[package - 120armv7-quarterly][biology/unanimity] Failed for unanimity-3.4.1_1 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Fri Jul 12 20:16:08 UTC 2019
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: jwb at FreeBSD.org
Last committer: jbeich at FreeBSD.org
Ident: $FreeBSD: branches/2019Q3/biology/unanimity/Makefile 498698 2019-04-12 06:36:31Z jbeich $
Log URL: http://beefy13.nyi.freebsd.org/data/120armv7-quarterly/506385/logs/unanimity-3.4.1_1.log
Build URL: http://beefy13.nyi.freebsd.org/build.html?mastername=120armv7-quarterly&build=506385
Log:
=>> Building biology/unanimity
build started at Fri Jul 12 20:12:29 UTC 2019
port directory: /usr/ports/biology/unanimity
package name: unanimity-3.4.1_1
building for: FreeBSD 120armv7-quarterly-job-12 12.0-RELEASE-p7 FreeBSD 12.0-RELEASE-p7 1200086 arm
maintained by: jwb at FreeBSD.org
Makefile ident: $FreeBSD: branches/2019Q3/biology/unanimity/Makefile 498698 2019-04-12 06:36:31Z jbeich $
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=======================<phase: check-sanity >============================
===> License BSD3CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> unanimity-3.4.1_1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.11.1.txz
[120armv7-quarterly-job-12] Installing pkg-1.11.1...
[120armv7-quarterly-job-12] Extracting pkg-1.11.1: .......... done
===> unanimity-3.4.1_1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of unanimity-3.4.1_1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by unanimity-3.4.1_1 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by unanimity-3.4.1_1 for building
=> SHA256 Checksum OK for PacificBiosciences-unanimity-v3.4.1_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
<snip>
/usr/include/c++/v1/iterator:1425:74: note: in instantiation of member function 'std::__1::__vector_base<PacBio::Consensus::Mutation, std::__1::allocator<PacBio::Consensus::Mutation> >::~__vector_base' requested here
template <class _Tp, class _Alloc> friend class _LIBCPP_TEMPLATE_VIS vector;
^
/usr/include/c++/v1/memory:1860:64: note: qualify call to silence this warning
_LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
^
1 warning generated.
[35/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/Integrator.cpp.o' -MF 'src/25a6634@@unanimity at sha/Integrator.cpp.o.d' -o 'src/25a6634@@unanimity at sha/Integrator.cpp.o' -c ../src/Integrator.cpp
In file included from ../src/Integrator.cpp:7:
In file included from /usr/include/c++/v1/numeric:144:
In file included from /usr/include/c++/v1/functional:487:
/usr/include/c++/v1/memory:1860:58: warning: destructor called on non-final 'PacBio::Consensus::Mutation' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
_LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
^
/usr/include/c++/v1/memory:1727:18: note: in instantiation of member function 'std::__1::allocator<PacBio::Consensus::Mutation>::destroy' requested here
{__a.destroy(__p);}
^
/usr/include/c++/v1/memory:1595:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<PacBio::Consensus::Mutation> >::__destroy<PacBio::Consensus::Mutation>' requested here
{__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
^
/usr/include/c++/v1/vector:413:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<PacBio::Consensus::Mutation> >::destroy<PacBio::Consensus::Mutation>' requested here
__alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end));
^
/usr/include/c++/v1/vector:356:29: note: in instantiation of member function 'std::__1::__vector_base<PacBio::Consensus::Mutation, std::__1::allocator<PacBio::Consensus::Mutation> >::__destruct_at_end' requested here
void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
^
/usr/include/c++/v1/vector:441:9: note: in instantiation of member function 'std::__1::__vector_base<PacBio::Consensus::Mutation, std::__1::allocator<PacBio::Consensus::Mutation> >::clear' requested here
clear();
^
/usr/include/c++/v1/iterator:1425:74: note: in instantiation of member function 'std::__1::__vector_base<PacBio::Consensus::Mutation, std::__1::allocator<PacBio::Consensus::Mutation> >::~__vector_base' requested here
template <class _Tp, class _Alloc> friend class _LIBCPP_TEMPLATE_VIS vector;
^
/usr/include/c++/v1/memory:1860:64: note: qualify call to silence this warning
_LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
^
1 warning generated.
[36/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/IntervalMask.cpp.o' -MF 'src/25a6634@@unanimity at sha/IntervalMask.cpp.o.d' -o 'src/25a6634@@unanimity at sha/IntervalMask.cpp.o' -c ../src/IntervalMask.cpp
[37/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/ModelConfig.cpp.o' -MF 'src/25a6634@@unanimity at sha/ModelConfig.cpp.o.d' -o 'src/25a6634@@unanimity at sha/ModelConfig.cpp.o' -c ../src/ModelConfig.cpp
[38/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/ModelFactory.cpp.o' -MF 'src/25a6634@@unanimity at sha/ModelFactory.cpp.o.d' -o 'src/25a6634@@unanimity at sha/ModelFactory.cpp.o' -c ../src/ModelFactory.cpp
[39/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/ModelFormFactory.cpp.o' -MF 'src/25a6634@@unanimity at sha/ModelFormFactory.cpp.o.d' -o 'src/25a6634@@unanimity at sha/ModelFormFactory.cpp.o' -c ../src/ModelFormFactory.cpp
[40/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/ModelSelection.cpp.o' -MF 'src/25a6634@@unanimity at sha/ModelSelection.cpp.o.d' -o 'src/25a6634@@unanimity at sha/ModelSelection.cpp.o' -c ../src/ModelSelection.cpp
[41/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/Mutation.cpp.o' -MF 'src/25a6634@@unanimity at sha/Mutation.cpp.o.d' -o 'src/25a6634@@unanimity at sha/Mutation.cpp.o' -c ../src/Mutation.cpp
[42/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/Polish.cpp.o' -MF 'src/25a6634@@unanimity at sha/Polish.cpp.o.d' -o 'src/25a6634@@unanimity at sha/Polish.cpp.o' -c ../src/Polish.cpp
In file included from ../src/Polish.cpp:3:
In file included from /usr/include/c++/v1/algorithm:643:
/usr/include/c++/v1/memory:1860:58: warning: destructor called on non-final 'PacBio::Consensus::Mutation' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
_LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
^
/usr/include/c++/v1/memory:1727:18: note: in instantiation of member function 'std::__1::allocator<PacBio::Consensus::Mutation>::destroy' requested here
{__a.destroy(__p);}
^
/usr/include/c++/v1/memory:1595:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<PacBio::Consensus::Mutation> >::__destroy<PacBio::Consensus::Mutation>' requested here
{__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
^
/usr/include/c++/v1/__split_buffer:296:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<PacBio::Consensus::Mutation> >::destroy<PacBio::Consensus::Mutation>' requested here
__alloc_traits::destroy(__alloc(), __to_raw_pointer(--__end_));
^
/usr/include/c++/v1/__split_buffer:141:10: note: in instantiation of member function 'std::__1::__split_buffer<PacBio::Consensus::Mutation, std::__1::allocator<PacBio::Consensus::Mutation> &>::__destruct_at_end' requested here
{__destruct_at_end(__new_last, false_type());}
^
/usr/include/c++/v1/__split_buffer:88:10: note: in instantiation of member function 'std::__1::__split_buffer<PacBio::Consensus::Mutation, std::__1::allocator<PacBio::Consensus::Mutation> &>::__destruct_at_end' requested here
{__destruct_at_end(__begin_);}
^
/usr/include/c++/v1/__split_buffer:341:5: note: in instantiation of member function 'std::__1::__split_buffer<PacBio::Consensus::Mutation, std::__1::allocator<PacBio::Consensus::Mutation> &>::clear' requested here
clear();
^
/usr/include/c++/v1/vector:1628:49: note: in instantiation of member function 'std::__1::__split_buffer<PacBio::Consensus::Mutation, std::__1::allocator<PacBio::Consensus::Mutation> &>::~__split_buffer' requested here
__split_buffer<value_type, allocator_type&> __v(__recommend(size() + 1), size(), __a);
^
/usr/include/c++/v1/vector:1655:9: note: in instantiation of function template specialization 'std::__1::vector<PacBio::Consensus::Mutation, std::__1::allocator<PacBio::Consensus::Mutation> >::__emplace_back_slow_path<PacBio::Consensus::Mutation>' requested here
__emplace_back_slow_path(_VSTD::forward<_Args>(__args)...);
^
./src/Polish.cpp:87:50: note: in instantiation of function template specialization 'std::__1::vector<PacBio::Consensus::Mutation, std::__1::allocator<PacBio::Consensus::Mutation> >::emplace_back<PacBio::Consensus::Mutation>' requested here
if (!containedWithin(last, j)) muts->emplace_back(Mutation::Insertion(i, j));
^
/usr/include/c++/v1/memory:1860:64: note: qualify call to silence this warning
_LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
^
/usr/include/c++/v1/memory:1732:17: warning: destructor called on non-final 'PacBio::Consensus::ScoredMutation' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
__p->~_Tp();
^
/usr/include/c++/v1/memory:1595:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<std::__1::__list_node<PacBio::Consensus::ScoredMutation, void *> > >::__destroy<PacBio::Consensus::ScoredMutation>' requested here
{__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
^
/usr/include/c++/v1/list:1830:34: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<std::__1::__list_node<PacBio::Consensus::ScoredMutation, void *> > >::destroy<PacBio::Consensus::ScoredMutation>' requested here
__node_alloc_traits::destroy(__na, _VSTD::addressof(__np->__value_));
^
/usr/include/c++/v1/list:2131:19: note: in instantiation of member function 'std::__1::list<PacBio::Consensus::ScoredMutation, std::__1::allocator<PacBio::Consensus::ScoredMutation> >::erase' requested here
__i = erase(__i, __j);
^
./src/Polish.cpp:181:21: note: in instantiation of function template specialization 'std::__1::list<PacBio::Consensus::ScoredMutation, std::__1::allocator<PacBio::Consensus::ScoredMutation> >::remove_if<(lambda at ../src/Polish.cpp:182:13)>' requested here
scoredMuts->remove_if(
^
/usr/include/c++/v1/memory:1732:23: note: qualify call to silence this warning
__p->~_Tp();
^
2 warnings generated.
[43/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/PolishResult.cpp.o' -MF 'src/25a6634@@unanimity at sha/PolishResult.cpp.o.d' -o 'src/25a6634@@unanimity at sha/PolishResult.cpp.o' -c ../src/PolishResult.cpp
[44/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/Read.cpp.o' -MF 'src/25a6634@@unanimity at sha/Read.cpp.o.d' -o 'src/25a6634@@unanimity at sha/Read.cpp.o' -c ../src/Read.cpp
[45/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/Recursor.cpp.o' -MF 'src/25a6634@@unanimity at sha/Recursor.cpp.o.d' -o 'src/25a6634@@unanimity at sha/Recursor.cpp.o' -c ../src/Recursor.cpp
[46/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/Sequence.cpp.o' -MF 'src/25a6634@@unanimity at sha/Sequence.cpp.o.d' -o 'src/25a6634@@unanimity at sha/Sequence.cpp.o' -c ../src/Sequence.cpp
[47/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/Template.cpp.o' -MF 'src/25a6634@@unanimity at sha/Template.cpp.o.d' -o 'src/25a6634@@unanimity at sha/Template.cpp.o' -c ../src/Template.cpp
[48/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/genomicconsensus_experimental_io_FastaWriter.cpp.o' -MF 'src/25a6634@@unanimity at sha/genomicconsensus_experimental_io_FastaWriter.cpp.o.d' -o 'src/25a6634@@unanimity at sha/genomicconsensus_experimental_io_FastaWriter.cpp.o' -c ../src/genomicconsensus/experimental/io/FastaWriter.cpp
[49/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/genomicconsensus_experimental_io_FastqWriter.cpp.o' -MF 'src/25a6634@@unanimity at sha/genomicconsensus_experimental_io_FastqWriter.cpp.o.d' -o 'src/25a6634@@unanimity at sha/genomicconsensus_experimental_io_FastqWriter.cpp.o' -c ../src/genomicconsensus/experimental/io/FastqWriter.cpp
[50/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/genomicconsensus_experimental_io_GffWriter.cpp.o' -MF 'src/25a6634@@unanimity at sha/genomicconsensus_experimental_io_GffWriter.cpp.o.d' -o 'src/25a6634@@unanimity at sha/genomicconsensus_experimental_io_GffWriter.cpp.o' -c ../src/genomicconsensus/experimental/io/GffWriter.cpp
[51/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/genomicconsensus_experimental_io_VcfWriter.cpp.o' -MF 'src/25a6634@@unanimity at sha/genomicconsensus_experimental_io_VcfWriter.cpp.o.d' -o 'src/25a6634@@unanimity at sha/genomicconsensus_experimental_io_VcfWriter.cpp.o' -c ../src/genomicconsensus/experimental/io/VcfWriter.cpp
[52/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/.._third-party_cpp-optparse_OptionParser.cpp.o' -MF 'src/25a6634@@unanimity at sha/.._third-party_cpp-optparse_OptionParser.cpp.o.d' -o 'src/25a6634@@unanimity at sha/.._third-party_cpp-optparse_OptionParser.cpp.o' -c ../third-party/cpp-optparse/OptionParser.cpp
[53/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/ChemistryMapping.cpp.o' -MF 'src/25a6634@@unanimity at sha/ChemistryMapping.cpp.o.d' -o 'src/25a6634@@unanimity at sha/ChemistryMapping.cpp.o' -c ../src/ChemistryMapping.cpp
[54/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/ChemistryTriple.cpp.o' -MF 'src/25a6634@@unanimity at sha/ChemistryTriple.cpp.o.d' -o 'src/25a6634@@unanimity at sha/ChemistryTriple.cpp.o' -c ../src/ChemistryTriple.cpp
[55/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/Interval.cpp.o' -MF 'src/25a6634@@unanimity at sha/Interval.cpp.o.d' -o 'src/25a6634@@unanimity at sha/Interval.cpp.o' -c ../src/Interval.cpp
[56/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/ReadId.cpp.o' -MF 'src/25a6634@@unanimity at sha/ReadId.cpp.o.d' -o 'src/25a6634@@unanimity at sha/ReadId.cpp.o' -c ../src/ReadId.cpp
[57/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/SparsePoa.cpp.o' -MF 'src/25a6634@@unanimity at sha/SparsePoa.cpp.o.d' -o 'src/25a6634@@unanimity at sha/SparsePoa.cpp.o' -c ../src/SparsePoa.cpp
[58/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/SubreadResultCounter.cpp.o' -MF 'src/25a6634@@unanimity at sha/SubreadResultCounter.cpp.o.d' -o 'src/25a6634@@unanimity at sha/SubreadResultCounter.cpp.o' -c ../src/SubreadResultCounter.cpp
[59/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/Timer.cpp.o' -MF 'src/25a6634@@unanimity at sha/Timer.cpp.o.d' -o 'src/25a6634@@unanimity at sha/Timer.cpp.o' -c ../src/Timer.cpp
[60/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/Utility.cpp.o' -MF 'src/25a6634@@unanimity at sha/Utility.cpp.o.d' -o 'src/25a6634@@unanimity at sha/Utility.cpp.o' -c ../src/Utility.cpp
[61/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/ConsensusSettings.cpp.o' -MF 'src/25a6634@@unanimity at sha/ConsensusSettings.cpp.o.d' -o 'src/25a6634@@unanimity at sha/ConsensusSettings.cpp.o' -c ../src/ConsensusSettings.cpp
[62/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/LocalAlignment.cpp.o' -MF 'src/25a6634@@unanimity at sha/LocalAlignment.cpp.o.d' -o 'src/25a6634@@unanimity at sha/LocalAlignment.cpp.o' -c ../src/LocalAlignment.cpp
[63/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/models_P6C4NoCov_Model.cpp.o' -MF 'src/25a6634@@unanimity at sha/models_P6C4NoCov_Model.cpp.o.d' -o 'src/25a6634@@unanimity at sha/models_P6C4NoCov_Model.cpp.o' -c ../src/models/P6C4NoCov_Model.cpp
[64/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/models_S_P1C1Beta_Model.cpp.o' -MF 'src/25a6634@@unanimity at sha/models_S_P1C1Beta_Model.cpp.o.d' -o 'src/25a6634@@unanimity at sha/models_S_P1C1Beta_Model.cpp.o' -c ../src/models/S_P1C1Beta_Model.cpp
[65/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/models_S_P1C1v1_Model.cpp.o' -MF 'src/25a6634@@unanimity at sha/models_S_P1C1v1_Model.cpp.o.d' -o 'src/25a6634@@unanimity at sha/models_S_P1C1v1_Model.cpp.o' -c ../src/models/S_P1C1v1_Model.cpp
[66/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/models_S_P1C1v2_Model.cpp.o' -MF 'src/25a6634@@unanimity at sha/models_S_P1C1v2_Model.cpp.o.d' -o 'src/25a6634@@unanimity at sha/models_S_P1C1v2_Model.cpp.o' -c ../src/models/S_P1C1v2_Model.cpp
[67/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/models_S_P2C2v5_Model.cpp.o' -MF 'src/25a6634@@unanimity at sha/models_S_P2C2v5_Model.cpp.o.d' -o 'src/25a6634@@unanimity at sha/models_S_P2C2v5_Model.cpp.o' -c ../src/models/S_P2C2v5_Model.cpp
[68/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/models_MarginalModelForm.cpp.o' -MF 'src/25a6634@@unanimity at sha/models_MarginalModelForm.cpp.o.d' -o 'src/25a6634@@unanimity at sha/models_MarginalModelForm.cpp.o' -c ../src/models/MarginalModelForm.cpp
[69/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/models_PwSnrAModelForm.cpp.o' -MF 'src/25a6634@@unanimity at sha/models_PwSnrAModelForm.cpp.o.d' -o 'src/25a6634@@unanimity at sha/models_PwSnrAModelForm.cpp.o' -c ../src/models/PwSnrAModelForm.cpp
[70/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/models_PwSnrModelForm.cpp.o' -MF 'src/25a6634@@unanimity at sha/models_PwSnrModelForm.cpp.o.d' -o 'src/25a6634@@unanimity at sha/models_PwSnrModelForm.cpp.o' -c ../src/models/PwSnrModelForm.cpp
[71/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/models_SnrModelForm.cpp.o' -MF 'src/25a6634@@unanimity at sha/models_SnrModelForm.cpp.o.d' -o 'src/25a6634@@unanimity at sha/models_SnrModelForm.cpp.o' -c ../src/models/SnrModelForm.cpp
[72/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/meson-generated_.._ModelInternalInitializer.cpp.o' -MF 'src/25a6634@@unanimity at sha/meson-generated_.._ModelInternalInitializer.cpp.o.d' -o 'src/25a6634@@unanimity at sha/meson-generated_.._ModelInternalInitializer.cpp.o' -c src/ModelInternalInitializer.cpp
[73/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/meson-generated_.._UnanimityVersion.cpp.o' -MF 'src/25a6634@@unanimity at sha/meson-generated_.._UnanimityVersion.cpp.o.d' -o 'src/25a6634@@unanimity at sha/meson-generated_.._UnanimityVersion.cpp.o' -c src/UnanimityVersion.cpp
[74/97] /nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/.._third-party_cssw_ssw_cpp.cpp.o' -MF 'src/25a6634@@unanimity at sha/.._third-party_cssw_ssw_cpp.cpp.o.d' -o 'src/25a6634@@unanimity at sha/.._third-party_cssw_ssw_cpp.cpp.o' -c ../third-party/cssw/ssw_cpp.cpp
FAILED: src/25a6634@@unanimity at sha/.._third-party_cssw_ssw_cpp.cpp.o
/nxb-bin/usr/bin/c++ -Isrc/25a6634@@unanimity at sha -Isrc -I../src -Iinclude -I../include -I../include/pacbio -I../third-party/cssw/ -I/usr/local/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -O3 -O2 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -pthread -Wno-unused-parameter -Wno-non-virtual-dtor -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedef -MD -MQ 'src/25a6634@@unanimity at sha/.._third-party_cssw_ssw_cpp.cpp.o' -MF 'src/25a6634@@unanimity at sha/.._third-party_cssw_ssw_cpp.cpp.o.d' -o 'src/25a6634@@unanimity at sha/.._third-party_cssw_ssw_cpp.cpp.o' -c ../third-party/cssw/ssw_cpp.cpp
In file included from ../third-party/cssw/ssw_cpp.cpp:2:
In file included from ../third-party/cssw/ssw.h:17:
In file included from /nxb-bin/usr/lib/clang/6.0.1/include/emmintrin.h:27:
In file included from /nxb-bin/usr/lib/clang/6.0.1/include/xmmintrin.h:27:
/nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:47:5: error: use of undeclared identifier '__builtin_ia32_emms'; did you mean '__builtin_isless'?
__builtin_ia32_emms();
^
/nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:47:5: note: '__builtin_isless' declared here
/nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:47:25: error: too few arguments to function call, expected 2, have 0
__builtin_ia32_emms();
^
/nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:64:19: error: use of undeclared identifier '__builtin_ia32_vec_init_v2si'
return (__m64)__builtin_ia32_vec_init_v2si(__i, 0);
^
/nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:81:12: error: use of undeclared identifier '__builtin_ia32_vec_ext_v2si'
return __builtin_ia32_vec_ext_v2si((__v2si)__m, 0);
^
/nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:143:19: error: use of undeclared identifier '__builtin_ia32_packsswb'
return (__m64)__builtin_ia32_packsswb((__v4hi)__m1, (__v4hi)__m2);
^
/nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:173:19: error: use of undeclared identifier '__builtin_ia32_packssdw'
return (__m64)__builtin_ia32_packssdw((__v2si)__m1, (__v2si)__m2);
^
/nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:203:19: error: use of undeclared identifier '__builtin_ia32_packuswb'
return (__m64)__builtin_ia32_packuswb((__v4hi)__m1, (__v4hi)__m2);
^
/nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:230:19: error: use of undeclared identifier '__builtin_ia32_punpckhbw'
return (__m64)__builtin_ia32_punpckhbw((__v8qi)__m1, (__v8qi)__m2);
^
/nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:253:19: error: use of undeclared identifier '__builtin_ia32_punpckhwd'
return (__m64)__builtin_ia32_punpckhwd((__v4hi)__m1, (__v4hi)__m2);
^
/nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:274:19: error: use of undeclared identifier '__builtin_ia32_punpckhdq'
return (__m64)__builtin_ia32_punpckhdq((__v2si)__m1, (__v2si)__m2);
^
/nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:301:19: error: use of undeclared identifier '__builtin_ia32_punpcklbw'
return (__m64)__builtin_ia32_punpcklbw((__v8qi)__m1, (__v8qi)__m2);
^
/nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:324:19: error: use of undeclared identifier '__builtin_ia32_punpcklwd'
return (__m64)__builtin_ia32_punpcklwd((__v4hi)__m1, (__v4hi)__m2);
^
/nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:345:19: error: use of undeclared identifier '__builtin_ia32_punpckldq'
return (__m64)__builtin_ia32_punpckldq((__v2si)__m1, (__v2si)__m2);
^
/nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:366:19: error: use of undeclared identifier '__builtin_ia32_paddb'
return (__m64)__builtin_ia32_paddb((__v8qi)__m1, (__v8qi)__m2);
^
/nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:387:19: error: use of undeclared identifier '__builtin_ia32_paddw'
return (__m64)__builtin_ia32_paddw((__v4hi)__m1, (__v4hi)__m2);
^
/nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:408:19: error: use of undeclared identifier '__builtin_ia32_paddd'
return (__m64)__builtin_ia32_paddd((__v2si)__m1, (__v2si)__m2);
^
/nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:430:19: error: use of undeclared identifier '__builtin_ia32_paddsb'
return (__m64)__builtin_ia32_paddsb((__v8qi)__m1, (__v8qi)__m2);
^
/nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:453:19: error: use of undeclared identifier '__builtin_ia32_paddsw'
return (__m64)__builtin_ia32_paddsw((__v4hi)__m1, (__v4hi)__m2);
^
/nxb-bin/usr/lib/clang/6.0.1/include/mmintrin.h:475:19: error: use of undeclared identifier '__builtin_ia32_paddusb'
return (__m64)__builtin_ia32_paddusb((__v8qi)__m1, (__v8qi)__m2);
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
ninja: build stopped: subcommand failed.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/unanimity
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