############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf DeMixT.buildbin-libdir && mkdir DeMixT.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DeMixT_1.14.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R DeMixT.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=DeMixT.buildbin-libdir DeMixT_1.14.0.tar.gz' >>>>>>> * installing *source* package ‘DeMixT’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c DeMixT.c -o DeMixT.o DeMixT.c:37:33: warning: variable 'st1_sig_2' set but not used [-Wunused-but-set-variable] double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2; ^ DeMixT.c:37:45: warning: variable 'st2_sig_2' set but not used [-Wunused-but-set-variable] double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2; ^ DeMixT.c:37:11: warning: variable 'st1_mu_2' set but not used [-Wunused-but-set-variable] double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2; ^ DeMixT.c:37:22: warning: variable 'st2_mu_2' set but not used [-Wunused-but-set-variable] double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2; ^ DeMixT.c:591:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable] double obj_old, obj_new; ^ DeMixT.c:591:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable] double obj_old, obj_new; ^ DeMixT.c:1280:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable] double obj_old, obj_new; ^ DeMixT.c:1280:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable] double obj_old, obj_new; ^ DeMixT.c:1307:9: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable] double obj_old, obj_new; ^ DeMixT.c:1307:18: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable] double obj_old, obj_new; ^ DeMixT.c:1322:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable] double obj_old, obj_new; ^ DeMixT.c:1322:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable] double obj_old, obj_new; ^ 12 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c Profile_2D.cpp -o Profile_2D.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o DeMixT.so DeMixT.o Profile_2D.o RcppExports.o init.o registerDynamicSymbol.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.16-bioc/meat/DeMixT.buildbin-libdir/00LOCK-DeMixT/00new/DeMixT/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘ggplot2::alpha’ by ‘psych::alpha’ when loading ‘DeMixT’ Warning: replacing previous import ‘SummarizedExperiment::distance’ by ‘psych::distance’ when loading ‘DeMixT’ Warning: replacing previous import ‘ggplot2::%+%’ by ‘psych::%+%’ when loading ‘DeMixT’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘ggplot2::alpha’ by ‘psych::alpha’ when loading ‘DeMixT’ Warning: replacing previous import ‘SummarizedExperiment::distance’ by ‘psych::distance’ when loading ‘DeMixT’ Warning: replacing previous import ‘ggplot2::%+%’ by ‘psych::%+%’ when loading ‘DeMixT’ ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: replacing previous import ‘ggplot2::alpha’ by ‘psych::alpha’ when loading ‘DeMixT’ Warning: replacing previous import ‘SummarizedExperiment::distance’ by ‘psych::distance’ when loading ‘DeMixT’ Warning: replacing previous import ‘ggplot2::%+%’ by ‘psych::%+%’ when loading ‘DeMixT’ ** testing if installed package keeps a record of temporary installation path * DONE (DeMixT) >>>>>>> >>>>>>> FIXING LINKS FOR DeMixT.buildbin-libdir/DeMixT/libs/DeMixT.so >>>>>>> install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib" "DeMixT.buildbin-libdir/DeMixT/libs/DeMixT.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "DeMixT.buildbin-libdir/DeMixT/libs/DeMixT.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "DeMixT.buildbin-libdir/DeMixT/libs/DeMixT.so"