[package - main-armv7-default][biology/seqan-apps] Failed for seqan-apps-2.4.0_11 in build
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Date: Tue, 12 Nov 2024 17:49:43 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/ampere2/data/main-armv7-default/p380be9c7980a_s5036d9652a/logs/seqan-apps-2.4.0_11.log
Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-armv7-default&build=p380be9c7980a_s5036d9652a
Log:
=>> Building biology/seqan-apps
build started at Tue Nov 12 17:37:24 UTC 2024
port directory: /usr/ports/biology/seqan-apps
package name: seqan-apps-2.4.0_11
building for: FreeBSD main-armv7-default-job-01 15.0-CURRENT FreeBSD 15.0-CURRENT 1500026 arm
maintained by: h2+fbsdports@fsfe.org
Makefile datestamp: -rw-r--r-- 1 root wheel 1045 Aug 12 2023 /usr/ports/biology/seqan-apps/Makefile
Ports top last git commit: 380be9c7980
Ports top unclean checkout: no
Port dir last git commit: 6d558714dfd
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.2
Host OSVERSION: 1500023
Jail OSVERSION: 1500026
Job Id: 01
!!! Jail is newer than host. (Jail: 1500026, Host: 1500023) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/sh
OSVERSION=1500026
UNAME_v=FreeBSD 15.0-CURRENT 1500026
UNAME_r=15.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
MM_CHARSET=UTF-8
LANG=C.UTF-8
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
MAKE_OBJDIR_CHECK_WRITABLE=0
LOCALBASE=/usr/local
USER=root
POUDRIERE_NAME=poudriere-git
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.4.2
MASTERMNT=/usr/local/poudriere/data/.m/main-armv7-default/ref
LC_COLLATE=C
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
OUTPUT_REDIRECTED_STDERR=4
OUTPUT_REDIRECTED=1
PWD=/usr/local/poudriere/data/.m/main-armv7-default/01/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=main-armv7-default
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/main-armv7-default/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.2
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---
---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
MAKE_ARGS=
---End Poudriere Port Flags/Env---
---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---
--MAINTAINER--
h2+fbsdports@fsfe.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work/.cache HOME=/wrkdirs/usr/ports/biology/seqan-apps/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/seqan-apps/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/seqan-apps/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--
--MAKE_ENV--
NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work/.cache HOME=/wrkdirs/usr/ports/biology/seqan-apps/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/seqan-apps/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/seqan-apps/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DESTDIR=/wrkdirs/usr/ports/biology/seqan-apps/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 " BSD_INSTALL_PROGRAM="install -s -m 555"
BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444"
--End MAKE_ENV--
--PLIST_SUB--
CMAKE_BUILD_TYPE="release" RM_I386="@comment " OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/seqan-apps" EXAMPLESDIR="share/examples/seqan-apps" DATADIR="share/seqan-apps" WWWDIR="www/seqan-apps" ETCDIR="etc/seqan-apps"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/seqan-apps DOCSDIR=/usr/local/share/doc/seqan-apps EXAMPLESDIR=/usr/local/share/examples/seqan-apps WWWDIR=/usr/local/www/seqan-apps ETCDIR=/usr/local/etc/seqan-apps
--End SUB_LIST--
---Begin make.conf---
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure. It currently retries the same
# failed mirror and then fails rather then trying another. It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs
MAKE_JOBS_NUMBER=3
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
#### ####
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure. It currently retries the same
# failed mirror and then fails rather then trying another. It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs
MAKE_JOBS_NUMBER=3
#### Misc Poudriere ####
.include "/etc/make.conf.ports_env"
GID=0
UID=0
---End make.conf---
--Resource limits--
ulimit: can't get limit: Invalid argument
cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 524288
stack size (kbytes, -s) 65536
core file size (512-blocks, -c) unlimited
max memory size (kbytes, -m) unlimited
locked memory (kbytes, -l) unlimited
max user processes (-u) 89999
open files (-n) 8192
virtual mem size (kbytes, -v) unlimited
swap limit (kbytes, -w) unlimited
socket buffer size (bytes, -b) unlimited
pseudo-terminals (-p) unlimited
kqueues (-k) unlimited
umtx shared locks (-o) unlimited
--End resource limits--
=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> seqan-apps-2.4.0_11 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.21.3.pkg
[main-armv7-default-job-01] Installing pkg-1.21.3...
[main-armv7-default-job-01] Extracting pkg-1.21.3: .......... 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 >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: fetch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
===> Fetching all distfiles required by seqan-apps-2.4.0_11 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> 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>============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: extract >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> 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 >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: patch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Patching for seqan-apps-2.4.0_11
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> seqan-apps-2.4.0_11 depends on package: boost-libs>0 - not found
===> Installing existing package /packages/All/boost-libs-1.85.0.pkg
[main-armv7-default-job-01] Installing boost-libs-1.85.0...
<snip>
551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options);
| ^
/usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function<seqan::ReadMatch<int>, seqan::ReadMatch<int>, bool>' has been explicitly marked deprecated here
24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function {
| ^
/usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
| ^
/usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED'
713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:30:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:91:
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:268:5: warning: definition of implicit copy assignment operator for 'Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::OneGappedShape>>>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy]
268 | Index(Index &other):
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: in implicit copy assignment operator for 'seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::OneGappedShape>>>' first required here
110 | target = source;
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:9: note: in instantiation of function template specialization 'seqan::assign<seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::OneGappedShape>>>, seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::OneGappedShape>>>>' requested here
645 | assign(_dataValue(me), value_);
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:13: note: in instantiation of function template specialization 'seqan::create<seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::OneGappedShape>>>, seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::OneGappedShape>>>>' requested here
594 | create(me, _dataValue(me));
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:9: note: in instantiation of function template specialization 'seqan::create<seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::OneGappedShape>>>>' requested here
863 | create(me);
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:12: note: in instantiation of function template specialization 'seqan::value<seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::OneGappedShape>>>>' requested here
339 | return value(me.data_host);
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1666:27: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)
1666 | TReadSet &readSet = host(host(swiftPattern));
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:5: note: in instantiation of function template specialization 'seqan::mapSingleReads<seqan::String<seqan::ReadMatch<int>>, seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>>, seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::OneGappedShape>>>, seqan::Tag<seqan::SwiftSemiGlobal_<seqan::Hamming_>>, seqan::String<seqan::Pattern<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>>, seqan::Myers<seqan::FindInfix, seqan::True, void>>>, seqan::String<seqan::String<unsigned short>>, seqan::RazerSSpec<>>' requested here
2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options);
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:10: note: in instantiation of function template specialization 'seqan::mapSingleReads<seqan::String<seqan::ReadMatch<int>>, seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::String<seqan::String<unsigned short>>, seqan::RazerSSpec<>, seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::OneGappedShape>, seqan::Tag<seqan::SwiftSemiGlobal_<seqan::Hamming_>>>' requested here
2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift<TSwiftSpec>());
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2268:11: note: in instantiation of function template specialization 'seqan::mapReads<seqan::String<seqan::ReadMatch<int>>, seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::String<seqan::String<unsigned short>>, seqan::RazerSSpec<>, seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::OneGappedShape>, seqan::Tag<seqan::SwiftSemiGlobal_<seqan::Hamming_>>>' requested here
2268 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift<SwiftSemiGlobalHamming>());
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:17: note: in instantiation of function template specialization 'seqan::mapReads<seqan::String<seqan::ReadMatch<int>>, seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::String<seqan::String<unsigned short>>, seqan::RazerSSpec<>>' requested here
165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options);
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:18: note: in instantiation of function template specialization 'mapMicroRNAReads<seqan::RazerSSpec<>>' requested here
551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options);
| ^
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:30:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:87:
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: warning: definition of implicit copy assignment operator for 'Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::OneGappedShape>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy]
107 | Shape(Shape const &other):
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:52:57: note: in implicit copy assignment operator for 'seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::OneGappedShape>' first required here
52 | template < typename TObject, typename TSpec > class Index;
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: in implicit copy assignment operator for 'seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::OneGappedShape>>>' first required here
110 | target = source;
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:9: note: in instantiation of function template specialization 'seqan::assign<seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::OneGappedShape>>>, seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::OneGappedShape>>>>' requested here
645 | assign(_dataValue(me), value_);
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:13: note: in instantiation of function template specialization 'seqan::create<seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::OneGappedShape>>>, seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::OneGappedShape>>>>' requested here
594 | create(me, _dataValue(me));
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:9: note: in instantiation of function template specialization 'seqan::create<seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::OneGappedShape>>>>' requested here
863 | create(me);
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:12: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
339 | return value(me.data_host);
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:5: note: in instantiation of function template specialization 'seqan::mapSingleReads<seqan::String<seqan::ReadMatch<int>>, seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>>, seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::OneGappedShape>>>, seqan::Tag<seqan::SwiftSemiGlobal_<seqan::Hamming_>>, seqan::String<seqan::Pattern<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>>, seqan::Myers<seqan::FindInfix, seqan::True, void>>>, seqan::String<seqan::String<unsigned short>>, seqan::RazerSSpec<>>' requested here
2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options);
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:10: note: in instantiation of function template specialization 'seqan::mapSingleReads<seqan::String<seqan::ReadMatch<int>>, seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::String<seqan::String<unsigned short>>, seqan::RazerSSpec<>, seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::OneGappedShape>, seqan::Tag<seqan::SwiftSemiGlobal_<seqan::Hamming_>>>' requested here
2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift<TSwiftSpec>());
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2268:11: note: in instantiation of function template specialization 'seqan::mapReads<seqan::String<seqan::ReadMatch<int>>, seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::String<seqan::String<unsigned short>>, seqan::RazerSSpec<>, seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::OneGappedShape>, seqan::Tag<seqan::SwiftSemiGlobal_<seqan::Hamming_>>>' requested here
2268 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift<SwiftSemiGlobalHamming>());
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:17: note: in instantiation of function template specialization 'seqan::mapReads<seqan::String<seqan::ReadMatch<int>>, seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::String<seqan::String<unsigned short>>, seqan::RazerSSpec<>>' requested here
165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options);
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:18: note: in instantiation of function template specialization 'mapMicroRNAReads<seqan::RazerSSpec<>>' requested here
551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options);
| ^
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:30:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:91:
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:268:5: warning: definition of implicit copy assignment operator for 'Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::GappedShape<seqan::Tag<seqan::Default_>>>>>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy]
268 | Index(Index &other):
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: in implicit copy assignment operator for 'seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::GappedShape<seqan::Tag<seqan::Default_>>>>>' first required here
110 | target = source;
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:9: note: in instantiation of function template specialization 'seqan::assign<seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::GappedShape<seqan::Tag<seqan::Default_>>>>>, seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::GappedShape<seqan::Tag<seqan::Default_>>>>>>' requested here
645 | assign(_dataValue(me), value_);
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:13: note: in instantiation of function template specialization 'seqan::create<seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::GappedShape<seqan::Tag<seqan::Default_>>>>>, seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::GappedShape<seqan::Tag<seqan::Default_>>>>>>' requested here
594 | create(me, _dataValue(me));
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:9: note: in instantiation of function template specialization 'seqan::create<seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::GappedShape<seqan::Tag<seqan::Default_>>>>>>' requested here
863 | create(me);
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:12: note: in instantiation of function template specialization 'seqan::value<seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::GappedShape<seqan::Tag<seqan::Default_>>>>>>' requested here
339 | return value(me.data_host);
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1666:27: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)
1666 | TReadSet &readSet = host(host(swiftPattern));
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:5: note: in instantiation of function template specialization 'seqan::mapSingleReads<seqan::String<seqan::ReadMatch<int>>, seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>>, seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::GappedShape<seqan::Tag<seqan::Default_>>>>>, seqan::Tag<seqan::SwiftSemiGlobal_<seqan::Hamming_>>, seqan::String<seqan::Pattern<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>>, seqan::Myers<seqan::FindInfix, seqan::True, void>>>, seqan::String<seqan::String<unsigned short>>, seqan::RazerSSpec<>>' requested here
2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options);
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:10: note: in instantiation of function template specialization 'seqan::mapSingleReads<seqan::String<seqan::ReadMatch<int>>, seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::String<seqan::String<unsigned short>>, seqan::RazerSSpec<>, seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::GappedShape<seqan::Tag<seqan::Default_>>>, seqan::Tag<seqan::SwiftSemiGlobal_<seqan::Hamming_>>>' requested here
2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift<TSwiftSpec>());
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2271:11: note: in instantiation of function template specialization 'seqan::mapReads<seqan::String<seqan::ReadMatch<int>>, seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::String<seqan::String<unsigned short>>, seqan::RazerSSpec<>, seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::GappedShape<seqan::Tag<seqan::Default_>>>, seqan::Tag<seqan::SwiftSemiGlobal_<seqan::Hamming_>>>' requested here
2271 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift<SwiftSemiGlobalHamming>());
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:17: note: in instantiation of function template specialization 'seqan::mapReads<seqan::String<seqan::ReadMatch<int>>, seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::String<seqan::String<unsigned short>>, seqan::RazerSSpec<>>' requested here
165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options);
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:18: note: in instantiation of function template specialization 'mapMicroRNAReads<seqan::RazerSSpec<>>' requested here
551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options);
| ^
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:28:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:44:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:68:
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/cyclic_shape.h:41:
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: warning: definition of implicit copy assignment operator for 'Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::GappedShape<seqan::Tag<seqan::Default_>>>' is deprecated because it has a user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy]
281 | Shape(Shape const &other):
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:52:57: note: in implicit copy assignment operator for 'seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::GappedShape<seqan::Tag<seqan::Default_>>>' first required here
52 | template < typename TObject, typename TSpec > class Index;
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: in implicit copy assignment operator for 'seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::GappedShape<seqan::Tag<seqan::Default_>>>>>' first required here
110 | target = source;
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:9: note: in instantiation of function template specialization 'seqan::assign<seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::GappedShape<seqan::Tag<seqan::Default_>>>>>, seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::GappedShape<seqan::Tag<seqan::Default_>>>>>>' requested here
645 | assign(_dataValue(me), value_);
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:13: note: in instantiation of function template specialization 'seqan::create<seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::GappedShape<seqan::Tag<seqan::Default_>>>>>, seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::GappedShape<seqan::Tag<seqan::Default_>>>>>>' requested here
594 | create(me, _dataValue(me));
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:9: note: in instantiation of function template specialization 'seqan::create<seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::GappedShape<seqan::Tag<seqan::Default_>>>>>>' requested here
863 | create(me);
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:12: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
339 | return value(me.data_host);
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:5: note: in instantiation of function template specialization 'seqan::mapSingleReads<seqan::String<seqan::ReadMatch<int>>, seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>>, seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::GappedShape<seqan::Tag<seqan::Default_>>>>>, seqan::Tag<seqan::SwiftSemiGlobal_<seqan::Hamming_>>, seqan::String<seqan::Pattern<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>>, seqan::Myers<seqan::FindInfix, seqan::True, void>>>, seqan::String<seqan::String<unsigned short>>, seqan::RazerSSpec<>>' requested here
2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options);
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:10: note: in instantiation of function template specialization 'seqan::mapSingleReads<seqan::String<seqan::ReadMatch<int>>, seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::String<seqan::String<unsigned short>>, seqan::RazerSSpec<>, seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::GappedShape<seqan::Tag<seqan::Default_>>>, seqan::Tag<seqan::SwiftSemiGlobal_<seqan::Hamming_>>>' requested here
2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift<TSwiftSpec>());
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2271:11: note: in instantiation of function template specialization 'seqan::mapReads<seqan::String<seqan::ReadMatch<int>>, seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::String<seqan::String<unsigned short>>, seqan::RazerSSpec<>, seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::GappedShape<seqan::Tag<seqan::Default_>>>, seqan::Tag<seqan::SwiftSemiGlobal_<seqan::Hamming_>>>' requested here
2271 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift<SwiftSemiGlobalHamming>());
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:17: note: in instantiation of function template specialization 'seqan::mapReads<seqan::String<seqan::ReadMatch<int>>, seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::String<seqan::String<unsigned short>>, seqan::RazerSSpec<>>' requested here
165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options);
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:18: note: in instantiation of function template specialization 'mapMicroRNAReads<seqan::RazerSSpec<>>' requested here
551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options);
| ^
In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:38:
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/outputFormat.h:126:37: warning: 'binary_function<seqan::ReadMatch<int>, seqan::ReadMatch<int>, bool>' is deprecated [-Wdeprecated-declarations]
126 | struct LessGPosRNo : public ::std::binary_function < TReadMatch, TReadMatch, bool >
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/outputFormat.h:388:5: note: in instantiation of template class 'seqan::LessGPosRNo<seqan::ReadMatch<int>>' requested here
388 | LessGPosRNo<TMatch>());
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:184:9: note: in instantiation of function template specialization 'seqan::dumpMatches<seqan::String<seqan::ReadMatch<int>>, seqan::StringSet<seqan::String<char>>, seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>>, seqan::Owner<seqan::ConcatDirect<>>>, seqan::StringSet<seqan::String<char>>, seqan::String<seqan::String<unsigned short>>, seqan::RazerSSpec<>>' requested here
184 | dumpMatches(matches, genomeNames, genomeFileNameList, gnoToFileMap, readSet, stats, readNames, readFileNames[0], errorPrbFileName, options);
| ^
/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:18: note: in instantiation of function template specialization 'mapMicroRNAReads<seqan::RazerSSpec<>>' requested here
551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options);
| ^
/usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function<seqan::ReadMatch<int>, seqan::ReadMatch<int>, bool>' has been explicitly marked deprecated here
24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function {
| ^
/usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
| ^
/usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED'
713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__))
| ^
35 warnings 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 making "build" in /usr/ports/biology/seqan-apps