=> 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
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
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/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 <boost/bind/bind.hpp> + 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<std::__cxx11::basic_string<char>, 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<boost::asio::io_service::work> 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<boost::asio::io_service::work> 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<boost::asio::io_service::work> 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<boost::asio::io_service::work> 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<std::__cxx11::basic_string<char>, 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<boost::asio::io_service::work> 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<boost::asio::io_service::work> 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<boost::asio::io_service::work> 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<boost::asio::io_service::work> 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