===> Building for haplohseq-0.1.2.2nb2 mkdir -p build build/bin build/obj clang++ -pipe -Os -I/opt/pkg/include -D_REENTRANT -I/opt/pkg/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/Hmm.o src/hmm/Hmm.cpp clang++ -pipe -Os -I/opt/pkg/include -D_REENTRANT -I/opt/pkg/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/DataStructures.o src/hmm/DataStructures.cpp clang++ -pipe -Os -I/opt/pkg/include -D_REENTRANT -I/opt/pkg/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/MathUtil.o src/hmm/MathUtil.cpp clang++ -pipe -Os -I/opt/pkg/include -D_REENTRANT -I/opt/pkg/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/StringUtil.o src/util/StringUtil.cpp src/util/StringUtil.cpp:51:76: warning: 'ptr_fun' is deprecated [-Wdeprecated-declarations] s.erase(s.begin(), std::find_if(s.begin(), s.end(), std::not1(std::ptr_fun(std::isspace)))); ^ /Applications/Xcode-13.4.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__functional/pointer_to_unary_function.h:37:1: note: 'ptr_fun' has been explicitly marked deprecated here _LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_INLINE_VISIBILITY ^ /Applications/Xcode-13.4.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Applications/Xcode-13.4.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ src/util/StringUtil.cpp:57:67: warning: 'ptr_fun' is deprecated [-Wdeprecated-declarations] s.erase(std::find_if(s.rbegin(), s.rend(), std::not1(std::ptr_fun(std::isspace))).base(), s.end()); ^ /Applications/Xcode-13.4.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__functional/pointer_to_unary_function.h:37:1: note: 'ptr_fun' has been explicitly marked deprecated here _LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_INLINE_VISIBILITY ^ /Applications/Xcode-13.4.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__config:1054:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED ^ /Applications/Xcode-13.4.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ 2 warnings generated. clang++ -pipe -Os -I/opt/pkg/include -D_REENTRANT -I/opt/pkg/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/InputProcessor.o src/util/InputProcessor.cpp clang++ -pipe -Os -I/opt/pkg/include -D_REENTRANT -I/opt/pkg/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/Reporter.o src/Reporter.cpp clang++ -pipe -Os -I/opt/pkg/include -D_REENTRANT -I/opt/pkg/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/FreqPhase.o src/FreqPhase.cpp clang++ -pipe -Os -I/opt/pkg/include -D_REENTRANT -I/opt/pkg/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/VcfUtil.o src/util/VcfUtil.cpp clang++ -pipe -Os -I/opt/pkg/include -D_REENTRANT -I/opt/pkg/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/HaplohSeq.o src/HaplohSeq.cpp In file included from src/HaplohSeq.cpp:9: In file included from ./src/HaplohSeq.h:13: /Users/pbulk/build/biology/haplohseq/work/.buildlink/include/boost/bind.hpp:36:1: warning: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages] BOOST_PRAGMA_MESSAGE( ^ /Users/pbulk/build/biology/haplohseq/work/.buildlink/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ :250:2: note: expanded from here message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " " + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.") ^ src/HaplohSeq.cpp:198:16: error: no type named 'io_service' in namespace 'boost::asio' boost::asio::io_service ioService; ~~~~~~~~~~~~~^ src/HaplohSeq.cpp:200:34: error: no member named 'io_service' in namespace 'boost::asio' boost::shared_ptr work(new boost::asio::io_service::work(ioService)); ~~~~~~~~~~~~~^ src/HaplohSeq.cpp:200:74: error: no member named 'io_service' in namespace 'boost::asio' boost::shared_ptr work(new boost::asio::io_service::work(ioService)); ~~~~~~~~~~~~~^ src/HaplohSeq.cpp:205:92: error: no member named 'io_service' in namespace 'boost::asio' threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService)); ~~~~~~~~~~~~~^ src/HaplohSeq.cpp:205:123: error: no member named 'io_service' in namespace 'boost::asio' threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService)); ~~~~~~~~~~~~~^ src/HaplohSeq.cpp:416:16: error: no type named 'io_service' in namespace 'boost::asio' boost::asio::io_service ioService; ~~~~~~~~~~~~~^ src/HaplohSeq.cpp:418:34: error: no member named 'io_service' in namespace 'boost::asio' boost::shared_ptr work(new boost::asio::io_service::work(ioService)); ~~~~~~~~~~~~~^ src/HaplohSeq.cpp:418:74: error: no member named 'io_service' in namespace 'boost::asio' boost::shared_ptr work(new boost::asio::io_service::work(ioService)); ~~~~~~~~~~~~~^ src/HaplohSeq.cpp:423:92: error: no member named 'io_service' in namespace 'boost::asio' threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService)); ~~~~~~~~~~~~~^ src/HaplohSeq.cpp:423:123: error: no member named 'io_service' in namespace 'boost::asio' threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService)); ~~~~~~~~~~~~~^ 1 warning and 10 errors generated. gmake: *** [makefile:47: build/obj/HaplohSeq.o] Error 1 *** Error code 2 Stop. bmake[1]: stopped making "all" in /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/haplohseq *** Error code 1 Stop. bmake: stopped making "all" in /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/haplohseq