Back to Mac ARM64 build report for BioC 3.16 |
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This page was generated on 2023-04-19 11:01:54 -0400 (Wed, 19 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson | macOS 13.0 Ventura | arm64 | 4.2.2 (2022-10-31) -- "Innocent and Trusting" | 4256 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the CytoML package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 469/2183 | Hostname | OS / Arch | INSTALL | BUILD | BUILD BIN | ||||||||
CytoML 2.10.0 (landing page) Mike Jiang
| kjohnson | macOS 13.0 Ventura / arm64 | OK | OK | OK | ||||||||
Package: CytoML |
Version: 2.10.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CytoML |
StartedAt: 2023-04-16 15:40:21 -0400 (Sun, 16 Apr 2023) |
EndedAt: 2023-04-16 15:42:08 -0400 (Sun, 16 Apr 2023) |
EllapsedTime: 107.1 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CytoML ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library’ * 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 arm64 -std=gnu++11 accepts -g... yes checking for gcc... clang -arch arm64 checking whether we are using the GNU C compiler... yes checking whether clang -arch arm64 accepts -g... yes checking for clang -arch arm64 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/MacOSX.sdk/usr/include -ftemplate-depth=900 configure: PKG_LIBS=-L/Library/Developer/CommandLineTools/SDKs/MacOSX.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 clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include/ -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -ftemplate-depth=900 -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/flowWorkspace/include' -I/opt/R/arm64/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/4.2-arm64/Resources/library/flowWorkspace/include/flowWorkspace.h:5: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/MemCytoFrame.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/compensation.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/transformation.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/split.hpp:16: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/iter_find.hpp:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/find_iterator.hpp:24: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/function.hpp:30: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/function/detail/prologue.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/throw_exception.hpp:24: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/assert/source_location.hpp:75:14: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] std::sprintf( buffer, ":%ld", static_cast<long>( line() ) ); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from cpp11.cpp:4: In file included from ./CytoML_types.h:4: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/flowWorkspace/include/flowWorkspace.h:5: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/MemCytoFrame.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/compensation.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/transformation.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/split.hpp:16: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/iter_find.hpp:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/find_iterator.hpp:24: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/function.hpp:30: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/function/detail/prologue.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/throw_exception.hpp:24: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/assert/source_location.hpp:80:18: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] std::sprintf( buffer, ":%ld", static_cast<long>( column() ) ); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from cpp11.cpp:4: In file included from ./CytoML_types.h:4: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/flowWorkspace/include/flowWorkspace.h:5: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/MemCytoFrame.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/compensation.hpp:16: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast.hpp:32: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] sprintf(begin, ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from cpp11.cpp:4: In file included from ./CytoML_types.h:4: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/flowWorkspace/include/flowWorkspace.h:5: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/MemCytoFrame.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/compensation.hpp:16: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast.hpp:32: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] sprintf(begin, ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from cpp11.cpp:4: In file included from ./CytoML_types.h:4: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/flowWorkspace/include/flowWorkspace.h:5: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/MemCytoFrame.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/compensation.hpp:16: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast.hpp:32: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] sprintf(begin, ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_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 ^ 6 warnings generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include/ -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -ftemplate-depth=900 -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/flowWorkspace/include' -I/opt/R/arm64/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/4.2-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/MemCytoFrame.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/compensation.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/transformation.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/split.hpp:16: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/iter_find.hpp:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/find_iterator.hpp:24: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/function.hpp:30: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/function/detail/prologue.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/throw_exception.hpp:24: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/assert/source_location.hpp:75:14: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] std::sprintf( buffer, ":%ld", static_cast<long>( line() ) ); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_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: 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/4.2-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/MemCytoFrame.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/compensation.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/transformation.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/split.hpp:16: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/iter_find.hpp:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/find_iterator.hpp:24: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/function.hpp:30: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/function/detail/prologue.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/throw_exception.hpp:24: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/assert/source_location.hpp:80:18: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] std::sprintf( buffer, ":%ld", static_cast<long>( column() ) ); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_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: 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/4.2-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/MemCytoFrame.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/compensation.hpp:16: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast.hpp:32: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:285:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] sprintf(begin, ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_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: 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/4.2-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/MemCytoFrame.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/compensation.hpp:16: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast.hpp:32: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:297:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] sprintf(begin, ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_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: 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/4.2-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/MemCytoFrame.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/include/cytolib/compensation.hpp:16: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast.hpp:32: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:310:21: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] sprintf(begin, ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_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 ^ 6 warnings generated. clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o CytoML.so cpp11.o parseFlowJoWorkspace.o /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cytolib/lib/libcytolib.a /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/lib -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/MacOSX.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: -undefined dynamic_lookup may not work with chained fixups installing to /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/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)