hello
At 2026-05-28 14:02:38, [email protected] wrote: >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: [email protected] >Log URL: >https://pkg-status.freebsd.org/beefy18/data/143i386-default/50aa2c1cc258/logs/seqan-apps-2.4.0_11.log >Build URL: >https://pkg-status.freebsd.org/beefy18/build.html?mastername=143i386-default&build=50aa2c1cc258 >Log: > >=>> Building biology/seqan-apps >build started at Thu May 28 05:56:15 UTC 2026 >port directory: /usr/ports/biology/seqan-apps >package name: seqan-apps-2.4.0_11 >building for: FreeBSD 143i386-default-job-05 14.3-RELEASE-p14 FreeBSD >14.3-RELEASE-p14 i386 >maintained by: [email protected] >Makefile datestamp: -rw-r--r-- 1 root wheel 1045 Aug 8 2023 >/usr/ports/biology/seqan-apps/Makefile >Ports top last git commit: 50aa2c1cc258dd977967f6babe3f9efd5038a269 >Ports top unclean checkout: no >Port dir last git commit: 6d558714dfde336df111103f873cef02d65c64c4 >Port dir unclean checkout: no >Poudriere version: poudriere-git-3.4.8 >Host OSVERSION: 1600018 >Jail OSVERSION: 1403000 >Job Id: 05 > >---Begin Environment--- >SHELL=/bin/sh >BLOCKSIZE=K >MAIL=/var/mail/root >MM_CHARSET=UTF-8 >LANG=C.UTF-8 >OSVERSION=1403000 >STATUS=1 >HOME=/root >PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin >MAKE_OBJDIR_CHECK_WRITABLE=0 >UNAME_m=i386 >UNAME_p=i386 >UNAME_r=14.3-RELEASE-p14 >LOCALBASE=/usr/local >UNAME_v=FreeBSD 14.3-RELEASE-p14 >USER=root >POUDRIERE_NAME=poudriere-git >LIBEXECPREFIX=/usr/local/libexec/poudriere >POUDRIERE_VERSION=3.4.8 >MASTERMNT=/usr/local/poudriere/data/.m/143i386-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/143i386-default/05/.p >OUTPUT_REDIRECTED_STDOUT=3 >P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS >MASTERNAME=143i386-default >SCRIPTPREFIX=/usr/local/share/poudriere >SCRIPTNAME=bulk.sh >OLDPWD=/usr/local/poudriere/data/.m/143i386-default/ref/.p/pool >POUDRIERE_PKGNAME=poudriere-git-3.4.8 >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-- >[email protected] >--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=" " LIBS="" CXX="c++" >CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing >-std=c++14 " CXXSTD=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=14.3 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--- >USE_PACKAGE_DEPENDS=yes >BATCH=yes >WRKDIRPREFIX=/wrkdirs >PORTSDIR=/usr/ports >PACKAGES=/packages >DISTDIR=/distfiles >PACKAGE_BUILDING=yes >PACKAGE_BUILDING_FLAVORS=yes >MACHINE=i386 >MACHINE_ARCH=i386 >ARCH=${MACHINE_ARCH} >#### #### ># 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-- >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 >pipebuf (-y) 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-2.7.5.pkg >[143i386-default-job-05] Installing pkg-2.7.5... >[143i386-default-job-05] Extracting pkg-2.7.5: .......... 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-1.89.0_2.pkg >[143i386-default-job-05] Installing boost-libs-1.89.0_2... >[143i386-default-job-05] `-- Installing icu-76.1,1... >[143i386-default-job-05] `-- Extracting icu-76.1,1: .......... done >[143i386-default-job-05] `-- Installing zstd-1.5.7_2... >[143i386-default-job-05] | `-- Installing liblz4-1.10.0_2,1... >[143i386-default-job-05] | `-- Extracting liblz4-1.10.0_2,1: .......... done >[143i386-default-job-05] `-- Extracting zstd-1.5.7_2: .......... done >[143i386-default-job-05] Extracting boost-libs-1.89.0_2: .......... done >===== >Message from boost-libs-1.89.0_2: > >-- >You have built the Boost library with thread support. ><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 in /usr/ports/biology/seqan-apps
