=> Bootstrap dependency digest>=20211023: found digest-20220214 ===> Skipping vulnerability checks. WARNING: No /usr/pkg/pkgdb/pkg-vulnerabilities file found. WARNING: To fix run: `/usr/sbin/pkg_admin -K /usr/pkg/pkgdb fetch-pkg-vulnerabilities'. ===> Building for haplohseq-0.1.2.2nb2 mkdir -p build build/bin build/obj mkdir -p build/test c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/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 c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/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 c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/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 c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/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 c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/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 cp -r src/test/resources build/test c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/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 c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/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 c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/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 c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/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 c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -isystem/usr/local/boost_1_52_0 -c -o build/test/FreqPhaseTest.o src/test/FreqPhaseTest.cpp c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -isystem/usr/local/boost_1_52_0 -c -o build/test/HaplohSeqTest.o src/test/HaplohSeqTest.cpp c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -isystem/usr/local/boost_1_52_0 -c -o build/test/HmmTest.o src/test/HmmTest.cpp c++ -O2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.12 -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -isystem/usr/local/boost_1_52_0 -c -o build/test/InputProcessorTest.o src/test/InputProcessorTest.cpp In file included from src/HaplohSeq.h:13:0, from src/HaplohSeq.cpp:9: /pbulk/work/biology/haplohseq/work/.buildlink/include/boost/bind.hpp:41:1: note: #pragma 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: In member function 'void HaplohSeq::runBafHaplohseq(std::__cxx11::string&, unsigned int&, double&, unsigned int&, double&, unsigned int&, unsigned int&, double&, double&, double&, unsigned int&, std::__cxx11::string&, unsigned int&, std::__cxx11::string&, std::__cxx11::string&, std::map, bool>&, std::__cxx11::string&, const unsigned int&)': src/HaplohSeq.cpp:198:16: error: 'io_service' is not a member of 'boost::asio' boost::asio::io_service ioService; ^~~~~~~~~~ src/HaplohSeq.cpp:198:16: note: suggested alternative: 'has_service' boost::asio::io_service ioService; ^~~~~~~~~~ has_service src/HaplohSeq.cpp:200:34: error: 'io_service' is not a member of 'boost::asio' boost::shared_ptr work(new boost::asio::io_service::work(ioService)); ^~~~~~~~~~ src/HaplohSeq.cpp:200:34: note: suggested alternative: 'has_service' boost::shared_ptr work(new boost::asio::io_service::work(ioService)); ^~~~~~~~~~ has_service src/HaplohSeq.cpp:200:34: error: 'io_service' is not a member of 'boost::asio' src/HaplohSeq.cpp:200:34: note: suggested alternative: 'has_service' boost::shared_ptr work(new boost::asio::io_service::work(ioService)); ^~~~~~~~~~ has_service src/HaplohSeq.cpp:200:50: error: template argument 1 is invalid boost::shared_ptr work(new boost::asio::io_service::work(ioService)); ^ src/HaplohSeq.cpp:200:74: error: 'io_service' in namespace 'boost::asio' does not name a type boost::shared_ptr work(new boost::asio::io_service::work(ioService)); ^~~~~~~~~~ src/HaplohSeq.cpp:205:92: error: 'io_service' is not a member of '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:205:92: note: suggested alternative: 'has_service' threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService)); ^~~~~~~~~~ has_service src/HaplohSeq.cpp:205:123: error: 'boost::asio::io_service' has not been declared threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService)); ^~~~~~~~~~ src/HaplohSeq.cpp:205:141: error: 'ioService' was not declared in this scope threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService)); ^~~~~~~~~ src/HaplohSeq.cpp:223:4: error: 'ioService' was not declared in this scope ioService.post(boost::bind(&HaplohSeq::runBafHaplohseqChr, this, ^~~~~~~~~ src/HaplohSeq.cpp:234:8: error: request for member 'reset' in 'work', which is of non-class type 'int' work.reset(); ^~~~~ src/HaplohSeq.cpp: In member function 'void HaplohSeq::runVcfHaplohseq(std::__cxx11::string&, unsigned int&, double&, unsigned int&, double&, unsigned int&, unsigned int&, double&, double&, double&, unsigned int&, std::__cxx11::string&, std::__cxx11::string&, unsigned int&, unsigned int&, std::__cxx11::string&, std::__cxx11::string&, std::map, bool>&, std::__cxx11::string&, const unsigned int&)': src/HaplohSeq.cpp:416:16: error: 'io_service' is not a member of 'boost::asio' boost::asio::io_service ioService; ^~~~~~~~~~ src/HaplohSeq.cpp:416:16: note: suggested alternative: 'has_service' boost::asio::io_service ioService; ^~~~~~~~~~ has_service src/HaplohSeq.cpp:418:34: error: 'io_service' is not a member of 'boost::asio' boost::shared_ptr work(new boost::asio::io_service::work(ioService)); ^~~~~~~~~~ src/HaplohSeq.cpp:418:34: note: suggested alternative: 'has_service' boost::shared_ptr work(new boost::asio::io_service::work(ioService)); ^~~~~~~~~~ has_service src/HaplohSeq.cpp:418:34: error: 'io_service' is not a member of 'boost::asio' src/HaplohSeq.cpp:418:34: note: suggested alternative: 'has_service' boost::shared_ptr work(new boost::asio::io_service::work(ioService)); ^~~~~~~~~~ has_service src/HaplohSeq.cpp:418:50: error: template argument 1 is invalid boost::shared_ptr work(new boost::asio::io_service::work(ioService)); ^ src/HaplohSeq.cpp:418:74: error: 'io_service' in namespace 'boost::asio' does not name a type boost::shared_ptr work(new boost::asio::io_service::work(ioService)); ^~~~~~~~~~ src/HaplohSeq.cpp:423:92: error: 'io_service' is not a member of '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:423:92: note: suggested alternative: 'has_service' threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService)); ^~~~~~~~~~ has_service src/HaplohSeq.cpp:423:123: error: 'boost::asio::io_service' has not been declared threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService)); ^~~~~~~~~~ src/HaplohSeq.cpp:423:141: error: 'ioService' was not declared in this scope threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService)); ^~~~~~~~~ src/HaplohSeq.cpp:441:4: error: 'ioService' was not declared in this scope ioService.post(boost::bind(&HaplohSeq::runVcfHaplohseqChr, this, ^~~~~~~~~ src/HaplohSeq.cpp:452:8: error: request for member 'reset' in 'work', which is of non-class type 'int' work.reset(); ^~~~~ gmake: *** [makefile:47: build/obj/HaplohSeq.o] Error 1 gmake: *** Waiting for unfinished jobs.... *** Error code 2 Stop. make[1]: stopped in /usr/pkgsrc/biology/haplohseq *** Error code 1 Stop. make: stopped in /usr/pkgsrc/biology/haplohseq