############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf martini.buildbin-libdir && mkdir martini.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh martini_1.26.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R martini.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=martini.buildbin-libdir martini_1.26.0.tar.gz' >>>>>>> * installing *source* package ‘martini’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -std=c++11 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -I./lib `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"` -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: In file included from ./../inst/include/martini.h:7: In file included from ./../inst/include/martini_RcppExports.h:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] Index count = 0; ^ In file included from RcppExports.cpp:4: In file included from ./../inst/include/martini.h:7: In file included from ./../inst/include/martini_RcppExports.h:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] Index nsuper_et = 0; // Number of relaxed snodes in the original etree ^ In file included from RcppExports.cpp:4: In file included from ./../inst/include/martini.h:7: In file included from ./../inst/include/martini_RcppExports.h:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] Index replacements = 0; ^ In file included from RcppExports.cpp:4: In file included from ./../inst/include/martini.h:7: In file included from ./../inst/include/martini_RcppExports.h:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] int count = 0; ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -std=c++11 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -I./lib `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"` -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fPIC -falign-functions=64 -Wall -g -O2 -c mincut.cpp -o mincut.o In file included from mincut.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] Index count = 0; ^ In file included from mincut.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] Index nsuper_et = 0; // Number of relaxed snodes in the original etree ^ In file included from mincut.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] Index replacements = 0; ^ In file included from mincut.cpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] int count = 0; ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -std=c++11 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -I./lib `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"` -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -fPIC -falign-functions=64 -Wall -g -O2 -c lib/maxflow/maxflow.cpp -o lib/maxflow/maxflow.o lib/maxflow/maxflow.cpp:628:6: warning: variable 'num1' set but not used [-Wunused-but-set-variable] int num1 = 0, num2 = 0; ^ lib/maxflow/maxflow.cpp:628:16: warning: variable 'num2' set but not used [-Wunused-but-set-variable] int num1 = 0, num2 = 0; ^ lib/maxflow/maxflow.cpp:555:19: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion] j -> is_sink = 1; ^ ~ lib/maxflow/instances.inc:15:16: note: in instantiation of member function 'Graph::maxflow' requested here template class Graph; ^ In file included from lib/maxflow/maxflow.cpp:7: lib/maxflow/maxflow.h:510:15: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion] i->is_marked = 1; ^ ~ lib/maxflow/instances.inc:15:16: note: in instantiation of member function 'Graph::mark_node' requested here template class Graph; ^ lib/maxflow/maxflow.cpp:159:17: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion] i -> is_sink = 1; ^ ~ lib/maxflow/instances.inc:15:16: note: in instantiation of member function 'Graph::maxflow_init' requested here template class Graph; ^ lib/maxflow/maxflow.cpp:221:16: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion] i->is_sink = 1; ^ ~ lib/maxflow/instances.inc:15:16: note: in instantiation of member function 'Graph::maxflow_reuse_trees_init' requested here template class Graph; ^ lib/maxflow/maxflow.cpp:555:19: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion] j -> is_sink = 1; ^ ~ lib/maxflow/instances.inc:16:16: note: in instantiation of member function 'Graph::maxflow' requested here template class Graph; ^ In file included from lib/maxflow/maxflow.cpp:7: lib/maxflow/maxflow.h:510:15: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion] i->is_marked = 1; ^ ~ lib/maxflow/instances.inc:16:16: note: in instantiation of member function 'Graph::mark_node' requested here template class Graph; ^ lib/maxflow/maxflow.cpp:159:17: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion] i -> is_sink = 1; ^ ~ lib/maxflow/instances.inc:16:16: note: in instantiation of member function 'Graph::maxflow_init' requested here template class Graph; ^ lib/maxflow/maxflow.cpp:221:16: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion] i->is_sink = 1; ^ ~ lib/maxflow/instances.inc:16:16: note: in instantiation of member function 'Graph::maxflow_reuse_trees_init' requested here template class Graph; ^ lib/maxflow/maxflow.cpp:555:19: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion] j -> is_sink = 1; ^ ~ lib/maxflow/instances.inc:17:16: note: in instantiation of member function 'Graph::maxflow' requested here template class Graph; ^ In file included from lib/maxflow/maxflow.cpp:7: lib/maxflow/maxflow.h:510:15: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion] i->is_marked = 1; ^ ~ lib/maxflow/instances.inc:17:16: note: in instantiation of member function 'Graph::mark_node' requested here template class Graph; ^ lib/maxflow/maxflow.cpp:159:17: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion] i -> is_sink = 1; ^ ~ lib/maxflow/instances.inc:17:16: note: in instantiation of member function 'Graph::maxflow_init' requested here template class Graph; ^ lib/maxflow/maxflow.cpp:221:16: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion] i->is_sink = 1; ^ ~ lib/maxflow/instances.inc:17:16: note: in instantiation of member function 'Graph::maxflow_reuse_trees_init' requested here template class Graph; ^ lib/maxflow/maxflow.cpp:555:19: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion] j -> is_sink = 1; ^ ~ lib/maxflow/instances.inc:18:16: note: in instantiation of member function 'Graph::maxflow' requested here template class Graph; ^ In file included from lib/maxflow/maxflow.cpp:7: lib/maxflow/maxflow.h:510:15: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion] i->is_marked = 1; ^ ~ lib/maxflow/instances.inc:18:16: note: in instantiation of member function 'Graph::mark_node' requested here template class Graph; ^ lib/maxflow/maxflow.cpp:159:17: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion] i -> is_sink = 1; ^ ~ lib/maxflow/instances.inc:18:16: note: in instantiation of member function 'Graph::maxflow_init' requested here template class Graph; ^ lib/maxflow/maxflow.cpp:221:16: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion] i->is_sink = 1; ^ ~ lib/maxflow/instances.inc:18:16: note: in instantiation of member function 'Graph::maxflow_reuse_trees_init' requested here template class Graph; ^ 18 warnings generated. ar -crus libmaxflow.a lib/maxflow/maxflow.o cp -r lib/maxflow "/Users/biocbuild/bbs-3.20-bioc/meat/martini.buildbin-libdir/00LOCK-martini/00new/martini/include" mkdir -p "/Users/biocbuild/bbs-3.20-bioc/meat/martini.buildbin-libdir/00LOCK-martini/00new/martini/usrlib" cp libmaxflow.a "/Users/biocbuild/bbs-3.20-bioc/meat/martini.buildbin-libdir/00LOCK-martini/00new/martini/usrlib" clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o martini.so RcppExports.o mincut.o -pthread /Users/biocbuild/bbs-3.20-bioc/meat/martini.buildbin-libdir/00LOCK-martini/00new/martini/usrlib/libmaxflow.a -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/martini.buildbin-libdir/00LOCK-martini/00new/martini/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 (martini) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR martini.buildbin-libdir/martini/libs/martini.so >>>>>>> >>>>>>> Paths before fix: martini.buildbin-libdir/martini/libs/martini.so: martini.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "martini.buildbin-libdir/martini/libs/martini.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "martini.buildbin-libdir/martini/libs/martini.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "martini.buildbin-libdir/martini/libs/martini.so" >>>>>>> Paths after fix: martini.buildbin-libdir/martini/libs/martini.so: martini.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)