############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf CytoML.buildbin-libdir && mkdir CytoML.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CytoML_2.17.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CytoML.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CytoML.buildbin-libdir CytoML_2.17.0.tar.gz' >>>>>>> * installing *source* package ‘CytoML’ ... ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether clang++ -arch x86_64 -std=gnu++11 accepts -g... yes checking for gcc... clang -arch x86_64 checking whether we are using the GNU C compiler... yes checking whether clang -arch x86_64 accepts -g... yes checking for clang -arch x86_64 option to accept ISO C89... none needed configure: setting xml2 flags... configure: No directory was specified for --with-xml2. Trying to find xml2 using other methods. checking for xml2-config... /usr/bin/xml2-config configure: setting cytolib-ml commandline tool path... configure: Using the following compilation and linking flags configure: PKG_CPPFLAGS=-I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include -ftemplate-depth=900 configure: PKG_LIBS=-L/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm configure: CYTOLIBML_BIN=/usr/local/bin configure: creating ./config.status config.status: creating src/Makevars config.status: creating R/cytolibml_bin_path.R ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include/ -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include -ftemplate-depth=900 -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/flowWorkspace/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cpp11.cpp -o cpp11.o In file included from cpp11.cpp:4: In file included from ./CytoML_types.h:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/flowWorkspace/include/flowWorkspace.h:5: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct] for (const pb::Range range : gate_pb.mrg().ranges()) { ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying for (const pb::Range range : gate_pb.mrg().ranges()) { ^~~~~~~~~~~~~~~~~~~~~~~ & In file included from cpp11.cpp:4: In file included from ./CytoML_types.h:5: In file included from ../inst/include/CytoML/openWorkspace.hpp:11: In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10: In file included from ../inst/include/CytoML/flowJoWorkspace.hpp:11: In file included from ../inst/include/CytoML/workspace.hpp:10: In file included from ../inst/include/CytoML/workspace_type.hpp:4: ../inst/include/CytoML/wsNode.hpp:27:20: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat] Rprintf("%.*s", n, s); ~~^~ ~ In file included from cpp11.cpp:4: In file included from ./CytoML_types.h:5: In file included from ../inst/include/CytoML/openWorkspace.hpp:11: In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10: In file included from ../inst/include/CytoML/flowJoWorkspace.hpp:11: In file included from ../inst/include/CytoML/workspace.hpp:10: ../inst/include/CytoML/workspace_type.hpp:67:44: warning: 'recursive_directory_iterator' is deprecated: Use directory_options instead of symlink_option [-Wdeprecated-declarations] for(const fs::directory_entry & i: fs::recursive_directory_iterator(fs::path(data_dir), fs::symlink_option::recurse)) ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/filesystem/directory.hpp:922:5: note: 'recursive_directory_iterator' has been explicitly marked deprecated here BOOST_FILESYSTEM_DETAIL_DEPRECATED("Use directory_options instead of symlink_option") ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/filesystem/config.hpp:73:49: note: expanded from macro 'BOOST_FILESYSTEM_DETAIL_DEPRECATED' #define BOOST_FILESYSTEM_DETAIL_DEPRECATED(msg) BOOST_DEPRECATED(msg) ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/config/compiler/clang.hpp:342:46: note: expanded from macro 'BOOST_DEPRECATED' #define BOOST_DEPRECATED(msg) __attribute__((deprecated(msg))) ^ In file included from cpp11.cpp:4: In file included from ./CytoML_types.h:5: In file included from ../inst/include/CytoML/openWorkspace.hpp:11: In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10: In file included from ../inst/include/CytoML/flowJoWorkspace.hpp:11: In file included from ../inst/include/CytoML/workspace.hpp:10: ../inst/include/CytoML/workspace_type.hpp:67:44: warning: 'recursive_directory_iterator' is deprecated: Use directory_options instead of symlink_option [-Wdeprecated-declarations] for(const fs::directory_entry & i: fs::recursive_directory_iterator(fs::path(data_dir), fs::symlink_option::recurse)) ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/filesystem/directory.hpp:922:5: note: 'recursive_directory_iterator' has been explicitly marked deprecated here BOOST_FILESYSTEM_DETAIL_DEPRECATED("Use directory_options instead of symlink_option") ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/filesystem/config.hpp:73:49: note: expanded from macro 'BOOST_FILESYSTEM_DETAIL_DEPRECATED' #define BOOST_FILESYSTEM_DETAIL_DEPRECATED(msg) BOOST_DEPRECATED(msg) ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/config/compiler/clang.hpp:342:46: note: expanded from macro 'BOOST_DEPRECATED' #define BOOST_DEPRECATED(msg) __attribute__((deprecated(msg))) ^ In file included from cpp11.cpp:4: In file included from ./CytoML_types.h:5: In file included from ../inst/include/CytoML/openWorkspace.hpp:12: ../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: warning: '/*' within block comment [-Wcomment] * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate ^ 5 warnings generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include/ -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include -ftemplate-depth=900 -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/flowWorkspace/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c parseFlowJoWorkspace.cpp -o parseFlowJoWorkspace.o In file included from parseFlowJoWorkspace.cpp:10: In file included from ../inst/include/CytoML/openWorkspace.hpp:11: In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10: In file included from ../inst/include/CytoML/flowJoWorkspace.hpp:11: In file included from ../inst/include/CytoML/workspace.hpp:10: In file included from ../inst/include/CytoML/workspace_type.hpp:4: In file included from ../inst/include/CytoML/wsNode.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct] for (const pb::Range range : gate_pb.mrg().ranges()) { ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying for (const pb::Range range : gate_pb.mrg().ranges()) { ^~~~~~~~~~~~~~~~~~~~~~~ & In file included from parseFlowJoWorkspace.cpp:10: In file included from ../inst/include/CytoML/openWorkspace.hpp:11: In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10: In file included from ../inst/include/CytoML/flowJoWorkspace.hpp:11: In file included from ../inst/include/CytoML/workspace.hpp:10: In file included from ../inst/include/CytoML/workspace_type.hpp:4: ../inst/include/CytoML/wsNode.hpp:27:20: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat] Rprintf("%.*s", n, s); ~~^~ ~ In file included from parseFlowJoWorkspace.cpp:10: In file included from ../inst/include/CytoML/openWorkspace.hpp:11: In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10: In file included from ../inst/include/CytoML/flowJoWorkspace.hpp:11: In file included from ../inst/include/CytoML/workspace.hpp:10: ../inst/include/CytoML/workspace_type.hpp:67:44: warning: 'recursive_directory_iterator' is deprecated: Use directory_options instead of symlink_option [-Wdeprecated-declarations] for(const fs::directory_entry & i: fs::recursive_directory_iterator(fs::path(data_dir), fs::symlink_option::recurse)) ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/filesystem/directory.hpp:922:5: note: 'recursive_directory_iterator' has been explicitly marked deprecated here BOOST_FILESYSTEM_DETAIL_DEPRECATED("Use directory_options instead of symlink_option") ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/filesystem/config.hpp:73:49: note: expanded from macro 'BOOST_FILESYSTEM_DETAIL_DEPRECATED' #define BOOST_FILESYSTEM_DETAIL_DEPRECATED(msg) BOOST_DEPRECATED(msg) ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/config/compiler/clang.hpp:342:46: note: expanded from macro 'BOOST_DEPRECATED' #define BOOST_DEPRECATED(msg) __attribute__((deprecated(msg))) ^ In file included from parseFlowJoWorkspace.cpp:10: In file included from ../inst/include/CytoML/openWorkspace.hpp:11: In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10: In file included from ../inst/include/CytoML/flowJoWorkspace.hpp:11: In file included from ../inst/include/CytoML/workspace.hpp:10: ../inst/include/CytoML/workspace_type.hpp:67:44: warning: 'recursive_directory_iterator' is deprecated: Use directory_options instead of symlink_option [-Wdeprecated-declarations] for(const fs::directory_entry & i: fs::recursive_directory_iterator(fs::path(data_dir), fs::symlink_option::recurse)) ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/filesystem/directory.hpp:922:5: note: 'recursive_directory_iterator' has been explicitly marked deprecated here BOOST_FILESYSTEM_DETAIL_DEPRECATED("Use directory_options instead of symlink_option") ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/filesystem/config.hpp:73:49: note: expanded from macro 'BOOST_FILESYSTEM_DETAIL_DEPRECATED' #define BOOST_FILESYSTEM_DETAIL_DEPRECATED(msg) BOOST_DEPRECATED(msg) ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/config/compiler/clang.hpp:342:46: note: expanded from macro 'BOOST_DEPRECATED' #define BOOST_DEPRECATED(msg) __attribute__((deprecated(msg))) ^ In file included from parseFlowJoWorkspace.cpp:10: In file included from ../inst/include/CytoML/openWorkspace.hpp:12: ../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: warning: '/*' within block comment [-Wcomment] * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate ^ 5 warnings generated. clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o CytoML.so cpp11.o parseFlowJoWorkspace.o /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/lib/libcytolib.a /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/CytoML.buildbin-libdir/00LOCK-CytoML/00new/CytoML/libs ** R ** 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 (CytoML) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR CytoML.buildbin-libdir/CytoML/libs/CytoML.so >>>>>>> >>>>>>> Paths before fix: CytoML.buildbin-libdir/CytoML/libs/CytoML.so: CytoML.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libxml2.2.dylib (compatibility version 10.0.0, current version 10.9.0) /usr/lib/libicucore.A.dylib (compatibility version 1.0.0, current version 66.1.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgcc_s.1.1.dylib" "CytoML.buildbin-libdir/CytoML/libs/CytoML.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "CytoML.buildbin-libdir/CytoML/libs/CytoML.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "CytoML.buildbin-libdir/CytoML/libs/CytoML.so" >>>>>>> Paths after fix: CytoML.buildbin-libdir/CytoML/libs/CytoML.so: CytoML.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libxml2.2.dylib (compatibility version 10.0.0, current version 10.9.0) /usr/lib/libicucore.A.dylib (compatibility version 1.0.0, current version 66.1.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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)