=> 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 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/InputProcessor.o src/util/InputProcessor.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/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 /pbulk/work/biology/haplohseq/work/.buildlink/include/boost/smart_ptr/detail/deprecated_macros.hpp:8, from /pbulk/work/biology/haplohseq/work/.buildlink/include/boost/smart_ptr/detail/sp_counted_base.hpp:22, from /pbulk/work/biology/haplohseq/work/.buildlink/include/boost/smart_ptr/detail/shared_count.hpp:22, from /pbulk/work/biology/haplohseq/work/.buildlink/include/boost/smart_ptr/shared_ptr.hpp:17, from /pbulk/work/biology/haplohseq/work/.buildlink/include/boost/shared_ptr.hpp:17, from /pbulk/work/biology/haplohseq/work/.buildlink/include/boost/date_time/time_clock.hpp:17, from /pbulk/work/biology/haplohseq/work/.buildlink/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /pbulk/work/biology/haplohseq/work/.buildlink/include/boost/asio/time_traits.hpp:25, from /pbulk/work/biology/haplohseq/work/.buildlink/include/boost/asio/detail/timer_queue_ptime.hpp:24, from /pbulk/work/biology/haplohseq/work/.buildlink/include/boost/asio/detail/deadline_timer_service.hpp:31, from /pbulk/work/biology/haplohseq/work/.buildlink/include/boost/asio/basic_deadline_timer.hpp:27, from /pbulk/work/biology/haplohseq/work/.buildlink/include/boost/asio.hpp:33, from src/HaplohSeq.h:12, from src/HaplohSeq.cpp:9: /pbulk/work/biology/haplohseq/work/.buildlink/include/boost/config/pragma_message.hpp:24:34: 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.' 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^~~~~~~ /pbulk/work/biology/haplohseq/work/.buildlink/include/boost/bind.hpp:36:1: note: in expansion of macro 'BOOST_PRAGMA_MESSAGE' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ src/HaplohSeq.cpp: In member function 'void HaplohSeq::runBafHaplohseq(std::string&, unsigned int&, double&, unsigned int&, double&, unsigned int&, unsigned int&, double&, double&, double&, unsigned int&, std::string&, unsigned int&, std::string&, std::string&, std::map, bool>&, std::string&, const unsigned int&)': src/HaplohSeq.cpp:198:16: error: 'io_service' is not a member of 'boost::asio'; did you mean 'has_service'? 198 | boost::asio::io_service ioService; | ^~~~~~~~~~ | has_service src/HaplohSeq.cpp:200:34: error: 'io_service' is not a member of 'boost::asio'; did you mean 'has_service'? 200 | 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'; did you mean 'has_service'? 200 | boost::shared_ptr work(new boost::asio::io_service::work(ioService)); | ^~~~~~~~~~ | has_service src/HaplohSeq.cpp:200:50: error: template argument 1 is invalid 200 | 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; did you mean 'has_service'? 200 | boost::shared_ptr work(new boost::asio::io_service::work(ioService)); | ^~~~~~~~~~ | has_service src/HaplohSeq.cpp:205:92: error: 'io_service' is not a member of 'boost::asio'; did you mean 'has_service'? 205 | 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 205 | 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 205 | 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 223 | 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' 234 | work.reset(); | ^~~~~ src/HaplohSeq.cpp: In member function 'void HaplohSeq::runVcfHaplohseq(std::string&, unsigned int&, double&, unsigned int&, double&, unsigned int&, unsigned int&, double&, double&, double&, unsigned int&, std::string&, std::string&, unsigned int&, unsigned int&, std::string&, std::string&, std::map, bool>&, std::string&, const unsigned int&)': src/HaplohSeq.cpp:416:16: error: 'io_service' is not a member of 'boost::asio'; did you mean 'has_service'? 416 | boost::asio::io_service ioService; | ^~~~~~~~~~ | has_service src/HaplohSeq.cpp:418:34: error: 'io_service' is not a member of 'boost::asio'; did you mean 'has_service'? 418 | 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'; did you mean 'has_service'? 418 | boost::shared_ptr work(new boost::asio::io_service::work(ioService)); | ^~~~~~~~~~ | has_service src/HaplohSeq.cpp:418:50: error: template argument 1 is invalid 418 | 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; did you mean 'has_service'? 418 | boost::shared_ptr work(new boost::asio::io_service::work(ioService)); | ^~~~~~~~~~ | has_service src/HaplohSeq.cpp:423:92: error: 'io_service' is not a member of 'boost::asio'; did you mean 'has_service'? 423 | 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 423 | 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 423 | 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 441 | 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' 452 | 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