=> 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
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/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
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 <boost/bind/bind.hpp> + 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<std::__cxx11::basic_string<char>, 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<boost::asio::io_service::work> work(new boost::asio::io_service::work(ioService));
^~~~~~~~~~
src/HaplohSeq.cpp:200:34: note: suggested alternative: 'has_service'
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'
src/HaplohSeq.cpp:200:34: note: suggested alternative: 'has_service'
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
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
boost::shared_ptr<boost::asio::io_service::work> 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<std::__cxx11::basic_string<char>, 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<boost::asio::io_service::work> work(new boost::asio::io_service::work(ioService));
^~~~~~~~~~
src/HaplohSeq.cpp:418:34: note: suggested alternative: 'has_service'
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'
src/HaplohSeq.cpp:418:34: note: suggested alternative: 'has_service'
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
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
boost::shared_ptr<boost::asio::io_service::work> 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