~~~~~~~~~~~~~ "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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tsGates.cpp -o tsGates.o tsGates.cpp: In function 'std::vector findKmedGates(const std::vector&, const std::vector&, int)': tsGates.cpp:41:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (auto j = 0; j != classVector.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~ tsGates.cpp: In function 'std::vector tsGates(const std::vector&, int)': tsGates.cpp:81:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (auto i = 1; i != (localMins.size()-1); ++i) { ~~^~~~~~~~~~~~~~~~~~~~~~~ tsGates.cpp:86:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (auto i = 0; i != yvals.size(); ++i) ~~^~~~~~~~~~~~~~~ tsGates.cpp:96:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (auto j = 0; j != cutValues.size(); ++j) { ~~^~~~~~~~~~~~~~~~~~~ tsGates.cpp:99:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (auto i = 0; i != ys.size(); ++i) ~~^~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -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:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c unlockNamespace.c -o unlockNamespace.o C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o openCyto.dll tmp.def RcppExports.o cpPmden.o cppApprox.o cppdip.o dynamic_prog.o fill_SMAWK.o getTautStringApprox.o kMedDP.o kkuiper.o local_density.o medianAbsoluteDeviation.o misc.o rQuantile.o singleDip.o tautstring.o tsGates.o unlockNamespace.o -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/openCyto.buildbin-libdir/00LOCK-openCyto/00new/openCyto/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'openCyto' finding HTML links ... done CytoExploreR_exports html add html as.data.table html boolMethod-class html dims-gtMethod-method html dummyMethod-class html fcEllipsoidGate-class html fcEllipsoidGate html fcFilter-class html fcFilterList-class html fcFilterList html fcPolygonGate-class html fcPolygonGate html fcRectangleGate-class html fcRectangleGate html fcTree-class html fcTree html gate_flowclust_1d html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/openCyto.buildbin-libdir/00LOCK-openCyto/00new/openCyto/help/gate_flowClust_1d.html finding level-2 HTML links ... done gate_flowclust_2d html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/openCyto.buildbin-libdir/00LOCK-openCyto/00new/openCyto/help/gate_flowClust_2d.html gate_mindensity html gate_mindensity2 html gate_quad_sequential html gate_quad_tmix html gate_quantile html gate_tail html gate_tautstring html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/openCyto.buildbin-libdir/00LOCK-openCyto/00new/openCyto/help/tautString.html gatingTemplate-class html getGate-fcTree-character-method html getNodes-fcTree-method html gh_generate_template html groupBy-gtMethod-method html gs_add_gating_method html gs_add_gating_method_init html gs_remove_gating_method html gtMethod-class html gtPopulation-class html gtSubsets-class html gt_gating html gt_get_children html gt_get_gate html gt_get_nodes html gt_get_parent html gt_list_methods html gt_toggle_helpergates html isCollapse-gtMethod-method html names-gtMethod-method html names-gtPopulation-method html ocRectRefGate-class html ocRectRefGate html ocRectangleGate-class html openCyto-deprecated html openCyto html openCyto.options html parameters-gtMethod-method html plot-fcFilterList-ANY-method html plot-fcTree-character-method html plot-gatingTemplate-missing-method html polyFunctions-class html posteriors-fcFilter-ANY-method html ppMethod-class html ppMethod-gatingTemplate-character-method html preprocessing-ppMethod-GatingSet-method html prior_flowclust html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/openCyto.buildbin-libdir/00LOCK-openCyto/00new/openCyto/help/prior_flowClust.html priors-fcFilter-ANY-method html refGate-class html register_plugins html show-boolMethod-method html show-fcFilter-method html show-gatingTemplate-method html show-gtMethod-method 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 'openCyto' ... ** 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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cpPmden.cpp -o cpPmden.o cpPmden.cpp: In function 'stringInfo cpPmden(const std::vector&)': cpPmden.cpp:88:22: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] for (auto i = 0; i < (nsamp-1); i++) { ~~^~~~~~~~~~~ cpPmden.cpp:100:17: warning: variable 'newaccx' set but not used [-Wunused-but-set-variable] double rhs, newaccx; ^~~~~~~ cpPmden.cpp:157:24: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] for (auto i = 0; i < nsamp; i++) { ~~^~~~~~~ cpPmden.cpp:164:22: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] for (auto i=0; i < (nsamp-2); i++) { ~~^~~~~~~~~~~ cpPmden.cpp:193:24: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] for (auto i = 0; i < nsamp; i++) { ~~^~~~~~~ cpPmden.cpp:219:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] for (auto i = 0; i < nsamp; i++) { ~~^~~~~~~ cpPmden.cpp:251:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] for (auto i = 0; i < nsamp; i++) { ~~^~~~~~~ "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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cppApprox.cpp -o cppApprox.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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cppdip.cpp -o cppdip.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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dynamic_prog.cpp -o dynamic_prog.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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fill_SMAWK.cpp -o fill_SMAWK.o fill_SMAWK.cpp: In function 'void reduce_in_place(int, int, int, int, const std::vector&, std::vector&, const std::vector >&, const std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, DISSIMILARITY)': fill_SMAWK.cpp:80:8: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] if(N >= js.size()) { ~~^~~~~~~~~~~~ fill_SMAWK.cpp:90:11: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] while(m > N) { // js_reduced has more than N positions / columns ~~^~~ fill_SMAWK.cpp:121:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] for(int r=(left+1); r < m; ++r) { ~~^~~ fill_SMAWK.cpp: In function 'void fill_even_positions(int, int, int, int, const std::vector&, std::vector >&, std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, DISSIMILARITY)': fill_SMAWK.cpp:164:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] for(++ r; r < n && js[r]<=jmax; r++) { ~~^~~ fill_SMAWK.cpp:164:29: warning: comparison of integer expressions of different signedness: 'const value_type' {aka 'const long long unsigned int'} and 'int' [-Wsign-compare] for(++ r; r < n && js[r]<=jmax; r++) { fill_SMAWK.cpp:168:15: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'int' [-Wsign-compare] if(jabs > i) break; ~~~~~^~~ fill_SMAWK.cpp: In function 'void find_min_from_candidates(int, int, int, int, const std::vector&, std::vector >&, std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, DISSIMILARITY)': fill_SMAWK.cpp:218:16: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'int' [-Wsign-compare] if(j_abs > i) break; ~~~~~~^~~ "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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c getTautStringApprox.cpp -o getTautStringApprox.o getTautStringApprox.cpp: In function 'Rcpp::List getTautStringApprox(std::vector)': getTautStringApprox.cpp:32:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (int i = 1; i != fullString.size(); ++i) { ~~^~~~~~~~~~~~~~~~~~~~ getTautStringApprox.cpp:56:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (int i = 0; i != plotSpecs.size(); ++i) { ~~^~~~~~~~~~~~~~~~~~~ "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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c kMedDP.cpp -o kMedDP.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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c kkuiper.cpp -o kkuiper.o kkuiper.cpp: In function 'void difficultmax(std::vector&, long int, long int, long int, long int*, long int*, double*)': kkuiper.cpp:77:10: warning: variable 'min' set but not used [-Wunused-but-set-variable] double min, max; ^~~ kkuiper.cpp: In function 'void easymax(std::vector&, long int, long int, long int, long int*, long int*, double*)': kkuiper.cpp:64:10: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized] *erga=maxi; ~~~~~^~~~~ kkuiper.cpp:63:10: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized] *ergb=mini; ~~~~~^~~~~ kkuiper.cpp: In function 'void difficultmax(std::vector&, long int, long int, long int, long int*, long int*, double*)': kkuiper.cpp:161:23: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized] *erga=minis[maxi]; ^ kkuiper.cpp: In function 'std::vector kkuiper(std::vector&, long int, int)': kkuiper.cpp:64:10: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized] *erga=maxi; ~~~~~^~~~~ kkuiper.cpp:44:15: note: 'maxi' was declared here long i,mini,maxi; ^~~~ kkuiper.cpp:63:10: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized] *ergb=mini; ~~~~~^~~~~ kkuiper.cpp:44:10: note: 'mini' was declared here long i,mini,maxi; ^~~~ kkuiper.cpp:64:10: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized] *erga=maxi; ~~~~~^~~~~ kkuiper.cpp:44:15: note: 'maxi' was declared here long i,mini,maxi; ^~~~ kkuiper.cpp:63:10: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized] *ergb=mini; ~~~~~^~~~~ kkuiper.cpp:44:10: note: 'mini' was declared here long i,mini,maxi; ^~~~ kkuiper.cpp:58:3: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized] if(mini&)': medianAbsoluteDeviation.cpp:28:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (auto i = 0; i != devs.size(); ++i) ~~^~~~~~~~~~~~~~ "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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c misc.cpp -o misc.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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rQuantile.cpp -o rQuantile.o rQuantile.cpp: In function 'std::vector rQuantile(const std::vector&, std::vector)': rQuantile.cpp:35:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (auto i = 0; i != lowInd.size(); ++i) { ~~^~~~~~~~~~~~~~~~ rQuantile.cpp:41:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (auto i = 0; i != lowInd.size(); ++i) { ~~^~~~~~~~~~~~~~~~ rQuantile.cpp:47:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (auto i = 0; i != offSet.size(); ++i) ~~^~~~~~~~~~~~~~~~ "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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c singleDip.cpp -o singleDip.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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tautstring.cpp -o tautstring.o tautstring.cpp: In function 'stringInfo tautString(const std::vector&, const std::vector&, const std::vector&, const std::vector&, double, double, long int, int)': tautstring.cpp:148:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (auto i = 0; i < knotst.size(); i++) { ~~^~~~~~~~~~~~~~~ "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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tsGates.cpp -o tsGates.o tsGates.cpp: In function 'std::vector findKmedGates(const std::vector&, const std::vector&, int)': tsGates.cpp:41:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (auto j = 0; j != classVector.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~ tsGates.cpp: In function 'std::vector tsGates(const std::vector&, int)': tsGates.cpp:81:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (auto i = 1; i != (localMins.size()-1); ++i) { ~~^~~~~~~~~~~~~~~~~~~~~~~ tsGates.cpp:86:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (auto i = 0; i != yvals.size(); ++i) ~~^~~~~~~~~~~~~~~ tsGates.cpp:96:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (auto j = 0; j != cutValues.size(); ++j) { ~~^~~~~~~~~~~~~~~~~~~ tsGates.cpp:99:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (auto i = 0; i != ys.size(); ++i) ~~^~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -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:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c unlockNamespace.c -o unlockNamespace.o C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o openCyto.dll tmp.def RcppExports.o cpPmden.o cppApprox.o cppdip.o dynamic_prog.o fill_SMAWK.o getTautStringApprox.o kMedDP.o kkuiper.o local_density.o medianAbsoluteDeviation.o misc.o rQuantile.o singleDip.o tautstring.o tsGates.o unlockNamespace.o -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/openCyto.buildbin-libdir/openCyto/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'openCyto' as openCyto_2.6.0.zip * DONE (openCyto) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'openCyto' successfully unpacked and MD5 sums checked