[package - main-amd64-default][biology/canu] Failed for canu-2.2_2 in build
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Date: Mon, 26 Jun 2023 08:44:34 UTC
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
Log URL: https://pkg-status.freebsd.org/beefy18/data/main-amd64-default/p4785b313b958_se8efee297c/logs/canu-2.2_2.log
Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=p4785b313b958_se8efee297c
Log:
=>> Building biology/canu
build started at Mon Jun 26 08:43:31 UTC 2023
port directory: /usr/ports/biology/canu
package name: canu-2.2_2
building for: FreeBSD main-amd64-default-job-06 14.0-CURRENT FreeBSD 14.0-CURRENT 1400091 amd64
maintained by: jwb@FreeBSD.org
Makefile ident:
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!!! This is not supported. !!!
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!!! Expect build failures. !!!
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=======================<phase: check-sanity >============================
===> License GPLv2 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> canu-2.2_2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.19.1_1.pkg
[main-amd64-default-job-06] Installing pkg-1.19.1_1...
[main-amd64-default-job-06] Extracting pkg-1.19.1_1: .......... done
===> canu-2.2_2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of canu-2.2_2
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by canu-2.2_2 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by canu-2.2_2 for building
=> SHA256 Checksum OK for canu-2.2.tar.xz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by canu-2.2_2 for building
===> Extracting for canu-2.2_2
=> SHA256 Checksum OK for canu-2.2.tar.xz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for canu-2.2_2
===> Applying FreeBSD patches for canu-2.2_2 from /usr/ports/biology/canu/files
===========================================================================
=======================<phase: build-depends >============================
===> canu-2.2_2 depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.pkg
[main-amd64-default-job-06] Installing gmake-4.3_2...
[main-amd64-default-job-06] `-- Installing gettext-runtime-0.21.1...
<snip>
: public std::unary_function<type, std::size_t> \
~~~~~^
/usr/include/c++/v1/__functional/unary_function.h:46:1: note: '__unary_function' declared here
using __unary_function = __unary_function_keep_layout_base<_Arg, _Result>;
^
In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59:
In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21:
In file included from utgcns/libboost/boost/unordered_set.hpp:17:
In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21:
In file included from utgcns/libboost/boost/functional/hash.hpp:6:
utgcns/libboost/boost/functional/hash/hash.hpp:446:5: error: no template named 'unary_function' in namespace 'std'; did you mean '__unary_function'?
BOOST_HASH_SPECIALIZE(unsigned short)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE'
: public std::unary_function<type, std::size_t> \
~~~~~^
/usr/include/c++/v1/__functional/unary_function.h:46:1: note: '__unary_function' declared here
using __unary_function = __unary_function_keep_layout_base<_Arg, _Result>;
^
In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59:
In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21:
In file included from utgcns/libboost/boost/unordered_set.hpp:17:
In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21:
In file included from utgcns/libboost/boost/functional/hash.hpp:6:
utgcns/libboost/boost/functional/hash/hash.hpp:447:5: error: no template named 'unary_function' in namespace 'std'; did you mean '__unary_function'?
BOOST_HASH_SPECIALIZE(int)
^~~~~~~~~~~~~~~~~~~~~~~~~~
utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE'
: public std::unary_function<type, std::size_t> \
~~~~~^
/usr/include/c++/v1/__functional/unary_function.h:46:1: note: '__unary_function' declared here
using __unary_function = __unary_function_keep_layout_base<_Arg, _Result>;
^
In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59:
In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21:
In file included from utgcns/libboost/boost/unordered_set.hpp:17:
In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21:
In file included from utgcns/libboost/boost/functional/hash.hpp:6:
utgcns/libboost/boost/functional/hash/hash.hpp:448:5: error: no template named 'unary_function' in namespace 'std'; did you mean '__unary_function'?
BOOST_HASH_SPECIALIZE(unsigned int)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE'
: public std::unary_function<type, std::size_t> \
~~~~~^
/usr/include/c++/v1/__functional/unary_function.h:46:1: note: '__unary_function' declared here
using __unary_function = __unary_function_keep_layout_base<_Arg, _Result>;
^
In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59:
In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21:
In file included from utgcns/libboost/boost/unordered_set.hpp:17:
In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21:
In file included from utgcns/libboost/boost/functional/hash.hpp:6:
utgcns/libboost/boost/functional/hash/hash.hpp:449:5: error: no template named 'unary_function' in namespace 'std'; did you mean '__unary_function'?
BOOST_HASH_SPECIALIZE(long)
^~~~~~~~~~~~~~~~~~~~~~~~~~~
utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE'
: public std::unary_function<type, std::size_t> \
~~~~~^
/usr/include/c++/v1/__functional/unary_function.h:46:1: note: '__unary_function' declared here
using __unary_function = __unary_function_keep_layout_base<_Arg, _Result>;
^
In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59:
In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21:
In file included from utgcns/libboost/boost/unordered_set.hpp:17:
In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21:
In file included from utgcns/libboost/boost/functional/hash.hpp:6:
utgcns/libboost/boost/functional/hash/hash.hpp:450:5: error: no template named 'unary_function' in namespace 'std'; did you mean '__unary_function'?
BOOST_HASH_SPECIALIZE(unsigned long)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE'
: public std::unary_function<type, std::size_t> \
~~~~~^
/usr/include/c++/v1/__functional/unary_function.h:46:1: note: '__unary_function' declared here
using __unary_function = __unary_function_keep_layout_base<_Arg, _Result>;
^
In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59:
In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21:
In file included from utgcns/libboost/boost/unordered_set.hpp:17:
In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21:
In file included from utgcns/libboost/boost/functional/hash.hpp:6:
utgcns/libboost/boost/functional/hash/hash.hpp:452:5: error: no template named 'unary_function' in namespace 'std'; did you mean '__unary_function'?
BOOST_HASH_SPECIALIZE(float)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE'
: public std::unary_function<type, std::size_t> \
~~~~~^
/usr/include/c++/v1/__functional/unary_function.h:46:1: note: '__unary_function' declared here
using __unary_function = __unary_function_keep_layout_base<_Arg, _Result>;
^
In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59:
In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21:
In file included from utgcns/libboost/boost/unordered_set.hpp:17:
In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21:
In file included from utgcns/libboost/boost/functional/hash.hpp:6:
utgcns/libboost/boost/functional/hash/hash.hpp:453:5: error: no template named 'unary_function' in namespace 'std'; did you mean '__unary_function'?
BOOST_HASH_SPECIALIZE(double)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE'
: public std::unary_function<type, std::size_t> \
~~~~~^
/usr/include/c++/v1/__functional/unary_function.h:46:1: note: '__unary_function' declared here
using __unary_function = __unary_function_keep_layout_base<_Arg, _Result>;
^
In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59:
In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21:
In file included from utgcns/libboost/boost/unordered_set.hpp:17:
In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21:
In file included from utgcns/libboost/boost/functional/hash.hpp:6:
utgcns/libboost/boost/functional/hash/hash.hpp:454:5: error: no template named 'unary_function' in namespace 'std'; did you mean '__unary_function'?
BOOST_HASH_SPECIALIZE(long double)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE'
: public std::unary_function<type, std::size_t> \
~~~~~^
/usr/include/c++/v1/__functional/unary_function.h:46:1: note: '__unary_function' declared here
using __unary_function = __unary_function_keep_layout_base<_Arg, _Result>;
^
In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59:
In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21:
In file included from utgcns/libboost/boost/unordered_set.hpp:17:
In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21:
In file included from utgcns/libboost/boost/functional/hash.hpp:6:
utgcns/libboost/boost/functional/hash/hash.hpp:456:5: error: no template named 'unary_function' in namespace 'std'; did you mean '__unary_function'?
BOOST_HASH_SPECIALIZE_REF(std::string)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utgcns/libboost/boost/functional/hash/hash.hpp:430:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE_REF'
: public std::unary_function<type, std::size_t> \
~~~~~^
/usr/include/c++/v1/__functional/unary_function.h:46:1: note: '__unary_function' declared here
using __unary_function = __unary_function_keep_layout_base<_Arg, _Result>;
^
In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59:
In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21:
In file included from utgcns/libboost/boost/unordered_set.hpp:17:
In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21:
In file included from utgcns/libboost/boost/functional/hash.hpp:6:
utgcns/libboost/boost/functional/hash/hash.hpp:458:5: error: no template named 'unary_function' in namespace 'std'; did you mean '__unary_function'?
BOOST_HASH_SPECIALIZE_REF(std::wstring)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utgcns/libboost/boost/functional/hash/hash.hpp:430:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE_REF'
: public std::unary_function<type, std::size_t> \
~~~~~^
/usr/include/c++/v1/__functional/unary_function.h:46:1: note: '__unary_function' declared here
using __unary_function = __unary_function_keep_layout_base<_Arg, _Result>;
^
In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59:
In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21:
In file included from utgcns/libboost/boost/unordered_set.hpp:17:
In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21:
In file included from utgcns/libboost/boost/functional/hash.hpp:6:
utgcns/libboost/boost/functional/hash/hash.hpp:462:5: error: no template named 'unary_function' in namespace 'std'; did you mean '__unary_function'?
BOOST_HASH_SPECIALIZE(boost::long_long_type)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE'
: public std::unary_function<type, std::size_t> \
~~~~~^
/usr/include/c++/v1/__functional/unary_function.h:46:1: note: '__unary_function' declared here
using __unary_function = __unary_function_keep_layout_base<_Arg, _Result>;
^
In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59:
In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21:
In file included from utgcns/libboost/boost/unordered_set.hpp:17:
In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21:
In file included from utgcns/libboost/boost/functional/hash.hpp:6:
utgcns/libboost/boost/functional/hash/hash.hpp:463:5: error: no template named 'unary_function' in namespace 'std'; did you mean '__unary_function'?
BOOST_HASH_SPECIALIZE(boost::ulong_long_type)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE'
: public std::unary_function<type, std::size_t> \
~~~~~^
/usr/include/c++/v1/__functional/unary_function.h:46:1: note: '__unary_function' declared here
using __unary_function = __unary_function_keep_layout_base<_Arg, _Result>;
^
In file included from utgcns/libpbutgcns/AlnGraphBoost.C:59:
In file included from utgcns/libboost/boost/graph/adjacency_list.hpp:21:
In file included from utgcns/libboost/boost/unordered_set.hpp:17:
In file included from utgcns/libboost/boost/unordered/unordered_set.hpp:21:
In file included from utgcns/libboost/boost/functional/hash.hpp:6:
utgcns/libboost/boost/functional/hash/hash.hpp:467:5: error: no template named 'unary_function' in namespace 'std'; did you mean '__unary_function'?
BOOST_HASH_SPECIALIZE(boost::int128_type)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utgcns/libboost/boost/functional/hash/hash.hpp:420:24: note: expanded from macro 'BOOST_HASH_SPECIALIZE'
: public std::unary_function<type, std::size_t> \
~~~~~^
/usr/include/c++/v1/__functional/unary_function.h:46:1: note: '__unary_function' declared here
using __unary_function = __unary_function_keep_layout_base<_Arg, _Result>;
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
c++ -o /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/gfa/bed.o -c -MD -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pthread -fopenmp -fPIC -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/bed.C
10 warnings and 20 errors generated.
gmake[1]: *** [Makefile:725: /wrkdirs/usr/ports/biology/canu/work/canu-2.2/src//build/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o] Error 1
gmake[1]: *** Waiting for unfinished jobs....
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/canu/work/canu-2.2/src'
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/canu