[package - main-i386-default][biology/seqan-apps] Failed for seqan-apps-2.4.0_11 in build
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Date: Thu, 27 Jul 2023 11:40:18 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: h2+fbsdports@fsfe.org
Log URL: https://pkg-status.freebsd.org/beefy17/data/main-i386-default/p5cfda4f9e5a4_s474708c334/logs/seqan-apps-2.4.0_11.log
Build URL: https://pkg-status.freebsd.org/beefy17/build.html?mastername=main-i386-default&build=p5cfda4f9e5a4_s474708c334
Log:
=>> Building biology/seqan-apps
build started at Thu Jul 27 11:40:01 UTC 2023
port directory: /usr/ports/biology/seqan-apps
package name: seqan-apps-2.4.0_11
building for: FreeBSD main-i386-default-job-06 14.0-CURRENT FreeBSD 14.0-CURRENT 1400093 i386
maintained by: h2+fbsdports@fsfe.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400089
Jail OSVERSION: 1400093
Job Id: 06
!!! Jail is newer than host. (Jail: 1400093, Host: 1400089) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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---Begin OPTIONS List---
===> The following configuration options are available for seqan-apps-2.4.0_11:
====> Options available for the radio ARCH: you can only select none or one of them
SSE4=off: Use SSE4 and POPCNT instructions
AVX2=off: Use SSE4, AVX2 and POPCNT instructions
NATIVE=off: Use all available instruction sets (-march=native)
===> Use 'make config' to modify these settings
---End OPTIONS List---
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h2+fbsdports@fsfe.org
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--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
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--End PLIST_SUB--
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=======================<phase: check-sanity >============================
===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> seqan-apps-2.4.0_11 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.4.pkg
[main-i386-default-job-06] Installing pkg-1.20.4...
[main-i386-default-job-06] Extracting pkg-1.20.4: .......... done
===> seqan-apps-2.4.0_11 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of seqan-apps-2.4.0_11
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
===> Fetching all distfiles required by seqan-apps-2.4.0_11 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
===> Fetching all distfiles required by seqan-apps-2.4.0_11 for building
=> SHA256 Checksum OK for seqan-seqan-seqan-v2.4.0_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
===> Fetching all distfiles required by seqan-apps-2.4.0_11 for building
===> Extracting for seqan-apps-2.4.0_11
=> SHA256 Checksum OK for seqan-seqan-seqan-v2.4.0_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
<snip>
^
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74:
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: error: no template named 'unary_function' in namespace 'std'; did you mean '__unary_function'?
struct FunctorComplement<Dna> : public std::unary_function<Dna,Dna>
~~~~~^~~~~~~~~~~~~~
__unary_function
/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 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74:
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: error: no template named 'unary_function' in namespace 'std'; did you mean '__unary_function'?
struct FunctorComplement<Dna5> : public std::unary_function<Dna5,Dna5>
~~~~~^~~~~~~~~~~~~~
__unary_function
/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 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74:
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: error: no template named 'unary_function' in namespace 'std'; did you mean '__unary_function'?
struct FunctorComplement<Rna> : public std::unary_function<Rna,Rna>
~~~~~^~~~~~~~~~~~~~
__unary_function
/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 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74:
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: error: no template named 'unary_function' in namespace 'std'; did you mean '__unary_function'?
struct FunctorComplement<Rna5> : public std::unary_function<Rna5,Rna5>
~~~~~^~~~~~~~~~~~~~
__unary_function
/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 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74:
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: error: no template named 'unary_function' in namespace 'std'; did you mean '__unary_function'?
struct FunctorComplement<DnaQ> : public std::unary_function<DnaQ,DnaQ>
~~~~~^~~~~~~~~~~~~~
__unary_function
/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 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74:
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: error: no template named 'unary_function' in namespace 'std'; did you mean '__unary_function'?
struct FunctorComplement<Dna5Q> : public std::unary_function<Dna5Q,Dna5Q>
~~~~~^~~~~~~~~~~~~~
__unary_function
/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 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74:
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: error: no template named 'unary_function' in namespace 'std'; did you mean '__unary_function'?
struct FunctorComplement<Iupac> : public std::unary_function<Iupac,Iupac>
~~~~~^~~~~~~~~~~~~~
__unary_function
/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 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:79:
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
struct PosLess_ : public std::binary_function<TPos, TPos, bool>
~~~~~^~~~~~~~~~~~~~~
__binary_function
/usr/include/c++/v1/__functional/binary_function.h:49:1: note: '__binary_function' declared here
using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg2, _Result>;
^
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:92:
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: error: no template named 'unary_function' in namespace 'std'; did you mean '__unary_function'?
struct testIODone : public std::unary_function<TPageFrame&,bool>
~~~~~^~~~~~~~~~~~~~
__unary_function
/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 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52:
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: error: no template named 'unary_function' in namespace 'std'; did you mean '__unary_function'?
struct QualityExtractor : public std::unary_function<TValue, char>
~~~~~^~~~~~~~~~~~~~
__unary_function
/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 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score.h:48:
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable]
for (unsigned row = 0; !atEnd(reader); ++row)
^
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48:
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: error: no template named 'unary_function' in namespace 'std'; did you mean '__unary_function'?
public std::unary_function<Pair<TKey, TValue>, bool>
~~~~~^~~~~~~~~~~~~~
__unary_function
/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 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:59:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62:
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: error: no template named 'unary_function' in namespace 'std'; did you mean '__unary_function'?
struct LessPairI1_ : public std::unary_function<Pair<TWeight, TPair>, bool>
~~~~~^~~~~~~~~~~~~~
__unary_function
/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 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:88:
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
public std::binary_function<TGapAnchor, TGapAnchor, bool>
~~~~~^~~~~~~~~~~~~~~
__binary_function
/usr/include/c++/v1/__functional/binary_function.h:49:1: note: '__binary_function' declared here
using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg2, _Result>;
^
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align.h:88:
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
public std::binary_function<TGapAnchor, TGapAnchor, bool>
~~~~~^~~~~~~~~~~~~~~
__binary_function
/usr/include/c++/v1/__functional/binary_function.h:49:1: note: '__binary_function' declared here
using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg2, _Result>;
^
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store.h:60:
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
public std::binary_function<TAlignedRead, TAlignedRead, bool>
~~~~~^~~~~~~~~~~~~~~
__binary_function
/usr/include/c++/v1/__functional/binary_function.h:49:1: note: '__binary_function' declared here
using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg2, _Result>;
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
2 warnings and 20 errors generated.
ninja: build stopped: subcommand failed.
===> 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/seqan-apps