=> Building biology/bowtie Started : Wednesday, 24 JUL 2019 at 16:44:24 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.83.g49866-DEVELOPMENT #40: Sun Jun 30 03:00:04 PDT 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.6-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.6-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- ===> The following configuration options are available for bowtie-1.1.2_8: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings -------------------------------------------------- -- 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/python3.6" XDG_DATA_HOME=/construction/biology/bowtie XDG_CONFIG_HOME=/construction/biology/bowtie HOME=/construction/biology/bowtie TMPDIR="/tmp" PATH=/construction/biology/bowtie/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/biology/bowtie XDG_CONFIG_HOME=/construction/biology/bowtie HOME=/construction/biology/bowtie TMPDIR="/tmp" PATH=/construction/biology/bowtie/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local 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" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/bowtie/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PYTHON_INCLUDEDIR=include/python3.6m PYTHON_LIBDIR=lib/python3.6 PYTHON_PLATFORM=dragonfly5 PYTHON_SITELIBDIR=lib/python3.6/site-packages PYTHON_SUFFIX=36 PYTHON_VER=3.6 PYTHON_VERSION=python3.6 PYTHON2="@comment " PYTHON3="" OSREL=5.6 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.28.2 PERL_VER=5.28 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/5.28 PROFILE="@comment " DOCSDIR="share/doc/bowtie" EXAMPLESDIR="share/examples/bowtie" DATADIR="share/bowtie" WWWDIR="www/bowtie" ETCDIR="etc/bowtie" -------------------------------------------------- -- 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 -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.6 USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.28.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500601 OSVERSION=9999999 OSREL=5.6 _OSRELEASE=5.6-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License ART10 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> bowtie-1.1.2_8 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.11.1.txz Installing pkg-1.11.1... Extracting pkg-1.11.1: .......... done ===> bowtie-1.1.2_8 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bowtie-1.1.2_8 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License ART10 accepted by the user ===> Fetching all distfiles required by bowtie-1.1.2_8 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License ART10 accepted by the user ===> Fetching all distfiles required by bowtie-1.1.2_8 for building => SHA256 Checksum OK for BenLangmead-bowtie-v1.1.2_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License ART10 accepted by the user ===> Fetching all distfiles required by bowtie-1.1.2_8 for building ===> Extracting for bowtie-1.1.2_8 ===> License ART10 accepted by the user ===> Fetching all distfiles required by bowtie-1.1.2_8 for building => SHA256 Checksum OK for BenLangmead-bowtie-v1.1.2_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for bowtie-1.1.2_8 ===> Applying ports patches for bowtie-1.1.2_8 /usr/bin/sed -i.bak -e 's@amd64@x86_64@g' /construction/biology/bowtie/bowtie-1.1.2/Makefile -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> bowtie-1.1.2_8 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz Installing gmake-4.2.1_3... `-- Installing gettext-runtime-0.20.1... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: .... done `-- Extracting gettext-runtime-0.20.1: .......... done Extracting gmake-4.2.1_3: .......... done ===> bowtie-1.1.2_8 depends on executable: gmake - found ===> Returning to build of bowtie-1.1.2_8 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for bowtie-1.1.2_8 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for bowtie-1.1.2_8 gmake[2]: Entering directory '/construction/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, 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, 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, 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/basic.h:64, 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:53, 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, 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, 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:38, 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/index.h:82, 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, 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/sequence.h:51, 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/basic.h:64, 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:53, 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/file.h:66, 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, 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/basic.h:64, 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:57, 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, 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:38, 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, 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, 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, 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, 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/index.h:82, 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, 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/sequence.h:51, 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:62, 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/sequence.h:53, 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/basic.h:64, 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:57, 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, 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, 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/find.h:62, 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/file.h:66, 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, 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/sequence.h:38, 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, 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, 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, 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, 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, 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/file.h:66, 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, 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/index.h:82, 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, 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 blockwise_sa.h:13, from ebwt.h:27, from ebwt_build.cpp:11: diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': diff_sample.h:157:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:157:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:158:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:158:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~~~~ In file included from SeqAn-1.1/seqan/index.h:82, 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, 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/file.h:66, 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, 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, from ebwt_build.cpp:11: blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()': blockwise_sa.h:206:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~ blockwise_sa.h:206:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~~ 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, 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 blockwise_sa.h:13, from ebwt.h:27, from ebwt_build.cpp:11: diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': diff_sample.h:157:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:157:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:158:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:158:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~~~~ In file included from ebwt.h:27, from ebwt_build.cpp:11: blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()': blockwise_sa.h:206:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~ blockwise_sa.h:206:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~~ In file included from blockwise_sa.h:13, from ebwt.h:27, from ebwt_search.cpp:14: diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': diff_sample.h:157:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:157:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:158:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:158:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~~~~ 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, from ebwt_search.cpp:14: blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()': blockwise_sa.h:206:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~ blockwise_sa.h:206:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~~ In file included from ebwt.h:27, 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; ^~~~~~~~~ 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, 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 SeqAn-1.1/seqan/file.h:66, 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, 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 ebwt.h:40, 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 ebwt.h:40, 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 ebwt.h:40, 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 ebwt_search.cpp:14: ebwt.h: In destructor 'Ebwt::~Ebwt()': ebwt.h:823:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~ ebwt.h:823:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~~~~ ebwt.h:824:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~ ebwt.h:824:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~~~~ ebwt.h:825:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~ ebwt.h:825:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~~~~~ ebwt.h:831:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_isa != NULL) delete[] _isa; _isa = NULL; ^~ ebwt.h:831:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_isa != NULL) delete[] _isa; _isa = NULL; ^~~~ ebwt.h:832:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_plen != NULL) delete[] _plen; _plen = NULL; ^~ ebwt.h:832:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_plen != NULL) delete[] _plen; _plen = NULL; ^~~~~ ebwt.h:833:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~ ebwt.h:833:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~~~~~~~ In file included from SeqAn-1.1/seqan/index.h:82, 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, 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_build.cpp:11: ebwt.h: In destructor 'Ebwt::~Ebwt()': ebwt.h:823:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~ ebwt.h:823:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~~~~ ebwt.h:824:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~ ebwt.h:824:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~~~~ ebwt.h:825:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~ ebwt.h:825:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~~~~~ ebwt.h:831:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_isa != NULL) delete[] _isa; _isa = NULL; ^~ ebwt.h:831:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_isa != NULL) delete[] _isa; _isa = NULL; ^~~~ ebwt.h:832:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_plen != NULL) delete[] _plen; _plen = NULL; ^~ ebwt.h:832:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_plen != NULL) delete[] _plen; _plen = NULL; ^~~~~ ebwt.h:833:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~ ebwt.h:833:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~~~~~~~ In file included from ebwt_build.cpp:11: ebwt.h: In destructor 'Ebwt::~Ebwt()': ebwt.h:823:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~ ebwt.h:823:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~~~~ ebwt.h:824:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~ ebwt.h:824:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~~~~ ebwt.h:825:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~ ebwt.h:825:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~~~~~ ebwt.h:831:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_isa != NULL) delete[] _isa; _isa = NULL; ^~ ebwt.h:831:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_isa != NULL) delete[] _isa; _isa = NULL; ^~~~ ebwt.h:832:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_plen != NULL) delete[] _plen; _plen = NULL; ^~ ebwt.h:832:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_plen != NULL) delete[] _plen; _plen = NULL; ^~~~~ ebwt.h:833:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~ ebwt.h:833:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~~~~~~~ In file included from blockwise_sa.h:13, from ebwt.h:27, from ebwt_search.cpp:14: diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': diff_sample.h:157:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:157:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:158:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:158:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~~~~ In file included from ebwt.h:27, from ebwt_search.cpp:14: blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()': blockwise_sa.h:206:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~ blockwise_sa.h:206:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~~ 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, 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, 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 ebwt_search.cpp:14: ebwt.h: In destructor 'Ebwt::~Ebwt()': ebwt.h:823:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~ ebwt.h:823:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~~~~ ebwt.h:824:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~ ebwt.h:824:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~~~~ ebwt.h:825:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~ ebwt.h:825:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~~~~~ ebwt.h:831:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_isa != NULL) delete[] _isa; _isa = NULL; ^~ ebwt.h:831:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_isa != NULL) delete[] _isa; _isa = NULL; ^~~~ ebwt.h:832:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_plen != NULL) delete[] _plen; _plen = NULL; ^~ ebwt.h:832:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_plen != NULL) delete[] _plen; _plen = NULL; ^~~~~ ebwt.h:833:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~ ebwt.h:833:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~~~~~~~ In file included from blockwise_sa.h:13, from ebwt.h:27, from bowtie_inspect.cpp:10: diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': diff_sample.h:157:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:157:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:158:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:158:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~~~~ In file included from SeqAn-1.1/seqan/sequence.h:57, 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), ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ In file included from ebwt.h:27, from bowtie_inspect.cpp:10: blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()': blockwise_sa.h:206:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~ blockwise_sa.h:206:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~~ 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; ^~~~~~~~~ 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 SeqAn-1.1/seqan/sequence.h:57, 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/basic.h:101, 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_alphabet_trait_basic.h: In instantiation of 'void seqan::_arrayCopyForward_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]': SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:27: required from 'void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:18: required from 'void seqan::_arrayConstructCopy_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:29: required from 'void seqan::arrayConstructCopy(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/sequence/string_alloc.h:421:21: required from 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = void; _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::Alloc >; 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::Alloc >; std::__cxx11::string = std::__cxx11::basic_string]' ebwt_build.cpp:611:61: required from here SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:9: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'struct seqan::SimpleType' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:106, 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_alphabet_simple.h:57:8: note: 'struct seqan::SimpleType' declared here struct SimpleType ^~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:101, 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_alphabet_trait_basic.h: In instantiation of 'void seqan::_arrayCopyForward_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]': SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:27: required from 'void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:18: required from 'void seqan::_arrayConstructCopy_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:29: required from 'void seqan::arrayConstructCopy(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/sequence/string_alloc.h:421:21: required from 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = void; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size > >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_base.h:1433:33: required from 'static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc >; 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::Alloc; TSize = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:15: required from 'typename seqan::Size::Type seqan::resize(T&, TSize) [with T = seqan::String, seqan::Alloc >; TSize = unsigned int; typename seqan::Size::Type = long unsigned int]' hit_set.h:284:24: required from here SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:9: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'struct seqan::SimpleType' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:106, 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_alphabet_simple.h:57:8: note: 'struct seqan::SimpleType' declared here struct SimpleType ^~~~~~~~~~ In file included from ebwt.h:27, 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:101, 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_alphabet_trait_basic.h: In instantiation of 'void seqan::_arrayCopyForward_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]': SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:27: required from 'void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:18: required from 'void seqan::_arrayConstructCopy_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:29: required from 'void seqan::arrayConstructCopy(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/sequence/string_alloc.h:421:21: required from 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = void; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size > >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_base.h:1433:33: required from 'static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc >; 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::Alloc; TSize = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:15: required from 'typename seqan::Size::Type seqan::resize(T&, TSize) [with T = seqan::String, seqan::Alloc >; TSize = unsigned int; typename seqan::Size::Type = long unsigned int]' hit_set.h:284:24: required from here SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:9: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'struct seqan::SimpleType' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:106, 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_alphabet_simple.h:57:8: note: 'struct seqan::SimpleType' declared here struct SimpleType ^~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:101, 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_alphabet_trait_basic.h: In instantiation of 'void seqan::_arrayCopyForward_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]': SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:27: required from 'void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:18: required from 'void seqan::_arrayConstructCopy_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:29: required from 'void seqan::arrayConstructCopy(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/sequence/string_alloc.h:421:21: required from 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = void; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size > >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_base.h:1433:33: required from 'static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc >; 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::Alloc; 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::Alloc >]' ebwt.h:2992:2: required from 'void Ebwt::checkOrigs(const std::vector, seqan::Alloc > >&, bool, bool) const [with TStr = seqan::String, seqan::Alloc >]' ebwt_search.cpp:2659:3: required from 'void driver(const char*, const string&, const string&, const std::vector >&, const std::vector >&, const string&) [with TStr = seqan::String, seqan::Alloc >; std::__cxx11::string = std::__cxx11::basic_string]' ebwt_search.cpp:2933:86: required from here SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:9: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'struct seqan::SimpleType' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:106, 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_alphabet_simple.h:57:8: note: 'struct seqan::SimpleType' declared here struct SimpleType ^~~~~~~~~~ In file included from SeqAn-1.1/seqan/sequence.h:57, 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), ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ In file included from SeqAn-1.1/seqan/sequence.h:57, 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), ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 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 bowtie_inspect.cpp:10: ebwt.h: In destructor 'Ebwt::~Ebwt()': ebwt.h:823:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~ ebwt.h:823:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~~~~ ebwt.h:824:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~ ebwt.h:824:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~~~~ ebwt.h:825:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~ ebwt.h:825:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~~~~~ ebwt.h:831:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_isa != NULL) delete[] _isa; _isa = NULL; ^~ ebwt.h:831:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_isa != NULL) delete[] _isa; _isa = NULL; ^~~~ ebwt.h:832:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_plen != NULL) delete[] _plen; _plen = NULL; ^~ ebwt.h:832:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_plen != NULL) delete[] _plen; _plen = NULL; ^~~~~ ebwt.h:833:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~ ebwt.h:833:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:101, 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_alphabet_trait_basic.h: In instantiation of 'void seqan::_arrayCopyForward_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]': SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:27: required from 'void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:18: required from 'void seqan::_arrayConstructCopy_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:29: required from 'void seqan::arrayConstructCopy(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/sequence/string_alloc.h:421:21: required from 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = void; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size > >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_base.h:1433:33: required from 'static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc >; 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::Alloc; TSize = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:15: required from 'typename seqan::Size::Type seqan::resize(T&, TSize) [with T = seqan::String, seqan::Alloc >; TSize = unsigned int; typename seqan::Size::Type = long unsigned int]' hit_set.h:284:24: required from here SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:9: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'struct seqan::SimpleType' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:106, 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_alphabet_simple.h:57:8: note: 'struct seqan::SimpleType' declared here struct SimpleType ^~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:101, 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_alphabet_trait_basic.h: In instantiation of 'void seqan::_arrayCopyForward_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]': SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:27: required from 'void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:18: required from 'void seqan::_arrayConstructCopy_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:29: required from 'void seqan::arrayConstructCopy(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/sequence/string_alloc.h:421:21: required from 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = void; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size > >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_base.h:1433:33: required from 'static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc >; 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::Alloc; 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::Alloc >]' ebwt.h:2992:2: required from 'void Ebwt::checkOrigs(const std::vector, seqan::Alloc > >&, bool, bool) const [with TStr = seqan::String, seqan::Alloc >]' ebwt_search.cpp:2659:3: required from 'void driver(const char*, const string&, const string&, const std::vector >&, const std::vector >&, const string&) [with TStr = seqan::String, seqan::Alloc >; std::__cxx11::string = std::__cxx11::basic_string]' ebwt_search.cpp:2933:86: required from here SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:9: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'struct seqan::SimpleType' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:106, 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_alphabet_simple.h:57:8: note: 'struct seqan::SimpleType' declared here struct SimpleType ^~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:101, 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_alphabet_trait_basic.h: In instantiation of 'void seqan::_arrayCopyForward_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]': SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:27: required from 'void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:18: required from 'void seqan::_arrayConstructCopy_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:29: required from 'void seqan::arrayConstructCopy(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/sequence/string_alloc.h:421:21: required from 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = void; _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::Alloc >; 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::Alloc >; std::__cxx11::string = std::__cxx11::basic_string]' ebwt_build.cpp:611:61: required from here SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:9: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'struct seqan::SimpleType' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:106, 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_alphabet_simple.h:57:8: note: 'struct seqan::SimpleType' declared here struct SimpleType ^~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:101, 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_alphabet_trait_basic.h: In instantiation of 'void seqan::_arrayCopyForward_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]': SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:27: required from 'void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:18: required from 'void seqan::_arrayConstructCopy_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:29: required from 'void seqan::arrayConstructCopy(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/sequence/string_alloc.h:421:21: required from 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = void; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size > >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_base.h:1433:33: required from 'static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc >; 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::Alloc; TSize = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:15: required from 'typename seqan::Size::Type seqan::resize(T&, TSize) [with T = seqan::String, seqan::Alloc >; TSize = unsigned int; typename seqan::Size::Type = long unsigned int]' hit_set.h:284:24: required from here SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:9: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'struct seqan::SimpleType' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:106, 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_alphabet_simple.h:57:8: note: 'struct seqan::SimpleType' declared here struct SimpleType ^~~~~~~~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::free(T*, uint32_t) [with T = Edit; uint32_t = unsigned int]': range_source.h:138:75: required from here pool.h:306:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(&pools_[curPool_][cur_], 0, num * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:20, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:8, from blockwise_sa.h:13, from ebwt.h:27, from bowtie_inspect.cpp:10: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'void AllocOnlyPool::free(T*) [with T = Branch]': range_source.h:852:18: required from here pool.h:286:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(&pools_[curPool_][cur_], 0, sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1656, from bowtie_inspect.cpp:10: range_source.h:556:7: note: 'class Branch' declared here class Branch { ^~~~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::lazyInit() [with T = Edit]': pool.h:238:7: required from 'T* AllocOnlyPool::alloc(uint32_t) [with T = Edit; uint32_t = unsigned int]' range_source.h:41:40: required from here pool.h:367:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:20, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:8, from blockwise_sa.h:13, from ebwt.h:27, from bowtie_inspect.cpp:10: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::allocNextPool() [with T = Edit]': pool.h:240:8: required from 'T* AllocOnlyPool::alloc(uint32_t) [with T = Edit; uint32_t = unsigned int]' range_source.h:41:40: required from here pool.h:347:21: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:20, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:8, from blockwise_sa.h:13, from ebwt.h:27, from bowtie_inspect.cpp:10: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::lazyInit() [with T = Branch]': pool.h:215:7: required from 'T* AllocOnlyPool::alloc() [with T = Branch]' range_source.h:699:35: required from here pool.h:367:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1656, from bowtie_inspect.cpp:10: range_source.h:556:7: note: 'class Branch' declared here class Branch { ^~~~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::allocNextPool() [with T = Branch]': pool.h:217:8: required from 'T* AllocOnlyPool::alloc() [with T = Branch]' range_source.h:699:35: required from here pool.h:347:21: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1656, from bowtie_inspect.cpp:10: range_source.h:556:7: note: 'class Branch' declared here class Branch { ^~~~~~ In file included from SeqAn-1.1/seqan/sequence.h:57, 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:101, 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_alphabet_trait_basic.h: In instantiation of 'void seqan::_arrayCopyForward_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]': SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:27: required from 'void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:18: required from 'void seqan::_arrayConstructCopy_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:29: required from 'void seqan::arrayConstructCopy(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/sequence/string_alloc.h:421:21: required from 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = void; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size > >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_base.h:1433:33: required from 'static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc >; 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::Alloc; TSize = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:15: required from 'typename seqan::Size::Type seqan::resize(T&, TSize) [with T = seqan::String, seqan::Alloc >; TSize = unsigned int; typename seqan::Size::Type = long unsigned int]' hit_set.h:284:24: required from here SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:9: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'struct seqan::SimpleType' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:106, 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_alphabet_simple.h:57:8: note: 'struct seqan::SimpleType' declared here struct SimpleType ^~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:64, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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 blockwise_sa.h:13, from ebwt.h:27, from bowtie_inspect.cpp:10: diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': diff_sample.h:157:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:157:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:158:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:158:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~~~~ In file included from SeqAn-1.1/seqan/basic.h:64, 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, 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, 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, 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, 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, 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 ebwt.h:27, from bowtie_inspect.cpp:10: blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()': blockwise_sa.h:206:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~ blockwise_sa.h:206:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~~ 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 SeqAn-1.1/seqan/file.h:66, 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, 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 ebwt.h:27, 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 bowtie_inspect.cpp:10: ebwt.h: In destructor 'Ebwt::~Ebwt()': ebwt.h:823:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~ ebwt.h:823:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_fchr != NULL) delete[] _fchr; _fchr = NULL; ^~~~~ ebwt.h:824:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~ ebwt.h:824:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~~~~ ebwt.h:825:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~ ebwt.h:825:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~~~~~ ebwt.h:831:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_isa != NULL) delete[] _isa; _isa = NULL; ^~ ebwt.h:831:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_isa != NULL) delete[] _isa; _isa = NULL; ^~~~ ebwt.h:832:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_plen != NULL) delete[] _plen; _plen = NULL; ^~ ebwt.h:832:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_plen != NULL) delete[] _plen; _plen = NULL; ^~~~~ ebwt.h:833:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~ ebwt.h:833:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~~~~~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::free(T*, uint32_t) [with T = Edit; uint32_t = unsigned int]': range_source.h:138:75: required from here pool.h:306:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(&pools_[curPool_][cur_], 0, num * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:20, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:8, from blockwise_sa.h:13, from ebwt.h:27, from bowtie_inspect.cpp:10: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'void AllocOnlyPool::free(T*) [with T = Branch]': range_source.h:852:18: required from here pool.h:286:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(&pools_[curPool_][cur_], 0, sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1656, from bowtie_inspect.cpp:10: range_source.h:556:7: note: 'class Branch' declared here class Branch { ^~~~~~ In file included from SeqAn-1.1/seqan/basic.h:64, 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, 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, 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, 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, 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, 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 bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::lazyInit() [with T = Edit]': pool.h:238:7: required from 'T* AllocOnlyPool::alloc(uint32_t) [with T = Edit; uint32_t = unsigned int]' range_source.h:41:40: required from here pool.h:367:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:20, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:8, from blockwise_sa.h:13, from ebwt.h:27, from bowtie_inspect.cpp:10: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::allocNextPool() [with T = Edit]': pool.h:240:8: required from 'T* AllocOnlyPool::alloc(uint32_t) [with T = Edit; uint32_t = unsigned int]' range_source.h:41:40: required from here pool.h:347:21: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Edit'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from hit_set.h:16, from pat.h:20, from sequence_io.h:12, from multikey_qsort.h:8, from diff_sample.h:8, from blockwise_sa.h:13, from ebwt.h:27, from bowtie_inspect.cpp:10: edit.h:31:8: note: 'struct Edit' declared here struct Edit { ^~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::lazyInit() [with T = Branch]': pool.h:215:7: required from 'T* AllocOnlyPool::alloc() [with T = Branch]' range_source.h:699:35: required from here pool.h:367:22: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1656, from bowtie_inspect.cpp:10: range_source.h:556:7: note: 'class Branch' declared here class Branch { ^~~~~~ In file included from bowtie_inspect.cpp:8: pool.h: In instantiation of 'bool AllocOnlyPool::allocNextPool() [with T = Branch]': pool.h:217:8: required from 'T* AllocOnlyPool::alloc() [with T = Branch]' range_source.h:699:35: required from here pool.h:347:21: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class Branch'; use assignment or value-initialization instead [-Wclass-memaccess] ASSERT_ONLY(memset(pool, 0, lim_ * sizeof(T))); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ assert_helpers.h:21:27: note: in definition of macro 'ASSERT_ONLY' #define ASSERT_ONLY(x...) x ^ In file included from ebwt_search_backtrack.h:10, from ebwt.h:1656, from bowtie_inspect.cpp:10: range_source.h:556:7: note: 'class Branch' declared here class Branch { ^~~~~~ In file included from SeqAn-1.1/seqan/file.h:66, 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, 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/sequence.h:57, 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:101, 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_alphabet_trait_basic.h: In instantiation of 'void seqan::_arrayCopyForward_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]': SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:27: required from 'void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:18: required from 'void seqan::_arrayConstructCopy_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:29: required from 'void seqan::arrayConstructCopy(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/sequence/string_alloc.h:421:21: required from 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = void; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size > >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_base.h:1433:33: required from 'static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc >; 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::Alloc; TSize = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:15: required from 'typename seqan::Size::Type seqan::resize(T&, TSize) [with T = seqan::String, seqan::Alloc >; TSize = unsigned int; typename seqan::Size::Type = long unsigned int]' hit_set.h:284:24: required from here SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:9: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'struct seqan::SimpleType' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:106, 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_alphabet_simple.h:57:8: note: 'struct seqan::SimpleType' declared here struct SimpleType ^~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:101, from SeqAn-1.1/seqan/sequence.h:27, from pat.cpp:5: SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h: In instantiation of 'void seqan::_arrayCopyForward_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]': SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:27: required from 'void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:18: required from 'void seqan::_arrayConstructCopy_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:29: required from 'void seqan::arrayConstructCopy(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/sequence/string_alloc.h:421:21: required from 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = void; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size > >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_base.h:1433:33: required from 'static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc >; 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::Alloc; TSize = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:15: required from 'typename seqan::Size::Type seqan::resize(T&, TSize) [with T = seqan::String, seqan::Alloc >; TSize = unsigned int; typename seqan::Size::Type = long unsigned int]' hit_set.h:284:24: required from here SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:9: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'struct seqan::SimpleType' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:106, from SeqAn-1.1/seqan/sequence.h:27, from pat.cpp:5: SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:57:8: note: 'struct seqan::SimpleType' declared here struct SimpleType ^~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:64, 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, 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, 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, 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, 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, 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, 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, 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:101, 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_alphabet_trait_basic.h: In instantiation of 'void seqan::_arrayCopyForward_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]': SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:27: required from 'void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:18: required from 'void seqan::_arrayConstructCopy_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:29: required from 'void seqan::arrayConstructCopy(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/sequence/string_alloc.h:421:21: required from 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = void; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size > >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_base.h:1433:33: required from 'static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc >; 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::Alloc; TSize = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:15: required from 'typename seqan::Size::Type seqan::resize(T&, TSize) [with T = seqan::String, seqan::Alloc >; TSize = unsigned int; typename seqan::Size::Type = long unsigned int]' hit_set.h:284:24: required from here SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:9: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'struct seqan::SimpleType' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:106, 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_alphabet_simple.h:57:8: note: 'struct seqan::SimpleType' declared here struct SimpleType ^~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:64, 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, 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, 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, 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, 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, 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/basic.h:64, 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/file.h:66, 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, 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:38, 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, 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, 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, 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, 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, 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, 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:101, from SeqAn-1.1/seqan/sequence.h:27, from hit_set.cpp:10: SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h: In instantiation of 'void seqan::_arrayCopyForward_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]': SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:27: required from 'void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:18: required from 'void seqan::_arrayConstructCopy_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:29: required from 'void seqan::arrayConstructCopy(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/sequence/string_alloc.h:421:21: required from 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = void; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size > >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_base.h:1433:33: required from 'static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc >; 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::Alloc; TSize = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:15: required from 'typename seqan::Size::Type seqan::resize(T&, TSize) [with T = seqan::String, seqan::Alloc >; TSize = unsigned int; typename seqan::Size::Type = long unsigned int]' hit_set.h:284:24: required from here SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:9: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'struct seqan::SimpleType' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:106, from SeqAn-1.1/seqan/sequence.h:27, from hit_set.cpp:10: SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:57:8: note: 'struct seqan::SimpleType' declared here struct SimpleType ^~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:64, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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/basic.h:101, from SeqAn-1.1/seqan/sequence.h:27, from pat.cpp:5: SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h: In instantiation of 'void seqan::_arrayCopyForward_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]': SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:27: required from 'void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:18: required from 'void seqan::_arrayConstructCopy_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:29: required from 'void seqan::arrayConstructCopy(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/sequence/string_alloc.h:421:21: required from 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = void; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size > >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_base.h:1433:33: required from 'static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc >; 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::Alloc; TSize = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:15: required from 'typename seqan::Size::Type seqan::resize(T&, TSize) [with T = seqan::String, seqan::Alloc >; TSize = unsigned int; typename seqan::Size::Type = long unsigned int]' hit_set.h:284:24: required from here SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:9: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'struct seqan::SimpleType' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:106, from SeqAn-1.1/seqan/sequence.h:27, from pat.cpp:5: SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:57:8: note: 'struct seqan::SimpleType' declared here struct SimpleType ^~~~~~~~~~ In file included from SeqAn-1.1/seqan/file.h:66, 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, 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:101, from SeqAn-1.1/seqan/sequence.h:27, from pat.h:12, from sam.cpp:11: SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h: In instantiation of 'void seqan::_arrayCopyForward_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]': SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:27: required from 'void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:18: required from 'void seqan::_arrayConstructCopy_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:29: required from 'void seqan::arrayConstructCopy(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/sequence/string_alloc.h:421:21: required from 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = void; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size > >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_base.h:1433:33: required from 'static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc >; 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::Alloc; TSize = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:15: required from 'typename seqan::Size::Type seqan::resize(T&, TSize) [with T = seqan::String, seqan::Alloc >; TSize = unsigned int; typename seqan::Size::Type = long unsigned int]' hit_set.h:284:24: required from here SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:9: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'struct seqan::SimpleType' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:106, from SeqAn-1.1/seqan/sequence.h:27, from pat.h:12, from sam.cpp:11: SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:57:8: note: 'struct seqan::SimpleType' declared here struct SimpleType ^~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:64, 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, 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, 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, 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, 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, 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, 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, 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:101, 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_alphabet_trait_basic.h: In instantiation of 'void seqan::_arrayCopyForward_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]': SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:27: required from 'void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:18: required from 'void seqan::_arrayConstructCopy_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:29: required from 'void seqan::arrayConstructCopy(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/sequence/string_alloc.h:421:21: required from 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = void; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size > >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_base.h:1433:33: required from 'static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc >; 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::Alloc; TSize = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:15: required from 'typename seqan::Size::Type seqan::resize(T&, TSize) [with T = seqan::String, seqan::Alloc >; TSize = unsigned int; typename seqan::Size::Type = long unsigned int]' hit_set.h:284:24: required from here SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:9: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'struct seqan::SimpleType' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:106, 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_alphabet_simple.h:57:8: note: 'struct seqan::SimpleType' declared here struct SimpleType ^~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:64, 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/basic.h:64, 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/basic.h:64, 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, 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:38, 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, 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; ^~~~~~~ In file included from SeqAn-1.1/seqan/sequence.h:51, 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::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; ^~~~~~~ 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, 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:53, 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, 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, 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:57, 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, 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/sequence.h:51, 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, 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, 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, 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/sequence.h:62, 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, 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, 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/file.h:66, 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, 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, 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, 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:101, from SeqAn-1.1/seqan/sequence.h:27, from hit_set.cpp:10: SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h: In instantiation of 'void seqan::_arrayCopyForward_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]': SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:27: required from 'void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:18: required from 'void seqan::_arrayConstructCopy_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:29: required from 'void seqan::arrayConstructCopy(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/sequence/string_alloc.h:421:21: required from 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = void; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size > >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_base.h:1433:33: required from 'static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc >; 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::Alloc; TSize = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:15: required from 'typename seqan::Size::Type seqan::resize(T&, TSize) [with T = seqan::String, seqan::Alloc >; TSize = unsigned int; typename seqan::Size::Type = long unsigned int]' hit_set.h:284:24: required from here SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:9: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'struct seqan::SimpleType' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:106, from SeqAn-1.1/seqan/sequence.h:27, from hit_set.cpp:10: SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:57:8: note: 'struct seqan::SimpleType' declared here struct SimpleType ^~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:64, 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, 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, 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, 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, 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, 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, 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, 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:101, from SeqAn-1.1/seqan/sequence.h:27, from hit.h:11, from hit.cpp:1: SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h: In instantiation of 'void seqan::_arrayCopyForward_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]': SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:27: required from 'void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:18: required from 'void seqan::_arrayConstructCopy_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:29: required from 'void seqan::arrayConstructCopy(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/sequence/string_alloc.h:421:21: required from 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = void; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size > >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_base.h:1433:33: required from 'static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc >; 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::Alloc; TSize = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:15: required from 'typename seqan::Size::Type seqan::resize(T&, TSize) [with T = seqan::String, seqan::Alloc >; TSize = unsigned int; typename seqan::Size::Type = long unsigned int]' hit_set.h:284:24: required from here SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:9: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'struct seqan::SimpleType' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:106, from SeqAn-1.1/seqan/sequence.h:27, from hit.h:11, from hit.cpp:1: SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:57:8: note: 'struct seqan::SimpleType' declared here struct SimpleType ^~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:64, 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, 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, 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, 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, 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, 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, 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, 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:101, from SeqAn-1.1/seqan/sequence.h:27, from pat.h:12, from sam.cpp:11: SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h: In instantiation of 'void seqan::_arrayCopyForward_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]': SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:27: required from 'void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:18: required from 'void seqan::_arrayConstructCopy_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:29: required from 'void seqan::arrayConstructCopy(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/sequence/string_alloc.h:421:21: required from 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = void; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size > >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_base.h:1433:33: required from 'static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc >; 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::Alloc; TSize = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:15: required from 'typename seqan::Size::Type seqan::resize(T&, TSize) [with T = seqan::String, seqan::Alloc >; TSize = unsigned int; typename seqan::Size::Type = long unsigned int]' hit_set.h:284:24: required from here SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:9: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'struct seqan::SimpleType' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:106, from SeqAn-1.1/seqan/sequence.h:27, from pat.h:12, from sam.cpp:11: SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:57:8: note: 'struct seqan::SimpleType' declared here struct SimpleType ^~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:64, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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:101, from SeqAn-1.1/seqan/sequence.h:27, from hit.h:11, from hit.cpp:1: SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h: In instantiation of 'void seqan::_arrayCopyForward_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]': SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:27: required from 'void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:18: required from 'void seqan::_arrayConstructCopy_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:29: required from 'void seqan::arrayConstructCopy(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' SeqAn-1.1/seqan/sequence/string_alloc.h:421:21: required from 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = void; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size > >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_base.h:1433:33: required from 'static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc >; 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::Alloc; TSize = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size >::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/sequence_interface.h:1360:15: required from 'typename seqan::Size::Type seqan::resize(T&, TSize) [with T = seqan::String, seqan::Alloc >; TSize = unsigned int; typename seqan::Size::Type = long unsigned int]' hit_set.h:284:24: required from here SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:9: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'struct seqan::SimpleType' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from SeqAn-1.1/seqan/basic.h:106, from SeqAn-1.1/seqan/sequence.h:27, from hit.h:11, from hit.cpp:1: SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:57:8: note: 'struct seqan::SimpleType' declared here struct SimpleType ^~~~~~~~~~ gmake[2]: Leaving directory '/construction/biology/bowtie/bowtie-1.1.2' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> bowtie-1.1.2_8 depends on file: /usr/local/bin/python3.6 - not found ===> Installing existing package /packages/All/python36-3.6.9.txz Installing python36-3.6.9... `-- Installing expat-2.2.6_1... `-- Extracting expat-2.2.6_1: .......... done `-- Installing libffi-3.2.1_3... `-- Extracting libffi-3.2.1_3: .......... done `-- Installing libressl-2.9.2... `-- Extracting libressl-2.9.2: .......... done `-- Installing ncurses-6.1.20190525... `-- Extracting ncurses-6.1.20190525: .......... done `-- Installing readline-8.0.0... `-- Extracting readline-8.0.0: .......... done Extracting python36-3.6.9: .......... done Message from python36-3.6.9: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py36-gdbm databases/py-gdbm@py36 py36-sqlite3 databases/py-sqlite3@py36 py36-tkinter x11-toolkits/py-tkinter@py36 =========================================================================== ===> bowtie-1.1.2_8 depends on file: /usr/local/bin/python3.6 - found ===> Returning to build of bowtie-1.1.2_8 ===> bowtie-1.1.2_8 depends on package: perl5>=5.28.r1<5.29 - not found ===> Installing existing package /packages/All/perl5-5.28.2.txz Installing perl5-5.28.2... Extracting perl5-5.28.2: .......... done Message from perl5-5.28.2: 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_8 depends on package: perl5>=5.28.r1<5.29 - found ===> Returning to build of bowtie-1.1.2_8 -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for bowtie-1.1.2_8 ===> Generating temporary packing list gmake[2]: Entering directory '/construction/biology/bowtie/bowtie-1.1.2' mkdir -p /construction/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 /construction/biology/bowtie/stage/usr/local/bin ; \ done gmake[2]: Leaving directory '/construction/biology/bowtie/bowtie-1.1.2' /bin/mkdir -p /construction/biology/bowtie/stage/usr/local/share/bowtie/scripts install -m 555 /construction/biology/bowtie/bowtie-1.1.2/bowtie /construction/biology/bowtie/bowtie-1.1.2/bowtie-build /construction/biology/bowtie/bowtie-1.1.2/bowtie-inspect /construction/biology/bowtie/stage/usr/local/bin install -m 555 /construction/biology/bowtie/bowtie-1.1.2/scripts/*.sh /construction/biology/bowtie/bowtie-1.1.2/scripts/*.pl /construction/biology/bowtie/stage/usr/local/share/bowtie/scripts cd /construction/biology/bowtie/bowtie-1.1.2 && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE 'genomes indexes reads' /construction/biology/bowtie/stage/usr/local/share/bowtie cd /construction/biology/bowtie/bowtie-1.1.2/doc && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE \* /construction/biology/bowtie/stage/usr/local/share/doc/bowtie /usr/bin/strip /construction/biology/bowtie/stage/usr/local/bin/*-[sl] ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for bowtie-1.1.2_8 file sizes/checksums [92]: . done packing files [92]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Wednesday, 24 JUL 2019 at 16:48:06 UTC Duration: 00:03:42