=> Building biology/bowtie build started at Mon Sep 18 18:39:51 PDT 2017 port directory: /usr/ports/biology/bowtie building for: DragonFly pkgbox64.dragonflybsd.org 4.9-DEVELOPMENT DragonFly v4.9.0.503.g33553-DEVELOPMENT #21: Fri Aug 4 16:51:32 PDT 2017 marino@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 maintained by: bacon4000@gmail.com ident warning: no id keywords in /build/boomdata/data/.m/Release48-default/ref/../04//usr/ports/biology/bowtie/Makefile Makefile ident: Poudriere version: 3.1-pre Host OSVERSION: 400908 Jail OSVERSION: 400801 ---Begin Environment--- STATUS=1 SAVED_TERM=screen MASTERMNT=/build/boomdata/data/.m/Release48-default/ref PATH=/usr/local/libexec/poudriere:/sbin:/bin:/usr/sbin:/usr/bin:/usr/pkg/bin:/usr/pkg/sbin:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/pkg/xorg/bin:/usr/X11R6/bin:/root/bin:/sbin:/usr/sbin POUDRIERE_BUILD_TYPE=bulk PKGNAME=bowtie-1.1.2_4 OLDPWD=/root/boom PWD=/build/boomdata/data/.m/Release48-default/ref/.p/pool MASTERNAME=Release48-default TERM=cons25 USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/wrkdirs/biology/bowtie XDG_CONFIG_HOME=/wrkdirs/biology/bowtie HOME=/wrkdirs/biology/bowtie TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/biology/bowtie XDG_CONFIG_HOME=/wrkdirs/biology/bowtie HOME=/wrkdirs/biology/bowtie TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc50 PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" NOPROFILE=1 CC="gcc" CFLAGS="-pipe -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="g++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing" MANPREFIX="/usr/local" 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-- PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=dragonfly4 PYTHON_PYOEXTENSION=pyo PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_SUFFIX=27 PYTHON_VER=2.7 PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " OSREL=4.8 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PERL_VERSION=5.24.2 PERL_VER=5.24 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.24 PROFILE="@comment " DOCSDIR="share/doc/bowtie" EXAMPLESDIR="share/examples/bowtie" DATADIR="share/bowtie" WWWDIR="www/bowtie" ETCDIR="etc/bowtie" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bowtie DOCSDIR=/usr/local/share/doc/bowtie EXAMPLESDIR=/usr/local/share/examples/bowtie WWWDIR=/usr/local/www/bowtie ETCDIR=/usr/local/etc/bowtie --End SUB_LIST-- ---Begin make.conf--- NO_BACKUP=yes USE_PACKAGE_DEPENDS=yes PKG_CREATE_VERBOSE=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORT_DBDIR=/options PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles MAKE_JOBS_NUMBER=5 ---End make.conf--- =================================================== ===> License ART10 accepted by the user =========================================================================== =================================================== ===> bowtie-1.1.2_4 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.1.txz Installing pkg-1.10.1... Extracting pkg-1.10.1: .......... done ===> bowtie-1.1.2_4 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bowtie-1.1.2_4 =========================================================================== =================================================== =========================================================================== =================================================== ===> License ART10 accepted by the user ===> Fetching all distfiles required by bowtie-1.1.2_4 for building =========================================================================== =================================================== ===> License ART10 accepted by the user ===> Fetching all distfiles required by bowtie-1.1.2_4 for building => SHA256 Checksum OK for BenLangmead-bowtie-v1.1.2_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License ART10 accepted by the user ===> Fetching all distfiles required by bowtie-1.1.2_4 for building ===> Extracting for bowtie-1.1.2_4 ===> License ART10 accepted by the user ===> Fetching all distfiles required by bowtie-1.1.2_4 for building => SHA256 Checksum OK for BenLangmead-bowtie-v1.1.2_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for bowtie-1.1.2_4 ===> Applying ports patches for bowtie-1.1.2_4 /usr/bin/sed -i.bak -e 's@amd64@x86_64@g' /wrkdirs/biology/bowtie/bowtie-1.1.2/Makefile =========================================================================== =================================================== ===> bowtie-1.1.2_4 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_1.txz Installing gmake-4.2.1_1... `-- Installing indexinfo-0.2.6... `-- Extracting indexinfo-0.2.6: .... done `-- Installing gettext-runtime-0.19.8.1_1... `-- Extracting gettext-runtime-0.19.8.1_1: .......... done Extracting gmake-4.2.1_1: .......... done ===> bowtie-1.1.2_4 depends on executable: gmake - found ===> Returning to build of bowtie-1.1.2_4 =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for bowtie-1.1.2_4 =========================================================================== =================================================== ===> Building for bowtie-1.1.2_4 gmake[2]: Entering directory '/wrkdirs/biology/bowtie/bowtie-1.1.2' g++ -O -DCOMPILER_OPTIONS="\"-O -DPOPCNT_CAPABILITY -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing \"" -DPOPCNT_CAPABILITY -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \ -I SeqAn-1.1 -I third_party -I third_party \ -o bowtie-build-s ebwt_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp bowtie_build_main.cpp \ -lpthread g++ -O -DCOMPILER_OPTIONS="\"-O -DPOPCNT_CAPABILITY -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing \"" -DPOPCNT_CAPABILITY -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I SeqAn-1.1 -I third_party -I third_party \ -o bowtie-build-l ebwt_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp bowtie_build_main.cpp \ -lpthread g++ -O -DCOMPILER_OPTIONS="\"-O -DPOPCNT_CAPABILITY -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing \"" -DPOPCNT_CAPABILITY -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \ -I SeqAn-1.1 -I third_party -I third_party \ -o bowtie-align-s ebwt_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \ -lpthread g++ -O -DCOMPILER_OPTIONS="\"-O -DPOPCNT_CAPABILITY -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing \"" -DPOPCNT_CAPABILITY -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -DBOWTIE_64BIT_INDEX -Wall \ -I SeqAn-1.1 -I third_party -I third_party \ -o bowtie-align-l ebwt_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \ -lpthread g++ -O \ -DCOMPILER_OPTIONS="\"-O -DPOPCNT_CAPABILITY -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing \"" -DPOPCNT_CAPABILITY -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -Wall \ -I SeqAn-1.1 -I third_party -I third_party -I . \ -o bowtie-inspect-s bowtie_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp \ -lpthread In file included from SeqAn-1.1/seqan/basic.h:64:0, from SeqAn-1.1/seqan/sequence.h:27, from SeqAn-1.1/seqan/find.h:31, from ebwt_search.cpp:8: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:38:0, from SeqAn-1.1/seqan/find.h:31, from ebwt_search.cpp:8: SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:51:0, from SeqAn-1.1/seqan/find.h:31, from ebwt_search.cpp:8: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ In file included from SeqAn-1.1/seqan/sequence.h:53:0, from SeqAn-1.1/seqan/find.h:31, from ebwt_search.cpp:8: SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from SeqAn-1.1/seqan/find.h:31, from ebwt_search.cpp:8: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^ SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:62:0, from SeqAn-1.1/seqan/find.h:31, from ebwt_search.cpp:8: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^ In file included from SeqAn-1.1/seqan/find.h:62:0, from ebwt_search.cpp:8: SeqAn-1.1/seqan/find/find_multiple_shiftand.h: In function 'void seqan::_patternInit(seqan::Pattern >&)': SeqAn-1.1/seqan/find/find_multiple_shiftand.h:220:23: warning: typedef 'TWord' locally defined but not used [-Wunused-local-typedefs] typedef unsigned int TWord; ^ In file included from SeqAn-1.1/seqan/basic.h:64:0, from SeqAn-1.1/seqan/sequence.h:27, from SeqAn-1.1/seqan/find.h:31, from bowtie_inspect.cpp:6: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^ In file included from SeqAn-1.1/seqan/file.h:66:0, from alphabet.h:7, from ebwt_search.cpp:11: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] typedef typename Position::Type TPosition; ^ In file included from SeqAn-1.1/seqan/file.h:69:0, from alphabet.h:7, from ebwt_search.cpp:11: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ In file included from SeqAn-1.1/seqan/sequence.h:38:0, from SeqAn-1.1/seqan/find.h:31, from bowtie_inspect.cpp:6: SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:51:0, from SeqAn-1.1/seqan/find.h:31, from bowtie_inspect.cpp:6: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ In file included from SeqAn-1.1/seqan/sequence.h:53:0, from SeqAn-1.1/seqan/find.h:31, from bowtie_inspect.cpp:6: SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/index.h:82:0, from ebwt.h:16, from ebwt_search.cpp:14: SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter)': SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter)': SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape > >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< Shape > >::Type TSize; ^ SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hash(seqan::Shape&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hashUpper(seqan::Shape&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hash2(seqan::Shape&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ In file included from SeqAn-1.1/seqan/index.h:83:0, from ebwt.h:16, from ebwt_search.cpp:14: SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value > > >::Type seqan::hash(seqan::Shape > >&, TIter)': SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape > >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value > >::Type seqan::hashUpper(seqan::Shape >&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape > >::Type THValue; ^ In file included from ebwt.h:27:0, from ebwt_search.cpp:14: blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA::buildSamples()': blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TAlphabet; ^ In file included from ebwt.h:27:0, from ebwt_search.cpp:14: blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA::nextBlock()': blockwise_sa.h:755:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TAlphabet; ^ In file included from ebwt.h:40:0, from ebwt_search.cpp:14: reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^ reference.h:528:15: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] bool binarySearched = false; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from SeqAn-1.1/seqan/find.h:31, from bowtie_inspect.cpp:6: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^ SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/basic.h:64:0, from SeqAn-1.1/seqan/sequence.h:27, from SeqAn-1.1/seqan/index.h:27, from ebwt_build.cpp:5: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^ In file included from SeqAn-1.1/seqan/basic.h:64:0, from SeqAn-1.1/seqan/sequence.h:27, from SeqAn-1.1/seqan/find.h:31, from ebwt_search.cpp:8: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:38:0, from SeqAn-1.1/seqan/find.h:31, from ebwt_search.cpp:8: SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:38:0, from SeqAn-1.1/seqan/index.h:27, from ebwt_build.cpp:5: SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:51:0, from SeqAn-1.1/seqan/index.h:27, from ebwt_build.cpp:5: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ In file included from SeqAn-1.1/seqan/sequence.h:51:0, from SeqAn-1.1/seqan/find.h:31, from ebwt_search.cpp:8: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ In file included from SeqAn-1.1/seqan/sequence.h:53:0, from SeqAn-1.1/seqan/index.h:27, from ebwt_build.cpp:5: SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:53:0, from SeqAn-1.1/seqan/find.h:31, from ebwt_search.cpp:8: SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from SeqAn-1.1/seqan/index.h:27, from ebwt_build.cpp:5: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^ SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from SeqAn-1.1/seqan/find.h:31, from ebwt_search.cpp:8: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^ SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:62:0, from SeqAn-1.1/seqan/find.h:31, from bowtie_inspect.cpp:6: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^ In file included from SeqAn-1.1/seqan/sequence.h:62:0, from SeqAn-1.1/seqan/index.h:27, from ebwt_build.cpp:5: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^ In file included from SeqAn-1.1/seqan/sequence.h:62:0, from SeqAn-1.1/seqan/find.h:31, from ebwt_search.cpp:8: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^ In file included from SeqAn-1.1/seqan/find.h:62:0, from ebwt_search.cpp:8: SeqAn-1.1/seqan/find/find_multiple_shiftand.h: In function 'void seqan::_patternInit(seqan::Pattern >&)': SeqAn-1.1/seqan/find/find_multiple_shiftand.h:220:23: warning: typedef 'TWord' locally defined but not used [-Wunused-local-typedefs] typedef unsigned int TWord; ^ In file included from SeqAn-1.1/seqan/index.h:82:0, from ebwt_build.cpp:5: SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter)': SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter)': SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape > >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< Shape > >::Type TSize; ^ SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hash(seqan::Shape&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hashUpper(seqan::Shape&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hash2(seqan::Shape&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ In file included from SeqAn-1.1/seqan/index.h:83:0, from ebwt_build.cpp:5: SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value > > >::Type seqan::hash(seqan::Shape > >&, TIter)': SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape > >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value > >::Type seqan::hashUpper(seqan::Shape >&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape > >::Type THValue; ^ In file included from SeqAn-1.1/seqan/file.h:66:0, from alphabet.h:7, from ebwt_search.cpp:11: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] typedef typename Position::Type TPosition; ^ In file included from SeqAn-1.1/seqan/file.h:69:0, from alphabet.h:7, from ebwt_search.cpp:11: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ In file included from SeqAn-1.1/seqan/file.h:66:0, from ebwt_build.cpp:7: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] typedef typename Position::Type TPosition; ^ In file included from SeqAn-1.1/seqan/file.h:69:0, from ebwt_build.cpp:7: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ In file included from SeqAn-1.1/seqan/find.h:62:0, from bowtie_inspect.cpp:6: SeqAn-1.1/seqan/find/find_multiple_shiftand.h: In function 'void seqan::_patternInit(seqan::Pattern >&)': SeqAn-1.1/seqan/find/find_multiple_shiftand.h:220:23: warning: typedef 'TWord' locally defined but not used [-Wunused-local-typedefs] typedef unsigned int TWord; ^ In file included from SeqAn-1.1/seqan/index.h:82:0, from ebwt.h:16, from ebwt_search.cpp:14: SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter)': SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter)': SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape > >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< Shape > >::Type TSize; ^ SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hash(seqan::Shape&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hashUpper(seqan::Shape&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hash2(seqan::Shape&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ In file included from SeqAn-1.1/seqan/index.h:83:0, from ebwt.h:16, from ebwt_search.cpp:14: SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value > > >::Type seqan::hash(seqan::Shape > >&, TIter)': SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape > >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value > >::Type seqan::hashUpper(seqan::Shape >&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape > >::Type THValue; ^ In file included from SeqAn-1.1/seqan/index.h:82:0, from ebwt.h:16, from bowtie_inspect.cpp:10: SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter)': SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter)': SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape > >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< Shape > >::Type TSize; ^ SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hash(seqan::Shape&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hashUpper(seqan::Shape&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hash2(seqan::Shape&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ In file included from SeqAn-1.1/seqan/index.h:83:0, from ebwt.h:16, from bowtie_inspect.cpp:10: SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value > > >::Type seqan::hash(seqan::Shape > >&, TIter)': SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape > >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value > >::Type seqan::hashUpper(seqan::Shape >&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape > >::Type THValue; ^ In file included from ebwt.h:27:0, from ebwt_build.cpp:11: blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA::buildSamples()': blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TAlphabet; ^ In file included from ebwt.h:27:0, from ebwt_build.cpp:11: blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA::nextBlock()': blockwise_sa.h:755:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TAlphabet; ^ In file included from SeqAn-1.1/seqan/file.h:66:0, from alphabet.h:7, from ebwt.h:24, from bowtie_inspect.cpp:10: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] typedef typename Position::Type TPosition; ^ In file included from SeqAn-1.1/seqan/file.h:69:0, from alphabet.h:7, from ebwt.h:24, from bowtie_inspect.cpp:10: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ In file included from ebwt.h:40:0, from ebwt_build.cpp:11: reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^ reference.h:528:15: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] bool binarySearched = false; ^ In file included from SeqAn-1.1/seqan/basic.h:64:0, from SeqAn-1.1/seqan/sequence.h:27, from SeqAn-1.1/seqan/index.h:27, from ebwt_build.cpp:5: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:38:0, from SeqAn-1.1/seqan/index.h:27, from ebwt_build.cpp:5: SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:51:0, from SeqAn-1.1/seqan/index.h:27, from ebwt_build.cpp:5: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ In file included from SeqAn-1.1/seqan/sequence.h:53:0, from SeqAn-1.1/seqan/index.h:27, from ebwt_build.cpp:5: SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from SeqAn-1.1/seqan/index.h:27, from ebwt_build.cpp:5: SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts, seqan::Packed<> > >': SeqAn-1.1/seqan/sequence/string_packed.h:906:43: required from 'typename seqan::Position > >::Type seqan::position(const seqan::Iter >&) [with TContainer = const seqan::String, seqan::Packed<> >; THostspec = seqan::Alloc; typename seqan::Position > >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_packed.h:1237:17: required from 'typename seqan::Difference > >::Type seqan::operator-(const seqan::Iter >&, const seqan::Iter >&) [with TContainer = const seqan::String, seqan::Packed<> >; THostspec = seqan::Alloc; typename seqan::Difference > >::Type = long int]' SeqAn-1.1/seqan/sequence/string_base.h:181:29: required from 'typename seqan::Size >::Type seqan::length(const seqan::String&) [with TValue = seqan::SimpleType; TSpec = seqan::Packed<>; typename seqan::Size >::Type = long unsigned int]' blockwise_sa.h:354:46: required from here SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue >::' and 'enum seqan::BitsPerValue::' [-Wenum-compare] VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE), ^ SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts, seqan::Packed<> > >': SeqAn-1.1/seqan/sequence/string_packed.h:731:75: required from 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = seqan::Alloc; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size > >::Type = long unsigned int]' ebwt.h:4032:9: required from 'static TStr Ebwt::join(std::vector&, std::vector&, TIndexOffU, const RefReadInParams&, uint32_t) [with TStr = seqan::String, seqan::Packed<> >; TIndexOffU = unsigned int; uint32_t = unsigned int]' ebwt_build.cpp:480:36: required from 'void driver(const string&, std::vector >&, const string&, bool) [with TStr = seqan::String, seqan::Packed<> >; std::__cxx11::string = std::__cxx11::basic_string]' ebwt_build.cpp:622:69: required from here SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue >::' and 'enum seqan::BitsPerValue::' [-Wenum-compare] In file included from ebwt.h:27:0, from ebwt_search.cpp:14: blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA::buildSamples()': blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TAlphabet; ^ In file included from ebwt.h:27:0, from ebwt_search.cpp:14: blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA::nextBlock()': blockwise_sa.h:755:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TAlphabet; ^ In file included from ebwt.h:40:0, from ebwt_search.cpp:14: reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^ reference.h:528:15: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] bool binarySearched = false; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from SeqAn-1.1/seqan/find.h:31, from ebwt_search.cpp:8: SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts, seqan::Packed<> > >': SeqAn-1.1/seqan/sequence/string_packed.h:906:43: required from 'typename seqan::Position > >::Type seqan::position(const seqan::Iter >&) [with TContainer = const seqan::String, seqan::Packed<> >; THostspec = seqan::Alloc; typename seqan::Position > >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_packed.h:1237:17: required from 'typename seqan::Difference > >::Type seqan::operator-(const seqan::Iter >&, const seqan::Iter >&) [with TContainer = const seqan::String, seqan::Packed<> >; THostspec = seqan::Alloc; typename seqan::Difference > >::Type = long int]' SeqAn-1.1/seqan/sequence/string_base.h:181:29: required from 'typename seqan::Size >::Type seqan::length(const seqan::String&) [with TValue = seqan::SimpleType; TSpec = seqan::Packed<>; typename seqan::Size >::Type = long unsigned int]' blockwise_sa.h:354:46: required from here SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue >::' and 'enum seqan::BitsPerValue::' [-Wenum-compare] VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE), ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from SeqAn-1.1/seqan/index.h:27, from ebwt_build.cpp:5: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^ SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:62:0, from SeqAn-1.1/seqan/index.h:27, from ebwt_build.cpp:5: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^ In file included from SeqAn-1.1/seqan/index.h:82:0, from ebwt_build.cpp:5: SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter)': SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter)': SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape > >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< Shape > >::Type TSize; ^ SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hash(seqan::Shape&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hashUpper(seqan::Shape&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hash2(seqan::Shape&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ In file included from ebwt.h:27:0, from bowtie_inspect.cpp:10: blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA::buildSamples()': blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TAlphabet; ^ In file included from ebwt.h:27:0, from bowtie_inspect.cpp:10: blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA::nextBlock()': blockwise_sa.h:755:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TAlphabet; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from SeqAn-1.1/seqan/find.h:31, from ebwt_search.cpp:8: SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts, seqan::Packed<> > >': SeqAn-1.1/seqan/sequence/string_packed.h:906:43: required from 'typename seqan::Position > >::Type seqan::position(const seqan::Iter >&) [with TContainer = const seqan::String, seqan::Packed<> >; THostspec = seqan::Alloc; typename seqan::Position > >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_packed.h:1237:17: required from 'typename seqan::Difference > >::Type seqan::operator-(const seqan::Iter >&, const seqan::Iter >&) [with TContainer = const seqan::String, seqan::Packed<> >; THostspec = seqan::Alloc; typename seqan::Difference > >::Type = long int]' SeqAn-1.1/seqan/sequence/string_base.h:181:29: required from 'typename seqan::Size >::Type seqan::length(const seqan::String&) [with TValue = seqan::SimpleType; TSpec = seqan::Packed<>; typename seqan::Size >::Type = long unsigned int]' blockwise_sa.h:354:46: required from here SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue >::' and 'enum seqan::BitsPerValue::' [-Wenum-compare] VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE), ^ In file included from SeqAn-1.1/seqan/index.h:83:0, from ebwt_build.cpp:5: SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value > > >::Type seqan::hash(seqan::Shape > >&, TIter)': SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape > >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value > >::Type seqan::hashUpper(seqan::Shape >&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape > >::Type THValue; ^ In file included from SeqAn-1.1/seqan/file.h:66:0, from ebwt_build.cpp:7: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] typedef typename Position::Type TPosition; ^ In file included from SeqAn-1.1/seqan/file.h:69:0, from ebwt_build.cpp:7: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ In file included from ebwt.h:27:0, from ebwt_build.cpp:11: blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA::buildSamples()': blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TAlphabet; ^ In file included from ebwt.h:27:0, from ebwt_build.cpp:11: blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA::nextBlock()': blockwise_sa.h:755:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TAlphabet; ^ In file included from ebwt.h:40:0, from ebwt_build.cpp:11: reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^ reference.h:528:15: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] bool binarySearched = false; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from SeqAn-1.1/seqan/index.h:27, from ebwt_build.cpp:5: SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts, seqan::Packed<> > >': SeqAn-1.1/seqan/sequence/string_packed.h:906:43: required from 'typename seqan::Position > >::Type seqan::position(const seqan::Iter >&) [with TContainer = const seqan::String, seqan::Packed<> >; THostspec = seqan::Alloc; typename seqan::Position > >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_packed.h:1237:17: required from 'typename seqan::Difference > >::Type seqan::operator-(const seqan::Iter >&, const seqan::Iter >&) [with TContainer = const seqan::String, seqan::Packed<> >; THostspec = seqan::Alloc; typename seqan::Difference > >::Type = long int]' SeqAn-1.1/seqan/sequence/string_base.h:181:29: required from 'typename seqan::Size >::Type seqan::length(const seqan::String&) [with TValue = seqan::SimpleType; TSpec = seqan::Packed<>; typename seqan::Size >::Type = long unsigned int]' blockwise_sa.h:354:46: required from here SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue >::' and 'enum seqan::BitsPerValue::' [-Wenum-compare] VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE), ^ SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts, seqan::Packed<> > >': SeqAn-1.1/seqan/sequence/string_packed.h:731:75: required from 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = seqan::Alloc; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size > >::Type = long unsigned int]' ebwt.h:4032:9: required from 'static TStr Ebwt::join(std::vector&, std::vector&, TIndexOffU, const RefReadInParams&, uint32_t) [with TStr = seqan::String, seqan::Packed<> >; TIndexOffU = long unsigned int; uint32_t = unsigned int]' ebwt_build.cpp:480:36: required from 'void driver(const string&, std::vector >&, const string&, bool) [with TStr = seqan::String, seqan::Packed<> >; std::__cxx11::string = std::__cxx11::basic_string]' ebwt_build.cpp:622:69: required from here SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue >::' and 'enum seqan::BitsPerValue::' [-Wenum-compare] In file included from SeqAn-1.1/seqan/sequence.h:57:0, from SeqAn-1.1/seqan/find.h:31, from bowtie_inspect.cpp:6: SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts, seqan::Packed<> > >': SeqAn-1.1/seqan/sequence/string_packed.h:906:43: required from 'typename seqan::Position > >::Type seqan::position(const seqan::Iter >&) [with TContainer = const seqan::String, seqan::Packed<> >; THostspec = seqan::Alloc; typename seqan::Position > >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_packed.h:1237:17: required from 'typename seqan::Difference > >::Type seqan::operator-(const seqan::Iter >&, const seqan::Iter >&) [with TContainer = const seqan::String, seqan::Packed<> >; THostspec = seqan::Alloc; typename seqan::Difference > >::Type = long int]' SeqAn-1.1/seqan/sequence/string_base.h:181:29: required from 'typename seqan::Size >::Type seqan::length(const seqan::String&) [with TValue = seqan::SimpleType; TSpec = seqan::Packed<>; typename seqan::Size >::Type = long unsigned int]' blockwise_sa.h:354:46: required from here SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue >::' and 'enum seqan::BitsPerValue::' [-Wenum-compare] VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE), ^ SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts, seqan::Packed<> > >': SeqAn-1.1/seqan/sequence/string_packed.h:509:6: required from 'typename seqan::Size > >::Type seqan::capacity(const seqan::String >&) [with TValue = seqan::SimpleType; THostspec = seqan::Alloc; typename seqan::Size > >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_base.h:1429:49: required from 'static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Packed<> >; TExpand = const seqan::Tag; typename seqan::Size::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_base.h:1459:52: required from 'typename seqan::Size >::Type seqan::resize(seqan::String&, TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = seqan::Packed<>; TSize = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size >::Type = long unsigned int]' ebwt.h:2965:8: required from 'void Ebwt::restore(TStr&) const [with TStr = seqan::String, seqan::Packed<> >]' bowtie_inspect.cpp:283:2: required from 'void print_index_sequences(std::ostream&, Ebwt&, const BitPairReference&) [with TStr = seqan::String, seqan::Packed<> >; std::ostream = std::basic_ostream]' bowtie_inspect.cpp:461:42: required from here SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue >::' and 'enum seqan::BitsPerValue::' [-Wenum-compare] In file included from SeqAn-1.1/seqan/basic.h:64:0, from SeqAn-1.1/seqan/sequence.h:27, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:38:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:51:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ In file included from SeqAn-1.1/seqan/sequence.h:53:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^ SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:62:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^ In file included from SeqAn-1.1/seqan/file.h:66:0, from alphabet.h:7, from ref_read.h:12, from ref_read.cpp:1: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] typedef typename Position::Type TPosition; ^ In file included from SeqAn-1.1/seqan/file.h:69:0, from alphabet.h:7, from ref_read.h:12, from ref_read.cpp:1: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ g++ -O \ -DCOMPILER_OPTIONS="\"-O -DPOPCNT_CAPABILITY -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing \"" -DPOPCNT_CAPABILITY -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DBOWTIE_64BIT_INDEX -Wall \ -I SeqAn-1.1 -I third_party -I third_party -I . \ -o bowtie-inspect-l bowtie_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp \ -lpthread In file included from SeqAn-1.1/seqan/basic.h:64:0, from SeqAn-1.1/seqan/sequence.h:27, from SeqAn-1.1/seqan/find.h:31, from bowtie_inspect.cpp:6: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:38:0, from SeqAn-1.1/seqan/find.h:31, from bowtie_inspect.cpp:6: SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:51:0, from SeqAn-1.1/seqan/find.h:31, from bowtie_inspect.cpp:6: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ In file included from SeqAn-1.1/seqan/sequence.h:53:0, from SeqAn-1.1/seqan/find.h:31, from bowtie_inspect.cpp:6: SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from SeqAn-1.1/seqan/find.h:31, from bowtie_inspect.cpp:6: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^ SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:62:0, from SeqAn-1.1/seqan/find.h:31, from bowtie_inspect.cpp:6: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^ In file included from SeqAn-1.1/seqan/find.h:62:0, from bowtie_inspect.cpp:6: SeqAn-1.1/seqan/find/find_multiple_shiftand.h: In function 'void seqan::_patternInit(seqan::Pattern >&)': SeqAn-1.1/seqan/find/find_multiple_shiftand.h:220:23: warning: typedef 'TWord' locally defined but not used [-Wunused-local-typedefs] typedef unsigned int TWord; ^ In file included from SeqAn-1.1/seqan/index.h:82:0, from ebwt.h:16, from bowtie_inspect.cpp:10: SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter)': SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter)': SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape > >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< Shape > >::Type TSize; ^ SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hash(seqan::Shape&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hashUpper(seqan::Shape&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hash2(seqan::Shape&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ In file included from SeqAn-1.1/seqan/index.h:83:0, from ebwt.h:16, from bowtie_inspect.cpp:10: SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value > > >::Type seqan::hash(seqan::Shape > >&, TIter)': SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape > >::Type THValue; ^ SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value > >::Type seqan::hashUpper(seqan::Shape >&, TIter, TSize)': SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape > >::Type THValue; ^ In file included from SeqAn-1.1/seqan/file.h:66:0, from alphabet.h:7, from ebwt.h:24, from bowtie_inspect.cpp:10: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] typedef typename Position::Type TPosition; ^ In file included from SeqAn-1.1/seqan/file.h:69:0, from alphabet.h:7, from ebwt.h:24, from bowtie_inspect.cpp:10: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ In file included from ebwt.h:27:0, from bowtie_inspect.cpp:10: blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA::buildSamples()': blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TAlphabet; ^ In file included from ebwt.h:27:0, from bowtie_inspect.cpp:10: blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA::nextBlock()': blockwise_sa.h:755:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TAlphabet; ^ In file included from SeqAn-1.1/seqan/basic.h:64:0, from SeqAn-1.1/seqan/sequence.h:27, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:38:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:51:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ In file included from SeqAn-1.1/seqan/sequence.h:53:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^ SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:62:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^ In file included from SeqAn-1.1/seqan/file.h:66:0, from alphabet.h:7, from ref_read.h:12, from ref_read.cpp:1: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] typedef typename Position::Type TPosition; ^ In file included from SeqAn-1.1/seqan/file.h:69:0, from alphabet.h:7, from ref_read.h:12, from ref_read.cpp:1: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ In file included from SeqAn-1.1/seqan/basic.h:64:0, from SeqAn-1.1/seqan/sequence.h:27, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:38:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:51:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ In file included from SeqAn-1.1/seqan/sequence.h:53:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^ SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:62:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^ In file included from SeqAn-1.1/seqan/file.h:66:0, from alphabet.h:7, from ref_read.h:12, from ref_read.cpp:1: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] typedef typename Position::Type TPosition; ^ In file included from SeqAn-1.1/seqan/file.h:69:0, from alphabet.h:7, from ref_read.h:12, from ref_read.cpp:1: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from SeqAn-1.1/seqan/find.h:31, from bowtie_inspect.cpp:6: SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts, seqan::Packed<> > >': SeqAn-1.1/seqan/sequence/string_packed.h:906:43: required from 'typename seqan::Position > >::Type seqan::position(const seqan::Iter >&) [with TContainer = const seqan::String, seqan::Packed<> >; THostspec = seqan::Alloc; typename seqan::Position > >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_packed.h:1237:17: required from 'typename seqan::Difference > >::Type seqan::operator-(const seqan::Iter >&, const seqan::Iter >&) [with TContainer = const seqan::String, seqan::Packed<> >; THostspec = seqan::Alloc; typename seqan::Difference > >::Type = long int]' SeqAn-1.1/seqan/sequence/string_base.h:181:29: required from 'typename seqan::Size >::Type seqan::length(const seqan::String&) [with TValue = seqan::SimpleType; TSpec = seqan::Packed<>; typename seqan::Size >::Type = long unsigned int]' blockwise_sa.h:354:46: required from here SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue >::' and 'enum seqan::BitsPerValue::' [-Wenum-compare] VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE), ^ SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts, seqan::Packed<> > >': SeqAn-1.1/seqan/sequence/string_packed.h:509:6: required from 'typename seqan::Size > >::Type seqan::capacity(const seqan::String >&) [with TValue = seqan::SimpleType; THostspec = seqan::Alloc; typename seqan::Size > >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_base.h:1429:49: required from 'static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Packed<> >; TExpand = const seqan::Tag; typename seqan::Size::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_base.h:1459:52: required from 'typename seqan::Size >::Type seqan::resize(seqan::String&, TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = seqan::Packed<>; TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size >::Type = long unsigned int]' ebwt.h:2965:8: required from 'void Ebwt::restore(TStr&) const [with TStr = seqan::String, seqan::Packed<> >]' bowtie_inspect.cpp:283:2: required from 'void print_index_sequences(std::ostream&, Ebwt&, const BitPairReference&) [with TStr = seqan::String, seqan::Packed<> >; std::ostream = std::basic_ostream]' bowtie_inspect.cpp:461:42: required from here SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue >::' and 'enum seqan::BitsPerValue::' [-Wenum-compare] In file included from SeqAn-1.1/seqan/basic.h:64:0, from SeqAn-1.1/seqan/sequence.h:27, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:38:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:51:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ In file included from SeqAn-1.1/seqan/sequence.h:53:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^ SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:62:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^ In file included from SeqAn-1.1/seqan/file.h:66:0, from alphabet.h:7, from ref_read.h:12, from ref_read.cpp:1: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] typedef typename Position::Type TPosition; ^ In file included from SeqAn-1.1/seqan/file.h:69:0, from alphabet.h:7, from ref_read.h:12, from ref_read.cpp:1: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ In file included from SeqAn-1.1/seqan/basic.h:64:0, from SeqAn-1.1/seqan/sequence.h:27, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:38:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:51:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ In file included from SeqAn-1.1/seqan/sequence.h:53:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^ SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:62:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^ In file included from SeqAn-1.1/seqan/file.h:66:0, from alphabet.h:7, from ref_read.h:12, from ref_read.cpp:1: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] typedef typename Position::Type TPosition; ^ In file included from SeqAn-1.1/seqan/file.h:69:0, from alphabet.h:7, from ref_read.h:12, from ref_read.cpp:1: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ In file included from SeqAn-1.1/seqan/basic.h:64:0, from SeqAn-1.1/seqan/sequence.h:27, from pat.cpp:5: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:38:0, from pat.cpp:5: SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:51:0, from pat.cpp:5: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ In file included from SeqAn-1.1/seqan/sequence.h:53:0, from pat.cpp:5: SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from pat.cpp:5: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^ SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:62:0, from pat.cpp:5: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^ In file included from SeqAn-1.1/seqan/file.h:66:0, from pat.cpp:6: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] typedef typename Position::Type TPosition; ^ In file included from SeqAn-1.1/seqan/file.h:69:0, from pat.cpp:6: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ In file included from SeqAn-1.1/seqan/basic.h:64:0, from SeqAn-1.1/seqan/sequence.h:27, from pat.cpp:5: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:38:0, from pat.cpp:5: SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:51:0, from pat.cpp:5: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ In file included from SeqAn-1.1/seqan/sequence.h:53:0, from pat.cpp:5: SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from pat.cpp:5: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^ SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:62:0, from pat.cpp:5: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^ In file included from SeqAn-1.1/seqan/file.h:66:0, from pat.cpp:6: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] typedef typename Position::Type TPosition; ^ In file included from SeqAn-1.1/seqan/file.h:69:0, from pat.cpp:6: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ In file included from SeqAn-1.1/seqan/basic.h:64:0, from SeqAn-1.1/seqan/sequence.h:27, from ebwt_search_util.h:8, from ebwt_search_util.cpp:1: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^ In file included from SeqAn-1.1/seqan/basic.h:64:0, from SeqAn-1.1/seqan/sequence.h:27, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:38:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:51:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ In file included from SeqAn-1.1/seqan/sequence.h:53:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^ SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:38:0, from ebwt_search_util.h:8, from ebwt_search_util.cpp:1: SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:51:0, from ebwt_search_util.h:8, from ebwt_search_util.cpp:1: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ In file included from SeqAn-1.1/seqan/sequence.h:53:0, from ebwt_search_util.h:8, from ebwt_search_util.cpp:1: SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from ebwt_search_util.h:8, from ebwt_search_util.cpp:1: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^ SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:62:0, from ebwt_search_util.h:8, from ebwt_search_util.cpp:1: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^ In file included from SeqAn-1.1/seqan/sequence.h:62:0, from ref_read.h:11, from ref_read.cpp:1: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^ In file included from SeqAn-1.1/seqan/file.h:66:0, from alphabet.h:7, from ref_read.h:12, from ref_read.cpp:1: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] typedef typename Position::Type TPosition; ^ In file included from SeqAn-1.1/seqan/file.h:69:0, from alphabet.h:7, from ref_read.h:12, from ref_read.cpp:1: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ In file included from SeqAn-1.1/seqan/file.h:66:0, from alphabet.h:7, from hit.h:12, from ebwt_search_util.h:9, from ebwt_search_util.cpp:1: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] typedef typename Position::Type TPosition; ^ In file included from SeqAn-1.1/seqan/file.h:69:0, from alphabet.h:7, from hit.h:12, from ebwt_search_util.h:9, from ebwt_search_util.cpp:1: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ In file included from SeqAn-1.1/seqan/basic.h:64:0, from SeqAn-1.1/seqan/sequence.h:27, from ebwt_search_util.h:8, from ebwt_search_util.cpp:1: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:38:0, from ebwt_search_util.h:8, from ebwt_search_util.cpp:1: SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:51:0, from ebwt_search_util.h:8, from ebwt_search_util.cpp:1: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ In file included from SeqAn-1.1/seqan/sequence.h:53:0, from ebwt_search_util.h:8, from ebwt_search_util.cpp:1: SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/basic.h:64:0, from SeqAn-1.1/seqan/sequence.h:27, from hit_set.cpp:10: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:38:0, from hit_set.cpp:10: SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:51:0, from hit_set.cpp:10: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ In file included from SeqAn-1.1/seqan/sequence.h:53:0, from hit_set.cpp:10: SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from hit_set.cpp:10: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^ SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:62:0, from hit_set.cpp:10: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^ In file included from SeqAn-1.1/seqan/file.h:66:0, from alphabet.h:7, from hit_set.cpp:11: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] typedef typename Position::Type TPosition; ^ In file included from SeqAn-1.1/seqan/file.h:69:0, from alphabet.h:7, from hit_set.cpp:11: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from ebwt_search_util.h:8, from ebwt_search_util.cpp:1: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^ SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:62:0, from ebwt_search_util.h:8, from ebwt_search_util.cpp:1: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^ In file included from SeqAn-1.1/seqan/file.h:66:0, from alphabet.h:7, from hit.h:12, from ebwt_search_util.h:9, from ebwt_search_util.cpp:1: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] typedef typename Position::Type TPosition; ^ In file included from SeqAn-1.1/seqan/file.h:69:0, from alphabet.h:7, from hit.h:12, from ebwt_search_util.h:9, from ebwt_search_util.cpp:1: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ In file included from SeqAn-1.1/seqan/basic.h:64:0, from SeqAn-1.1/seqan/sequence.h:27, from hit_set.cpp:10: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:38:0, from hit_set.cpp:10: SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:51:0, from hit_set.cpp:10: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ In file included from SeqAn-1.1/seqan/sequence.h:53:0, from hit_set.cpp:10: SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from hit_set.cpp:10: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^ SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:62:0, from hit_set.cpp:10: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^ In file included from SeqAn-1.1/seqan/file.h:66:0, from alphabet.h:7, from hit_set.cpp:11: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] typedef typename Position::Type TPosition; ^ In file included from SeqAn-1.1/seqan/file.h:69:0, from alphabet.h:7, from hit_set.cpp:11: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ In file included from SeqAn-1.1/seqan/basic.h:64:0, from SeqAn-1.1/seqan/sequence.h:27, from pat.h:12, from sam.cpp:11: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:38:0, from pat.h:12, from sam.cpp:11: SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:51:0, from pat.h:12, from sam.cpp:11: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ In file included from SeqAn-1.1/seqan/sequence.h:53:0, from pat.h:12, from sam.cpp:11: SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from pat.h:12, from sam.cpp:11: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^ SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:62:0, from pat.h:12, from sam.cpp:11: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^ In file included from SeqAn-1.1/seqan/file.h:66:0, from alphabet.h:7, from pat.h:13, from sam.cpp:11: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] typedef typename Position::Type TPosition; ^ In file included from SeqAn-1.1/seqan/file.h:69:0, from alphabet.h:7, from pat.h:13, from sam.cpp:11: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ In file included from SeqAn-1.1/seqan/basic.h:64:0, from SeqAn-1.1/seqan/sequence.h:27, from pat.h:12, from sam.cpp:11: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:38:0, from pat.h:12, from sam.cpp:11: SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:51:0, from pat.h:12, from sam.cpp:11: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ In file included from SeqAn-1.1/seqan/sequence.h:53:0, from pat.h:12, from sam.cpp:11: SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from pat.h:12, from sam.cpp:11: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^ SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:62:0, from pat.h:12, from sam.cpp:11: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^ In file included from SeqAn-1.1/seqan/file.h:66:0, from alphabet.h:7, from pat.h:13, from sam.cpp:11: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] typedef typename Position::Type TPosition; ^ In file included from SeqAn-1.1/seqan/file.h:69:0, from alphabet.h:7, from pat.h:13, from sam.cpp:11: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ In file included from SeqAn-1.1/seqan/basic.h:64:0, from SeqAn-1.1/seqan/sequence.h:27, from alphabet.h:6, from color_dec.cpp:11: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:38:0, from alphabet.h:6, from color_dec.cpp:11: SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:51:0, from alphabet.h:6, from color_dec.cpp:11: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ In file included from SeqAn-1.1/seqan/sequence.h:53:0, from alphabet.h:6, from color_dec.cpp:11: SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from alphabet.h:6, from color_dec.cpp:11: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^ SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:62:0, from alphabet.h:6, from color_dec.cpp:11: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^ In file included from SeqAn-1.1/seqan/file.h:66:0, from alphabet.h:7, from color_dec.cpp:11: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] typedef typename Position::Type TPosition; ^ In file included from SeqAn-1.1/seqan/file.h:69:0, from alphabet.h:7, from color_dec.cpp:11: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ In file included from SeqAn-1.1/seqan/basic.h:64:0, from SeqAn-1.1/seqan/sequence.h:27, from hit.h:11, from hit.cpp:1: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:38:0, from hit.h:11, from hit.cpp:1: SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:51:0, from hit.h:11, from hit.cpp:1: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ In file included from SeqAn-1.1/seqan/sequence.h:53:0, from hit.h:11, from hit.cpp:1: SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from hit.h:11, from hit.cpp:1: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^ SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:62:0, from hit.h:11, from hit.cpp:1: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^ In file included from SeqAn-1.1/seqan/file.h:66:0, from alphabet.h:7, from hit.h:12, from hit.cpp:1: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] typedef typename Position::Type TPosition; ^ In file included from SeqAn-1.1/seqan/file.h:69:0, from alphabet.h:7, from hit.h:12, from hit.cpp:1: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ In file included from SeqAn-1.1/seqan/basic.h:64:0, from SeqAn-1.1/seqan/sequence.h:27, from alphabet.h:6, from color_dec.cpp:11: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:38:0, from alphabet.h:6, from color_dec.cpp:11: SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:51:0, from alphabet.h:6, from color_dec.cpp:11: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ In file included from SeqAn-1.1/seqan/sequence.h:53:0, from alphabet.h:6, from color_dec.cpp:11: SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from alphabet.h:6, from color_dec.cpp:11: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^ SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:62:0, from alphabet.h:6, from color_dec.cpp:11: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^ In file included from SeqAn-1.1/seqan/file.h:66:0, from alphabet.h:7, from color_dec.cpp:11: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] typedef typename Position::Type TPosition; ^ In file included from SeqAn-1.1/seqan/file.h:69:0, from alphabet.h:7, from color_dec.cpp:11: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ In file included from SeqAn-1.1/seqan/basic.h:64:0, from SeqAn-1.1/seqan/sequence.h:27, from hit.h:11, from hit.cpp:1: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^ SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:38:0, from hit.h:11, from hit.cpp:1: SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^ In file included from SeqAn-1.1/seqan/sequence.h:51:0, from hit.h:11, from hit.cpp:1: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^ In file included from SeqAn-1.1/seqan/sequence.h:53:0, from hit.h:11, from hit.cpp:1: SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from hit.h:11, from hit.cpp:1: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^ SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^ In file included from SeqAn-1.1/seqan/sequence.h:62:0, from hit.h:11, from hit.cpp:1: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^ In file included from SeqAn-1.1/seqan/file.h:66:0, from alphabet.h:7, from hit.h:12, from hit.cpp:1: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] typedef typename Position::Type TPosition; ^ In file included from SeqAn-1.1/seqan/file.h:69:0, from alphabet.h:7, from hit.h:12, from hit.cpp:1: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^ gmake[2]: Leaving directory '/wrkdirs/biology/bowtie/bowtie-1.1.2' =========================================================================== =================================================== ===> bowtie-1.1.2_4 depends on file: /usr/local/bin/python2.7 - not found ===> Installing existing package /packages/All/python27-2.7.13_7.txz Installing python27-2.7.13_7... `-- Installing expat-2.2.1... `-- Extracting expat-2.2.1: .......... done `-- Installing libffi-3.2.1... `-- Extracting libffi-3.2.1: .......... done `-- Installing libressl-2.5.5... `-- Extracting libressl-2.5.5: .......... done `-- Installing ncurses-6.0_3... `-- Extracting ncurses-6.0_3: .......... done `-- Installing readline-7.0.3... `-- Extracting readline-7.0.3: .......... done Extracting python27-2.7.13_7: .......... done Message from ncurses-6.0_3: ===> NOTICE: The ncurses port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port Message from python27-2.7.13_7: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== ===> bowtie-1.1.2_4 depends on file: /usr/local/bin/python2.7 - found ===> Returning to build of bowtie-1.1.2_4 ===> bowtie-1.1.2_4 depends on package: perl5>=5.24<5.25 - not found ===> Installing existing package /packages/All/perl5-5.24.2.txz Installing perl5-5.24.2... Extracting perl5-5.24.2: .......... done Message from perl5-5.24.2: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. ===> bowtie-1.1.2_4 depends on package: perl5>=5.24<5.25 - found ===> Returning to build of bowtie-1.1.2_4 =========================================================================== =================================================== ===> Staging for bowtie-1.1.2_4 ===> Generating temporary packing list gmake[2]: Entering directory '/wrkdirs/biology/bowtie/bowtie-1.1.2' mkdir -p /wrkdirs/biology/bowtie/stage/usr/local/bin for file in bowtie-build-s bowtie-build-l bowtie-align-s bowtie-align-l bowtie-inspect-s bowtie-inspect-l bowtie-inspect bowtie-build bowtie ; do \ cp -f $file /wrkdirs/biology/bowtie/stage/usr/local/bin ; \ done gmake[2]: Leaving directory '/wrkdirs/biology/bowtie/bowtie-1.1.2' /bin/mkdir -p /wrkdirs/biology/bowtie/stage/usr/local/share/bowtie/scripts install -m 555 /wrkdirs/biology/bowtie/bowtie-1.1.2/bowtie /wrkdirs/biology/bowtie/bowtie-1.1.2/bowtie-build /wrkdirs/biology/bowtie/bowtie-1.1.2/bowtie-inspect /wrkdirs/biology/bowtie/stage/usr/local/bin install -m 555 /wrkdirs/biology/bowtie/bowtie-1.1.2/scripts/*.sh /wrkdirs/biology/bowtie/bowtie-1.1.2/scripts/*.pl /wrkdirs/biology/bowtie/stage/usr/local/share/bowtie/scripts cd /wrkdirs/biology/bowtie/bowtie-1.1.2 && /bin/sh -c '(/usr/bin/find -Ed $0 $2 | /usr/bin/cpio -dumpl $1 >/dev/null 2>&1) && /usr/bin/find -Ed $0 $2 \( -type d -exec /bin/sh -c '\''cd '\''$1'\'' && chmod 755 "$@"'\'' -- . {} + -o -type f -exec /bin/sh -c '\''cd '\''$1'\'' && chmod 0644 "$@"'\'' -- . {} + \)' -- 'genomes indexes reads' /wrkdirs/biology/bowtie/stage/usr/local/share/bowtie cd /wrkdirs/biology/bowtie/bowtie-1.1.2/doc && /bin/sh -c '(/usr/bin/find -Ed $0 $2 | /usr/bin/cpio -dumpl $1 >/dev/null 2>&1) && /usr/bin/find -Ed $0 $2 \( -type d -exec /bin/sh -c '\''cd '\''$1'\'' && chmod 755 "$@"'\'' -- . {} + -o -type f -exec /bin/sh -c '\''cd '\''$1'\'' && chmod 0644 "$@"'\'' -- . {} + \)' -- \* /wrkdirs/biology/bowtie/stage/usr/local/share/doc/bowtie /usr/bin/strip /wrkdirs/biology/bowtie/stage/usr/local/bin/*-[sl] ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===> Building package for bowtie-1.1.2_4 file sizes/checksums [92]: . done packing files [92]: . done packing directories [0]: . done =========================================================================== => Cleaning up wrkdir ===> Cleaning for bowtie-1.1.2_4 build of biology/bowtie ended at Mon Sep 18 18:43:44 PDT 2017 build time: 00:03:53