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Date:      Tue, 8 Oct 2019 16:25:21 GMT
From:      pkg-fallout@FreeBSD.org
To:        pkg-fallout@FreeBSD.org
Subject:   [package - 112arm64-quarterly][biology/canu] Failed for canu-1.8_5 in build
Message-ID:  <201910081625.x98GPLle085710@thunderx1.nyi.freebsd.org>

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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@FreeBSD.org
Last committer: jbeich@FreeBSD.org
Ident:          $FreeBSD: branches/2019Q4/biology/canu/Makefile 509290 2019-08-19 15:35:27Z jbeich $
Log URL:        http://thunderx1.nyi.freebsd.org/data/112arm64-quarterly/513847/logs/canu-1.8_5.log
Build URL:      http://thunderx1.nyi.freebsd.org/build.html?mastername=112arm64-quarterly&build=513847
Log:

=>> Building biology/canu
build started at Tue Oct  8 16:18:46 UTC 2019
port directory: /usr/ports/biology/canu
package name: canu-1.8_5
building for: FreeBSD 112arm64-quarterly-job-12 11.2-RELEASE-p14 FreeBSD 11.2-RELEASE-p14 1102000 arm64
maintained by: jwb@FreeBSD.org
Makefile ident:      $FreeBSD: branches/2019Q4/biology/canu/Makefile 509290 2019-08-19 15:35:27Z jbeich $
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=======================<phase: check-sanity   >============================
===>  License GPLv2 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   canu-1.8_5 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.12.0.txz
[112arm64-quarterly-job-12] Installing pkg-1.12.0...
[112arm64-quarterly-job-12] Extracting pkg-1.12.0: .......... done
===>   canu-1.8_5 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of canu-1.8_5
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by canu-1.8_5 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by canu-1.8_5 for building
=> SHA256 Checksum OK for marbl-canu-v1.8_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by canu-1.8_5 for building
===>  Extracting for canu-1.8_5
=> SHA256 Checksum OK for marbl-canu-v1.8_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for canu-1.8_5
===>  Applying FreeBSD patches for canu-1.8_5
===========================================================================
=======================<phase: build-depends  >============================
===>   canu-1.8_5 depends on executable: gmake - not found
===>   Installing existing package /packages/All/gmake-4.2.1_3.txz
[112arm64-quarterly-job-12] Installing gmake-4.2.1_3...
[112arm64-quarterly-job-12] `-- Installing gettext-runtime-0.20.1...
[112arm64-quarterly-job-12] |   `-- Installing indexinfo-0.3.1...
[112arm64-quarterly-job-12] |   `-- Extracting indexinfo-0.3.1: .... done
[112arm64-quarterly-job-12] `-- Extracting gettext-runtime-0.20.1: .......... done
[112arm64-quarterly-job-12] Extracting gmake-4.2.1_3: .......... done
===>   canu-1.8_5 depends on executable: gmake - found
===>   Returning to build of canu-1.8_5
===>   canu-1.8_5 depends on executable: gcc9 - not found
===>   Installing existing package /packages/All/gcc9-9.2.0.txz
[112arm64-quarterly-job-12] Installing gcc9-9.2.0...
[112arm64-quarterly-job-12] `-- Installing binutils-2.32_1,1...
<snip>
      |     ^~~~~~~
utgcns/libboost/boost/smart_ptr/detail/sp_counted_impl.hpp:252:20: error: expected ';' at end of member declaration
  252 |     virtual void * get_deleter( detail::sp_typeinfo const & ti )
      |                    ^~~~~~~~~~~
      |                               ;
utgcns/libboost/boost/smart_ptr/detail/sp_counted_impl.hpp:252:52: error: expected ')' before 'const'
  252 |     virtual void * get_deleter( detail::sp_typeinfo const & ti )
      |                               ~                    ^~~~~~
      |                                                    )
In file included from utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:28,
                 from utgcns/libboost/boost/shared_ptr.hpp:17,
                 from utgcns/libboost/boost/property_map/vector_property_map.hpp:14,
                 from utgcns/libboost/boost/property_map/property_map.hpp:600,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:36,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
utgcns/libboost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  395 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/local/lib/gcc9/include/c++/memory:80,
                 from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14,
                 from utgcns/libboost/boost/unordered/unordered_set.hpp:17,
                 from utgcns/libboost/boost/unordered_set.hpp:17,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:21,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
/usr/local/lib/gcc9/include/c++/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:28,
                 from utgcns/libboost/boost/shared_ptr.hpp:17,
                 from utgcns/libboost/boost/property_map/vector_property_map.hpp:14,
                 from utgcns/libboost/boost/property_map/property_map.hpp:600,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:36,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
utgcns/libboost/boost/smart_ptr/detail/shared_count.hpp:518:12: error: expected ';' at end of member declaration
  518 |     void * get_deleter( sp_typeinfo const & ti ) const
      |            ^~~~~~~~~~~
      |                       ;
utgcns/libboost/boost/smart_ptr/detail/shared_count.hpp:518:36: error: expected ')' before 'const'
  518 |     void * get_deleter( sp_typeinfo const & ti ) const
      |                       ~            ^~~~~~
      |                                    )
In file included from utgcns/libboost/boost/shared_ptr.hpp:17,
                 from utgcns/libboost/boost/property_map/vector_property_map.hpp:14,
                 from utgcns/libboost/boost/property_map/property_map.hpp:600,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:36,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  242 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/local/lib/gcc9/include/c++/memory:80,
                 from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14,
                 from utgcns/libboost/boost/unordered/unordered_set.hpp:17,
                 from utgcns/libboost/boost/unordered_set.hpp:17,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:21,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
/usr/local/lib/gcc9/include/c++/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from utgcns/libboost/boost/shared_ptr.hpp:17,
                 from utgcns/libboost/boost/property_map/vector_property_map.hpp:14,
                 from utgcns/libboost/boost/property_map/property_map.hpp:600,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:36,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  441 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/local/lib/gcc9/include/c++/memory:80,
                 from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14,
                 from utgcns/libboost/boost/unordered/unordered_set.hpp:17,
                 from utgcns/libboost/boost/unordered_set.hpp:17,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:21,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
/usr/local/lib/gcc9/include/c++/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from utgcns/libboost/boost/shared_ptr.hpp:17,
                 from utgcns/libboost/boost/property_map/vector_property_map.hpp:14,
                 from utgcns/libboost/boost/property_map/property_map.hpp:600,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:36,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  454 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/local/lib/gcc9/include/c++/memory:80,
                 from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14,
                 from utgcns/libboost/boost/unordered/unordered_set.hpp:17,
                 from utgcns/libboost/boost/unordered_set.hpp:17,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:21,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
/usr/local/lib/gcc9/include/c++/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from utgcns/libboost/boost/shared_ptr.hpp:17,
                 from utgcns/libboost/boost/property_map/vector_property_map.hpp:14,
                 from utgcns/libboost/boost/property_map/property_map.hpp:600,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:36,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  520 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/local/lib/gcc9/include/c++/memory:80,
                 from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14,
                 from utgcns/libboost/boost/unordered/unordered_set.hpp:17,
                 from utgcns/libboost/boost/unordered_set.hpp:17,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:21,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
/usr/local/lib/gcc9/include/c++/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from utgcns/libboost/boost/shared_ptr.hpp:17,
                 from utgcns/libboost/boost/property_map/vector_property_map.hpp:14,
                 from utgcns/libboost/boost/property_map/property_map.hpp:600,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:36,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  529 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/local/lib/gcc9/include/c++/memory:80,
                 from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14,
                 from utgcns/libboost/boost/unordered/unordered_set.hpp:17,
                 from utgcns/libboost/boost/unordered_set.hpp:17,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:21,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
/usr/local/lib/gcc9/include/c++/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from utgcns/libboost/boost/shared_ptr.hpp:17,
                 from utgcns/libboost/boost/property_map/vector_property_map.hpp:14,
                 from utgcns/libboost/boost/property_map/property_map.hpp:600,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:36,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:695:12: error: expected ';' at end of member declaration
  695 |     void * _internal_get_deleter( boost::detail::sp_typeinfo const & ti ) const BOOST_NOEXCEPT
      |            ^~~~~~~~~~~~~~~~~~~~~
      |                                 ;
utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:695:61: error: expected ')' before 'const'
  695 |     void * _internal_get_deleter( boost::detail::sp_typeinfo const & ti ) const BOOST_NOEXCEPT
      |                                 ~                           ^~~~~~
      |                                                             )
In file included from utgcns/libboost/boost/shared_ptr.hpp:17,
                 from utgcns/libboost/boost/property_map/vector_property_map.hpp:14,
                 from utgcns/libboost/boost/property_map/property_map.hpp:600,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:36,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
utgcns/libboost/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  531 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/local/lib/gcc9/include/c++/memory:80,
                 from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14,
                 from utgcns/libboost/boost/unordered/unordered_set.hpp:17,
                 from utgcns/libboost/boost/unordered_set.hpp:17,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:21,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
/usr/local/lib/gcc9/include/c++/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from utgcns/libboost/boost/shared_ptr.hpp:17,
                 from utgcns/libboost/boost/property_map/vector_property_map.hpp:14,
                 from utgcns/libboost/boost/property_map/property_map.hpp:600,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:36,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
utgcns/libboost/boost/smart_ptr/shared_ptr.hpp: In function 'D* boost::detail::basic_get_deleter(const boost::shared_ptr<U>&)':
utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:887:71: error: expected primary-expression before ')' token
  887 |     return static_cast<D *>( p._internal_get_deleter(BOOST_SP_TYPEID(D)) );
      |                                                                       ^
utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:887:54: error: there are no arguments to 'BOOST_SP_TYPEID' that depend on a template parameter, so a declaration of 'BOOST_SP_TYPEID' must be available [-fpermissive]
  887 |     return static_cast<D *>( p._internal_get_deleter(BOOST_SP_TYPEID(D)) );
      |                                                      ^~~~~~~~~~~~~~~
utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:887:54: note: (if you use '-fpermissive', G++ will accept your code, but allowing the use of an undeclared name is deprecated)
utgcns/libcns/unitigConsensus.C: In member function 'bool unitigConsensus::alignFragment(bool)':
utgcns/libcns/unitigConsensus.C:1562:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
 1562 |       oaFull->display("utgCns::alignFragment()--", true);
      |                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~
utgcns/libcns/unitigConsensus.C:1660:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
 1660 |       oaFull->display("utgCns::alignFragment()-- ", true);
      |                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
gmake[1]: *** [Makefile:705: /wrkdirs/usr/ports/biology/canu/work/canu-1.8/src/usr/local/FreeBSD-aarch64/obj/lib/libcanu.a/utgcns/libcns/unitigConsensus.o] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/canu/work/canu-1.8/src'
*** Error code 1

Stop.
make: stopped in /usr/ports/biology/canu



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